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Conserved domains on  [gi|57530702|ref|NP_001006359|]
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insulin-like growth factor 2 mRNA-binding protein 3 [Gallus gallus]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
KH-I super family cl00098
K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found ...
276-370 1.12e-59

K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include an N-terminal extension and type I KH domains (e.g. hnRNP K) contain a C-terminal extension. Some KH-I superfamily members contain a divergent KH domain that lacks the RNA-binding GXXG motif. Some others have a mutated GXXG motif which may or may not have nucleic acid binding ability.


The actual alignment was detected with superfamily member cd22493:

Pssm-ID: 444693  Cd Length: 97  Bit Score: 193.35  E-value: 1.12e-59
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57530702 276 EEIPLKILAHNNFVGRLIGKEGRNLKKIEQDTDTKITISPLQDLTLYNPERTITVKGSIETCAKAEEEIMKKIRESYEND 355
Cdd:cd22493   3 DEVPLKILAHNNFVGRLIGKEGRNLKKVEQDTETKITISPLQDLTLYNPERTITVKGSIEACCRAEQEIMKKVREAYEND 82
                        90
                ....*....|....*
gi 57530702 356 IAAMNLQAHLIPGLN 370
Cdd:cd22493  83 VAAMNLQSHLIPGLN 97
RRM1_IGF2BP3 cd12627
RNA recognition motif 1 (RRM1) found in vertebrate insulin-like growth factor 2 mRNA-binding ...
1-77 6.43e-54

RNA recognition motif 1 (RRM1) found in vertebrate insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3); This subgroup corresponds to the RRM1 of IGF2BP3 (IGF2 mRNA-binding protein 3 or IMP-3), also termed KH domain-containing protein overexpressed in cancer (KOC), or VICKZ family member 3, an RNA-binding protein that plays an important role in the differentiation process during early embryogenesis. It is known to bind to and repress the translation of IGF2 leader 3 mRNA. IGF2BP3 also acts as a Glioblastoma-specific proproliferative and proinvasive marker acting through IGF2 resulting in the activation of oncogenic phosphatidylinositol 3-kinase/mitogen-activated protein kinase (PI3K/MAPK) pathways. IGF2BP3 contains four hnRNP K-homology (KH) domains, two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a RGG RNA-binding domain.


:

Pssm-ID: 410036 [Multi-domain]  Cd Length: 77  Bit Score: 177.47  E-value: 6.43e-54
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 57530702   1 MNKLYIGNLGENVSPLDLESLFKDSKIPFSGQFLVKTGYAFVDCPDESWAMKAIEALSGKVELHGKLIEVEHSVPKR 77
Cdd:cd12627   1 MNKLYIGNLSENASPLDLESIFKDWKIPFSGPFLVKTGYAFVDCPDESWAMKAIDTLSGKVELHGKVIEVEHSVPKR 77
RRM2_IGF2BP3 cd12630
RNA recognition motif 2 (RRM2) found in vertebrate insulin-like growth factor 2 mRNA-binding ...
81-156 1.76e-53

RNA recognition motif 2 (RRM2) found in vertebrate insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3); This subgroup corresponds to the RRM2 of IGF2BP3 (IGF2 mRNA-binding protein 3 or IMP-3), also termed KH domain-containing protein overexpressed in cancer (KOC), or VICKZ family member 3, an RNA-binding protein that plays an important role in the differentiation process during early embryogenesis. It is known to bind to and repress the translation of IGF2 leader 3 mRNA. IGF2BP3 also acts as a Glioblastoma-specific proproliferative and proinvasive marker acting through IGF2 resulting in the activation of oncogenic phosphatidylinositol 3-kinase/mitogen-activated protein kinase (PI3K/MAPK) pathways. IGF2BP3 contains four hnRNP K-homology (KH) domains, two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a RGG RNA-binding domain.


:

Pssm-ID: 410039 [Multi-domain]  Cd Length: 76  Bit Score: 176.36  E-value: 1.76e-53
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 57530702  81 RKLQIRNIPPHLQWEVLDSLLAQYGTVENCEQVNTDTETAVVNVTYGNKDQARQAIEKLNGFQLENYSLKVAYIPD 156
Cdd:cd12630   1 RKLQIRNIPPHLQWEVLDSLLAQYGTVENCEQVNTDTETAVVNVTYSTKDQARQAIEKLNGFQLENYSLKVTYIPD 76
KH-I_IGF2BP3_rpt3 cd22498
third type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 ...
406-483 1.26e-47

third type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3) and similar proteins; IGF2BP3, also called IGF2 mRNA-binding protein 3 (IMP-3), or hepatocellular carcinoma autoantigen p62, or IGF-II mRNA-binding protein 3, or VICKZ family member 3 (VICKZ3), or KH domain-containing protein overexpressed in cancer, or KOC, is primarily found in the nucleolus, where it can bind to the 5' UTR of the insulin-like growth factor II leader 3 mRNA and may repress translation of insulin-like growth factor II during late development. It acts as an RNA-binding factor that may recruit target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It also modulates the rate and location at which target transcripts encounter the translational apparatus and shields them from endonuclease attacks or microRNA-mediated degradation. IGF2BP3 binds to the 3'-UTR of CD44 mRNA and stabilizes it, hence promotes cell adhesion and invadopodia formation in cancer cells. It also binds to beta-actin/ACTB and MYC transcripts. IGF2BP3 can form homooligomers and heterooligomers with IGF2BP1 and IGF2BP2 in an RNA-dependent manner. IGF2BP3 contains four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the third one.


:

Pssm-ID: 411926  Cd Length: 78  Bit Score: 160.62  E-value: 1.26e-47
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 57530702 406 QPESETVHLFIPALAVGAIIGKQGQHIKQLSRFAGASIKIAPAEGPDAKLRMVIITGPPEAQFKAQGRIYGKLKEENF 483
Cdd:cd22498   1 QPESETVHLFIPALAVGAIIGKQGQHIKQLSRFAGASIKIAPAEGPDAKLRMVIITGPPEAQFKAQGRIYGKLKEENF 78
KH-I_IGF2BP1_rpt1 cd22490
first type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 ...
198-273 9.04e-47

first type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1) and similar proteins; IGF2BP1, also called IGF2 mRNA-binding protein 1 (IMP-1), or coding region determinant-binding protein (CRD-BP), or IGF-II mRNA-binding protein 1, or VICKZ family member 1 (VICKZ1), or zipcode-binding protein 1 (ZBP-1), is an RNA-binding factor that recruits target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It functions by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. It regulates localized beta-actin/ACTB mRNA translation, a crucial process for cell polarity, cell migration and neurite outgrowth. IGF2BP1 can form homodimers and heterodimers with IGF2BP1 and IGF2BP3. It contains four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the first one.


:

Pssm-ID: 411918 [Multi-domain]  Cd Length: 76  Bit Score: 158.33  E-value: 9.04e-47
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 57530702 198 PLRMLVPTQFVGAIIGKEGATIRNITKQTQSKIDIHRKENAGAAEKPITIHSTPEGCSTACKIIMEIMQKEAQDTK 273
Cdd:cd22490   1 PLRLLVPTQYVGAIIGKEGATIRNITKQTQSKIDVHRKENAGAAEKAISIHSTPEGCSAACKMILEIMQKEAKDTK 76
KH-I super family cl00098
K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found ...
491-562 4.88e-39

K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include an N-terminal extension and type I KH domains (e.g. hnRNP K) contain a C-terminal extension. Some KH-I superfamily members contain a divergent KH domain that lacks the RNA-binding GXXG motif. Some others have a mutated GXXG motif which may or may not have nucleic acid binding ability.


The actual alignment was detected with superfamily member cd22499:

Pssm-ID: 444693  Cd Length: 76  Bit Score: 137.47  E-value: 4.88e-39
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 57530702 491 KLEAHIKVPSYAAGRVIGKGGKTVNELQNLTSAEVVVPRDQTPDENDQVVVKITGHFYACQLAQRKIQEILA 562
Cdd:cd22499   1 KLETHIKVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQTPDENDQVIVKIIGHFYASQMAQRKIRDILA 72
 
Name Accession Description Interval E-value
KH-I_IGF2BP1_rpt2 cd22493
second type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 ...
276-370 1.12e-59

second type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1) and similar proteins; IGF2BP1, also called IGF2 mRNA-binding protein 1 (IMP-1), or coding region determinant-binding protein (CRD-BP), or IGF-II mRNA-binding protein 1, or VICKZ family member 1 (VICKZ1), or zipcode-binding protein 1 (ZBP-1), is an RNA-binding factor that recruits target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It functions by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. It regulates localized beta-actin/ACTB mRNA translation, a crucial process for cell polarity, cell migration and neurite outgrowth. IGF2BP1 can form homodimers and heterodimers with IGF2BP1 and IGF2BP3. It contains four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the second one.


Pssm-ID: 411921  Cd Length: 97  Bit Score: 193.35  E-value: 1.12e-59
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57530702 276 EEIPLKILAHNNFVGRLIGKEGRNLKKIEQDTDTKITISPLQDLTLYNPERTITVKGSIETCAKAEEEIMKKIRESYEND 355
Cdd:cd22493   3 DEVPLKILAHNNFVGRLIGKEGRNLKKVEQDTETKITISPLQDLTLYNPERTITVKGSIEACCRAEQEIMKKVREAYEND 82
                        90
                ....*....|....*
gi 57530702 356 IAAMNLQAHLIPGLN 370
Cdd:cd22493  83 VAAMNLQSHLIPGLN 97
RRM1_IGF2BP3 cd12627
RNA recognition motif 1 (RRM1) found in vertebrate insulin-like growth factor 2 mRNA-binding ...
1-77 6.43e-54

RNA recognition motif 1 (RRM1) found in vertebrate insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3); This subgroup corresponds to the RRM1 of IGF2BP3 (IGF2 mRNA-binding protein 3 or IMP-3), also termed KH domain-containing protein overexpressed in cancer (KOC), or VICKZ family member 3, an RNA-binding protein that plays an important role in the differentiation process during early embryogenesis. It is known to bind to and repress the translation of IGF2 leader 3 mRNA. IGF2BP3 also acts as a Glioblastoma-specific proproliferative and proinvasive marker acting through IGF2 resulting in the activation of oncogenic phosphatidylinositol 3-kinase/mitogen-activated protein kinase (PI3K/MAPK) pathways. IGF2BP3 contains four hnRNP K-homology (KH) domains, two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a RGG RNA-binding domain.


Pssm-ID: 410036 [Multi-domain]  Cd Length: 77  Bit Score: 177.47  E-value: 6.43e-54
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 57530702   1 MNKLYIGNLGENVSPLDLESLFKDSKIPFSGQFLVKTGYAFVDCPDESWAMKAIEALSGKVELHGKLIEVEHSVPKR 77
Cdd:cd12627   1 MNKLYIGNLSENASPLDLESIFKDWKIPFSGPFLVKTGYAFVDCPDESWAMKAIDTLSGKVELHGKVIEVEHSVPKR 77
RRM2_IGF2BP3 cd12630
RNA recognition motif 2 (RRM2) found in vertebrate insulin-like growth factor 2 mRNA-binding ...
81-156 1.76e-53

RNA recognition motif 2 (RRM2) found in vertebrate insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3); This subgroup corresponds to the RRM2 of IGF2BP3 (IGF2 mRNA-binding protein 3 or IMP-3), also termed KH domain-containing protein overexpressed in cancer (KOC), or VICKZ family member 3, an RNA-binding protein that plays an important role in the differentiation process during early embryogenesis. It is known to bind to and repress the translation of IGF2 leader 3 mRNA. IGF2BP3 also acts as a Glioblastoma-specific proproliferative and proinvasive marker acting through IGF2 resulting in the activation of oncogenic phosphatidylinositol 3-kinase/mitogen-activated protein kinase (PI3K/MAPK) pathways. IGF2BP3 contains four hnRNP K-homology (KH) domains, two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a RGG RNA-binding domain.


Pssm-ID: 410039 [Multi-domain]  Cd Length: 76  Bit Score: 176.36  E-value: 1.76e-53
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 57530702  81 RKLQIRNIPPHLQWEVLDSLLAQYGTVENCEQVNTDTETAVVNVTYGNKDQARQAIEKLNGFQLENYSLKVAYIPD 156
Cdd:cd12630   1 RKLQIRNIPPHLQWEVLDSLLAQYGTVENCEQVNTDTETAVVNVTYSTKDQARQAIEKLNGFQLENYSLKVTYIPD 76
KH-I_IGF2BP3_rpt3 cd22498
third type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 ...
406-483 1.26e-47

third type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3) and similar proteins; IGF2BP3, also called IGF2 mRNA-binding protein 3 (IMP-3), or hepatocellular carcinoma autoantigen p62, or IGF-II mRNA-binding protein 3, or VICKZ family member 3 (VICKZ3), or KH domain-containing protein overexpressed in cancer, or KOC, is primarily found in the nucleolus, where it can bind to the 5' UTR of the insulin-like growth factor II leader 3 mRNA and may repress translation of insulin-like growth factor II during late development. It acts as an RNA-binding factor that may recruit target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It also modulates the rate and location at which target transcripts encounter the translational apparatus and shields them from endonuclease attacks or microRNA-mediated degradation. IGF2BP3 binds to the 3'-UTR of CD44 mRNA and stabilizes it, hence promotes cell adhesion and invadopodia formation in cancer cells. It also binds to beta-actin/ACTB and MYC transcripts. IGF2BP3 can form homooligomers and heterooligomers with IGF2BP1 and IGF2BP2 in an RNA-dependent manner. IGF2BP3 contains four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the third one.


Pssm-ID: 411926  Cd Length: 78  Bit Score: 160.62  E-value: 1.26e-47
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 57530702 406 QPESETVHLFIPALAVGAIIGKQGQHIKQLSRFAGASIKIAPAEGPDAKLRMVIITGPPEAQFKAQGRIYGKLKEENF 483
Cdd:cd22498   1 QPESETVHLFIPALAVGAIIGKQGQHIKQLSRFAGASIKIAPAEGPDAKLRMVIITGPPEAQFKAQGRIYGKLKEENF 78
KH-I_IGF2BP1_rpt1 cd22490
first type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 ...
198-273 9.04e-47

first type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1) and similar proteins; IGF2BP1, also called IGF2 mRNA-binding protein 1 (IMP-1), or coding region determinant-binding protein (CRD-BP), or IGF-II mRNA-binding protein 1, or VICKZ family member 1 (VICKZ1), or zipcode-binding protein 1 (ZBP-1), is an RNA-binding factor that recruits target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It functions by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. It regulates localized beta-actin/ACTB mRNA translation, a crucial process for cell polarity, cell migration and neurite outgrowth. IGF2BP1 can form homodimers and heterodimers with IGF2BP1 and IGF2BP3. It contains four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the first one.


Pssm-ID: 411918 [Multi-domain]  Cd Length: 76  Bit Score: 158.33  E-value: 9.04e-47
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 57530702 198 PLRMLVPTQFVGAIIGKEGATIRNITKQTQSKIDIHRKENAGAAEKPITIHSTPEGCSTACKIIMEIMQKEAQDTK 273
Cdd:cd22490   1 PLRLLVPTQYVGAIIGKEGATIRNITKQTQSKIDVHRKENAGAAEKAISIHSTPEGCSAACKMILEIMQKEAKDTK 76
KH-I_IGF2BP1_rpt4 cd22499
fourth type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 ...
491-562 4.88e-39

fourth type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1) and similar proteins; IGF2BP1, also called IGF2 mRNA-binding protein 1 (IMP-1), or coding region determinant-binding protein (CRD-BP), or IGF-II mRNA-binding protein 1, or VICKZ family member 1 (VICKZ1), or zipcode-binding protein 1 (ZBP-1), is an RNA-binding factor that recruits target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It functions by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. It regulates localized beta-actin/ACTB mRNA translation, a crucial process for cell polarity, cell migration and neurite outgrowth. IGF2BP1 can form homodimers and heterodimers with IGF2BP1 and IGF2BP3. It contains four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the fourth one.


Pssm-ID: 411927  Cd Length: 76  Bit Score: 137.47  E-value: 4.88e-39
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 57530702 491 KLEAHIKVPSYAAGRVIGKGGKTVNELQNLTSAEVVVPRDQTPDENDQVVVKITGHFYACQLAQRKIQEILA 562
Cdd:cd22499   1 KLETHIKVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQTPDENDQVIVKIIGHFYASQMAQRKIRDILA 72
KH_1 pfam00013
KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause ...
199-263 2.03e-12

KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia.


Pssm-ID: 425420 [Multi-domain]  Cd Length: 65  Bit Score: 62.30  E-value: 2.03e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 57530702   199 LRMLVPTQFVGAIIGKEGATIRNITKQTQSKIDIHRKENaGAAEKPITIHSTPEGCSTACKIIME 263
Cdd:pfam00013   2 VEILVPSSLVGLIIGKGGSNIKEIREETGAKIQIPPSES-EGNERVVTITGTPEAVEAAKALIEE 65
KH_1 pfam00013
KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause ...
280-346 9.51e-12

KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia.


Pssm-ID: 425420 [Multi-domain]  Cd Length: 65  Bit Score: 60.37  E-value: 9.51e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 57530702   280 LKILAHNNFVGRLIGKEGRNLKKIEQDTDTKITISPLQDltlYNPERTITVKGSIETCAKAEEEIMK 346
Cdd:pfam00013   2 VEILVPSSLVGLIIGKGGSNIKEIREETGAKIQIPPSES---EGNERVVTITGTPEAVEAAKALIEE 65
KH smart00322
K homology RNA-binding domain;
276-348 1.11e-11

K homology RNA-binding domain;


Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 60.39  E-value: 1.11e-11
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 57530702    276 EEIPLKILAHNNFVGRLIGKEGRNLKKIEQDTDTKITISPLQdltlyNPERTITVKGSIETCAKAEEEIMKKI 348
Cdd:smart00322   1 DPVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPG-----SEERVVEITGPPENVEKAAELILEIL 68
KH smart00322
K homology RNA-binding domain;
195-265 2.02e-11

K homology RNA-binding domain;


Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 59.62  E-value: 2.02e-11
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 57530702    195 SDVPLRMLVPTQFVGAIIGKEGATIRNITKQTQSKIDIHRKENagaAEKPITIHSTPEGCSTACKIIMEIM 265
Cdd:smart00322   1 DPVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPGS---EERVVEITGPPENVEKAAELILEIL 68
KH_1 pfam00013
KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause ...
411-475 4.04e-11

KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia.


Pssm-ID: 425420 [Multi-domain]  Cd Length: 65  Bit Score: 58.45  E-value: 4.04e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 57530702   411 TVHLFIPALAVGAIIGKQGQHIKQLSRFAGASIKIaPAEGPDAKLRMVIITGPPEAQFKAQGRIY 475
Cdd:pfam00013   1 TVEILVPSSLVGLIIGKGGSNIKEIREETGAKIQI-PPSESEGNERVVTITGTPEAVEAAKALIE 64
KH smart00322
K homology RNA-binding domain;
491-561 4.24e-11

K homology RNA-binding domain;


Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 58.46  E-value: 4.24e-11
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 57530702    491 KLEAHIKVPSYAAGRVIGKGGKTVNELQNLTSAEVVVPRDQTPDEndqvVVKITGHFYACQLAQRKIQEIL 561
Cdd:smart00322   2 PVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPGSEER----VVEITGPPENVEKAAELILEIL 68
KH_1 pfam00013
KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause ...
496-559 7.33e-11

KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia.


Pssm-ID: 425420 [Multi-domain]  Cd Length: 65  Bit Score: 57.67  E-value: 7.33e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 57530702   496 IKVPSYAAGRVIGKGGKTVNELQNLTSAEVVVPRDQTPDENDqvVVKITGHFYACQLAQRKIQE 559
Cdd:pfam00013   4 ILVPSSLVGLIIGKGGSNIKEIREETGAKIQIPPSESEGNER--VVTITGTPEAVEAAKALIEE 65
RRM smart00360
RNA recognition motif;
3-70 4.81e-10

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 55.68  E-value: 4.81e-10
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 57530702      3 KLYIGNLGENVSPLDLESLF------KDSKIPFSGQFLVKTGYAFVDCPDESWAMKAIEALSGKvELHGKLIEV 70
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFskfgkvESVRLVRDKETGKSKGFAFVEFESEEDAEKALEALNGK-ELDGRPLKV 73
RRM smart00360
RNA recognition motif;
82-151 2.66e-09

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 53.75  E-value: 2.66e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 57530702     82 KLQIRNIPPHLQWEVLDSLLAQYGTVENCeQVNTDTETAVVN----VTYGNKDQARQAIEKLNGFQLENYSLKV 151
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFGKVESV-RLVRDKETGKSKgfafVEFESEEDAEKALEALNGKELDGRPLKV 73
KH smart00322
K homology RNA-binding domain;
408-478 1.65e-08

K homology RNA-binding domain;


Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 51.14  E-value: 1.65e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 57530702    408 ESETVHLFIPALAVGAIIGKQGQHIKQLSRFAGASIKIapaEGPDAKLRMVIITGPPEAQFKAQGRIYGKL 478
Cdd:smart00322   1 DPVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDI---PGPGSEERVVEITGPPENVEKAAELILEIL 68
sex-lethal TIGR01659
sex-lethal family splicing factor; This model describes the sex-lethal family of splicing ...
13-194 6.65e-07

sex-lethal family splicing factor; This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661).


Pssm-ID: 273740 [Multi-domain]  Cd Length: 346  Bit Score: 51.56  E-value: 6.65e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57530702    13 VSPLDLESLFKDSKIPFSgqflvkTGYAFVDCPDESWAMKAIEALSGkVELHGKLIEVEHSVP--KRQRSRKLQIRNIPP 90
Cdd:TIGR01659 131 IGPINTCRIMRDYKTGYS------FGYAFVDFGSEADSQRAIKNLNG-ITVRNKRLKVSYARPggESIKDTNLYVTNLPR 203
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57530702    91 HLQWEVLDSLLAQYGTVencEQVN------TDTETAVVNVTYGNKDQARQAIEKLNGFQLENYS--LKVAYIPDEMAAQQ 162
Cdd:TIGR01659 204 TITDDQLDTIFGKYGQI---VQKNilrdklTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSqpLTVRLAEEHGKAKA 280
                         170       180       190
                  ....*....|....*....|....*....|..
gi 57530702   163 PPQQHPQGRRGFGQRGPPRQGSPSATTRQKPQ 194
Cdd:TIGR01659 281 HHYMSQMGHGNMGNMGHGNMGMAGGSGMNPPN 312
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
85-150 1.22e-06

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C-terminus that has some features characteristic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 46.07  E-value: 1.22e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 57530702    85 IRNIPPHLQWEVLDSLLAQYGTVENCEQVNTDTETA--VVNVTYGNKDQARQAIEKLNGFQLENYSLK 150
Cdd:pfam00076   3 VGNLPPDTTEEDLKDLFSKFGPIKSIRLVRDETGRSkgFAFVEFEDEEDAEKAIEALNGKELGGRELK 70
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
4-69 1.66e-06

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C-terminus that has some features characteristic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 45.69  E-value: 1.66e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 57530702     4 LYIGNLGENVSPLDLESLF------KDSKIPfSGQFLVKTGYAFVDCPDESWAMKAIEALSGKvELHGKLIE 69
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFskfgpiKSIRLV-RDETGRSKGFAFVEFEDEEDAEKAIEALNGK-ELGGRELK 70
ELAV_HUD_SF TIGR01661
ELAV/HuD family splicing factor; This model describes the ELAV/HuD subfamily of splicing ...
30-141 2.09e-06

ELAV/HuD family splicing factor; This model describes the ELAV/HuD subfamily of splicing factors found in metazoa. HuD stands for the human paraneoplastic encephalomyelitis antigen D of which there are 4 variants in human. ELAV stnds for the Drosophila Embryonic lethal abnormal visual protein. ELAV-like splicing factors are also known in human as HuB (ELAV-like protein 2), HuC (ELAV-like protein 3, Paraneoplastic cerebellar degeneration-associated antigen) and HuR (ELAV-like protein 1). These genes are most closely related to the sex-lethal subfamily of splicing factors found in Dipteran insects (TIGR01659). These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).


Pssm-ID: 273741 [Multi-domain]  Cd Length: 352  Bit Score: 49.94  E-value: 2.09e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57530702    30 SGQFLvktGYAFVDCPDESWAMKAIEALSGkVELHGKLIEVEHSVPKRQ--RSRKLQIRNIPPHLQWEVLDSLLAQYGTV 107
Cdd:TIGR01661  41 TGQSL---GYGFVNYVRPEDAEKAVNSLNG-LRLQNKTIKVSYARPSSDsiKGANLYVSGLPKTMTQHELESIFSPFGQI 116
                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 57530702   108 EN----CEQVnTDTETAVVNVTYGNKDQARQAIEKLNG 141
Cdd:TIGR01661 117 ITsrilSDNV-TGLSKGVGFIRFDKRDEADRAIKTLNG 153
PRK13763 PRK13763
putative RNA-processing protein; Provisional
203-335 1.32e-05

putative RNA-processing protein; Provisional


Pssm-ID: 237494 [Multi-domain]  Cd Length: 180  Bit Score: 46.01  E-value: 1.32e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57530702  203 VPTQFVGAIIGKEGATIRNITKQTQSKIDIHRKENAgaaekpITIhsTPEGCSTACKII--MEIMQkeAQDTKFTEEIPL 280
Cdd:PRK13763   9 IPKDRIGVLIGKKGETKKEIEERTGVKLEIDSETGE------VII--EPTDGEDPLAVLkaRDIVK--AIGRGFSPEKAL 78
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 57530702  281 KILAHNNFV-------------------GRLIGKEGRNLKKIEQDTDTKITISplqDLTLY---NPERTITVKGSIE 335
Cdd:PRK13763  79 RLLDDDYVLevidlsdygdspnalrrikGRIIGEGGKTRRIIEELTGVDISVY---GKTVAiigDPEQVEIAREAIE 152
PRK13763 PRK13763
putative RNA-processing protein; Provisional
411-561 2.43e-05

putative RNA-processing protein; Provisional


Pssm-ID: 237494 [Multi-domain]  Cd Length: 180  Bit Score: 45.24  E-value: 2.43e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57530702  411 TVHLFIPALAVGAIIGKQGQHIKQLSRFAGASIKIapaegpDAKLRMVIIT----GPPEAQFKAQGRI----YGklkeen 482
Cdd:PRK13763   4 MEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEI------DSETGEVIIEptdgEDPLAVLKARDIVkaigRG------ 71
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57530702  483 fFGPKEEVKLEAH------IKVPSYAA---------GRVIGKGGKTVNELQNLTSAEVVVpRDQTpdendqvvVKITGHF 547
Cdd:PRK13763  72 -FSPEKALRLLDDdyvlevIDLSDYGDspnalrrikGRIIGEGGKTRRIIEELTGVDISV-YGKT--------VAIIGDP 141
                        170
                 ....*....|....
gi 57530702  548 YACQLAQRKIQEIL 561
Cdd:PRK13763 142 EQVEIAREAIEMLI 155
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
2-87 2.91e-05

RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];


Pssm-ID: 223796 [Multi-domain]  Cd Length: 306  Bit Score: 46.09  E-value: 2.91e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57530702   2 NKLYIGNLGENVSPLDLESLFKDS------KIPFSGQFLVKTGYAFVDCPDESWAMKAIEALSGKvELHGKLIEVEHSVP 75
Cdd:COG0724 116 NTLFVGNLPYDVTEEDLRELFKKFgpvkrvRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGK-ELEGRPLRVQKAQP 194
                        90
                ....*....|..
gi 57530702  76 KRQRSRKLQIRN 87
Cdd:COG0724 195 ASQPRSELSNNL 206
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
71-151 1.00e-04

RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];


Pssm-ID: 223796 [Multi-domain]  Cd Length: 306  Bit Score: 44.55  E-value: 1.00e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57530702  71 EHSVPKRQRSRKLQIRNIPPHLQWEVLDSLLAQYGTVENCeQVNTDTETAVV----NVTYGNKDQARQAIEKLNGFQLEN 146
Cdd:COG0724 106 KSRQKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRV-RLVRDRETGKSrgfaFVEFESEESAEKAIEELNGKELEG 184

                ....*
gi 57530702 147 YSLKV 151
Cdd:COG0724 185 RPLRV 189
arCOG04150 TIGR03665
arCOG04150 universal archaeal KH domain protein; This family of proteins is universal among ...
413-527 1.14e-04

arCOG04150 universal archaeal KH domain protein; This family of proteins is universal among the 41 archaeal genomes analyzed, and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.


Pssm-ID: 274711 [Multi-domain]  Cd Length: 172  Bit Score: 42.94  E-value: 1.14e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57530702   413 HLFIPALAVGAIIGKQGQHIKQLSRFAGASIKIapaegpDAKLRMVII---TGPPEAQFKAQGRI----YGklkeenfFG 485
Cdd:TIGR03665   1 YVKIPKDRIGVLIGKGGETKKEIEERTGVKLDI------DSETGEVKIepeDEDPLAVMKAREVVkaigRG-------FS 67
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 57530702   486 PKEEVKLEAH------IKVPSYAA---------GRVIGKGGKTVNELQNLTSAEVVV 527
Cdd:TIGR03665  68 PEKALKLLDDdymlevIDLKEYGKspnalrrikGRIIGEGGKTRRIIEELTGVSISV 124
MSL5 COG5176
Splicing factor (branch point binding protein) [RNA processing and modification];
272-313 1.94e-04

Splicing factor (branch point binding protein) [RNA processing and modification];


Pssm-ID: 227503 [Multi-domain]  Cd Length: 269  Bit Score: 43.42  E-value: 1.94e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
gi 57530702 272 TKFTEE--IPLKILAHNNFVGRLIGKEGRNLKKIEQDTDTKITI 313
Cdd:COG5176 146 SKYQNKiyIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAI 189
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
3-72 7.79e-04

splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed.


Pssm-ID: 273721 [Multi-domain]  Cd Length: 494  Bit Score: 42.21  E-value: 7.79e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57530702     3 KLYIGNLGENVSPLDLESLFKdskiPFSGQFLVK----------TGYAFVDCPDESWAMKAIEALSGkVELHGKLIEVEH 72
Cdd:TIGR01622 216 RLYVGNLHFNITEQDLRQIFE----PFGEIEFVQlqkdpetgrsKGYGFIQFRDAEQAKEALEKMNG-FELAGRPIKVGL 290
Pnp COG1185
Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ...
201-297 8.84e-03

Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis];


Pssm-ID: 224106 [Multi-domain]  Cd Length: 692  Bit Score: 39.10  E-value: 8.84e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57530702 201 MLVPTQFVGAIIGKEGATIRNITKQTQSKIDIhrkENAGAaekpITIHSTPEGCSTACKIIMEIMQKEAQDTKFTEEIPL 280
Cdd:COG1185 556 IKIDPDKIRDVIGPGGKTIKAITEETGVKIDI---EDDGT----VKIAASDGESAKKAKERIEAITREVEVGEVYEGTVV 628
                        90
                ....*....|....*..
gi 57530702 281 KILAHNNFVGRLIGKEG 297
Cdd:COG1185 629 RIVDFGAFVELLPGKDG 645
 
Name Accession Description Interval E-value
KH-I_IGF2BP1_rpt2 cd22493
second type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 ...
276-370 1.12e-59

second type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1) and similar proteins; IGF2BP1, also called IGF2 mRNA-binding protein 1 (IMP-1), or coding region determinant-binding protein (CRD-BP), or IGF-II mRNA-binding protein 1, or VICKZ family member 1 (VICKZ1), or zipcode-binding protein 1 (ZBP-1), is an RNA-binding factor that recruits target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It functions by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. It regulates localized beta-actin/ACTB mRNA translation, a crucial process for cell polarity, cell migration and neurite outgrowth. IGF2BP1 can form homodimers and heterodimers with IGF2BP1 and IGF2BP3. It contains four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the second one.


Pssm-ID: 411921  Cd Length: 97  Bit Score: 193.35  E-value: 1.12e-59
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57530702 276 EEIPLKILAHNNFVGRLIGKEGRNLKKIEQDTDTKITISPLQDLTLYNPERTITVKGSIETCAKAEEEIMKKIRESYEND 355
Cdd:cd22493   3 DEVPLKILAHNNFVGRLIGKEGRNLKKVEQDTETKITISPLQDLTLYNPERTITVKGSIEACCRAEQEIMKKVREAYEND 82
                        90
                ....*....|....*
gi 57530702 356 IAAMNLQAHLIPGLN 370
Cdd:cd22493  83 VAAMNLQSHLIPGLN 97
RRM1_IGF2BP3 cd12627
RNA recognition motif 1 (RRM1) found in vertebrate insulin-like growth factor 2 mRNA-binding ...
1-77 6.43e-54

RNA recognition motif 1 (RRM1) found in vertebrate insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3); This subgroup corresponds to the RRM1 of IGF2BP3 (IGF2 mRNA-binding protein 3 or IMP-3), also termed KH domain-containing protein overexpressed in cancer (KOC), or VICKZ family member 3, an RNA-binding protein that plays an important role in the differentiation process during early embryogenesis. It is known to bind to and repress the translation of IGF2 leader 3 mRNA. IGF2BP3 also acts as a Glioblastoma-specific proproliferative and proinvasive marker acting through IGF2 resulting in the activation of oncogenic phosphatidylinositol 3-kinase/mitogen-activated protein kinase (PI3K/MAPK) pathways. IGF2BP3 contains four hnRNP K-homology (KH) domains, two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a RGG RNA-binding domain.


Pssm-ID: 410036 [Multi-domain]  Cd Length: 77  Bit Score: 177.47  E-value: 6.43e-54
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 57530702   1 MNKLYIGNLGENVSPLDLESLFKDSKIPFSGQFLVKTGYAFVDCPDESWAMKAIEALSGKVELHGKLIEVEHSVPKR 77
Cdd:cd12627   1 MNKLYIGNLSENASPLDLESIFKDWKIPFSGPFLVKTGYAFVDCPDESWAMKAIDTLSGKVELHGKVIEVEHSVPKR 77
RRM2_IGF2BP3 cd12630
RNA recognition motif 2 (RRM2) found in vertebrate insulin-like growth factor 2 mRNA-binding ...
81-156 1.76e-53

RNA recognition motif 2 (RRM2) found in vertebrate insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3); This subgroup corresponds to the RRM2 of IGF2BP3 (IGF2 mRNA-binding protein 3 or IMP-3), also termed KH domain-containing protein overexpressed in cancer (KOC), or VICKZ family member 3, an RNA-binding protein that plays an important role in the differentiation process during early embryogenesis. It is known to bind to and repress the translation of IGF2 leader 3 mRNA. IGF2BP3 also acts as a Glioblastoma-specific proproliferative and proinvasive marker acting through IGF2 resulting in the activation of oncogenic phosphatidylinositol 3-kinase/mitogen-activated protein kinase (PI3K/MAPK) pathways. IGF2BP3 contains four hnRNP K-homology (KH) domains, two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a RGG RNA-binding domain.


Pssm-ID: 410039 [Multi-domain]  Cd Length: 76  Bit Score: 176.36  E-value: 1.76e-53
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 57530702  81 RKLQIRNIPPHLQWEVLDSLLAQYGTVENCEQVNTDTETAVVNVTYGNKDQARQAIEKLNGFQLENYSLKVAYIPD 156
Cdd:cd12630   1 RKLQIRNIPPHLQWEVLDSLLAQYGTVENCEQVNTDTETAVVNVTYSTKDQARQAIEKLNGFQLENYSLKVTYIPD 76
KH-I_IGF2BP3_rpt2 cd22495
second type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 ...
279-355 4.05e-49

second type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3) and similar proteins; IGF2BP3, also called IGF2 mRNA-binding protein 3 (IMP-3), or hepatocellular carcinoma autoantigen p62, or IGF-II mRNA-binding protein 3, or VICKZ family member 3 (VICKZ3), or KH domain-containing protein overexpressed in cancer, or KOC, is primarily found in the nucleolus, where it can bind to the 5' UTR of the insulin-like growth factor II leader 3 mRNA and may repress translation of insulin-like growth factor II during late development. It acts as an RNA-binding factor that may recruit target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It also modulates the rate and location at which target transcripts encounter the translational apparatus and shields them from endonuclease attacks or microRNA-mediated degradation. IGF2BP3 binds to the 3'-UTR of CD44 mRNA and stabilizes it, hence promotes cell adhesion and invadopodia formation in cancer cells. It also binds to beta-actin/ACTB and MYC transcripts. IGF2BP3 can form homooligomers and heterooligomers with IGF2BP1 and IGF2BP2 in an RNA-dependent manner. IGF2BP3 contains four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the second one.


Pssm-ID: 411923  Cd Length: 77  Bit Score: 164.83  E-value: 4.05e-49
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 57530702 279 PLKILAHNNFVGRLIGKEGRNLKKIEQDTDTKITISPLQDLTLYNPERTITVKGSIETCAKAEEEIMKKIRESYEND 355
Cdd:cd22495   1 PLKILAHNNFVGRLIGKEGRNLKKIEQDTDTKITISPLQDLTLYNPERTITVKGSIETCAKAEEEIMKKIRESYEND 77
KH-I_IGF2BP3_rpt3 cd22498
third type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 ...
406-483 1.26e-47

third type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3) and similar proteins; IGF2BP3, also called IGF2 mRNA-binding protein 3 (IMP-3), or hepatocellular carcinoma autoantigen p62, or IGF-II mRNA-binding protein 3, or VICKZ family member 3 (VICKZ3), or KH domain-containing protein overexpressed in cancer, or KOC, is primarily found in the nucleolus, where it can bind to the 5' UTR of the insulin-like growth factor II leader 3 mRNA and may repress translation of insulin-like growth factor II during late development. It acts as an RNA-binding factor that may recruit target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It also modulates the rate and location at which target transcripts encounter the translational apparatus and shields them from endonuclease attacks or microRNA-mediated degradation. IGF2BP3 binds to the 3'-UTR of CD44 mRNA and stabilizes it, hence promotes cell adhesion and invadopodia formation in cancer cells. It also binds to beta-actin/ACTB and MYC transcripts. IGF2BP3 can form homooligomers and heterooligomers with IGF2BP1 and IGF2BP2 in an RNA-dependent manner. IGF2BP3 contains four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the third one.


Pssm-ID: 411926  Cd Length: 78  Bit Score: 160.62  E-value: 1.26e-47
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 57530702 406 QPESETVHLFIPALAVGAIIGKQGQHIKQLSRFAGASIKIAPAEGPDAKLRMVIITGPPEAQFKAQGRIYGKLKEENF 483
Cdd:cd22498   1 QPESETVHLFIPALAVGAIIGKQGQHIKQLSRFAGASIKIAPAEGPDAKLRMVIITGPPEAQFKAQGRIYGKLKEENF 78
KH-I_IGF2BP1_rpt1 cd22490
first type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 ...
198-273 9.04e-47

first type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1) and similar proteins; IGF2BP1, also called IGF2 mRNA-binding protein 1 (IMP-1), or coding region determinant-binding protein (CRD-BP), or IGF-II mRNA-binding protein 1, or VICKZ family member 1 (VICKZ1), or zipcode-binding protein 1 (ZBP-1), is an RNA-binding factor that recruits target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It functions by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. It regulates localized beta-actin/ACTB mRNA translation, a crucial process for cell polarity, cell migration and neurite outgrowth. IGF2BP1 can form homodimers and heterodimers with IGF2BP1 and IGF2BP3. It contains four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the first one.


Pssm-ID: 411918 [Multi-domain]  Cd Length: 76  Bit Score: 158.33  E-value: 9.04e-47
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 57530702 198 PLRMLVPTQFVGAIIGKEGATIRNITKQTQSKIDIHRKENAGAAEKPITIHSTPEGCSTACKIIMEIMQKEAQDTK 273
Cdd:cd22490   1 PLRLLVPTQYVGAIIGKEGATIRNITKQTQSKIDVHRKENAGAAEKAISIHSTPEGCSAACKMILEIMQKEAKDTK 76
KH-I_IGF2BP2_rpt2 cd22494
second type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 ...
279-355 1.16e-45

second type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2) and similar proteins; IGF2BP2, also called IGF2 mRNA-binding protein 2 (IMP-2), or hepatocellular carcinoma autoantigen p62, or IGF-II mRNA-binding protein 2, or VICKZ family member 2 (VICKZ2), is an RNA-binding factor that recruits target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It functions by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. It also binds to beta-actin/ACTB and MYC transcripts. IGF2BP2 can form homooligomers and heterooligomers with IGF2BP1 and IGF2BP3 in an RNA-dependent manner. It contains four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the second one.


Pssm-ID: 411922  Cd Length: 77  Bit Score: 155.57  E-value: 1.16e-45
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 57530702 279 PLKILAHNNFVGRLIGKEGRNLKKIEQDTDTKITISPLQDLTLYNPERTITVKGSIETCAKAEEEIMKKIRESYEND 355
Cdd:cd22494   1 PLKILAHNSLVGRLIGKEGRNLKKIEQDTGTKITISSLQDLTIYNPERTITVKGSIEACSSAEVEIMKKLREAYEND 77
KH-I_IGF2BP2_rpt1 cd22491
first type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 ...
198-271 2.71e-44

first type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2) and similar proteins; IGF2BP2, also called IGF2 mRNA-binding protein 2 (IMP-2), or hepatocellular carcinoma autoantigen p62, or IGF-II mRNA-binding protein 2, or VICKZ family member 2 (VICKZ2), is an RNA-binding factor that recruits target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It functions by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. It also binds to beta-actin/ACTB and MYC transcripts. IGF2BP2 can form homooligomers and heterooligomers with IGF2BP1 and IGF2BP3 in an RNA-dependent manner. It contains four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the first one.


Pssm-ID: 411919  Cd Length: 74  Bit Score: 151.75  E-value: 2.71e-44
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 57530702 198 PLRMLVPTQFVGAIIGKEGATIRNITKQTQSKIDIHRKENAGAAEKPITIHSTPEGCSTACKIIMEIMQKEAQD 271
Cdd:cd22491   1 PLRILVPTQFVGAIIGKEGLTIKNITKQTQSKVDIHRKENAGAAEKPITIHATPEGCSAACRMILEIMQKEANE 74
RRM1_IGF2BP1 cd12625
RNA recognition motif 1 (RRM1) found in vertebrate insulin-like growth factor 2 mRNA-binding ...
1-77 4.99e-44

RNA recognition motif 1 (RRM1) found in vertebrate insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1); This subgroup corresponds to the RRM1 of IGF2BP1 (IGF2 mRNA-binding protein 1 or IMP-1), also termed coding region determinant-binding protein (CRD-BP), or VICKZ family member 1, or zipcode-binding protein 1 (ZBP-1). IGF2BP1 is a multi-functional regulator of RNA metabolism that has been implicated in the control of aspects of localization, stability, and translation for many mRNAs. It is predominantly located in cytoplasm and was initially identified as a trans-acting factor that interacts with the zipcode in the 3'- untranslated region (UTR) of the beta-actin mRNA, which is important for its localization and translational regulation. It inhibits IGF-II mRNA translation through binding to the 5'-UTR of the transcript. IGF2BP1 also acts as human immunodeficiency virus type 1 (HIV-1) Gag-binding factor that interacts with HIV-1 Gag protein and blocks the formation of infectious HIV-1 particles. IGF2BP1 promotes mRNA stabilization; it functions as a coding region determinant (CRD)-binding protein that binds to the coding region of betaTrCP1 mRNA and prevents miR-183-mediated degradation of betaTrCP1 mRNA. It also promotes c-myc mRNA stability by associating with the CRD and stabilizes CD44 mRNA via interaction with the 3'-UTR of the transcript. In addition, IGF2BP1 specifically interacts with both Hepatitis C virus (HCV) 5'-UTR and 3'-UTR, further recruiting eIF3 and enhancing HCV internal ribosome entry site (IRES)-mediated translation initiation via the 3'-UTR. IGF2BP1 contains four hnRNP K-homology (KH) domains, two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a RGG RNA-binding domain. It also contains two putative nuclear export signals (NESs) and a putative nuclear localization signal (NLS).


Pssm-ID: 241069 [Multi-domain]  Cd Length: 77  Bit Score: 150.95  E-value: 4.99e-44
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 57530702   1 MNKLYIGNLGENVSPLDLESLFKDSKIPFSGQFLVKTGYAFVDCPDESWAMKAIEALSGKVELHGKLIEVEHSVPKR 77
Cdd:cd12625   1 MNKLYIGNLNESVTPADLEKVFEDHKISYSGQFLVKSGYAFVDCPDEQWAMKAIETFSGKVELHGKRLEIEHSVPKK 77
RRM2_IGF2BP2 cd12629
RNA recognition motif 2 (RRM2) found in vertebrate insulin-like growth factor 2 mRNA-binding ...
81-156 3.80e-43

RNA recognition motif 2 (RRM2) found in vertebrate insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2); This subgroup corresponds to the RRM2 of IGF2BP2 (IGF2 mRNA-binding protein 2 or IMP-2), also termed hepatocellular carcinoma autoantigen p62, or VICKZ family member 2, a ubiquitously expressed RNA-binding protein involved in the stimulation of insulin action. It is predominantly nuclear. SNPs in IGF2BP2 gene are implicated in susceptibility to type 2 diabetes. IGF2BP2 plays an important role in cellular motility; it regulates the expression of PINCH-2, an important mediator of cell adhesion and motility, and MURF-3, a microtubule-stabilizing protein, through direct binding to their mRNAs. IGF2BP2 may be involved in the regulation of mRNA stability through the interaction with the AU-rich element-binding factor AUF1. In addition, IGF2BP2 binds initially to nascent beta-actin transcripts and facilitates the subsequent binding of the shuttling IGF2BP1. IGF2BP2 contains four hnRNP K-homology (KH) domains, two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a RGG RNA-binding domain.


Pssm-ID: 410038 [Multi-domain]  Cd Length: 76  Bit Score: 148.66  E-value: 3.80e-43
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 57530702  81 RKLQIRNIPPHLQWEVLDSLLAQYGTVENCEQVNTDTETAVVNVTYGNKDQARQAIEKLNGFQLENYSLKVAYIPD 156
Cdd:cd12629   1 RKIQIRNIPPHLQWEVLDGLLAQYGTVENVEQVNTDTETAVVNVTYATKEEAKVAVEKLSGHQFENYSFKISYIPD 76
RRM2_VICKZ cd12359
RNA recognition motif 2 (RRM2) found in the VICKZ family proteins; This subfamily corresponds ...
81-156 1.89e-42

RNA recognition motif 2 (RRM2) found in the VICKZ family proteins; This subfamily corresponds to the RRM2 of IGF-II mRNA-binding proteins (IGF2BPs or IMPs) in the VICKZ family that have been implicated in the post-transcriptional regulation of several different RNAs and in subcytoplasmic localization of mRNAs during embryogenesis. IGF2BPs are composed of two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and four hnRNP K homology (KH) domains.


Pssm-ID: 409794 [Multi-domain]  Cd Length: 76  Bit Score: 146.75  E-value: 1.89e-42
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 57530702  81 RKLQIRNIPPHLQWEVLDSLLAQYGTVENCEQVNTDTETAVVNVTYGNKDQARQAIEKLNGFQLENYSLKVAYIPD 156
Cdd:cd12359   1 RKIQIRNIPPHARWEDLDSLLSTYGTVENCEQVNTKSETATVNVTYESPEQAQQAVNKLNGYQYEGSALKVSYIPD 76
RRM2_IGF2BP1 cd12628
RNA recognition motif 2 (RRM2) found in vertebrate insulin-like growth factor 2 mRNA-binding ...
81-156 3.09e-42

RNA recognition motif 2 (RRM2) found in vertebrate insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1); This subgroup corresponds to the RRM2 of IGF2BP1 (IGF2 mRNA-binding protein 1 or IMP-1), also termed coding region determinant-binding protein (CRD-BP), or VICKZ family member 1, or zipcode-binding protein 1 (ZBP-1). IGF2BP1 is a multi-functional regulator of RNA metabolism that has been implicated in the control of aspects of localization, stability, and translation for many mRNAs. It is predominantly located in cytoplasm and was initially identified as a trans-acting factor that interacts with the zipcode in the 3'- untranslated region (UTR) of the beta-actin mRNA, which is important for its localization and translational regulation. It inhibits IGF-II mRNA translation through binding to the 5'-UTR of the transcript. IGF2BP1 also acts as human immunodeficiency virus type 1 (HIV-1) Gag-binding factor that interacts with HIV-1 Gag protein and blocks the formation of infectious HIV-1 particles. It promotes mRNA stabilization and functions as a coding region determinant (CRD)-binding protein that binds to the coding region of betaTrCP1 mRNA and prevents miR-183-mediated degradation of betaTrCP1 mRNA. It also promotes c-myc mRNA stability by associating with the CRD. It stabilizes CD44 mRNA via interaction with the 3'-UTR of the transcript. In addition, IGF2BP1 specifically interacts with both Hepatitis C virus (HCV) 5'-UTR and 3'-UTR, further recruiting eIF3 and enhancing HCV internal ribosome entry site (IRES)-mediated translation initiation via the 3'-UTR. IGF2BP1 contains four hnRNP K-homology (KH) domains, two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a RGG RNA-binding domain. It also contains two putative nuclear export signals (NESs) and a putative nuclear localization signal (NLS).


Pssm-ID: 410037 [Multi-domain]  Cd Length: 76  Bit Score: 146.36  E-value: 3.09e-42
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 57530702  81 RKLQIRNIPPHLQWEVLDSLLAQYGTVENCEQVNTDTETAVVNVTYGNKDQARQAIEKLNGFQLENYSLKVAYIPD 156
Cdd:cd12628   1 RKIQIRNIPPQLRWEVLDGLLAQYGTVENCEQVNTDSETAVVNVTYGNREQTRQAIMKLNGHQLENHVLKVSYIPD 76
KH-I_IGF2BP1_rpt3 cd22496
third type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 ...
408-483 3.79e-42

third type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1) and similar proteins; IGF2BP1, also called IGF2 mRNA-binding protein 1 (IMP-1), or coding region determinant-binding protein (CRD-BP), or IGF-II mRNA-binding protein 1, or VICKZ family member 1 (VICKZ1), or zipcode-binding protein 1 (ZBP-1), is an RNA-binding factor that recruits target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It functions by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. It regulates localized beta-actin/ACTB mRNA translation, a crucial process for cell polarity, cell migration and neurite outgrowth. IGF2BP1 can form homodimers and heterodimers with IGF2BP1 and IGF2BP3. It contains four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the third one.


Pssm-ID: 411924  Cd Length: 76  Bit Score: 145.93  E-value: 3.79e-42
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 57530702 408 ESETVHLFIPALAVGAIIGKQGQHIKQLSRFAGASIKIAPAEGPDAKLRMVIITGPPEAQFKAQGRIYGKLKEENF 483
Cdd:cd22496   1 EQETVHVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGPPEAQFKAQGRIYGKLKEENF 76
KH-I_IGF2BP3_rpt1 cd22492
first type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 ...
198-273 4.33e-40

first type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3) and similar proteins; IGF2BP3, also called IGF2 mRNA-binding protein 3 (IMP-3), or hepatocellular carcinoma autoantigen p62, or IGF-II mRNA-binding protein 3, or VICKZ family member 3 (VICKZ3), or KH domain-containing protein overexpressed in cancer, or KOC, is primarily found in the nucleolus, where it can bind to the 5' UTR of the insulin-like growth factor II leader 3 mRNA and may repress translation of insulin-like growth factor II during late development. It acts as an RNA-binding factor that may recruit target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It also modulates the rate and location at which target transcripts encounter the translational apparatus and shields them from endonuclease attacks or microRNA-mediated degradation. IGF2BP3 binds to the 3'-UTR of CD44 mRNA and stabilizes it, hence promotes cell adhesion and invadopodia formation in cancer cells. It also binds to beta-actin/ACTB and MYC transcripts. IGF2BP3 can form homooligomers and heterooligomers with IGF2BP1 and IGF2BP2 in an RNA-dependent manner. IGF2BP3 contains four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the first one.


Pssm-ID: 411920  Cd Length: 76  Bit Score: 140.33  E-value: 4.33e-40
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 57530702 198 PLRMLVPTQFVGAIIGKEGATIRNITKQTQSKIDIHRKENAGAAEKPITIHSTPEGCSTACKIIMEIMQKEAQDTK 273
Cdd:cd22492   1 PLRLLVPTQFVGAIIGKEGATIRNITKQTQSKIDVHRKENAGAAEKSITILSTPEGTSAACKSILEIMHKEAQDIK 76
KH-I_IGF2BP_rpt1 cd22400
first type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 ...
198-265 4.62e-39

first type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 mRNA-binding protein (IGF2BP) family; The IGF2BP family includes three members: IGF2BP1/IMP-1/ CRD-BP/ VICKZ1, IGF2BP2/IMP-2/ VICKZ2, and IGF2BP3/IMP-3/VICKZ3, which are RNA-binding factors that recruit target transcripts to cytoplasmic protein-RNA complexes (mRNPs). They function by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. IGF2BP proteins contain four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the first one.


Pssm-ID: 411828 [Multi-domain]  Cd Length: 68  Bit Score: 137.02  E-value: 4.62e-39
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 57530702 198 PLRMLVPTQFVGAIIGKEGATIRNITKQTQSKIDIHRKENAGAAEKPITIHSTPEGCSTACKIIMEIM 265
Cdd:cd22400   1 PLRILVPSEFVGAIIGKGGATIRQITQQTGARIDIHRKENAGAAEKAITIYGTPEGCSSACKQILEIM 68
KH-I_IGF2BP1_rpt4 cd22499
fourth type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 ...
491-562 4.88e-39

fourth type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1) and similar proteins; IGF2BP1, also called IGF2 mRNA-binding protein 1 (IMP-1), or coding region determinant-binding protein (CRD-BP), or IGF-II mRNA-binding protein 1, or VICKZ family member 1 (VICKZ1), or zipcode-binding protein 1 (ZBP-1), is an RNA-binding factor that recruits target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It functions by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. It regulates localized beta-actin/ACTB mRNA translation, a crucial process for cell polarity, cell migration and neurite outgrowth. IGF2BP1 can form homodimers and heterodimers with IGF2BP1 and IGF2BP3. It contains four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the fourth one.


Pssm-ID: 411927  Cd Length: 76  Bit Score: 137.47  E-value: 4.88e-39
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 57530702 491 KLEAHIKVPSYAAGRVIGKGGKTVNELQNLTSAEVVVPRDQTPDENDQVVVKITGHFYACQLAQRKIQEILA 562
Cdd:cd22499   1 KLETHIKVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQTPDENDQVIVKIIGHFYASQMAQRKIRDILA 72
KH-I_IGF2BP_rpt2 cd22401
second type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 ...
279-350 1.22e-38

second type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 mRNA-binding protein (IGF2BP) family; The IGF2BP family includes three members: IGF2BP1/IMP-1/ CRD-BP/ VICKZ1, IGF2BP2/IMP-2/ VICKZ2, and IGF2BP3/IMP-3/VICKZ3, which are RNA-binding factors that recruit target transcripts to cytoplasmic protein-RNA complexes (mRNPs). They function by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. IGF2BP proteins contain four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the second one.


Pssm-ID: 411829 [Multi-domain]  Cd Length: 72  Bit Score: 136.20  E-value: 1.22e-38
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 57530702 279 PLKILAHNNFVGRLIGKEGRNLKKIEQDTDTKITISPLQDLTLYNPERTITVKGSIETCAKAEEEIMKKIRE 350
Cdd:cd22401   1 PLKILAHNNLCGRLIGKDGRNIKKIMEDTNTKITISSLQDLTSYNPERTITIKGSLEAMSEAESLISEKLRE 72
KH-I_IGF2BP3_rpt4 cd22501
fourth type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 ...
493-558 1.29e-38

fourth type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3) and similar proteins; IGF2BP3, also called IGF2 mRNA-binding protein 3 (IMP-3), or hepatocellular carcinoma autoantigen p62, or IGF-II mRNA-binding protein 3, or VICKZ family member 3 (VICKZ3), or KH domain-containing protein overexpressed in cancer, or KOC, is primarily found in the nucleolus, where it can bind to the 5' UTR of the insulin-like growth factor II leader 3 mRNA and may repress translation of insulin-like growth factor II during late development. It acts as an RNA-binding factor that may recruit target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It also modulates the rate and location at which target transcripts encounter the translational apparatus and shields them from endonuclease attacks or microRNA-mediated degradation. IGF2BP3 binds to the 3'-UTR of CD44 mRNA and stabilizes it, hence promotes cell adhesion and invadopodia formation in cancer cells. It also binds to beta-actin/ACTB and MYC transcripts. IGF2BP3 can form homooligomers and heterooligomers with IGF2BP1 and IGF2BP2 in an RNA-dependent manner. IGF2BP3 contains four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the fourth one.


Pssm-ID: 411929  Cd Length: 66  Bit Score: 135.97  E-value: 1.29e-38
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 57530702 493 EAHIKVPSYAAGRVIGKGGKTVNELQNLTSAEVVVPRDQTPDENDQVVVKITGHFYACQLAQRKIQ 558
Cdd:cd22501   1 EAHIKVPSYAAGRVIGKGGKTVNELQNLTSAEVVVPRDQTPDENDQVVVKITGHFYASQLAQRKIQ 66
KH-I_IGF2BP2_rpt3 cd22497
third type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 ...
408-484 3.38e-38

third type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2) and similar proteins; IGF2BP2, also called IGF2 mRNA-binding protein 2 (IMP-2), or hepatocellular carcinoma autoantigen p62, or IGF-II mRNA-binding protein 2, or VICKZ family member 2 (VICKZ2), is an RNA-binding factor that recruits target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It functions by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. It also binds to beta-actin/ACTB and MYC transcripts. IGF2BP2 can form homooligomers and heterooligomers with IGF2BP1 and IGF2BP3 in an RNA-dependent manner. It contains four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the third one.


Pssm-ID: 411925  Cd Length: 77  Bit Score: 135.22  E-value: 3.38e-38
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 57530702 408 ESETVHLFIPALAVGAIIGKQGQHIKQLSRFAGASIKIAPAEGPDAKLRMVIITGPPEAQFKAQGRIYGKLKEENFF 484
Cdd:cd22497   1 EQEVVYLFIPTQAVGAIIGKKGQHIKQLARFAGASIKIAPAEGPDVSERMVIITGPPEAQFKAQGRIFGKLKEENFF 77
KH-I_IGF2BP2_rpt4 cd22500
fourth type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 ...
491-561 4.12e-36

fourth type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2) and similar proteins; IGF2BP2, also called IGF2 mRNA-binding protein 2 (IMP-2), or hepatocellular carcinoma autoantigen p62, or IGF-II mRNA-binding protein 2, or VICKZ family member 2 (VICKZ2), is an RNA-binding factor that recruits target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It functions by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. It also binds to beta-actin/ACTB and MYC transcripts. IGF2BP2 can form homooligomers and heterooligomers with IGF2BP1 and IGF2BP3 in an RNA-dependent manner. It contains four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the fourth one.


Pssm-ID: 411928  Cd Length: 78  Bit Score: 129.48  E-value: 4.12e-36
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 57530702 491 KLEAHIKVPSYAAGRVIGKGGKTVNELQNLTSAEVVVPRDQTPDENDQVVVKITGHFYACQLAQRKIQEIL 561
Cdd:cd22500   1 KLEAHIKVPSSAAGRVIGKGGKTVNELQNLTSAEVIVPRDQTPDENEEVIVKIIGHFFASQTAQRKIREIV 71
RRM1_VICKZ cd12358
RNA recognition motif 1 (RRM1) found in the VICKZ family proteins; Thid subfamily corresponds ...
4-77 1.61e-34

RNA recognition motif 1 (RRM1) found in the VICKZ family proteins; Thid subfamily corresponds to the RRM1 of IGF2BPs (or IMPs) found in the VICKZ family that have been implicated in the post-transcriptional regulation of several different RNAs and in subcytoplasmic localization of mRNAs during embryogenesis. IGF2BPs are composed of two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and four hnRNP K homology (KH) domains.


Pssm-ID: 240804 [Multi-domain]  Cd Length: 73  Bit Score: 124.79  E-value: 1.61e-34
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 57530702   4 LYIGNLGENVSPLDLESLFKDSKIPFSGQFLVKTGYAFVDCPDESWAMKAIEALSGKVeLHGKLIEVEHSVPKR 77
Cdd:cd12358   1 LYIGNLSSDVNESDLRQLFEEHKIPVSSVLVKKGGYAFVDCPDQSWADKAIEKLNGKI-LQGKVIEVEHSVPKK 73
RRM1_IGF2BP2 cd12626
RNA recognition motif 1 (RRM1) found in vertebrate insulin-like growth factor 2 mRNA-binding ...
1-77 3.07e-33

RNA recognition motif 1 (RRM1) found in vertebrate insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2); This subgroup corresponds to the RRM1 of IGF2BP2 (IGF2 mRNA-binding protein 2 or IMP-2), also termed hepatocellular carcinoma autoantigen p62, or VICKZ family member 2, which is a ubiquitously expressed RNA-binding protein involved in the stimulation of insulin action. It is predominantly nuclear. SNPs in IGF2BP2 gene are implicated in susceptibility to type 2 diabetes. IGF2BP2 plays an important role in cellular motility; it regulates the expression of PINCH-2, an important mediator of cell adhesion and motility, and MURF-3, a microtubule-stabilizing protein, through direct binding to their mRNAs. IGF2BP2 may be involved in the regulation of mRNA stability through the interaction with the AU-rich element-binding factor AUF1. IGF2BP2 binds initially to nascent beta-actin transcripts and facilitates the subsequent binding of the shuttling IGF2BP1. IGF2BP2 contains four hnRNP K-homology (KH) domains, two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a RGG RNA-binding domain.


Pssm-ID: 241070 [Multi-domain]  Cd Length: 77  Bit Score: 121.64  E-value: 3.07e-33
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 57530702   1 MNKLYIGNLGENVSPLDLESLFKDSKIPFSGQFLVKTGYAFVDCPDESWAMKAIEALSGKVELHGKLIEVEHSVPKR 77
Cdd:cd12626   1 MNKLYIGNLSPAVTAEDLRQLFGDRKLPLTGQVLLKSGYAFVDYPDQNWAIRAIETLSGKVELHGKVMEVDYSVPKK 77
KH-I_IGF2BP_rpt3 cd22402
third type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 ...
410-475 1.62e-32

third type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 mRNA-binding protein (IGF2BP) family; The IGF2BP family includes three members: IGF2BP1/IMP-1/ CRD-BP/ VICKZ1, IGF2BP2/IMP-2/ VICKZ2, and IGF2BP3/IMP-3/VICKZ3, which are RNA-binding factors that recruit target transcripts to cytoplasmic protein-RNA complexes (mRNPs). They function by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. IGF2BP proteins contain four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the third one.


Pssm-ID: 411830  Cd Length: 66  Bit Score: 119.28  E-value: 1.62e-32
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 57530702 410 ETVHLFIPALAVGAIIGKQGQHIKQLSRFAGASIKIAPAEGPDAKLRMVIITGPPEAQFKAQGRIY 475
Cdd:cd22402   1 ETTYLYIPNKAVGAIIGTKGSHIRYIKRFSGASIKIAPADSPDAPERKVTITGPPEAQWKAQLCIF 66
KH-I_IGF2BP_rpt4 cd22403
fourth type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 ...
493-558 2.12e-29

fourth type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 mRNA-binding protein (IGF2BP) family; The IGF2BP family includes three members: IGF2BP1/IMP-1/CRD-BP/VICKZ1, IGF2BP2/IMP-2/VICKZ2, and IGF2BP3/IMP-3/VICKZ3, which are RNA-binding factors that recruit target transcripts to cytoplasmic protein-RNA complexes (mRNPs). They function by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. IGF2BP proteins contain four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the fourth one.


Pssm-ID: 411831 [Multi-domain]  Cd Length: 66  Bit Score: 110.41  E-value: 2.12e-29
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 57530702 493 EAHIKVPSYAAGRVIGKGGKTVNELQNLTSAEVVVPRDQTPDENDQVVVKITGHFYACQLAQRKIQ 558
Cdd:cd22403   1 RTEIRVPSSMVGRIIGKGGQNVRELQRLTGAIIKLPRDQTPDEGDEVPVEIIGNFYATQSAQRRIR 66
KH_1 pfam00013
KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause ...
199-263 2.03e-12

KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia.


Pssm-ID: 425420 [Multi-domain]  Cd Length: 65  Bit Score: 62.30  E-value: 2.03e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 57530702   199 LRMLVPTQFVGAIIGKEGATIRNITKQTQSKIDIHRKENaGAAEKPITIHSTPEGCSTACKIIME 263
Cdd:pfam00013   2 VEILVPSSLVGLIIGKGGSNIKEIREETGAKIQIPPSES-EGNERVVTITGTPEAVEAAKALIEE 65
KH-I_BTR1_rpt2 cd22437
second type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana protein BTR1 ...
280-348 4.90e-12

second type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana protein BTR1 and similar proteins; BTR1, also called Binding to ToMV RNA 1, is a negative regulator of tomato mosaic virus (ToMV) multiplication but has no effect on the multiplication of cucumber mosaic virus (CMV). BTR1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411865 [Multi-domain]  Cd Length: 69  Bit Score: 61.46  E-value: 4.90e-12
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 57530702 280 LKILAHNNFVGRLIGKEGRNLKKIEQDTDTKITISPLQDLTLYNPERTITVKGSIETCAKAEEEIMKKI 348
Cdd:cd22437   1 VRLLVPNSSCGLIIGKGGSTIKELREDSNANIKISPKDQLLPGSSERIVTITGSFDQVVKAVALILEKL 69
KH_1 pfam00013
KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause ...
280-346 9.51e-12

KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia.


Pssm-ID: 425420 [Multi-domain]  Cd Length: 65  Bit Score: 60.37  E-value: 9.51e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 57530702   280 LKILAHNNFVGRLIGKEGRNLKKIEQDTDTKITISPLQDltlYNPERTITVKGSIETCAKAEEEIMK 346
Cdd:pfam00013   2 VEILVPSSLVGLIIGKGGSNIKEIREETGAKIQIPPSES---EGNERVVTITGTPEAVEAAKALIEE 65
KH smart00322
K homology RNA-binding domain;
276-348 1.11e-11

K homology RNA-binding domain;


Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 60.39  E-value: 1.11e-11
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 57530702    276 EEIPLKILAHNNFVGRLIGKEGRNLKKIEQDTDTKITISPLQdltlyNPERTITVKGSIETCAKAEEEIMKKI 348
Cdd:smart00322   1 DPVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPG-----SEERVVEITGPPENVEKAAELILEIL 68
KH smart00322
K homology RNA-binding domain;
195-265 2.02e-11

K homology RNA-binding domain;


Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 59.62  E-value: 2.02e-11
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 57530702    195 SDVPLRMLVPTQFVGAIIGKEGATIRNITKQTQSKIDIHRKENagaAEKPITIHSTPEGCSTACKIIMEIM 265
Cdd:smart00322   1 DPVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPGS---EERVVEITGPPENVEKAAELILEIL 68
KH_1 pfam00013
KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause ...
411-475 4.04e-11

KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia.


Pssm-ID: 425420 [Multi-domain]  Cd Length: 65  Bit Score: 58.45  E-value: 4.04e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 57530702   411 TVHLFIPALAVGAIIGKQGQHIKQLSRFAGASIKIaPAEGPDAKLRMVIITGPPEAQFKAQGRIY 475
Cdd:pfam00013   1 TVEILVPSSLVGLIIGKGGSNIKEIREETGAKIQI-PPSESEGNERVVTITGTPEAVEAAKALIE 64
KH smart00322
K homology RNA-binding domain;
491-561 4.24e-11

K homology RNA-binding domain;


Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 58.46  E-value: 4.24e-11
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 57530702    491 KLEAHIKVPSYAAGRVIGKGGKTVNELQNLTSAEVVVPRDQTPDEndqvVVKITGHFYACQLAQRKIQEIL 561
Cdd:smart00322   2 PVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPGSEER----VVEITGPPENVEKAAELILEIL 68
KH-I cd00105
K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found ...
199-262 4.51e-11

K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include an N-terminal extension and type I KH domains (e.g. hnRNP K) contain a C-terminal extension. Some KH-I superfamily members contain a divergent KH domain that lacks the RNA-binding GXXG motif. Some others have a mutated GXXG motif which may or may not have nucleic acid binding ability.


Pssm-ID: 411802 [Multi-domain]  Cd Length: 63  Bit Score: 58.46  E-value: 4.51e-11
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 57530702 199 LRMLVPTQFVGAIIGKEGATIRNITKQTQSKIDIHRKENaGAAEKPITIHSTPEGCSTACKIIM 262
Cdd:cd00105   1 EEIEVPSELVGLIIGKGGSTIKEIEEETGARIQIPKEGE-GSGERVVTITGTPEAVEKAKELIE 63
KH_1 pfam00013
KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause ...
496-559 7.33e-11

KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia.


Pssm-ID: 425420 [Multi-domain]  Cd Length: 65  Bit Score: 57.67  E-value: 7.33e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 57530702   496 IKVPSYAAGRVIGKGGKTVNELQNLTSAEVVVPRDQTPDENDqvVVKITGHFYACQLAQRKIQE 559
Cdd:pfam00013   4 ILVPSSLVGLIIGKGGSNIKEIREETGAKIQIPPSESEGNER--VVTITGTPEAVEAAKALIEE 65
KH-I cd00105
K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found ...
280-345 8.11e-11

K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include an N-terminal extension and type I KH domains (e.g. hnRNP K) contain a C-terminal extension. Some KH-I superfamily members contain a divergent KH domain that lacks the RNA-binding GXXG motif. Some others have a mutated GXXG motif which may or may not have nucleic acid binding ability.


Pssm-ID: 411802 [Multi-domain]  Cd Length: 63  Bit Score: 57.69  E-value: 8.11e-11
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 57530702 280 LKILAHNNFVGRLIGKEGRNLKKIEQDTDTKITISPLQDltlYNPERTITVKGSIETCAKAEEEIM 345
Cdd:cd00105   1 EEIEVPSELVGLIIGKGGSTIKEIEEETGARIQIPKEGE---GSGERVVTITGTPEAVEKAKELIE 63
KH-I_IGF2BP_rpt1 cd22400
first type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 ...
279-346 1.17e-10

first type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 mRNA-binding protein (IGF2BP) family; The IGF2BP family includes three members: IGF2BP1/IMP-1/ CRD-BP/ VICKZ1, IGF2BP2/IMP-2/ VICKZ2, and IGF2BP3/IMP-3/VICKZ3, which are RNA-binding factors that recruit target transcripts to cytoplasmic protein-RNA complexes (mRNPs). They function by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. IGF2BP proteins contain four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the first one.


Pssm-ID: 411828 [Multi-domain]  Cd Length: 68  Bit Score: 57.28  E-value: 1.17e-10
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 57530702 279 PLKILAHNNFVGRLIGKEGRNLKKIEQDTDTKITISPLQDLTLynPERTITVKGSIETCAKAEEEIMK 346
Cdd:cd22400   1 PLRILVPSEFVGAIIGKGGATIRQITQQTGARIDIHRKENAGA--AEKAITIYGTPEGCSSACKQILE 66
KH-I_BTR1_rpt2 cd22437
second type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana protein BTR1 ...
199-265 4.48e-10

second type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana protein BTR1 and similar proteins; BTR1, also called Binding to ToMV RNA 1, is a negative regulator of tomato mosaic virus (ToMV) multiplication but has no effect on the multiplication of cucumber mosaic virus (CMV). BTR1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411865 [Multi-domain]  Cd Length: 69  Bit Score: 55.69  E-value: 4.48e-10
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 57530702 199 LRMLVPTQFVGAIIGKEGATIRNITKQTQSKIDIHRKENA--GAAEKPITIHSTPEGCSTACKIIMEIM 265
Cdd:cd22437   1 VRLLVPNSSCGLIIGKGGSTIKELREDSNANIKISPKDQLlpGSSERIVTITGSFDQVVKAVALILEKL 69
RRM smart00360
RNA recognition motif;
3-70 4.81e-10

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 55.68  E-value: 4.81e-10
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 57530702      3 KLYIGNLGENVSPLDLESLF------KDSKIPFSGQFLVKTGYAFVDCPDESWAMKAIEALSGKvELHGKLIEV 70
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFskfgkvESVRLVRDKETGKSKGFAFVEFESEEDAEKALEALNGK-ELDGRPLKV 73
KH-I cd00105
K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found ...
412-474 5.52e-10

K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include an N-terminal extension and type I KH domains (e.g. hnRNP K) contain a C-terminal extension. Some KH-I superfamily members contain a divergent KH domain that lacks the RNA-binding GXXG motif. Some others have a mutated GXXG motif which may or may not have nucleic acid binding ability.


Pssm-ID: 411802 [Multi-domain]  Cd Length: 63  Bit Score: 55.38  E-value: 5.52e-10
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 57530702 412 VHLFIPALAVGAIIGKQGQHIKQLSRFAGASIKIaPAEGPDAKLRMVIITGPPEAQFKAQGRI 474
Cdd:cd00105   1 EEIEVPSELVGLIIGKGGSTIKEIEEETGARIQI-PKEGEGSGERVVTITGTPEAVEKAKELI 62
KH-I cd00105
K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found ...
495-558 6.02e-10

K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include an N-terminal extension and type I KH domains (e.g. hnRNP K) contain a C-terminal extension. Some KH-I superfamily members contain a divergent KH domain that lacks the RNA-binding GXXG motif. Some others have a mutated GXXG motif which may or may not have nucleic acid binding ability.


Pssm-ID: 411802 [Multi-domain]  Cd Length: 63  Bit Score: 55.38  E-value: 6.02e-10
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 57530702 495 HIKVPSYAAGRVIGKGGKTVNELQNLTSAEVVVPRDQTPDENDqvVVKITGHFYACQLAQRKIQ 558
Cdd:cd00105   2 EIEVPSELVGLIIGKGGSTIKEIEEETGARIQIPKEGEGSGER--VVTITGTPEAVEKAKELIE 63
KH-I_PCBP_rpt3 cd22439
third type I K homology (KH) RNA-binding domain found in the family of poly(C)-binding ...
410-475 7.05e-10

third type I K homology (KH) RNA-binding domain found in the family of poly(C)-binding proteins (PCBPs); The PCBP family, also known as hnRNP E family, comprises four members, PCBP1-4, which are RNA-binding proteins that interact in a sequence-specific manner with single-stranded poly(C) sequences. They are mainly involved in various posttranscriptional regulations, including mRNA stabilization or translational activation/silencing. Besides, PCBPs may share iron chaperone activity. PCBPs contain three K-homology (KH) RNA-binding domains. The model corresponds to the third one.


Pssm-ID: 411867 [Multi-domain]  Cd Length: 68  Bit Score: 55.31  E-value: 7.05e-10
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 57530702 410 ETVHLFIPALAVGAIIGKQGQHIKQLSRFAGASIKIAPAEGpDAKLRMVIITGPPEAQFKAQGRIY 475
Cdd:cd22439   2 TTQEITIPNDLIGCIIGKGGTKINEIRQLSGATIKIANSED-GSTERSVTITGTPEAVSLAQYLIN 66
RRM smart00360
RNA recognition motif;
82-151 2.66e-09

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 53.75  E-value: 2.66e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 57530702     82 KLQIRNIPPHLQWEVLDSLLAQYGTVENCeQVNTDTETAVVN----VTYGNKDQARQAIEKLNGFQLENYSLKV 151
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFGKVESV-RLVRDKETGKSKgfafVEFESEEDAEKALEALNGKELDGRPLKV 73
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
83-151 4.30e-09

RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).


Pssm-ID: 409669 [Multi-domain]  Cd Length: 72  Bit Score: 53.06  E-value: 4.30e-09
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 57530702  83 LQIRNIPPHLQWEVLDSLLAQYGTVENCEqVNTDTETAVVN---VTYGNKDQARQAIEKLNGFQLENYSLKV 151
Cdd:cd00590   1 LFVGNLPPDTTEEDLRELFSKFGEVVSVR-IVRDRDGKSKGfafVEFESPEDAEKALEALNGTELGGRPLKV 71
KH-I_NOVA_rpt1 cd22435
first type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ...
414-479 5.18e-09

first type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ventral antigen (Nova); The family includes two related neuronal RNA-binding proteins, Nova-1 and Nova-2. Nova-1, also called onconeural ventral antigen 1, or paraneoplastic Ri antigen, or ventral neuron-specific protein 1, may regulate RNA splicing or metabolism in a specific subset of developing neurons. It interacts with RNA containing repeats of the YCAY sequence. It is a brain-enriched splicing factor regulating neuronal alternative splicing. Nova-1 is involved in neurological disorders and carcinogenesis. Nova-2, also called astrocytic NOVA1-like RNA-binding protein, is a neuronal RNA-binding protein expressed in a broader central nervous system (CNS) distribution than Nova-1. It functions in neuronal RNA metabolism. NOVA family proteins contain three K-homology (KH) RNA-binding domains. The model corresponds to the first one.


Pssm-ID: 411863 [Multi-domain]  Cd Length: 73  Bit Score: 52.93  E-value: 5.18e-09
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 57530702 414 LFIPALAVGAIIGKQGQHIKQLSRFAGASIKIAPAEG--PDAKLRMVIITGPPEAQFKAQGRIYGKLK 479
Cdd:cd22435   6 LLVPNYAAGSIIGKGGQTIAQLQKETGARIKLSKNNDfyPGTTERVCLIQGEVEAVNAVLDFILEKIR 73
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
4-71 6.62e-09

RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).


Pssm-ID: 409669 [Multi-domain]  Cd Length: 72  Bit Score: 52.67  E-value: 6.62e-09
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 57530702   4 LYIGNLGENVSPLDLESLF------KDSKIPFSGQFLVKtGYAFVDCPDESWAMKAIEALSGKvELHGKLIEVE 71
Cdd:cd00590   1 LFVGNLPPDTTEEDLRELFskfgevVSVRIVRDRDGKSK-GFAFVEFESPEDAEKALEALNGT-ELGGRPLKVS 72
KH-I_Rnc1_rpt3 cd22457
third type I K homology (KH) RNA-binding domain found in Schizosaccharomyces pombe RNA-binding ...
414-470 6.97e-09

third type I K homology (KH) RNA-binding domain found in Schizosaccharomyces pombe RNA-binding protein Rnc1 and similar proteins; Rnc1, also called RNA-binding protein that suppresses calcineurin deletion 1, is an RNA-binding protein that acts as an important regulator of the posttranscriptional expression of the MAPK phosphatase Pmp1 in fission yeast. It binds and stabilizes pmp1 mRNA and hence acts as a negative regulator of pmk1 signaling. Overexpression of Rnc1 suppresses the Cl(-) sensitivity of calcineurin deletion. The nuclear export of Rnc1 requires mRNA-binding ability and the mRNA export factor Rae1. Rnc1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the third one.


Pssm-ID: 411885 [Multi-domain]  Cd Length: 64  Bit Score: 52.08  E-value: 6.97e-09
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 57530702 414 LFIPALAVGAIIGKQGQHIKQLSRFAGASIKIAPAEGPDAKLRMVIITGPPEAQFKA 470
Cdd:cd22457   3 ISIPPDMVGCIIGKGGSKIQEIRRLSGCKISIAKAPHDETGERMFTITGTPEANDRA 59
KH smart00322
K homology RNA-binding domain;
408-478 1.65e-08

K homology RNA-binding domain;


Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 51.14  E-value: 1.65e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 57530702    408 ESETVHLFIPALAVGAIIGKQGQHIKQLSRFAGASIKIapaEGPDAKLRMVIITGPPEAQFKAQGRIYGKL 478
Cdd:smart00322   1 DPVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDI---PGPGSEERVVEITGPPENVEKAAELILEIL 68
KH-I_PCBP1_2_rpt1 cd22515
first type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 1 (PCBP1) ...
411-481 1.79e-08

first type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 1 (PCBP1) and similar proteins; The family includes PCBP1 (also called alpha-CP1, or heterogeneous nuclear ribonucleoprotein E1, or hnRNP E1, or nucleic acid-binding protein SUB2.3) and PCBP2 (also called alpha-CP2, or heterogeneous nuclear ribonucleoprotein E2, or hnRNP E2). They are single-stranded nucleic acid binding proteins that bind preferentially to oligo dC. They act as iron chaperones for ferritin. In case of infection by poliovirus, PCBP1 plays a role in initiation of viral RNA replication in concert with the viral protein 3CD. PCBP2 is a major cellular poly(rC)-binding protein. It also binds poly(rU). PCBP2 negatively regulates cellular antiviral responses mediated by MAVS signaling. It acts as an adapter between MAVS and the E3 ubiquitin ligase ITCH, therefore triggering MAVS ubiquitination and degradation. PCBP2 forms a metabolon with the heme oxygenase 1/cytochrome P450 reductase complex for heme catabolism and iron transfer. Both PCBP1 and PCBP2 contain three K-homology (KH) RNA-binding domains. The model corresponds to the first one.


Pssm-ID: 411943  Cd Length: 70  Bit Score: 51.17  E-value: 1.79e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 57530702 411 TVHLFIPALAVGAIIGKQGQHIKQLSRFAGASIKIAPAEGPDaklRMVIITGPPEAQFKAQGRIYGKLKEE 481
Cdd:cd22515   3 TIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCPE---RIITLAGPTNAIFKAFAMIIDKLEED 70
KH-I_PCBP_rpt1 cd22438
first type I K homology (KH) RNA-binding domain found in the family of poly(C)-binding ...
280-350 2.13e-08

first type I K homology (KH) RNA-binding domain found in the family of poly(C)-binding proteins (PCBPs); The PCBP family, also known as hnRNP E family, comprises four members, PCBP1-4, which are RNA-binding proteins that interact in a sequence-specific manner with single-stranded poly(C) sequences. They are mainly involved in various posttranscriptional regulations, including mRNA stabilization or translational activation/silencing. Besides, PCBPs may share iron chaperone activity. PCBPs contain three K-homology (KH) RNA-binding domains. The model corresponds to the first one.


Pssm-ID: 411866 [Multi-domain]  Cd Length: 67  Bit Score: 51.10  E-value: 2.13e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 57530702 280 LKILAHNNFVGRLIGKEGRNLKKIEQDTDTKITISplqDLTLynPERTITVKGSIETCAKAEEEIMKKIRE 350
Cdd:cd22438   1 IRMLMQGKEVGSIIGKKGETIKKFREESGARINIS---DGSC--PERIVTVTGTTDAVFKAFELICRKLEE 66
KH-I_PCBP3_rpt1 cd22516
first type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) ...
411-481 2.20e-08

first type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) and similar proteins; PCBP3, also called alpha-CP3, or PCBP3-overlapping transcript, or PCBP3-overlapping transcript 1, or heterogeneous nuclear ribonucleoprotein E3, or hnRNP E3, is a single-stranded nucleic acid binding protein that binds preferentially to oligo dC. It can function as a repressor dependent on binding to single-strand and double-stranded poly(C) sequences. PCBP3 contains three K-homology (KH) RNA-binding domains. The model corresponds to the first one.


Pssm-ID: 411944  Cd Length: 77  Bit Score: 51.26  E-value: 2.20e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 57530702 411 TVHLFIPALAVGAIIGKQGQHIKQLSRFAGASIKIAPAEGPDaklRMVIITGPPEAQFKAQGRIYGKLKEE 481
Cdd:cd22516  10 TIRLLMHGKEVGSIIGKKGETVKKMREESGARINISEGNCPE---RIVTITGPTDAIFKAFAMIAYKFEED 77
KH-I_FUBP_rpt1 cd22396
first type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding ...
416-474 2.44e-08

first type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding proteins; The far upstream element-binding protein (FUBP) family includes FUBP1-3. FUBP1, also called FBP, or FUSE-binding protein 1, or DNA helicase V, or DH V, binds RNA and single-stranded DNA (ssDNA) and may act both as activator and repressor of transcription. It regulates MYC expression by binding to a single-stranded far-upstream element (FUSE) upstream of the MYC promoter. FUBP2, also called FUSE-binding protein 2, or KH type-splicing regulatory protein (KSRP), or p75, is a single-strand nucleic acid binding protein implicated in a variety of cellular processes, including splicing in the nucleus, mRNA decay, maturation of miRNA, and transcriptional control of proto-oncogenes such as c-myc. It regulates the stability and/or translatability of many mRNA species, encoding immune-relevant proteins, either by binding to AU-rich elements (AREs) of mRNA 3'UTR or by facilitating miRNA biogenesis to target mRNA. FUBP3, also called FUSE-binding protein 3, or MARTA2, was previously shown to mediate dendritic targeting of MAP2 mRNA in neurons. It may interact with single-stranded DNA from the far-upstream element (FUSE) and activate gene expression. It is required for beta-actin mRNA localization. It also interacts with fibroblast growth factor 9 (FGF9) 3'-UTR UG repeats and positively controls FGF9 expression through increasing translation of FGF9 mRNA. FUBP proteins contain four K-homology (KH) RNA-binding domains. The model corresponds to the first one.


Pssm-ID: 411824 [Multi-domain]  Cd Length: 68  Bit Score: 50.72  E-value: 2.44e-08
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 57530702 416 IPALAVGAIIGKQGQHIKQLSRFAGASIKIAPAEGPDAKlRMVIITGPPEAQFKAQGRI 474
Cdd:cd22396   7 VPDKMVGLIIGRGGEQINRLQAESGAKIQIAPDSGGLPE-RPCTLTGTPDAIETAKRLI 64
KH-I_PEPPER_rpt2_like cd22460
second type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH ...
498-553 2.50e-08

second type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH domain-containing protein PEPPER and similar proteins; The family includes a group of plant RNA-binding KH domain-containing proteins, such as PEPPER, flowering locus K homology domain protein (FLK), RNA-binding KH domain-containing protein RCF3 and KH domain-containing protein HEN4. PEPPER regulates vegetative and gynoecium development. It acts as a positive regulator of the central floral repressor FLOWERING LOCUS C. In concert with HUA2, PEPPER antagonizes FLK by positively regulating FLC probably at transcriptional and post-transcriptional levels, and thus acts as a negative regulator of flowering. FLK, also called flowering locus KH domain protein, regulates positively flowering by repressing FLC expression and post-transcriptional modification. PEPPER and FLK contain three K-homology (KH) RNA-binding domains. RCF3, also called protein ENHANCED STRESS RESPONSE 1 (ESR1), or protein HIGH OSMOTIC STRESS GENE EXPRESSION 5 (HOS5), or protein REGULATOR OF CBF GENE EXPRESSION 3, or protein SHINY 1 (SHI1), acts as negative regulator of osmotic stress-induced gene expression. It is involved in the regulation of thermotolerance responses under heat stress. It functions as an upstream regulator of heat stress transcription factor (HSF) genes. HEN4, also called protein HUA ENHANCER 4, plays a role in floral reproductive organ identity in the third whorl and floral determinacy specification by specifically promoting the processing of AGAMOUS (AG) pre-mRNA. It functions in association with HUA1 and HUA2. RCF3 and HEN4 contain five KH RNA-binding domains. The model corresponds to the KH2 domain of PEPPER and FLK, as well as KH2 and KH4 domains of RCF3 and HEN4.


Pssm-ID: 411888 [Multi-domain]  Cd Length: 73  Bit Score: 51.08  E-value: 2.50e-08
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 57530702 498 VPSYAAGRVIGKGGKTVNELQNLTSAEV-VVPRDQTP---DENDQvVVKITGHFYACQLA 553
Cdd:cd22460   6 VASSQAGSLIGKGGAIIKQIREESGASVrILPEEELPpcaSPDDR-VVQISGEAQAVKKA 64
RRM1_CoAA cd12608
RNA recognition motif 1 (RRM1) found in vertebrate RRM-containing coactivator activator ...
3-73 3.67e-08

RNA recognition motif 1 (RRM1) found in vertebrate RRM-containing coactivator activator/modulator (CoAA); This subgroup corresponds to the RRM1 of CoAA, also termed RNA-binding protein 14 (RBM14), or paraspeckle protein 2 (PSP2), or synaptotagmin-interacting protein (SYT-interacting protein), a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. It stimulates transcription through its interactions with coactivators, such as TRBP and CREB-binding protein CBP/p300, via the TRBP-interacting domain and interaction with an RNA-containing complex, such as DNA-dependent protein kinase-poly(ADP-ribose) polymerase complexes, via the RRMs.


Pssm-ID: 410020 [Multi-domain]  Cd Length: 69  Bit Score: 50.19  E-value: 3.67e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 57530702   3 KLYIGNLGENVSPLDLESLFKdskiPFsGQFL---VKTGYAFVDCPDESWAMKAIEALSGKvELHGKLIEVEHS 73
Cdd:cd12608   2 KIFVGNVDEDTSQEELSALFE----PY-GAVLscaVMKQFAFVHMRGEAAADRAIRELNGR-ELHGRALVVEES 69
KH-I_PEPPER_rpt1_like cd22459
first type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH ...
196-252 4.47e-08

first type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH domain-containing protein PEPPER and similar proteins; The family includes a group of plant RNA-binding KH domain-containing proteins, such as PEPPER, flowering locus K homology domain protein (FLK), RNA-binding KH domain-containing protein RCF3 and KH domain-containing protein HEN4. PEPPER regulates vegetative and gynoecium development. It acts as a positive regulator of the central floral repressor FLOWERING LOCUS C. In concert with HUA2, PEPPER antagonizes FLK by positively regulating FLC probably at transcriptional and post-transcriptional levels, and thus acts as a negative regulator of flowering. FLK, also called flowering locus KH domain protein, regulates positively flowering by repressing FLC expression and post-transcriptional modification. PEPPER and FLK contain three K-homology (KH) RNA-binding domains. RCF3, also called protein ENHANCED STRESS RESPONSE 1 (ESR1), or protein HIGH OSMOTIC STRESS GENE EXPRESSION 5 (HOS5), or protein REGULATOR OF CBF GENE EXPRESSION 3, or protein SHINY 1 (SHI1), acts as negative regulator of osmotic stress-induced gene expression. It is involved in the regulation of thermotolerance responses under heat stress. It functions as an upstream regulator of heat stress transcription factor (HSF) genes. HEN4, also called protein HUA ENHANCER 4, plays a role in floral reproductive organ identity in the third whorl and floral determinacy specification by specifically promoting the processing of AGAMOUS (AG) pre-mRNA. It functions in association with HUA1 and HUA2. RCF3 and HEN4 contain five KH RNA-binding domains. The model corresponds to the KH1 domain of PEPPER and FLK, as well as KH1 and KH3 domains of RCF3 and HEN4.


Pssm-ID: 411887 [Multi-domain]  Cd Length: 69  Bit Score: 49.92  E-value: 4.47e-08
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 57530702 196 DVPLRMLVPTQFVGAIIGKEGATIRNITKQTQSKIDIHrKENAGAAEKPITIHSTPE 252
Cdd:cd22459   1 EVVFRLLCPVSKAGSVIGKGGEIIKQLRQETGARIKVE-DGVPGTEERVITISSSEA 56
KH-I_BTR1_rpt2 cd22437
second type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana protein BTR1 ...
412-470 5.30e-08

second type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana protein BTR1 and similar proteins; BTR1, also called Binding to ToMV RNA 1, is a negative regulator of tomato mosaic virus (ToMV) multiplication but has no effect on the multiplication of cucumber mosaic virus (CMV). BTR1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411865 [Multi-domain]  Cd Length: 69  Bit Score: 49.91  E-value: 5.30e-08
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 57530702 412 VHLFIPALAVGAIIGKQGQHIKQLSRFAGASIKIAP--AEGPDAKLRMVIITGPPEAQFKA 470
Cdd:cd22437   1 VRLLVPNSSCGLIIGKGGSTIKELREDSNANIKISPkdQLLPGSSERIVTITGSFDQVVKA 61
KH-I_NOVA_rpt2 cd22436
second type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ...
198-263 7.65e-08

second type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ventral antigen (Nova); The family includes two related neuronal RNA-binding proteins, Nova-1 and Nova-2. Nova-1, also called onconeural ventral antigen 1, or paraneoplastic Ri antigen, or ventral neuron-specific protein 1, may regulate RNA splicing or metabolism in a specific subset of developing neurons. It interacts with RNA containing repeats of the YCAY sequence. It is a brain-enriched splicing factor regulating neuronal alternative splicing. Nova-1 is involved in neurological disorders and carcinogenesis. Nova-2, also called astrocytic NOVA1-like RNA-binding protein, is a neuronal RNA-binding protein expressed in a broader central nervous system (CNS) distribution than Nova-1. It functions in neuronal RNA metabolism. NOVA family proteins contain three K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411864 [Multi-domain]  Cd Length: 70  Bit Score: 49.54  E-value: 7.65e-08
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 57530702 198 PLRMLVPTQFVGAIIGKEGATIRNITKQTQSKIDIHRK-ENAGAAEKPITIHSTPEGCSTACKIIME 263
Cdd:cd22436   2 QVKILVPNSTAGMIIGKGGATIKAIMEQSGARVQISQKpESINLQERVVTVTGEPEANRKAVSLILQ 68
KH-I_NOVA_rpt1 cd22435
first type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ...
280-349 8.58e-08

first type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ventral antigen (Nova); The family includes two related neuronal RNA-binding proteins, Nova-1 and Nova-2. Nova-1, also called onconeural ventral antigen 1, or paraneoplastic Ri antigen, or ventral neuron-specific protein 1, may regulate RNA splicing or metabolism in a specific subset of developing neurons. It interacts with RNA containing repeats of the YCAY sequence. It is a brain-enriched splicing factor regulating neuronal alternative splicing. Nova-1 is involved in neurological disorders and carcinogenesis. Nova-2, also called astrocytic NOVA1-like RNA-binding protein, is a neuronal RNA-binding protein expressed in a broader central nervous system (CNS) distribution than Nova-1. It functions in neuronal RNA metabolism. NOVA family proteins contain three K-homology (KH) RNA-binding domains. The model corresponds to the first one.


Pssm-ID: 411863 [Multi-domain]  Cd Length: 73  Bit Score: 49.46  E-value: 8.58e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 57530702 280 LKILAHNNFVGRLIGKEGRNLKKIEQDTDTKITISPLQDltlYNP---ERTITVKGSIETCAKAEEEIMKKIR 349
Cdd:cd22435   4 LKLLVPNYAAGSIIGKGGQTIAQLQKETGARIKLSKNND---FYPgttERVCLIQGEVEAVNAVLDFILEKIR 73
KH-I_ScSCP160_rpt2 cd22447
second type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein ...
498-562 9.90e-08

second type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411875 [Multi-domain]  Cd Length: 80  Bit Score: 49.34  E-value: 9.90e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 57530702 498 VPSYAAGRVIGKGGKTVNELQNLTSAEVVVPR------DQTPDENDQVVVKITGHFYACQLAQRKIQEILA 562
Cdd:cd22447  10 IPASTRARIIGKKGANLKQIREKTGVRIDIPPrdadaaPADEDDDTMVEVTITGDEFNVQHAKQRIEEIIS 80
KH-I_HEN4_like_rpt5 cd22462
fifth type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana KH ...
412-474 1.15e-07

fifth type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana KH domain-containing protein HEN4 and similar protein; HEN4, also called protein HUA ENHANCER 4, plays a role in floral reproductive organ identity in the third whorl and floral determinacy specification by specifically promoting the processing of AGAMOUS (AG) pre-mRNA. It functions in association with HUA1 and HUA2. HEN4 contains five K-homology (KH) RNA-binding domains. The model corresponds to the KH5 domain of HEN4.


Pssm-ID: 411890 [Multi-domain]  Cd Length: 66  Bit Score: 48.78  E-value: 1.15e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 57530702 412 VHLFIPALAVGAIIGKQGQHIKQLSRFAGASIKIAPAEgPDAKLRMVIITGPPEAQFKAQGRI 474
Cdd:cd22462   1 IEILIPAHAVGSVIGRGGSNINQIREISGAKVEVLKPD-SATGERIVLISGTPDQARHAQNLI 62
KH-I_FUBP_rpt1 cd22396
first type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding ...
200-264 1.44e-07

first type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding proteins; The far upstream element-binding protein (FUBP) family includes FUBP1-3. FUBP1, also called FBP, or FUSE-binding protein 1, or DNA helicase V, or DH V, binds RNA and single-stranded DNA (ssDNA) and may act both as activator and repressor of transcription. It regulates MYC expression by binding to a single-stranded far-upstream element (FUSE) upstream of the MYC promoter. FUBP2, also called FUSE-binding protein 2, or KH type-splicing regulatory protein (KSRP), or p75, is a single-strand nucleic acid binding protein implicated in a variety of cellular processes, including splicing in the nucleus, mRNA decay, maturation of miRNA, and transcriptional control of proto-oncogenes such as c-myc. It regulates the stability and/or translatability of many mRNA species, encoding immune-relevant proteins, either by binding to AU-rich elements (AREs) of mRNA 3'UTR or by facilitating miRNA biogenesis to target mRNA. FUBP3, also called FUSE-binding protein 3, or MARTA2, was previously shown to mediate dendritic targeting of MAP2 mRNA in neurons. It may interact with single-stranded DNA from the far-upstream element (FUSE) and activate gene expression. It is required for beta-actin mRNA localization. It also interacts with fibroblast growth factor 9 (FGF9) 3'-UTR UG repeats and positively controls FGF9 expression through increasing translation of FGF9 mRNA. FUBP proteins contain four K-homology (KH) RNA-binding domains. The model corresponds to the first one.


Pssm-ID: 411824 [Multi-domain]  Cd Length: 68  Bit Score: 48.79  E-value: 1.44e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 57530702 200 RMLVPTQFVGAIIGKEGATIRNITKQTQSKIDIHRkENAGAAEKPITIHSTPEGCSTACKIIMEI 264
Cdd:cd22396   4 EYKVPDKMVGLIIGRGGEQINRLQAESGAKIQIAP-DSGGLPERPCTLTGTPDAIETAKRLIDQI 67
KH-I_TDRKH_rpt1 cd22428
first type I K homology (KH) RNA-binding domain found in tudor and KH domain-containing ...
193-265 2.61e-07

first type I K homology (KH) RNA-binding domain found in tudor and KH domain-containing protein (TDRKH) and similar proteins; TDRKH, also called tudor domain-containing protein 2 (TDRD2), is a mitochondria-anchored RNA-binding protein that is required for spermatogenesis and involved in piRNA biogenesis. It specifically recruits MIWI, but not MILI, to engage the piRNA pathway. TDRKH contains two K-homology (KH) RNA-binding domains and one tudor domain, which are involved in binding to RNA or single-strand DNA. The model corresponds to the first one.


Pssm-ID: 411856 [Multi-domain]  Cd Length: 74  Bit Score: 48.10  E-value: 2.61e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 57530702 193 PQSDVPLRMLVPTQFVGAIIGKEGATIRNITKQTQSKIDIHRKENAG-AAEKPITIHSTPEGCSTACKIIMEIM 265
Cdd:cd22428   1 GSRQIEIEMKVPREAVGLIIGRQGATIKQIQKETGARIDFKDEGSGGeLPERVLLIQGNPVQAQRAEEAIHQII 74
KH-I_NOVA_rpt3 cd09031
third type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ...
410-478 2.75e-07

third type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ventral antigen (Nova); The family includes two related neuronal RNA-binding proteins, Nova-1 and Nova-2. Nova-1, also called onconeural ventral antigen 1, or paraneoplastic Ri antigen, or ventral neuron-specific protein 1, may regulate RNA splicing or metabolism in a specific subset of developing neurons. It interacts with RNA containing repeats of the YCAY sequence. It is a brain-enriched splicing factor regulating neuronal alternative splicing. Nova-1 is involved in neurological disorders and carcinogenesis. Nova-2, also called astrocytic NOVA1-like RNA-binding protein, is a neuronal RNA-binding protein expressed in a broader central nervous system (CNS) distribution than Nova-1. It functions in neuronal RNA metabolism. NOVA family proteins contain three K-homology (KH) RNA-binding domains. The model corresponds to the third one.


Pssm-ID: 411807 [Multi-domain]  Cd Length: 71  Bit Score: 47.96  E-value: 2.75e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 57530702 410 ETVHLFIPALAVGAIIGKQGQHIKQLSRFAGASIKIApAEG---PDAKLRMVIITGPPEAQFKAQGRIYGKL 478
Cdd:cd09031   1 TVIELEVPENLVGAILGKGGKTLVEIQELTGARIQIS-KKGefvPGTRNRKVTITGTPAAVQAAQYLIEQRI 71
KH-I_PEPPER_rpt2_like cd22460
second type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH ...
411-478 2.98e-07

second type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH domain-containing protein PEPPER and similar proteins; The family includes a group of plant RNA-binding KH domain-containing proteins, such as PEPPER, flowering locus K homology domain protein (FLK), RNA-binding KH domain-containing protein RCF3 and KH domain-containing protein HEN4. PEPPER regulates vegetative and gynoecium development. It acts as a positive regulator of the central floral repressor FLOWERING LOCUS C. In concert with HUA2, PEPPER antagonizes FLK by positively regulating FLC probably at transcriptional and post-transcriptional levels, and thus acts as a negative regulator of flowering. FLK, also called flowering locus KH domain protein, regulates positively flowering by repressing FLC expression and post-transcriptional modification. PEPPER and FLK contain three K-homology (KH) RNA-binding domains. RCF3, also called protein ENHANCED STRESS RESPONSE 1 (ESR1), or protein HIGH OSMOTIC STRESS GENE EXPRESSION 5 (HOS5), or protein REGULATOR OF CBF GENE EXPRESSION 3, or protein SHINY 1 (SHI1), acts as negative regulator of osmotic stress-induced gene expression. It is involved in the regulation of thermotolerance responses under heat stress. It functions as an upstream regulator of heat stress transcription factor (HSF) genes. HEN4, also called protein HUA ENHANCER 4, plays a role in floral reproductive organ identity in the third whorl and floral determinacy specification by specifically promoting the processing of AGAMOUS (AG) pre-mRNA. It functions in association with HUA1 and HUA2. RCF3 and HEN4 contain five KH RNA-binding domains. The model corresponds to the KH2 domain of PEPPER and FLK, as well as KH2 and KH4 domains of RCF3 and HEN4.


Pssm-ID: 411888 [Multi-domain]  Cd Length: 73  Bit Score: 48.00  E-value: 2.98e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 57530702 411 TVHLFIPALAVGAIIGKQGQHIKQLSRFAGASIKIAPAEGP----DAKLRMVIITGPPEAQFKAQGRIYGKL 478
Cdd:cd22460   1 SARLLVASSQAGSLIGKGGAIIKQIREESGASVRILPEEELppcaSPDDRVVQISGEAQAVKKALELVSSRL 72
KH-I_NOVA_rpt2 cd22436
second type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ...
411-478 3.04e-07

second type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ventral antigen (Nova); The family includes two related neuronal RNA-binding proteins, Nova-1 and Nova-2. Nova-1, also called onconeural ventral antigen 1, or paraneoplastic Ri antigen, or ventral neuron-specific protein 1, may regulate RNA splicing or metabolism in a specific subset of developing neurons. It interacts with RNA containing repeats of the YCAY sequence. It is a brain-enriched splicing factor regulating neuronal alternative splicing. Nova-1 is involved in neurological disorders and carcinogenesis. Nova-2, also called astrocytic NOVA1-like RNA-binding protein, is a neuronal RNA-binding protein expressed in a broader central nervous system (CNS) distribution than Nova-1. It functions in neuronal RNA metabolism. NOVA family proteins contain three K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411864 [Multi-domain]  Cd Length: 70  Bit Score: 47.61  E-value: 3.04e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 57530702 411 TVHLFIPALAVGAIIGKQGQHIKQLSRFAGASIKIA-PAEGPDAKLRMVIITGPPEAQFKAQGRIYGKL 478
Cdd:cd22436   2 QVKILVPNSTAGMIIGKGGATIKAIMEQSGARVQISqKPESINLQERVVTVTGEPEANRKAVSLILQKI 70
KH-I_PCBP4_rpt1 cd22517
first type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 4 (PCBP4) ...
278-350 3.15e-07

first type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 4 (PCBP4) and similar proteins; PCBP4, also called alpha-CP4, or heterogeneous nuclear ribonucleoprotein E4, or hnRNP E4, is a single-stranded nucleic acid binding protein that binds preferentially to oligo dC. It regulates both basal and stress-induced p21 expression through binding p21 3'-UTR and modulating p21 mRNA stability. It also plays a role in the cell cycle and is implicated in lung tumor suppression. PCBP4 contains three K-homology (KH) RNA-binding domains. The model corresponds to the first one.


Pssm-ID: 411945  Cd Length: 70  Bit Score: 47.72  E-value: 3.15e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 57530702 278 IPLKILAHNNFVGRLIGKEGRNLKKIEQDTDTKITISPLQdltlyNPERTITVKGSIETCAKAEEEIMKKIRE 350
Cdd:cd22517   2 LTLRLLMHGKEVGSIIGKKGETVKRIREESSARITISEGS-----CPERITTITGSTDAVFRAFSMIAFKLEE 69
KH-I_HNRNPK_rpt3 cd22434
third type I K homology (KH) RNA-binding domain found in heterogeneous nuclear ...
409-471 3.24e-07

third type I K homology (KH) RNA-binding domain found in heterogeneous nuclear ribonucleoprotein K (hnRNP K) and similar proteins; hnRNP K, also called transformation up-regulated nuclear protein (TUNP), is a pre-mRNA binding protein that binds tenaciously to poly(C) sequences. It may be involved in the nuclear metabolism of hnRNAs, particularly for pre-mRNAs that contain cytidine-rich sequences. It can also bind poly(C) single-stranded DNA. hnRNP K plays an important role in p53/TP53 response to DNA damage, acting at the level of both transcription activation and repression. hnRNP K contains three K-homology (KH) RNA-binding domains. The model corresponds to the third one.


Pssm-ID: 411862 [Multi-domain]  Cd Length: 74  Bit Score: 47.70  E-value: 3.24e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 57530702 409 SETVHLFIPALAVGAIIGKQGQHIKQLSRFAGASIKIAPAEgPDAKLRMVIITGPPE----AQFKAQ 471
Cdd:cd22434   1 TTTTQVTIPKDLAGSIIGKGGQRIRQIRHESGASIKIDEPL-PGSEDRIITITGTQDqiqnAQYLLQ 66
KH-I_TDRKH_rpt2 cd22429
second type I K homology (KH) RNA-binding domain found in tudor and KH domain-containing ...
201-278 3.57e-07

second type I K homology (KH) RNA-binding domain found in tudor and KH domain-containing protein (TDRKH) and similar proteins; TDRKH, also called tudor domain-containing protein 2 (TDRD2), is a mitochondria-anchored RNA-binding protein that is required for spermatogenesis and involved in piRNA biogenesis. It specifically recruits MIWI, but not MILI, to engage the piRNA pathway. TDRKH contains two K-homology (KH) RNA-binding domains and one tudor domain, which are involved in binding to RNA or single-strand DNA. The model corresponds to the second one.


Pssm-ID: 411857 [Multi-domain]  Cd Length: 82  Bit Score: 48.10  E-value: 3.57e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 57530702 201 MLVPTQFVGAIIGKEGATIRNITKQTQSKIDIHRKENAGAAE-KPITIHSTPEGCSTACKIIMEimqKEAQDTKFTEEI 278
Cdd:cd22429   6 LHVPQRAVGRIIGRGGETIRSICRTSGAKVKCDRESDDTLDLvRLITITGTKKEVDAAKSLILE---KVSEEEEFRQRL 81
KH-I_FUBP_rpt1 cd22396
first type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding ...
496-560 3.86e-07

first type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding proteins; The far upstream element-binding protein (FUBP) family includes FUBP1-3. FUBP1, also called FBP, or FUSE-binding protein 1, or DNA helicase V, or DH V, binds RNA and single-stranded DNA (ssDNA) and may act both as activator and repressor of transcription. It regulates MYC expression by binding to a single-stranded far-upstream element (FUSE) upstream of the MYC promoter. FUBP2, also called FUSE-binding protein 2, or KH type-splicing regulatory protein (KSRP), or p75, is a single-strand nucleic acid binding protein implicated in a variety of cellular processes, including splicing in the nucleus, mRNA decay, maturation of miRNA, and transcriptional control of proto-oncogenes such as c-myc. It regulates the stability and/or translatability of many mRNA species, encoding immune-relevant proteins, either by binding to AU-rich elements (AREs) of mRNA 3'UTR or by facilitating miRNA biogenesis to target mRNA. FUBP3, also called FUSE-binding protein 3, or MARTA2, was previously shown to mediate dendritic targeting of MAP2 mRNA in neurons. It may interact with single-stranded DNA from the far-upstream element (FUSE) and activate gene expression. It is required for beta-actin mRNA localization. It also interacts with fibroblast growth factor 9 (FGF9) 3'-UTR UG repeats and positively controls FGF9 expression through increasing translation of FGF9 mRNA. FUBP proteins contain four K-homology (KH) RNA-binding domains. The model corresponds to the first one.


Pssm-ID: 411824 [Multi-domain]  Cd Length: 68  Bit Score: 47.25  E-value: 3.86e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 57530702 496 IKVPSYAAGRVIGKGGKTVNELQNLTSAEVVVPRDqtPDENDQVVVKITGHFYACQLAQRKIQEI 560
Cdd:cd22396   5 YKVPDKMVGLIIGRGGEQINRLQAESGAKIQIAPD--SGGLPERPCTLTGTPDAIETAKRLIDQI 67
KH-I_ScSCP160_rpt1 cd22446
first type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein ...
485-562 4.39e-07

first type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the first one.


Pssm-ID: 411874 [Multi-domain]  Cd Length: 86  Bit Score: 47.79  E-value: 4.39e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57530702 485 GPKEEVKLEahikVPSYAAGRVIGKGGKTVNELQNLTSAEVVVPR---DQTPDENDQ---VVVKITGHFYACQLAQRKIQ 558
Cdd:cd22446   4 SPKVTITIS----VPSSVRGAIIGSRGKNLKSIQDKTGTKIQIPKrneEGNYDEDDDdetVEISIEGDAEGVELAKKEIE 79

                ....
gi 57530702 559 EILA 562
Cdd:cd22446  80 AIVK 83
KH-I_PCBP3_rpt3 cd22522
third type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) ...
407-464 4.95e-07

third type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) and similar proteins; PCBP3, also called alpha-CP3, or PCBP3-overlapping transcript, or PCBP3-overlapping transcript 1, or heterogeneous nuclear ribonucleoprotein E3, or hnRNP E3, is a single-stranded nucleic acid binding protein that binds preferentially to oligo dC. It can function as a repressor dependent on binding to single-strand and double-stranded poly(C) sequences. PCBP3 contains three K-homology (KH) RNA-binding domains. The model corresponds to the third one.


Pssm-ID: 411950  Cd Length: 75  Bit Score: 47.42  E-value: 4.95e-07
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 57530702 407 PESETVHLFIPALAVGAIIGKQGQHIKQLSRFAGASIKIAPA-EGpdAKLRMVIITGPP 464
Cdd:cd22522   6 PPASTHELTIPNDLIGCIIGRQGTKINEIRQMSGAQIKIANAtEG--SSERQITITGSP 62
KH-I_Mextli_like cd22454
type I K homology (KH) RNA-binding domain found in Drosophila melanogaster eukaryotic ...
277-348 5.11e-07

type I K homology (KH) RNA-binding domain found in Drosophila melanogaster eukaryotic translation initiation factor 4E-binding protein Mextli and similar proteins; Mextli is a novel eukaryotic translation initiation factor 4E-binding protein that promotes translation in Drosophila melanogaster.


Pssm-ID: 411882 [Multi-domain]  Cd Length: 71  Bit Score: 47.31  E-value: 5.11e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 57530702 277 EIPLKILAHNNFVGRLIGKEGRNLKKIEQDTDTKITISPLQDltlYNPERTITVKGSIETCAKAEEEIMKKI 348
Cdd:cd22454   3 QTTIEVVIPNADVGKVIGKGGETIKRIEALTDTVITFERVNG---GSPNREVQITGSPDNVAAAKRLIEDTI 71
sex-lethal TIGR01659
sex-lethal family splicing factor; This model describes the sex-lethal family of splicing ...
13-194 6.65e-07

sex-lethal family splicing factor; This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661).


Pssm-ID: 273740 [Multi-domain]  Cd Length: 346  Bit Score: 51.56  E-value: 6.65e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57530702    13 VSPLDLESLFKDSKIPFSgqflvkTGYAFVDCPDESWAMKAIEALSGkVELHGKLIEVEHSVP--KRQRSRKLQIRNIPP 90
Cdd:TIGR01659 131 IGPINTCRIMRDYKTGYS------FGYAFVDFGSEADSQRAIKNLNG-ITVRNKRLKVSYARPggESIKDTNLYVTNLPR 203
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57530702    91 HLQWEVLDSLLAQYGTVencEQVN------TDTETAVVNVTYGNKDQARQAIEKLNGFQLENYS--LKVAYIPDEMAAQQ 162
Cdd:TIGR01659 204 TITDDQLDTIFGKYGQI---VQKNilrdklTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSqpLTVRLAEEHGKAKA 280
                         170       180       190
                  ....*....|....*....|....*....|..
gi 57530702   163 PPQQHPQGRRGFGQRGPPRQGSPSATTRQKPQ 194
Cdd:TIGR01659 281 HHYMSQMGHGNMGNMGHGNMGMAGGSGMNPPN 312
KH-I_ScSCP160_rpt2 cd22447
second type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein ...
199-264 7.50e-07

second type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411875 [Multi-domain]  Cd Length: 80  Bit Score: 47.03  E-value: 7.50e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 57530702 199 LRMLVPTQFVGAIIGKEGATIRNITKQTQSKIDIHRKENAGAAEK-------PITIHSTPEGCSTACKIIMEI 264
Cdd:cd22447   6 LTVPIPASTRARIIGKKGANLKQIREKTGVRIDIPPRDADAAPADedddtmvEVTITGDEFNVQHAKQRIEEI 78
KH-I_IGF2BP_rpt3 cd22402
third type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 ...
200-254 9.52e-07

third type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 mRNA-binding protein (IGF2BP) family; The IGF2BP family includes three members: IGF2BP1/IMP-1/ CRD-BP/ VICKZ1, IGF2BP2/IMP-2/ VICKZ2, and IGF2BP3/IMP-3/VICKZ3, which are RNA-binding factors that recruit target transcripts to cytoplasmic protein-RNA complexes (mRNPs). They function by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. IGF2BP proteins contain four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the third one.


Pssm-ID: 411830  Cd Length: 66  Bit Score: 46.09  E-value: 9.52e-07
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 57530702 200 RMLVPTQFVGAIIGKEGATIRNITKQTQSKIDIHRKENAGAAEKPITIHSTPEGC 254
Cdd:cd22402   4 YLYIPNKAVGAIIGTKGSHIRYIKRFSGASIKIAPADSPDAPERKVTITGPPEAQ 58
KH-I_PCBP_rpt1 cd22438
first type I K homology (KH) RNA-binding domain found in the family of poly(C)-binding ...
421-481 9.72e-07

first type I K homology (KH) RNA-binding domain found in the family of poly(C)-binding proteins (PCBPs); The PCBP family, also known as hnRNP E family, comprises four members, PCBP1-4, which are RNA-binding proteins that interact in a sequence-specific manner with single-stranded poly(C) sequences. They are mainly involved in various posttranscriptional regulations, including mRNA stabilization or translational activation/silencing. Besides, PCBPs may share iron chaperone activity. PCBPs contain three K-homology (KH) RNA-binding domains. The model corresponds to the first one.


Pssm-ID: 411866 [Multi-domain]  Cd Length: 67  Bit Score: 46.10  E-value: 9.72e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 57530702 421 VGAIIGKQGQHIKQLSRFAGASIKIAPAEGPDaklRMVIITGPPEAQFKAQGRIYGKLKEE 481
Cdd:cd22438  10 VGSIIGKKGETIKKFREESGARINISDGSCPE---RIVTVTGTTDAVFKAFELICRKLEED 67
KH-I_TDRKH_rpt1 cd22428
first type I K homology (KH) RNA-binding domain found in tudor and KH domain-containing ...
496-561 9.90e-07

first type I K homology (KH) RNA-binding domain found in tudor and KH domain-containing protein (TDRKH) and similar proteins; TDRKH, also called tudor domain-containing protein 2 (TDRD2), is a mitochondria-anchored RNA-binding protein that is required for spermatogenesis and involved in piRNA biogenesis. It specifically recruits MIWI, but not MILI, to engage the piRNA pathway. TDRKH contains two K-homology (KH) RNA-binding domains and one tudor domain, which are involved in binding to RNA or single-strand DNA. The model corresponds to the first one.


Pssm-ID: 411856 [Multi-domain]  Cd Length: 74  Bit Score: 46.56  E-value: 9.90e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 57530702 496 IKVPSYAAGRVIGKGGKTVNELQNLTSAEVVVPRDQTPDENDQVVVKITGHFYACQLAQRKIQEIL 561
Cdd:cd22428   9 MKVPREAVGLIIGRQGATIKQIQKETGARIDFKDEGSGGELPERVLLIQGNPVQAQRAEEAIHQII 74
KH-I_PCBP1_2_rpt3 cd22521
third type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 1 (PCBP1) ...
409-481 1.12e-06

third type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 1 (PCBP1) and similar proteins; The family includes PCBP1 (also called alpha-CP1, or heterogeneous nuclear ribonucleoprotein E1, or hnRNP E1, or nucleic acid-binding protein SUB2.3) and PCBP2 (also called alpha-CP2, or heterogeneous nuclear ribonucleoprotein E2, or hnRNP E2). They are single-stranded nucleic acid binding proteins that bind preferentially to oligo dC. They act as iron chaperones for ferritin. In case of infection by poliovirus, PCBP1 plays a role in initiation of viral RNA replication in concert with the viral protein 3CD. PCBP2 is a major cellular poly(rC)-binding protein. It also binds poly(rU). PCBP2 negatively regulates cellular antiviral responses mediated by MAVS signaling. It acts as an adapter between MAVS and the E3 ubiquitin ligase ITCH, therefore triggering MAVS ubiquitination and degradation. PCBP2 forms a metabolon with the heme oxygenase 1/cytochrome P450 reductase complex for heme catabolism and iron transfer. Both PCBP1 and PCBP2 contain three K-homology (KH) RNA-binding domains. The model corresponds to the third one.


Pssm-ID: 411949  Cd Length: 76  Bit Score: 46.59  E-value: 1.12e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 57530702 409 SETVH-LFIPALAVGAIIGKQGQHIKQLSRFAGASIKIA-PAEGPDAklRMVIITGPPEAQFKAQGRIYGKLKEE 481
Cdd:cd22521   3 QTTSHeLTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIAnPVEGSTD--RQVTITGSAASISLAQYLINARLSSE 75
KH-I_Vigilin_rpt8 cd22411
eighth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; ...
203-261 1.19e-06

eighth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the eighth one.


Pssm-ID: 411839 [Multi-domain]  Cd Length: 62  Bit Score: 45.66  E-value: 1.19e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 57530702 203 VPTQFVGAIIGKEGATIRNITKQTQSKIDIhrkENAGAAEKPITIHSTPEGCSTACKII 261
Cdd:cd22411   6 IFKQFHKNIIGKGGATIKKIREETNTRIDL---PEENSDSDVITITGKKEDVEKARERI 61
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
85-150 1.22e-06

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C-terminus that has some features characteristic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 46.07  E-value: 1.22e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 57530702    85 IRNIPPHLQWEVLDSLLAQYGTVENCEQVNTDTETA--VVNVTYGNKDQARQAIEKLNGFQLENYSLK 150
Cdd:pfam00076   3 VGNLPPDTTEEDLKDLFSKFGPIKSIRLVRDETGRSkgFAFVEFEDEEDAEKAIEALNGKELGGRELK 70
KH-I_FUBP_rpt2 cd22397
second type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding ...
201-265 1.25e-06

second type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding proteins; The far upstream element-binding protein (FUBP) family includes FUBP1-3. FUBP1, also called FBP, or FUSE-binding protein 1, or DNA helicase V, or DH V, binds RNA and single-stranded DNA (ssDNA) and may act both as activator and repressor of transcription. It regulates MYC expression by binding to a single-stranded far-upstream element (FUSE) upstream of the MYC promoter. FUBP2, also called FUSE-binding protein 2, or KH type-splicing regulatory protein (KSRP), or p75, is a single-strand nucleic acid binding protein implicated in a variety of cellular processes, including splicing in the nucleus, mRNA decay, maturation of miRNA, and transcriptional control of proto-oncogenes such as c-myc. It regulates the stability and/or translatability of many mRNA species, encoding immune-relevant proteins, either by binding to AU-rich elements (AREs) of mRNA 3'UTR or by facilitating miRNA biogenesis to target mRNA. FUBP3, also called FUSE-binding protein 3, or MARTA2, was previously shown to mediate dendritic targeting of MAP2 mRNA in neurons. It may interact with single-stranded DNA from the far-upstream element (FUSE) and activate gene expression. It is required for beta-actin mRNA localization. It also interacts with fibroblast growth factor 9 (FGF9) 3'-UTR UG repeats and positively controls FGF9 expression through increasing translation of FGF9 mRNA. FUBP proteins contain four K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411825 [Multi-domain]  Cd Length: 69  Bit Score: 46.08  E-value: 1.25e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 57530702 201 MLVPTQFVGAIIGKEGATIRNITKQTQSK-IDIHRKENAGAAEKPITIHSTPEGCSTACKIIMEIM 265
Cdd:cd22397   4 IMIPGNKVGLIIGKGGETIKQLQERAGVKmVMIQDGPQPTGQDKPLRITGDPQKVQRAKELVMELI 69
RRM1_2_CoAA_like cd12343
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in RRM-containing coactivator activator ...
3-71 1.31e-06

RNA recognition motif 1 (RRM1) and 2 (RRM2) found in RRM-containing coactivator activator/modulator (CoAA) and similar proteins; This subfamily corresponds to the RRM in CoAA (also known as RBM14 or PSP2) and RNA-binding protein 4 (RBM4). CoAA is a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner, and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. RBM4 is a ubiquitously expressed splicing factor with two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may also function as a translational regulator of stress-associated mRNAs as well as play a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RRMs, a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. This family also includes Drosophila RNA-binding protein lark (Dlark), a homolog of human RBM4. It plays an important role in embryonic development and in the circadian regulation of adult eclosion. Dlark shares high sequence similarity with RBM4 at the N-terminal region. However, Dlark has three proline-rich segments instead of three alanine-rich segments within the C-terminal region.


Pssm-ID: 409779 [Multi-domain]  Cd Length: 66  Bit Score: 45.68  E-value: 1.31e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 57530702   3 KLYIGNLGENVSPLDLESLFKdskiPFsGQFL----VKTgYAFVDCPDESWAMKAIEALSGKvELHGKLIEVE 71
Cdd:cd12343   1 KIFVGNLPDAATSEELRALFE----KY-GKVTecdiVKN-YAFVHMEKEEDAEDAIKALNGY-EFMGSRINVE 66
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
4-69 1.66e-06

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C-terminus that has some features characteristic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 45.69  E-value: 1.66e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 57530702     4 LYIGNLGENVSPLDLESLF------KDSKIPfSGQFLVKTGYAFVDCPDESWAMKAIEALSGKvELHGKLIE 69
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFskfgpiKSIRLV-RDETGRSKGFAFVEFEDEEDAEKAIEALNGK-ELGGRELK 70
KH-I_NOVA_rpt1 cd22435
first type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ...
495-561 1.75e-06

first type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ventral antigen (Nova); The family includes two related neuronal RNA-binding proteins, Nova-1 and Nova-2. Nova-1, also called onconeural ventral antigen 1, or paraneoplastic Ri antigen, or ventral neuron-specific protein 1, may regulate RNA splicing or metabolism in a specific subset of developing neurons. It interacts with RNA containing repeats of the YCAY sequence. It is a brain-enriched splicing factor regulating neuronal alternative splicing. Nova-1 is involved in neurological disorders and carcinogenesis. Nova-2, also called astrocytic NOVA1-like RNA-binding protein, is a neuronal RNA-binding protein expressed in a broader central nervous system (CNS) distribution than Nova-1. It functions in neuronal RNA metabolism. NOVA family proteins contain three K-homology (KH) RNA-binding domains. The model corresponds to the first one.


Pssm-ID: 411863 [Multi-domain]  Cd Length: 73  Bit Score: 45.61  E-value: 1.75e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 57530702 495 HIK--VPSYAAGRVIGKGGKTVNELQNLTSAEVVVPR--DQTPDENDQVVVkITGHFYACQLAQRKIQEIL 561
Cdd:cd22435   3 SLKllVPNYAAGSIIGKGGQTIAQLQKETGARIKLSKnnDFYPGTTERVCL-IQGEVEAVNAVLDFILEKI 72
KH-I_ScSCP160_rpt6 cd22451
sixth type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein ...
201-268 1.79e-06

sixth type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the sixth one.


Pssm-ID: 411879 [Multi-domain]  Cd Length: 69  Bit Score: 45.52  E-value: 1.79e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 57530702 201 MLVPTQFVGAIIGKEGATIRNITKQTQSKIDIHRKENAGAaekPITIHSTPEGCSTACKIIMEIMQKE 268
Cdd:cd22451   5 IDIPKEYHRAIIGKGGAVLRELEAETGCRIQVPKKDDPSG---KIRITGARDGVEAATAKILNISDEE 69
ELAV_HUD_SF TIGR01661
ELAV/HuD family splicing factor; This model describes the ELAV/HuD subfamily of splicing ...
30-141 2.09e-06

ELAV/HuD family splicing factor; This model describes the ELAV/HuD subfamily of splicing factors found in metazoa. HuD stands for the human paraneoplastic encephalomyelitis antigen D of which there are 4 variants in human. ELAV stnds for the Drosophila Embryonic lethal abnormal visual protein. ELAV-like splicing factors are also known in human as HuB (ELAV-like protein 2), HuC (ELAV-like protein 3, Paraneoplastic cerebellar degeneration-associated antigen) and HuR (ELAV-like protein 1). These genes are most closely related to the sex-lethal subfamily of splicing factors found in Dipteran insects (TIGR01659). These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).


Pssm-ID: 273741 [Multi-domain]  Cd Length: 352  Bit Score: 49.94  E-value: 2.09e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57530702    30 SGQFLvktGYAFVDCPDESWAMKAIEALSGkVELHGKLIEVEHSVPKRQ--RSRKLQIRNIPPHLQWEVLDSLLAQYGTV 107
Cdd:TIGR01661  41 TGQSL---GYGFVNYVRPEDAEKAVNSLNG-LRLQNKTIKVSYARPSSDsiKGANLYVSGLPKTMTQHELESIFSPFGQI 116
                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 57530702   108 EN----CEQVnTDTETAVVNVTYGNKDQARQAIEKLNG 141
Cdd:TIGR01661 117 ITsrilSDNV-TGLSKGVGFIRFDKRDEADRAIKTLNG 153
KH-I_NOVA_rpt3 cd09031
third type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ...
496-559 2.15e-06

third type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ventral antigen (Nova); The family includes two related neuronal RNA-binding proteins, Nova-1 and Nova-2. Nova-1, also called onconeural ventral antigen 1, or paraneoplastic Ri antigen, or ventral neuron-specific protein 1, may regulate RNA splicing or metabolism in a specific subset of developing neurons. It interacts with RNA containing repeats of the YCAY sequence. It is a brain-enriched splicing factor regulating neuronal alternative splicing. Nova-1 is involved in neurological disorders and carcinogenesis. Nova-2, also called astrocytic NOVA1-like RNA-binding protein, is a neuronal RNA-binding protein expressed in a broader central nervous system (CNS) distribution than Nova-1. It functions in neuronal RNA metabolism. NOVA family proteins contain three K-homology (KH) RNA-binding domains. The model corresponds to the third one.


Pssm-ID: 411807 [Multi-domain]  Cd Length: 71  Bit Score: 45.26  E-value: 2.15e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 57530702 496 IKVPSYAAGRVIGKGGKTVNELQNLTSAEVVVPR--DQTPDENDQVVVkITGHFYACQLAQRKIQE 559
Cdd:cd09031   5 LEVPENLVGAILGKGGKTLVEIQELTGARIQISKkgEFVPGTRNRKVT-ITGTPAAVQAAQYLIEQ 69
KH-I_PCBP4_rpt2 cd22520
second type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 4 (PCBP4) ...
411-466 2.21e-06

second type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 4 (PCBP4) and similar proteins; PCBP4, also called alpha-CP4, or heterogeneous nuclear ribonucleoprotein E4, or hnRNP E4, is a single-stranded nucleic acid binding protein that binds preferentially to oligo dC. It regulates both basal and stress-induced p21 expression through binding p21 3'-UTR and modulating p21 mRNA stability. It also plays a role in the cell cycle and is implicated in lung tumor suppression. PCBP4 contains three K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411948 [Multi-domain]  Cd Length: 72  Bit Score: 45.40  E-value: 2.21e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 57530702 411 TVHLFIPALAVGAIIGKQGQHIKQLSRFAGASIKIAPAEGPDAKLRMVIITGPPEA 466
Cdd:cd22520   3 TLRLVIPASQCGSLIGKAGSKIKEIRESTGAQVQVAGDLLPNSTERAVTVSGVPDA 58
KH-I_TDRKH_rpt2 cd22429
second type I K homology (KH) RNA-binding domain found in tudor and KH domain-containing ...
410-484 2.27e-06

second type I K homology (KH) RNA-binding domain found in tudor and KH domain-containing protein (TDRKH) and similar proteins; TDRKH, also called tudor domain-containing protein 2 (TDRD2), is a mitochondria-anchored RNA-binding protein that is required for spermatogenesis and involved in piRNA biogenesis. It specifically recruits MIWI, but not MILI, to engage the piRNA pathway. TDRKH contains two K-homology (KH) RNA-binding domains and one tudor domain, which are involved in binding to RNA or single-strand DNA. The model corresponds to the second one.


Pssm-ID: 411857 [Multi-domain]  Cd Length: 82  Bit Score: 45.79  E-value: 2.27e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 57530702 410 ETVHLFIPALAVGAIIGKQGQHIKQLSRFAGASIKIA-PAEGPDAKLRMVIITGPPEAQFKAQGRIYGKLKEENFF 484
Cdd:cd22429   2 ITEELHVPQRAVGRIIGRGGETIRSICRTSGAKVKCDrESDDTLDLVRLITITGTKKEVDAAKSLILEKVSEEEEF 77
KH-I_PCBP_rpt2 cd02396
second type I K homology (KH) RNA-binding domain found in the family of poly(C)-binding ...
197-265 2.31e-06

second type I K homology (KH) RNA-binding domain found in the family of poly(C)-binding proteins (PCBPs); The PCBP family, also known as hnRNP E family, comprises four members, PCBP1-4, which are RNA-binding proteins that interact in a sequence-specific manner with single-stranded poly(C) sequences. They are mainly involved in various posttranscriptional regulations, including mRNA stabilization or translational activation/silencing. Besides, PCBPs may share iron chaperone activity. PCBPs contain three K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411806 [Multi-domain]  Cd Length: 72  Bit Score: 45.34  E-value: 2.31e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 57530702 197 VPLRMLVPTQFVGAIIGKEGATIRNITKQTQSKIDIHRKENAGAAEKPITIHSTPEGCSTACKIIMEIM 265
Cdd:cd02396   2 ITLRLLVPASQCGSLIGKGGSKIKEIRESTGASVQVASEMLPNSTERAVTISGSPEAITKCVEQICCVM 70
KH-I_KHDRBS cd22384
type I K homology (KH) RNA-binding domain found in the KH domain-containing, RNA-binding, ...
277-365 2.39e-06

type I K homology (KH) RNA-binding domain found in the KH domain-containing, RNA-binding, signal transduction-associated protein (KHDRBS) family; The KHDRBS family includes three members, KHDRBS1-3. KHDRBS1, also called GAP-associated tyrosine phosphoprotein p62, or Src-associated in mitosis 68 kDa protein, or Sam68, or p21 Ras GTPase-activating protein-associated p62, or p68, is an RNA-binding protein that plays a role in the regulation of alternative splicing and influences mRNA splice site selection and exon inclusion. It binds to RNA containing 5'-[AU]UAA-3' as a bipartite motif spaced by more than 15 nucleotides. It also binds poly(A). KHDRBS1 acts as a putative regulator of mRNA stability and/or translation rates and mediates mRNA nuclear export. It is recruited and tyrosine phosphorylated by several receptor systems, for example the T-cell, leptin and insulin receptors. KHDRBS2, also called Sam68-like mammalian protein 1, or SLM-1, is an RNA-binding protein that plays a role in the regulation of alternative splicing and influences mRNA splice site selection and exon inclusion. It binds both poly(A) and poly(U) homopolymers. KHDRBS2 may function as an adapter protein for Src kinases during mitosis. KHDRBS3, also called RNA-binding protein T-Star, or Sam68-like mammalian protein 2, or SLM-2, or Sam68-like phosphotyrosine protein, is an RNA-binding protein that plays a role in the regulation of alternative splicing and influences mRNA splice site selection and exon inclusion. It binds optimally to RNA containing 5'-[AU]UAA-3' as a bipartite motif spaced by more than 15 nucleotides. It also binds poly(A). KHDRBS3 may play a role as a negative regulator of cell growth.


Pssm-ID: 411812 [Multi-domain]  Cd Length: 102  Bit Score: 46.12  E-value: 2.39e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57530702 277 EIPLKILAHNNFVGRLIGKEGRNLKKIEQDTDTKItisplqdltlynperTITVKGSIETCAKAEEeimkkIRESYENDI 356
Cdd:cd22384  10 LIPVKEFPKFNFVGKLLGPRGNTLKRLQEETGTKM---------------SILGKGSMRDKAKEEE-----LRKSGDPKY 69

                ....*....
gi 57530702 357 AAMNLQAHL 365
Cdd:cd22384  70 AHLNEDLHV 78
KH-I_PCBP4_rpt1 cd22517
first type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 4 (PCBP4) ...
411-481 2.59e-06

first type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 4 (PCBP4) and similar proteins; PCBP4, also called alpha-CP4, or heterogeneous nuclear ribonucleoprotein E4, or hnRNP E4, is a single-stranded nucleic acid binding protein that binds preferentially to oligo dC. It regulates both basal and stress-induced p21 expression through binding p21 3'-UTR and modulating p21 mRNA stability. It also plays a role in the cell cycle and is implicated in lung tumor suppression. PCBP4 contains three K-homology (KH) RNA-binding domains. The model corresponds to the first one.


Pssm-ID: 411945  Cd Length: 70  Bit Score: 45.02  E-value: 2.59e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 57530702 411 TVHLFIPALAVGAIIGKQGQHIKQLSRFAGASIKIAPAEGPDaklRMVIITGPPEAQFKAQGRIYGKLKEE 481
Cdd:cd22517   3 TLRLLMHGKEVGSIIGKKGETVKRIREESSARITISEGSCPE---RITTITGSTDAVFRAFSMIAFKLEED 70
KH-I_IGF2BP_rpt1 cd22400
first type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 ...
414-474 2.85e-06

first type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 mRNA-binding protein (IGF2BP) family; The IGF2BP family includes three members: IGF2BP1/IMP-1/ CRD-BP/ VICKZ1, IGF2BP2/IMP-2/ VICKZ2, and IGF2BP3/IMP-3/VICKZ3, which are RNA-binding factors that recruit target transcripts to cytoplasmic protein-RNA complexes (mRNPs). They function by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. IGF2BP proteins contain four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the first one.


Pssm-ID: 411828 [Multi-domain]  Cd Length: 68  Bit Score: 44.96  E-value: 2.85e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 57530702 414 LFIPALAVGAIIGKQGQHIKQLSRFAGASIKIAPAEGPDAKLRMVIITGPPEAQFKAQGRI 474
Cdd:cd22400   4 ILVPSEFVGAIIGKGGATIRQITQQTGARIDIHRKENAGAAEKAITIYGTPEGCSSACKQI 64
KH-I_RCF3_like_rpt5 cd22463
fifth type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH ...
498-561 3.16e-06

fifth type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH domain-containing protein RCF3 and similar protein; RCF3, also called protein ENHANCED STRESS RESPONSE 1 (ESR1), or protein HIGH OSMOTIC STRESS GENE EXPRESSION 5 (HOS5), or protein REGULATOR OF CBF GENE EXPRESSION 3, or protein SHINY 1 (SHI1), acts as negative regulator of osmotic stress-induced gene expression. It is involved in the regulation of thermotolerance responses under heat stress. It functions as an upstream regulator of heat stress transcription factor (HSF) genes. HEN4, also called protein HUA ENHANCER 4, plays a role in floral reproductive organ identity in the third whorl and floral determinacy specification by specifically promoting the processing of AGAMOUS (AG) pre-mRNA. It functions in association with HUA1 and HUA2. RCF3 contains five K-homology (KH) RNA-binding domains. The model corresponds to the KH5 domain of RCF3.


Pssm-ID: 411891  Cd Length: 71  Bit Score: 45.11  E-value: 3.16e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 57530702 498 VPSYAAGRVIGKGGKTVNELQNLTSAEVVVPRDQTPDENDQVVVKITGHFYACQLAQRKIQEIL 561
Cdd:cd22463   8 IPEAVVGLIIGKSGNTIKQISERSGAFVAIVQDRYPLEETQKILRISGTEEQLKRAQSLVEGLI 71
KH-I_Vigilin_rpt14 cd22417
fourteenth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; ...
199-268 3.20e-06

fourteenth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the fourteenth one.


Pssm-ID: 411845 [Multi-domain]  Cd Length: 72  Bit Score: 44.89  E-value: 3.20e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57530702 199 LRMLVPTQFVGAIIGKEGATIRNITKQTQSKIDIHRKENAGaaEKPITIHSTPEGCSTACKIIMEIMQKE 268
Cdd:cd22417   3 LTVEVDPKYHPKIIGRKGAVITKLRDDHDVNIQFPDKGDEN--DDEITITGYEKNAEAAKDAILKIVQEL 70
KH-I_PCBP_rpt2 cd02396
second type I K homology (KH) RNA-binding domain found in the family of poly(C)-binding ...
411-480 3.32e-06

second type I K homology (KH) RNA-binding domain found in the family of poly(C)-binding proteins (PCBPs); The PCBP family, also known as hnRNP E family, comprises four members, PCBP1-4, which are RNA-binding proteins that interact in a sequence-specific manner with single-stranded poly(C) sequences. They are mainly involved in various posttranscriptional regulations, including mRNA stabilization or translational activation/silencing. Besides, PCBPs may share iron chaperone activity. PCBPs contain three K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411806 [Multi-domain]  Cd Length: 72  Bit Score: 44.95  E-value: 3.32e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57530702 411 TVHLFIPALAVGAIIGKQGQHIKQLSRFAGASIKIAPAEGPDAKLRMVIITGPPEAQFKAQGRIYGKLKE 480
Cdd:cd02396   3 TLRLLVPASQCGSLIGKGGSKIKEIRESTGASVQVASEMLPNSTERAVTISGSPEAITKCVEQICCVMLE 72
KH-I_FUBP_rpt3 cd22398
third type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding ...
496-561 3.54e-06

third type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding proteins; The far upstream element-binding protein (FUBP) family includes FUBP1-3. FUBP1, also called FBP, or FUSE-binding protein 1, or DNA helicase V, or DH V, binds RNA and single-stranded DNA (ssDNA) and may act both as activator and repressor of transcription. It regulates MYC expression by binding to a single-stranded far-upstream element (FUSE) upstream of the MYC promoter. FUBP2, also called FUSE-binding protein 2, or KH type-splicing regulatory protein (KSRP), or p75, is a single-strand nucleic acid binding protein implicated in a variety of cellular processes, including splicing in the nucleus, mRNA decay, maturation of miRNA, and transcriptional control of proto-oncogenes such as c-myc. It regulates the stability and/or translatability of many mRNA species, encoding immune-relevant proteins, either by binding to AU-rich elements (AREs) of mRNA 3'UTR or by facilitating miRNA biogenesis to target mRNA. FUBP3, also called FUSE-binding protein 3, or MARTA2, was previously shown to mediate dendritic targeting of MAP2 mRNA in neurons. It may interact with single-stranded DNA from the far-upstream element (FUSE) and activate gene expression. It is required for beta-actin mRNA localization. It also interacts with fibroblast growth factor 9 (FGF9) 3'-UTR UG repeats and positively controls FGF9 expression through increasing translation of FGF9 mRNA. FUBP proteins contain four K-homology (KH) RNA-binding domains. The model corresponds to the third one.


Pssm-ID: 411826 [Multi-domain]  Cd Length: 67  Bit Score: 44.56  E-value: 3.54e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 57530702 496 IKVPSYAAGRVIGKGGKTVNELQNLTSAEVVV--PRDQTPDEndqvVVKITGHFYACQLAQRKIQEIL 561
Cdd:cd22398   4 VPVPRFAVGVVIGKGGEMIKKIQNETGARVQFkpDDGNSPDR----ICVITGPPDQVQHAARMIQELI 67
KH-I_HNRNPK_rpt1 cd22432
first type I K homology (KH) RNA-binding domain found in heterogeneous nuclear ...
491-533 4.06e-06

first type I K homology (KH) RNA-binding domain found in heterogeneous nuclear ribonucleoprotein K (hnRNP K) and similar proteins; hnRNP K, also called transformation up-regulated nuclear protein (TUNP), is a pre-mRNA binding protein that binds tenaciously to poly(C) sequences. It may be involved in the nuclear metabolism of hnRNAs, particularly for pre-mRNAs that contain cytidine-rich sequences. It can also bind poly(C) single-stranded DNA. hnRNP K plays an important role in p53/TP53 response to DNA damage, acting at the level of both transcription activation and repression. hnRNP K contains three K-homology (KH) RNA-binding domains. The model corresponds to the first one.


Pssm-ID: 411860 [Multi-domain]  Cd Length: 64  Bit Score: 44.48  E-value: 4.06e-06
                        10        20        30        40
                ....*....|....*....|....*....|....*....|...
gi 57530702 491 KLEAHIKVPSYAAGRVIGKGGKTVNELQNLTSAEVVVPRDQTP 533
Cdd:cd22432   1 VVELRLLIPSKAAGAIIGKGGENIKRLRTEYNASVSVPDSSGP 43
KH-I_PEPPER_rpt1_like cd22459
first type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH ...
498-541 4.79e-06

first type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH domain-containing protein PEPPER and similar proteins; The family includes a group of plant RNA-binding KH domain-containing proteins, such as PEPPER, flowering locus K homology domain protein (FLK), RNA-binding KH domain-containing protein RCF3 and KH domain-containing protein HEN4. PEPPER regulates vegetative and gynoecium development. It acts as a positive regulator of the central floral repressor FLOWERING LOCUS C. In concert with HUA2, PEPPER antagonizes FLK by positively regulating FLC probably at transcriptional and post-transcriptional levels, and thus acts as a negative regulator of flowering. FLK, also called flowering locus KH domain protein, regulates positively flowering by repressing FLC expression and post-transcriptional modification. PEPPER and FLK contain three K-homology (KH) RNA-binding domains. RCF3, also called protein ENHANCED STRESS RESPONSE 1 (ESR1), or protein HIGH OSMOTIC STRESS GENE EXPRESSION 5 (HOS5), or protein REGULATOR OF CBF GENE EXPRESSION 3, or protein SHINY 1 (SHI1), acts as negative regulator of osmotic stress-induced gene expression. It is involved in the regulation of thermotolerance responses under heat stress. It functions as an upstream regulator of heat stress transcription factor (HSF) genes. HEN4, also called protein HUA ENHANCER 4, plays a role in floral reproductive organ identity in the third whorl and floral determinacy specification by specifically promoting the processing of AGAMOUS (AG) pre-mRNA. It functions in association with HUA1 and HUA2. RCF3 and HEN4 contain five KH RNA-binding domains. The model corresponds to the KH1 domain of PEPPER and FLK, as well as KH1 and KH3 domains of RCF3 and HEN4.


Pssm-ID: 411887 [Multi-domain]  Cd Length: 69  Bit Score: 44.52  E-value: 4.79e-06
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
gi 57530702 498 VPSYAAGRVIGKGGKTVNELQNLTSAEVVVPrDQTPDENDQVVV 541
Cdd:cd22459   8 CPVSKAGSVIGKGGEIIKQLRQETGARIKVE-DGVPGTEERVIT 50
KH-I_ScSCP160_rpt2 cd22447
second type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein ...
416-474 4.91e-06

second type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411875 [Multi-domain]  Cd Length: 80  Bit Score: 44.72  E-value: 4.91e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 57530702 416 IPALAVGAIIGKQGQHIKQLSRFAGASIKIAPAEG-------PDAKLRMVIITGPPEAQFKAQGRI 474
Cdd:cd22447  10 IPASTRARIIGKKGANLKQIREKTGVRIDIPPRDAdaapadeDDDTMVEVTITGDEFNVQHAKQRI 75
KH-I_Rnc1_rpt3 cd22457
third type I K homology (KH) RNA-binding domain found in Schizosaccharomyces pombe RNA-binding ...
203-261 5.15e-06

third type I K homology (KH) RNA-binding domain found in Schizosaccharomyces pombe RNA-binding protein Rnc1 and similar proteins; Rnc1, also called RNA-binding protein that suppresses calcineurin deletion 1, is an RNA-binding protein that acts as an important regulator of the posttranscriptional expression of the MAPK phosphatase Pmp1 in fission yeast. It binds and stabilizes pmp1 mRNA and hence acts as a negative regulator of pmk1 signaling. Overexpression of Rnc1 suppresses the Cl(-) sensitivity of calcineurin deletion. The nuclear export of Rnc1 requires mRNA-binding ability and the mRNA export factor Rae1. Rnc1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the third one.


Pssm-ID: 411885 [Multi-domain]  Cd Length: 64  Bit Score: 43.99  E-value: 5.15e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 57530702 203 VPTQFVGAIIGKEGATIRNITKQTQSKIDIHRKENAGAAEKPITIHSTPEGCSTACKII 261
Cdd:cd22457   5 IPPDMVGCIIGKGGSKIQEIRRLSGCKISIAKAPHDETGERMFTITGTPEANDRALRLL 63
KH-I_PCBP3_rpt2 cd22519
second type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) ...
411-466 5.25e-06

second type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) and similar proteins; PCBP3, also called alpha-CP3, or PCBP3-overlapping transcript, or PCBP3-overlapping transcript 1, or heterogeneous nuclear ribonucleoprotein E3, or hnRNP E3, is a single-stranded nucleic acid binding protein that binds preferentially to oligo dC. It can function as a repressor dependent on binding to single-strand and double-stranded poly(C) sequences. PCBP3 contains three K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411947 [Multi-domain]  Cd Length: 79  Bit Score: 44.78  E-value: 5.25e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 57530702 411 TVHLFIPALAVGAIIGKQGQHIKQLSRFAGASIKIAPAEGPDAKLRMVIITGPPEA 466
Cdd:cd22519   7 TLRLVVPASQCGSLIGKGGSKIKEIRESTGAQVQVAGDMLPNSTERAVTISGTPDA 62
KH-I_Vigilin_rpt2 cd22406
second type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; ...
290-350 5.35e-06

second type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the second one.


Pssm-ID: 411834 [Multi-domain]  Cd Length: 75  Bit Score: 44.22  E-value: 5.35e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 57530702 290 GRLIGKEGRNLKKIEQDTDTKITISPLQDltlynPERTITVKGSIETCAKAEEEIMKKIRE 350
Cdd:cd22406  17 RFILGKKGKKLQELELKTATKIVIPRQED-----NSDEIKITGTKEGIEKARHEIQLISDE 72
KH-I_TDRKH_rpt1 cd22428
first type I K homology (KH) RNA-binding domain found in tudor and KH domain-containing ...
416-475 5.39e-06

first type I K homology (KH) RNA-binding domain found in tudor and KH domain-containing protein (TDRKH) and similar proteins; TDRKH, also called tudor domain-containing protein 2 (TDRD2), is a mitochondria-anchored RNA-binding protein that is required for spermatogenesis and involved in piRNA biogenesis. It specifically recruits MIWI, but not MILI, to engage the piRNA pathway. TDRKH contains two K-homology (KH) RNA-binding domains and one tudor domain, which are involved in binding to RNA or single-strand DNA. The model corresponds to the first one.


Pssm-ID: 411856 [Multi-domain]  Cd Length: 74  Bit Score: 44.25  E-value: 5.39e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 57530702 416 IPALAVGAIIGKQGQHIKQLSRFAGASIKI-APAEGPDAKLRMVIITGPPEAQFKAQGRIY 475
Cdd:cd22428  11 VPREAVGLIIGRQGATIKQIQKETGARIDFkDEGSGGELPERVLLIQGNPVQAQRAEEAIH 71
KH-I_Vigilin_rpt6 cd02394
sixth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, ...
493-560 6.07e-06

sixth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the sixth one.


Pssm-ID: 411804 [Multi-domain]  Cd Length: 68  Bit Score: 44.10  E-value: 6.07e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 57530702 493 EAHIKVPSYAAGRVIGKGGKTVNELQNLTSAEVVVPRDQTPDENdqvvVKITGHFYACQLAQRKIQEI 560
Cdd:cd02394   3 FTTIEIDPKFHGHIIGKGGANIKRIREESGVSIRIPDDEANSDE----IRIEGSPEGVKKAKAEILEL 66
KH-I_IGF2BP2_rpt1 cd22491
first type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 ...
279-347 6.45e-06

first type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2) and similar proteins; IGF2BP2, also called IGF2 mRNA-binding protein 2 (IMP-2), or hepatocellular carcinoma autoantigen p62, or IGF-II mRNA-binding protein 2, or VICKZ family member 2 (VICKZ2), is an RNA-binding factor that recruits target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It functions by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. It also binds to beta-actin/ACTB and MYC transcripts. IGF2BP2 can form homooligomers and heterooligomers with IGF2BP1 and IGF2BP3 in an RNA-dependent manner. It contains four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the first one.


Pssm-ID: 411919  Cd Length: 74  Bit Score: 44.28  E-value: 6.45e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 57530702 279 PLKILAHNNFVGRLIGKEGRNLKKIEQDTDTKITISPLQDLTLynPERTITVKGSIETCAKAEE---EIMKK 347
Cdd:cd22491   1 PLRILVPTQFVGAIIGKEGLTIKNITKQTQSKVDIHRKENAGA--AEKPITIHATPEGCSAACRmilEIMQK 70
KH-I_FUBP_rpt3 cd22398
third type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding ...
415-474 6.97e-06

third type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding proteins; The far upstream element-binding protein (FUBP) family includes FUBP1-3. FUBP1, also called FBP, or FUSE-binding protein 1, or DNA helicase V, or DH V, binds RNA and single-stranded DNA (ssDNA) and may act both as activator and repressor of transcription. It regulates MYC expression by binding to a single-stranded far-upstream element (FUSE) upstream of the MYC promoter. FUBP2, also called FUSE-binding protein 2, or KH type-splicing regulatory protein (KSRP), or p75, is a single-strand nucleic acid binding protein implicated in a variety of cellular processes, including splicing in the nucleus, mRNA decay, maturation of miRNA, and transcriptional control of proto-oncogenes such as c-myc. It regulates the stability and/or translatability of many mRNA species, encoding immune-relevant proteins, either by binding to AU-rich elements (AREs) of mRNA 3'UTR or by facilitating miRNA biogenesis to target mRNA. FUBP3, also called FUSE-binding protein 3, or MARTA2, was previously shown to mediate dendritic targeting of MAP2 mRNA in neurons. It may interact with single-stranded DNA from the far-upstream element (FUSE) and activate gene expression. It is required for beta-actin mRNA localization. It also interacts with fibroblast growth factor 9 (FGF9) 3'-UTR UG repeats and positively controls FGF9 expression through increasing translation of FGF9 mRNA. FUBP proteins contain four K-homology (KH) RNA-binding domains. The model corresponds to the third one.


Pssm-ID: 411826 [Multi-domain]  Cd Length: 67  Bit Score: 43.79  E-value: 6.97e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 57530702 415 FIPALAVGAIIGKQGQHIKQLSRFAGASIKIAP--AEGPDaklRMVIITGPPEAQFKAQGRI 474
Cdd:cd22398   5 PVPRFAVGVVIGKGGEMIKKIQNETGARVQFKPddGNSPD---RICVITGPPDQVQHAARMI 63
KH-I_ScSCP160_rpt6 cd22451
sixth type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein ...
416-481 7.06e-06

sixth type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the sixth one.


Pssm-ID: 411879 [Multi-domain]  Cd Length: 69  Bit Score: 43.98  E-value: 7.06e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 57530702 416 IPALAVGAIIGKQGQHIKQLSRFAGASIKIAPAEGPDAKLRmviITGPPEAQFKAQGRIYGKLKEE 481
Cdd:cd22451   7 IPKEYHRAIIGKGGAVLRELEAETGCRIQVPKKDDPSGKIR---ITGARDGVEAATAKILNISDEE 69
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
4-155 7.26e-06

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.


Pssm-ID: 130689 [Multi-domain]  Cd Length: 562  Bit Score: 48.65  E-value: 7.26e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57530702     4 LYIGNLGENVSPLDLESLFKdskiPFSGQFLVKT----------GYAFVDCPDESWAMKAIEALSGKVeLHGKLIEVEHS 73
Cdd:TIGR01628   3 LYVGDLDPDVTEAKLYDLFK----PFGPVLSVRVcrdsvtrrslGYGYVNFQNPADAERALETMNFKR-LGGKPIRIMWS 77
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57530702    74 V--PKRQRSRK--LQIRNIPPHLQWEVLDSLLAQYGTVENCeQVNTDTE---TAVVNVTYGNKDQARQAIEKLNGFQLEN 146
Cdd:TIGR01628  78 QrdPSLRRSGVgnIFVKNLDKSVDNKALFDTFSKFGNILSC-KVATDENgksRGYGFVHFEKEESAKAAIQKVNGMLLND 156
                         170
                  ....*....|
gi 57530702   147 YSLKVA-YIP 155
Cdd:TIGR01628 157 KEVYVGrFIK 166
RBD_RRM1_NPL3 cd12340
RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 3 (Npl3p) and similar proteins; ...
82-153 7.27e-06

RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 3 (Npl3p) and similar proteins; This subfamily corresponds to the RRM1 of Npl3p, also termed mitochondrial targeting suppressor 1 protein, or nuclear polyadenylated RNA-binding protein 1. Npl3p is a major yeast RNA-binding protein that competes with 3'-end processing factors, such as Rna15, for binding to the nascent RNA, protecting the transcript from premature termination and coordinating transcription termination and the packaging of the fully processed transcript for export. It specifically recognizes a class of G/U-rich RNAs. Npl3p is a multi-domain protein containing two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), separated by a short linker and a C-terminal domain rich in glycine, arginine and serine residues.


Pssm-ID: 409777 [Multi-domain]  Cd Length: 69  Bit Score: 43.93  E-value: 7.27e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 57530702  82 KLQIRNIPPHLQWEVLDSLLAQYGTVENCEQVNTDTETAVVnvtYGNKDQARQAIEKLNGFQLENYSLKVAY 153
Cdd:cd12340   1 RLFVRPFPPDTSESAIREIFSPYGPVKEVKMLSDSNFAFVE---FEELEDAIRAKDSVHGRVLNNEPLYVTY 69
KH-I_FUBP_rpt1 cd22396
first type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding ...
286-344 8.81e-06

first type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding proteins; The far upstream element-binding protein (FUBP) family includes FUBP1-3. FUBP1, also called FBP, or FUSE-binding protein 1, or DNA helicase V, or DH V, binds RNA and single-stranded DNA (ssDNA) and may act both as activator and repressor of transcription. It regulates MYC expression by binding to a single-stranded far-upstream element (FUSE) upstream of the MYC promoter. FUBP2, also called FUSE-binding protein 2, or KH type-splicing regulatory protein (KSRP), or p75, is a single-strand nucleic acid binding protein implicated in a variety of cellular processes, including splicing in the nucleus, mRNA decay, maturation of miRNA, and transcriptional control of proto-oncogenes such as c-myc. It regulates the stability and/or translatability of many mRNA species, encoding immune-relevant proteins, either by binding to AU-rich elements (AREs) of mRNA 3'UTR or by facilitating miRNA biogenesis to target mRNA. FUBP3, also called FUSE-binding protein 3, or MARTA2, was previously shown to mediate dendritic targeting of MAP2 mRNA in neurons. It may interact with single-stranded DNA from the far-upstream element (FUSE) and activate gene expression. It is required for beta-actin mRNA localization. It also interacts with fibroblast growth factor 9 (FGF9) 3'-UTR UG repeats and positively controls FGF9 expression through increasing translation of FGF9 mRNA. FUBP proteins contain four K-homology (KH) RNA-binding domains. The model corresponds to the first one.


Pssm-ID: 411824 [Multi-domain]  Cd Length: 68  Bit Score: 43.40  E-value: 8.81e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 57530702 286 NNFVGRLIGKEGRNLKKIEQDTDTKITISPLQDltlYNPERTITVKGSIETCAKAEEEI 344
Cdd:cd22396   9 DKMVGLIIGRGGEQINRLQAESGAKIQIAPDSG---GLPERPCTLTGTPDAIETAKRLI 64
KH-I_PCBP1_2_rpt1 cd22515
first type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 1 (PCBP1) ...
278-350 9.29e-06

first type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 1 (PCBP1) and similar proteins; The family includes PCBP1 (also called alpha-CP1, or heterogeneous nuclear ribonucleoprotein E1, or hnRNP E1, or nucleic acid-binding protein SUB2.3) and PCBP2 (also called alpha-CP2, or heterogeneous nuclear ribonucleoprotein E2, or hnRNP E2). They are single-stranded nucleic acid binding proteins that bind preferentially to oligo dC. They act as iron chaperones for ferritin. In case of infection by poliovirus, PCBP1 plays a role in initiation of viral RNA replication in concert with the viral protein 3CD. PCBP2 is a major cellular poly(rC)-binding protein. It also binds poly(rU). PCBP2 negatively regulates cellular antiviral responses mediated by MAVS signaling. It acts as an adapter between MAVS and the E3 ubiquitin ligase ITCH, therefore triggering MAVS ubiquitination and degradation. PCBP2 forms a metabolon with the heme oxygenase 1/cytochrome P450 reductase complex for heme catabolism and iron transfer. Both PCBP1 and PCBP2 contain three K-homology (KH) RNA-binding domains. The model corresponds to the first one.


Pssm-ID: 411943  Cd Length: 70  Bit Score: 43.46  E-value: 9.29e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 57530702 278 IPLKILAHNNFVGRLIGKEGRNLKKIEQDTDTKITISPLQdltlyNPERTITVKGSIETCAKAEEEIMKKIRE 350
Cdd:cd22515   2 LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGN-----CPERIITLAGPTNAIFKAFAMIIDKLEE 69
KH-I_Vigilin_rpt8 cd22411
eighth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; ...
287-344 9.93e-06

eighth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the eighth one.


Pssm-ID: 411839 [Multi-domain]  Cd Length: 62  Bit Score: 43.35  E-value: 9.93e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 57530702 287 NFVGRLIGKEGRNLKKIEQDTDTKITIsPLQDltlyNPERTITVKGSIETCAKAEEEI 344
Cdd:cd22411   9 QFHKNIIGKGGATIKKIREETNTRIDL-PEEN----SDSDVITITGKKEDVEKARERI 61
PRK13763 PRK13763
putative RNA-processing protein; Provisional
203-335 1.32e-05

putative RNA-processing protein; Provisional


Pssm-ID: 237494 [Multi-domain]  Cd Length: 180  Bit Score: 46.01  E-value: 1.32e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57530702  203 VPTQFVGAIIGKEGATIRNITKQTQSKIDIHRKENAgaaekpITIhsTPEGCSTACKII--MEIMQkeAQDTKFTEEIPL 280
Cdd:PRK13763   9 IPKDRIGVLIGKKGETKKEIEERTGVKLEIDSETGE------VII--EPTDGEDPLAVLkaRDIVK--AIGRGFSPEKAL 78
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 57530702  281 KILAHNNFV-------------------GRLIGKEGRNLKKIEQDTDTKITISplqDLTLY---NPERTITVKGSIE 335
Cdd:PRK13763  79 RLLDDDYVLevidlsdygdspnalrrikGRIIGEGGKTRRIIEELTGVDISVY---GKTVAiigDPEQVEIAREAIE 152
KH-I_PEPPER_rpt2_like cd22460
second type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH ...
200-261 1.39e-05

second type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH domain-containing protein PEPPER and similar proteins; The family includes a group of plant RNA-binding KH domain-containing proteins, such as PEPPER, flowering locus K homology domain protein (FLK), RNA-binding KH domain-containing protein RCF3 and KH domain-containing protein HEN4. PEPPER regulates vegetative and gynoecium development. It acts as a positive regulator of the central floral repressor FLOWERING LOCUS C. In concert with HUA2, PEPPER antagonizes FLK by positively regulating FLC probably at transcriptional and post-transcriptional levels, and thus acts as a negative regulator of flowering. FLK, also called flowering locus KH domain protein, regulates positively flowering by repressing FLC expression and post-transcriptional modification. PEPPER and FLK contain three K-homology (KH) RNA-binding domains. RCF3, also called protein ENHANCED STRESS RESPONSE 1 (ESR1), or protein HIGH OSMOTIC STRESS GENE EXPRESSION 5 (HOS5), or protein REGULATOR OF CBF GENE EXPRESSION 3, or protein SHINY 1 (SHI1), acts as negative regulator of osmotic stress-induced gene expression. It is involved in the regulation of thermotolerance responses under heat stress. It functions as an upstream regulator of heat stress transcription factor (HSF) genes. HEN4, also called protein HUA ENHANCER 4, plays a role in floral reproductive organ identity in the third whorl and floral determinacy specification by specifically promoting the processing of AGAMOUS (AG) pre-mRNA. It functions in association with HUA1 and HUA2. RCF3 and HEN4 contain five KH RNA-binding domains. The model corresponds to the KH2 domain of PEPPER and FLK, as well as KH2 and KH4 domains of RCF3 and HEN4.


Pssm-ID: 411888 [Multi-domain]  Cd Length: 73  Bit Score: 42.99  E-value: 1.39e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 57530702 200 RMLVPTQFVGAIIGKEGATIRNITKQTQSKIDIHRKEN----AGAAEKPITIHSTPEGCSTACKII 261
Cdd:cd22460   3 RLLVASSQAGSLIGKGGAIIKQIREESGASVRILPEEElppcASPDDRVVQISGEAQAVKKALELV 68
KH-I_TDRKH_rpt2 cd22429
second type I K homology (KH) RNA-binding domain found in tudor and KH domain-containing ...
289-350 1.43e-05

second type I K homology (KH) RNA-binding domain found in tudor and KH domain-containing protein (TDRKH) and similar proteins; TDRKH, also called tudor domain-containing protein 2 (TDRD2), is a mitochondria-anchored RNA-binding protein that is required for spermatogenesis and involved in piRNA biogenesis. It specifically recruits MIWI, but not MILI, to engage the piRNA pathway. TDRKH contains two K-homology (KH) RNA-binding domains and one tudor domain, which are involved in binding to RNA or single-strand DNA. The model corresponds to the second one.


Pssm-ID: 411857 [Multi-domain]  Cd Length: 82  Bit Score: 43.48  E-value: 1.43e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 57530702 289 VGRLIGKEGRNLKKIEQDTDTKITISPLQDLTLyNPERTITVKGSIETCAKAEEEIMKKIRE 350
Cdd:cd22429  13 VGRIIGRGGETIRSICRTSGAKVKCDRESDDTL-DLVRLITITGTKKEVDAAKSLILEKVSE 73
KH-I_NOVA_rpt1 cd22435
first type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ...
199-265 1.56e-05

first type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ventral antigen (Nova); The family includes two related neuronal RNA-binding proteins, Nova-1 and Nova-2. Nova-1, also called onconeural ventral antigen 1, or paraneoplastic Ri antigen, or ventral neuron-specific protein 1, may regulate RNA splicing or metabolism in a specific subset of developing neurons. It interacts with RNA containing repeats of the YCAY sequence. It is a brain-enriched splicing factor regulating neuronal alternative splicing. Nova-1 is involved in neurological disorders and carcinogenesis. Nova-2, also called astrocytic NOVA1-like RNA-binding protein, is a neuronal RNA-binding protein expressed in a broader central nervous system (CNS) distribution than Nova-1. It functions in neuronal RNA metabolism. NOVA family proteins contain three K-homology (KH) RNA-binding domains. The model corresponds to the first one.


Pssm-ID: 411863 [Multi-domain]  Cd Length: 73  Bit Score: 42.91  E-value: 1.56e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57530702 199 LRMLVPTQFVGAIIGKEGATIRNITKQTQSKIDIhRKENA---GAAEKPITIHSTPEGCSTACKIIMEIM 265
Cdd:cd22435   4 LKLLVPNYAAGSIIGKGGQTIAQLQKETGARIKL-SKNNDfypGTTERVCLIQGEVEAVNAVLDFILEKI 72
RRM1_PSRP2_like cd21609
RNA recognition motif 1 (RRM1) found in chloroplastic plastid-specific 30S ribosomal protein 2 ...
82-153 1.72e-05

RNA recognition motif 1 (RRM1) found in chloroplastic plastid-specific 30S ribosomal protein 2 (PSRP-2) and similar proteins; PSRP-2, also called chloroplastic 30S ribosomal protein 2, or chloroplastic small ribosomal subunit protein cS22, is a component of the chloroplast ribosome (chloro-ribosome), a dedicated translation machinery responsible for the synthesis of chloroplast genome-encoded proteins, including proteins of the transcription and translation machinery and components of the photosynthetic apparatus. It binds single strand DNA (ssDNA) and RNA in vitro. It exhibits RNA chaperone activity and regulates negatively resistance responses to abiotic stresses during seed germination (e.g. salt, dehydration, and low temperature) and seedling growth (e.g. salt). The family also includes Nicotiana sylvestris chloroplastic 33 kDa ribonucleoprotein (NsCP33) and Arabidopsis thaliana chloroplastic 31 kDa ribonucleoprotein (AtCP31A). NsCP33 may be involved in splicing and/or processing of chloroplast RNA's. AtCP31A, also called RNA-binding protein 1/2/3 (AtRBP33), or RNA-binding protein CP31A, or RNA-binding protein RNP-T, or RNA-binding protein cp31, is required for specific RNA editing events in chloroplasts and stabilizes specific chloroplast mRNAs, as well as for normal chloroplast development under cold stress conditions by stabilizing transcripts of numerous mRNAs under these conditions. CP31A may modulate telomere replication through RNA binding domains. Members in this family contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the first RRM motif.


Pssm-ID: 410188 [Multi-domain]  Cd Length: 80  Bit Score: 43.18  E-value: 1.72e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 57530702  82 KLQIRNIPPHLQWEVLDSLLAQYGTVENcEQVNTDTETAVVN----VTYGNKDQARQAIEKLNGFQLENYSLKVAY 153
Cdd:cd21609   1 RLYVGNIPRNVTSEELAKIFEEAGTVEI-AEVMYDRYTGRSRgfgfVTMGSVEDAKAAIEKLNGTEVGGREIKVNI 75
RRM1_Hu_like cd12375
RNA recognition motif 1 (RRM1) found in the Hu proteins family, Drosophila sex-lethal (SXL), ...
83-153 1.87e-05

RNA recognition motif 1 (RRM1) found in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins; This subfamily corresponds to the RRM1 of Hu proteins and SXL. The Hu proteins family represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. This family also includes the sex-lethal protein (SXL) from Drosophila melanogaster. SXL governs sexual differentiation and X chromosome dosage compensation in flies. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds to its own pre-mRNA and promotes female-specific alternative splicing. It contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RRMs that show high preference to bind single-stranded, uridine-rich target RNA transcripts.


Pssm-ID: 409810 [Multi-domain]  Cd Length: 76  Bit Score: 42.78  E-value: 1.87e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 57530702  83 LQIRNIPPHLQWEVLDSLLAQYGTVENCEQV---NTDTETAVVNVTYGNKDQARQAIEKLNGFQLENYSLKVAY 153
Cdd:cd12375   2 LIVNYLPQSMTQEELRSLFGAIGPIESCKLVrdkITGQSLGYGFVNYRDPNDARKAINTLNGLDLENKRLKVSY 75
KH-I_AKAP1 cd22395
type I K homology (KH) RNA-binding domain found in mitochondrial A-kinase anchor protein 1 ...
286-316 1.94e-05

type I K homology (KH) RNA-binding domain found in mitochondrial A-kinase anchor protein 1 (AKAP1) and similar proteins; AKAP1, also called A-kinase anchor protein 149 kDa, or AKAP 149, or dual specificity A-kinase-anchoring protein 1, or D-AKAP-1, or protein kinase A-anchoring protein 1 (PRKA1), or spermatid A-kinase anchor protein 84, or S-AKAP84, is a novel developmentally regulated A kinase anchor protein of male germ cells. It binds to type I and II regulatory subunits of protein kinase A and anchors them to the cytoplasmic face of the mitochondrial outer membrane.


Pssm-ID: 411823 [Multi-domain]  Cd Length: 68  Bit Score: 42.51  E-value: 1.94e-05
                        10        20        30
                ....*....|....*....|....*....|.
gi 57530702 286 NNFVGRLIGKEGRNLKKIEQDTDTKITISPL 316
Cdd:cd22395   8 SELVGRLIGKQGRNVKQLKQKSGAKIYIKPH 38
KH-I_Rnc1_rpt2 cd22456
second type I K homology (KH) RNA-binding domain found in Schizosaccharomyces pombe ...
198-257 2.23e-05

second type I K homology (KH) RNA-binding domain found in Schizosaccharomyces pombe RNA-binding protein Rnc1 and similar proteins; Rnc1, also called RNA-binding protein that suppresses calcineurin deletion 1, is an RNA-binding protein that acts as an important regulator of the posttranscriptional expression of the MAPK phosphatase Pmp1 in fission yeast. It binds and stabilizes pmp1 mRNA and hence acts as a negative regulator of pmk1 signaling. Overexpression of Rnc1 suppresses the Cl(-) sensitivity of calcineurin deletion. The nuclear export of Rnc1 requires mRNA-binding ability and the mRNA export factor Rae1. Rnc1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411884 [Multi-domain]  Cd Length: 69  Bit Score: 42.28  E-value: 2.23e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 57530702 198 PLRMLVPTQFVGAIIGKEGATIRNITKQTQSKIDIHRKENAGAAEKPITIHSTPEGCSTA 257
Cdd:cd22456   1 PIRLLIPHSLIGSIIGKGGARIKEIQDGSGARLVASKEFLPLSTERILEVQGTPDAIHNA 60
KH-I_Vigilin_rpt6 cd02394
sixth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, ...
288-344 2.24e-05

sixth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the sixth one.


Pssm-ID: 411804 [Multi-domain]  Cd Length: 68  Bit Score: 42.56  E-value: 2.24e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 57530702 288 FVGRLIGKEGRNLKKIEQDTDTKITISPLQDLTlynpeRTITVKGSIETCAKAEEEI 344
Cdd:cd02394  12 FHGHIIGKGGANIKRIREESGVSIRIPDDEANS-----DEIRIEGSPEGVKKAKAEI 63
RRM1_SRSF6 cd12596
RNA recognition motif 1 (RRM1) found in vertebrate serine/arginine-rich splicing factor 6 ...
1-73 2.29e-05

RNA recognition motif 1 (RRM1) found in vertebrate serine/arginine-rich splicing factor 6 (SRSF6); This subfamily corresponds to the RRM1 of SRSF6, also termed pre-mRNA-splicing factor SRp55, which is an essential splicing regulatory serine/arginine (SR) protein that preferentially interacts with a number of purine-rich splicing enhancers (ESEs) to activate splicing of the ESE-containing exon. It is the only protein from HeLa nuclear extract or purified SR proteins that specifically binds B element RNA after UV irradiation. SRSF6 may also recognize different types of RNA sites. For instance, it does not bind to the purine-rich sequence in the calcitonin-specific ESE, but binds to a region adjacent to the purine tract. Moreover, cellular levels of SRSF6 may control tissue-specific alternative splicing of the calcitonin/ calcitonin gene-related peptide (CGRP) pre-mRNA. SRSF6 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal SR domains rich in serine-arginine dipeptides.


Pssm-ID: 410009 [Multi-domain]  Cd Length: 72  Bit Score: 42.64  E-value: 2.29e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 57530702   1 MNKLYIGNLGENVSPLDLESLFKDskipfSGQFL---VKTGYAFVDCPDESWAMKAIEALSGKvELHGKLIEVEHS 73
Cdd:cd12596   1 MPRVYIGRLSYHVREKDIQRFFSG-----YGKLLevdLKNGYGFVEFEDSRDADDAVYELNGK-ELCGERVIVEHA 70
KH-I_BTR1_rpt1 cd22513
first type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana protein BTR1 and ...
498-545 2.33e-05

first type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana protein BTR1 and similar proteins; BTR1, also called Binding to ToMV RNA 1, is a negative regulator of tomato mosaic virus (ToMV) multiplication but has no effect on the multiplication of cucumber mosaic virus (CMV). BTR1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the first one.


Pssm-ID: 411941 [Multi-domain]  Cd Length: 73  Bit Score: 42.42  E-value: 2.33e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 57530702 498 VPSYAAGRVIGKGGKTVNELQNLTSAEVVVPRDQT--PDENDQVVVkITG 545
Cdd:cd22513   8 VSNAAAGSVIGKGGATINDFQAQSGARIQLSRAQEffPGTTDRVLL-VSG 56
KH-I_Mextli_like cd22454
type I K homology (KH) RNA-binding domain found in Drosophila melanogaster eukaryotic ...
410-474 2.36e-05

type I K homology (KH) RNA-binding domain found in Drosophila melanogaster eukaryotic translation initiation factor 4E-binding protein Mextli and similar proteins; Mextli is a novel eukaryotic translation initiation factor 4E-binding protein that promotes translation in Drosophila melanogaster.


Pssm-ID: 411882 [Multi-domain]  Cd Length: 71  Bit Score: 42.30  E-value: 2.36e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 57530702 410 ETVHLFIPALAVGAIIGKQGQHIKQLSRFAGASIKIAPaEGPDAKLRMVIITGPPEAQFKAQGRI 474
Cdd:cd22454   4 TTIEVVIPNADVGKVIGKGGETIKRIEALTDTVITFER-VNGGSPNREVQITGSPDNVAAAKRLI 67
PRK13763 PRK13763
putative RNA-processing protein; Provisional
411-561 2.43e-05

putative RNA-processing protein; Provisional


Pssm-ID: 237494 [Multi-domain]  Cd Length: 180  Bit Score: 45.24  E-value: 2.43e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57530702  411 TVHLFIPALAVGAIIGKQGQHIKQLSRFAGASIKIapaegpDAKLRMVIIT----GPPEAQFKAQGRI----YGklkeen 482
Cdd:PRK13763   4 MEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEI------DSETGEVIIEptdgEDPLAVLKARDIVkaigRG------ 71
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57530702  483 fFGPKEEVKLEAH------IKVPSYAA---------GRVIGKGGKTVNELQNLTSAEVVVpRDQTpdendqvvVKITGHF 547
Cdd:PRK13763  72 -FSPEKALRLLDDdyvlevIDLSDYGDspnalrrikGRIIGEGGKTRRIIEELTGVDISV-YGKT--------VAIIGDP 141
                        170
                 ....*....|....
gi 57530702  548 YACQLAQRKIQEIL 561
Cdd:PRK13763 142 EQVEIAREAIEMLI 155
KH-I_PEPPER_rpt2_like cd22460
second type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH ...
281-349 2.89e-05

second type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH domain-containing protein PEPPER and similar proteins; The family includes a group of plant RNA-binding KH domain-containing proteins, such as PEPPER, flowering locus K homology domain protein (FLK), RNA-binding KH domain-containing protein RCF3 and KH domain-containing protein HEN4. PEPPER regulates vegetative and gynoecium development. It acts as a positive regulator of the central floral repressor FLOWERING LOCUS C. In concert with HUA2, PEPPER antagonizes FLK by positively regulating FLC probably at transcriptional and post-transcriptional levels, and thus acts as a negative regulator of flowering. FLK, also called flowering locus KH domain protein, regulates positively flowering by repressing FLC expression and post-transcriptional modification. PEPPER and FLK contain three K-homology (KH) RNA-binding domains. RCF3, also called protein ENHANCED STRESS RESPONSE 1 (ESR1), or protein HIGH OSMOTIC STRESS GENE EXPRESSION 5 (HOS5), or protein REGULATOR OF CBF GENE EXPRESSION 3, or protein SHINY 1 (SHI1), acts as negative regulator of osmotic stress-induced gene expression. It is involved in the regulation of thermotolerance responses under heat stress. It functions as an upstream regulator of heat stress transcription factor (HSF) genes. HEN4, also called protein HUA ENHANCER 4, plays a role in floral reproductive organ identity in the third whorl and floral determinacy specification by specifically promoting the processing of AGAMOUS (AG) pre-mRNA. It functions in association with HUA1 and HUA2. RCF3 and HEN4 contain five KH RNA-binding domains. The model corresponds to the KH2 domain of PEPPER and FLK, as well as KH2 and KH4 domains of RCF3 and HEN4.


Pssm-ID: 411888 [Multi-domain]  Cd Length: 73  Bit Score: 42.22  E-value: 2.89e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 57530702 281 KILAHNNFVGRLIGKEGRNLKKIEQDTDTKITISPLQDLTLYNP--ERTITVKGSIETCAKAEEEIMKKIR 349
Cdd:cd22460   3 RLLVASSQAGSLIGKGGAIIKQIREESGASVRILPEEELPPCASpdDRVVQISGEAQAVKKALELVSSRLR 73
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
2-87 2.91e-05

RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];


Pssm-ID: 223796 [Multi-domain]  Cd Length: 306  Bit Score: 46.09  E-value: 2.91e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57530702   2 NKLYIGNLGENVSPLDLESLFKDS------KIPFSGQFLVKTGYAFVDCPDESWAMKAIEALSGKvELHGKLIEVEHSVP 75
Cdd:COG0724 116 NTLFVGNLPYDVTEEDLRELFKKFgpvkrvRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGK-ELEGRPLRVQKAQP 194
                        90
                ....*....|..
gi 57530702  76 KRQRSRKLQIRN 87
Cdd:COG0724 195 ASQPRSELSNNL 206
KH-I_TDRKH_rpt2 cd22429
second type I K homology (KH) RNA-binding domain found in tudor and KH domain-containing ...
492-559 2.91e-05

second type I K homology (KH) RNA-binding domain found in tudor and KH domain-containing protein (TDRKH) and similar proteins; TDRKH, also called tudor domain-containing protein 2 (TDRD2), is a mitochondria-anchored RNA-binding protein that is required for spermatogenesis and involved in piRNA biogenesis. It specifically recruits MIWI, but not MILI, to engage the piRNA pathway. TDRKH contains two K-homology (KH) RNA-binding domains and one tudor domain, which are involved in binding to RNA or single-strand DNA. The model corresponds to the second one.


Pssm-ID: 411857 [Multi-domain]  Cd Length: 82  Bit Score: 42.71  E-value: 2.91e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 57530702 492 LEAHIKVPSYAAGRVIGKGGKTVNELQNLTSAEVVVPRDQTPDENDQVVVKITGHF----YACQLAQRKIQE 559
Cdd:cd22429   2 ITEELHVPQRAVGRIIGRGGETIRSICRTSGAKVKCDRESDDTLDLVRLITITGTKkevdAAKSLILEKVSE 73
KH-I_FUBP1_rpt2 cd22481
second type I K homology (KH) RNA-binding domain found in far upstream element-binding protein ...
496-561 2.99e-05

second type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 1 (FUBP1) and similar proteins; FUBP1, also called FBP, or FUSE-binding protein 1, or DNA helicase V, or DH V, binds RNA and single-stranded DNA (ssDNA) and may act both as activator and repressor of transcription. It regulates MYC expression by binding to a single-stranded far-upstream element (FUSE) upstream of the MYC promoter. FUBP1 contains four K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411909 [Multi-domain]  Cd Length: 71  Bit Score: 42.30  E-value: 2.99e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 57530702 496 IKVPSYAAGRVIGKGGKTVNELQNLTSAEVVVPRDQTPDENDQVVVKITGHFYACQLAQRKIQEIL 561
Cdd:cd22481   6 IMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGDPYKVQQAKEMVLELI 71
KH-I_DDX43_DDX53 cd22430
type I K homology (KH) RNA-binding domain found in DEAD box protein 43 (DDX43), DEAD box ...
279-344 3.03e-05

type I K homology (KH) RNA-binding domain found in DEAD box protein 43 (DDX43), DEAD box protein 53 (DDX53) and similar proteins; DDX43 (also called cancer/testis antigen 13, or DEAD box protein HAGE, or helical antigen) displays tumor-specific expression. Diseases associated with DDX43 include rheumatoid lung disease. DDX53 (also called cancer-associated gene protein, or cancer/testis antigen 26, or DEAD box protein CAGE) shows high expression level in various tumors and is involved in anti-cancer drug resistance. Both DDX46 and DDX53 are members of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation.


Pssm-ID: 411858 [Multi-domain]  Cd Length: 66  Bit Score: 41.89  E-value: 3.03e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 57530702 279 PLKILAHNNFVGRLIGKEGRNLKKIEQDTDTKITISPLQDltlynpERTITVKGSIETCAKAEEEI 344
Cdd:cd22430   1 PLCFKIDSSLVGAVIGRGGSKIRELEESTGSKIKIIKGGQ------EAEVKIFGSDEAQQKAKELI 60
KH-I_HEN4_like_rpt5 cd22462
fifth type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana KH ...
199-265 3.63e-05

fifth type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana KH domain-containing protein HEN4 and similar protein; HEN4, also called protein HUA ENHANCER 4, plays a role in floral reproductive organ identity in the third whorl and floral determinacy specification by specifically promoting the processing of AGAMOUS (AG) pre-mRNA. It functions in association with HUA1 and HUA2. HEN4 contains five K-homology (KH) RNA-binding domains. The model corresponds to the KH5 domain of HEN4.


Pssm-ID: 411890 [Multi-domain]  Cd Length: 66  Bit Score: 41.85  E-value: 3.63e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 57530702 199 LRMLVPTQFVGAIIGKEGATIRNITKQTQSKIDIHrKENAGAAEKPITIHSTPEGCSTACKIIMEIM 265
Cdd:cd22462   1 IEILIPAHAVGSVIGRGGSNINQIREISGAKVEVL-KPDSATGERIVLISGTPDQARHAQNLIEAFI 66
KH-I_IGF2BP1_rpt1 cd22490
first type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 ...
279-347 3.81e-05

first type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1) and similar proteins; IGF2BP1, also called IGF2 mRNA-binding protein 1 (IMP-1), or coding region determinant-binding protein (CRD-BP), or IGF-II mRNA-binding protein 1, or VICKZ family member 1 (VICKZ1), or zipcode-binding protein 1 (ZBP-1), is an RNA-binding factor that recruits target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It functions by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. It regulates localized beta-actin/ACTB mRNA translation, a crucial process for cell polarity, cell migration and neurite outgrowth. IGF2BP1 can form homodimers and heterodimers with IGF2BP1 and IGF2BP3. It contains four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the first one.


Pssm-ID: 411918 [Multi-domain]  Cd Length: 76  Bit Score: 42.00  E-value: 3.81e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 57530702 279 PLKILAHNNFVGRLIGKEGRNLKKIEQDTDTKITISPLQDLTLynPERTITVKGSIETCAKAEE---EIMKK 347
Cdd:cd22490   1 PLRLLVPTQYVGAIIGKEGATIRNITKQTQSKIDVHRKENAGA--AEKAISIHSTPEGCSAACKmilEIMQK 70
KH-I_FUBP2_rpt2 cd22482
second type I K homology (KH) RNA-binding domain found in far upstream element-binding protein ...
496-561 3.92e-05

second type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 2 (FUBP2) and similar proteins; FUBP2, also called FUSE-binding protein 2, or KH type-splicing regulatory protein (KSRP), or p75, is a single-strand nucleic acid binding protein implicated in a variety of cellular processes, including splicing in the nucleus, mRNA decay, maturation of miRNA, and transcriptional control of proto-oncogenes such as c-myc. It regulates the stability and/or translatability of many mRNA species, encoding immune-relevant proteins, either by binding to AU-rich elements (AREs) of mRNA 3'UTR or by facilitating miRNA biogenesis to target mRNA. FUBP2 contains four K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411910  Cd Length: 73  Bit Score: 41.82  E-value: 3.92e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 57530702 496 IKVPSYAAGRVIGKGGKTVNELQNLTSAEVVVPRDQTPDENDQVVVKITGHFYACQLAQRKIQEIL 561
Cdd:cd22482   6 IMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQACEMVMDIL 71
KH-I_PNPase cd02393
type I K homology (KH) RNA-binding domain found in polyribonucleotide nucleotidyltransferase ...
199-233 3.94e-05

type I K homology (KH) RNA-binding domain found in polyribonucleotide nucleotidyltransferase (PNPase) and similar proteins; PNPase, also called polynucleotide phosphorylase, is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. It catalyzes the phosphorolysis of single-stranded polyribonucleotides processively in the 3'- to 5'-direction. It is also involved, along with RNase II, in tRNA processing. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. The model corresponds to the KH domain.


Pssm-ID: 411803 [Multi-domain]  Cd Length: 70  Bit Score: 41.69  E-value: 3.94e-05
                        10        20        30
                ....*....|....*....|....*....|....*
gi 57530702 199 LRMLVPTQFVGAIIGKEGATIRNITKQTQSKIDIH 233
Cdd:cd02393   6 TTIKIPPDKIGDVIGPGGKTIRAIIEETGAKIDIE 40
KH-I_FUBP_rpt2 cd22397
second type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding ...
496-561 4.13e-05

second type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding proteins; The far upstream element-binding protein (FUBP) family includes FUBP1-3. FUBP1, also called FBP, or FUSE-binding protein 1, or DNA helicase V, or DH V, binds RNA and single-stranded DNA (ssDNA) and may act both as activator and repressor of transcription. It regulates MYC expression by binding to a single-stranded far-upstream element (FUSE) upstream of the MYC promoter. FUBP2, also called FUSE-binding protein 2, or KH type-splicing regulatory protein (KSRP), or p75, is a single-strand nucleic acid binding protein implicated in a variety of cellular processes, including splicing in the nucleus, mRNA decay, maturation of miRNA, and transcriptional control of proto-oncogenes such as c-myc. It regulates the stability and/or translatability of many mRNA species, encoding immune-relevant proteins, either by binding to AU-rich elements (AREs) of mRNA 3'UTR or by facilitating miRNA biogenesis to target mRNA. FUBP3, also called FUSE-binding protein 3, or MARTA2, was previously shown to mediate dendritic targeting of MAP2 mRNA in neurons. It may interact with single-stranded DNA from the far-upstream element (FUSE) and activate gene expression. It is required for beta-actin mRNA localization. It also interacts with fibroblast growth factor 9 (FGF9) 3'-UTR UG repeats and positively controls FGF9 expression through increasing translation of FGF9 mRNA. FUBP proteins contain four K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411825 [Multi-domain]  Cd Length: 69  Bit Score: 41.84  E-value: 4.13e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 57530702 496 IKVPSYAAGRVIGKGGKTVNELQNLTSAEVVVPRDQTPDENDQVVVKITGHFYACQLAQRKIQEIL 561
Cdd:cd22397   4 IMIPGNKVGLIIGKGGETIKQLQERAGVKMVMIQDGPQPTGQDKPLRITGDPQKVQRAKELVMELI 69
KH-I_NOVA_rpt3 cd09031
third type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ...
199-263 4.28e-05

third type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ventral antigen (Nova); The family includes two related neuronal RNA-binding proteins, Nova-1 and Nova-2. Nova-1, also called onconeural ventral antigen 1, or paraneoplastic Ri antigen, or ventral neuron-specific protein 1, may regulate RNA splicing or metabolism in a specific subset of developing neurons. It interacts with RNA containing repeats of the YCAY sequence. It is a brain-enriched splicing factor regulating neuronal alternative splicing. Nova-1 is involved in neurological disorders and carcinogenesis. Nova-2, also called astrocytic NOVA1-like RNA-binding protein, is a neuronal RNA-binding protein expressed in a broader central nervous system (CNS) distribution than Nova-1. It functions in neuronal RNA metabolism. NOVA family proteins contain three K-homology (KH) RNA-binding domains. The model corresponds to the third one.


Pssm-ID: 411807 [Multi-domain]  Cd Length: 71  Bit Score: 41.79  E-value: 4.28e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 57530702 199 LRMLVPTQFVGAIIGKEGATIRNITKQTQSKIDIHRKEN--AGAAEKPITIHSTPEGCSTACKIIME 263
Cdd:cd09031   3 IELEVPENLVGAILGKGGKTLVEIQELTGARIQISKKGEfvPGTRNRKVTITGTPAAVQAAQYLIEQ 69
RRM2_RBM23_RBM39 cd12284
RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein RBM23, RBM39 and ...
83-157 5.03e-05

RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein RBM23, RBM39 and similar proteins; This subfamily corresponds to the RRM2 of RBM39 (also termed HCC1), a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Although the cellular function of RBM23 remains unclear, it shows high sequence homology to RBM39 and contains two RRMs. It may possibly function as a pre-mRNA splicing factor.


Pssm-ID: 409726 [Multi-domain]  Cd Length: 78  Bit Score: 41.84  E-value: 5.03e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 57530702  83 LQIRNIPPHLQWEVLDSLLAQYGTVENCeQVNTDTETAVVN----VTYGNKDQARQAIEKLNGFQLENYSLKVAYIPDE 157
Cdd:cd12284   1 LYVGSLHFNITEDMLRGIFEPFGKIEFV-QLQKDPETGRSKgygfIQFRDAEDAKKALEQLNGFELAGRPMKVGHVTER 78
KH-I_FUBP1_rpt3 cd22484
third type I K homology (KH) RNA-binding domain found in far upstream element-binding protein ...
410-465 5.03e-05

third type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 1 (FUBP1) and similar proteins; FUBP1, also called FBP, or FUSE-binding protein 1, or DNA helicase V, or DH V, binds RNA and single-stranded DNA (ssDNA) and may act both as activator and repressor of transcription. It regulates MYC expression by binding to a single-stranded far-upstream element (FUSE) upstream of the MYC promoter. FUBP1 contains four K-homology (KH) RNA-binding domains. The model corresponds to the third one.


Pssm-ID: 411912  Cd Length: 68  Bit Score: 41.43  E-value: 5.03e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 57530702 410 ETVHLFIPALAVGAIIGKQGQHIKQLSRFAGASIKIAPAEG--PDaklRMVIITGPPE 465
Cdd:cd22484   1 EGIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGttPE---RIAQITGPPD 55
KH-I_HNRNPK_rpt2 cd22433
second type I K homology (KH) RNA-binding domain found in heterogeneous nuclear ...
196-264 5.12e-05

second type I K homology (KH) RNA-binding domain found in heterogeneous nuclear ribonucleoprotein K (hnRNP K) and similar proteins; hnRNP K, also called transformation up-regulated nuclear protein (TUNP), is a pre-mRNA binding protein that binds tenaciously to poly(C) sequences. It may be involved in the nuclear metabolism of hnRNAs, particularly for pre-mRNAs that contain cytidine-rich sequences. It can also bind poly(C) single-stranded DNA. hnRNP K plays an important role in p53/TP53 response to DNA damage, acting at the level of both transcription activation and repression. hnRNP K contains three K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411861 [Multi-domain]  Cd Length: 70  Bit Score: 41.47  E-value: 5.12e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 57530702 196 DVPLRMLVPTQFVGAIIGKEGATIRNITKQTQSKIDIHRKENAGAAEKPITIHSTPEGCSTACKIIMEI 264
Cdd:cd22433   1 DCELRLLVHQSQAGCIIGRAGFKIKELREKTGATIKVYSECCPRSTDRVVQIGGKPDKVVECIREILEL 69
KH-I_HNRNPK_rpt1 cd22432
first type I K homology (KH) RNA-binding domain found in heterogeneous nuclear ...
409-466 5.31e-05

first type I K homology (KH) RNA-binding domain found in heterogeneous nuclear ribonucleoprotein K (hnRNP K) and similar proteins; hnRNP K, also called transformation up-regulated nuclear protein (TUNP), is a pre-mRNA binding protein that binds tenaciously to poly(C) sequences. It may be involved in the nuclear metabolism of hnRNAs, particularly for pre-mRNAs that contain cytidine-rich sequences. It can also bind poly(C) single-stranded DNA. hnRNP K plays an important role in p53/TP53 response to DNA damage, acting at the level of both transcription activation and repression. hnRNP K contains three K-homology (KH) RNA-binding domains. The model corresponds to the first one.


Pssm-ID: 411860 [Multi-domain]  Cd Length: 64  Bit Score: 41.40  E-value: 5.31e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 57530702 409 SETVHLFIPALAVGAIIGKQGQHIKQLSRFAGASIKIAPAEGPDaklRMVIITGPPEA 466
Cdd:cd22432   1 VVELRLLIPSKAAGAIIGKGGENIKRLRTEYNASVSVPDSSGPE---RILTISADRET 55
RRM_SAFB_like cd12417
RNA recognition motif (RRM) found in the scaffold attachment factor (SAFB) family; This ...
3-71 5.33e-05

RNA recognition motif (RRM) found in the scaffold attachment factor (SAFB) family; This subfamily corresponds to the RRM domain of the SAFB family, including scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), SAFB-like transcriptional modulator (SLTM), and similar proteins, which are ubiquitously expressed. SAFB1, SAFB2 and SLTM have been implicated in many diverse cellular processes including cell growth and transformation, stress response, and apoptosis. They share high sequence similarities and all contain a scaffold attachment factor-box (SAF-box, also known as SAP domain) DNA-binding motif, an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region rich in glutamine and arginine residues. SAFB1 is a nuclear protein with a distribution similar to that of SLTM, but unlike that of SAFB2, which is also found in the cytoplasm. To a large extent, SAFB1 and SLTM might share similar functions, such as the inhibition of an oestrogen reporter gene. The additional cytoplasmic localization of SAFB2 implies that it could play additional roles in the cytoplasmic compartment which are distinct from the nuclear functions shared with SAFB1 and SLTM.


Pssm-ID: 409851 [Multi-domain]  Cd Length: 74  Bit Score: 41.47  E-value: 5.33e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 57530702   3 KLYIGNLGENVSPLDLESLF------KDSKIPFSGQFLVKTGYAFVDCPDESWAMKAIEALSGKvELHGKLIEVE 71
Cdd:cd12417   1 NLWISGLSDTTKAADLKKIFskygkvVSAKVVTSARTPGSRCYGYVTMASVEEADLCIKSLNKT-ELHGRVITVE 74
KH-I_DDX43_DDX53 cd22430
type I K homology (KH) RNA-binding domain found in DEAD box protein 43 (DDX43), DEAD box ...
495-561 5.35e-05

type I K homology (KH) RNA-binding domain found in DEAD box protein 43 (DDX43), DEAD box protein 53 (DDX53) and similar proteins; DDX43 (also called cancer/testis antigen 13, or DEAD box protein HAGE, or helical antigen) displays tumor-specific expression. Diseases associated with DDX43 include rheumatoid lung disease. DDX53 (also called cancer-associated gene protein, or cancer/testis antigen 26, or DEAD box protein CAGE) shows high expression level in various tumors and is involved in anti-cancer drug resistance. Both DDX46 and DDX53 are members of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation.


Pssm-ID: 411858 [Multi-domain]  Cd Length: 66  Bit Score: 41.12  E-value: 5.35e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 57530702 495 HIKVPSYAAGRVIGKGGKTVNELQNLTSAEVVVPRDQtpdenDQVVVKITGHFYACQLAQRKIQEIL 561
Cdd:cd22430   3 CFKIDSSLVGAVIGRGGSKIRELEESTGSKIKIIKGG-----QEAEVKIFGSDEAQQKAKELIDELV 64
KH-I_PCBP_rpt1 cd22438
first type I K homology (KH) RNA-binding domain found in the family of poly(C)-binding ...
199-261 5.38e-05

first type I K homology (KH) RNA-binding domain found in the family of poly(C)-binding proteins (PCBPs); The PCBP family, also known as hnRNP E family, comprises four members, PCBP1-4, which are RNA-binding proteins that interact in a sequence-specific manner with single-stranded poly(C) sequences. They are mainly involved in various posttranscriptional regulations, including mRNA stabilization or translational activation/silencing. Besides, PCBPs may share iron chaperone activity. PCBPs contain three K-homology (KH) RNA-binding domains. The model corresponds to the first one.


Pssm-ID: 411866 [Multi-domain]  Cd Length: 67  Bit Score: 41.47  E-value: 5.38e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 57530702 199 LRMLVPTQFVGAIIGKEGATIRNITKQTQSKIDIhrkENAGAAEKPITIHSTPEGCSTACKII 261
Cdd:cd22438   1 IRMLMQGKEVGSIIGKKGETIKKFREESGARINI---SDGSCPERIVTVTGTTDAVFKAFELI 60
KH-I_PEPPER_rpt1_like cd22459
first type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH ...
410-471 5.45e-05

first type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH domain-containing protein PEPPER and similar proteins; The family includes a group of plant RNA-binding KH domain-containing proteins, such as PEPPER, flowering locus K homology domain protein (FLK), RNA-binding KH domain-containing protein RCF3 and KH domain-containing protein HEN4. PEPPER regulates vegetative and gynoecium development. It acts as a positive regulator of the central floral repressor FLOWERING LOCUS C. In concert with HUA2, PEPPER antagonizes FLK by positively regulating FLC probably at transcriptional and post-transcriptional levels, and thus acts as a negative regulator of flowering. FLK, also called flowering locus KH domain protein, regulates positively flowering by repressing FLC expression and post-transcriptional modification. PEPPER and FLK contain three K-homology (KH) RNA-binding domains. RCF3, also called protein ENHANCED STRESS RESPONSE 1 (ESR1), or protein HIGH OSMOTIC STRESS GENE EXPRESSION 5 (HOS5), or protein REGULATOR OF CBF GENE EXPRESSION 3, or protein SHINY 1 (SHI1), acts as negative regulator of osmotic stress-induced gene expression. It is involved in the regulation of thermotolerance responses under heat stress. It functions as an upstream regulator of heat stress transcription factor (HSF) genes. HEN4, also called protein HUA ENHANCER 4, plays a role in floral reproductive organ identity in the third whorl and floral determinacy specification by specifically promoting the processing of AGAMOUS (AG) pre-mRNA. It functions in association with HUA1 and HUA2. RCF3 and HEN4 contain five KH RNA-binding domains. The model corresponds to the KH1 domain of PEPPER and FLK, as well as KH1 and KH3 domains of RCF3 and HEN4.


Pssm-ID: 411887 [Multi-domain]  Cd Length: 69  Bit Score: 41.44  E-value: 5.45e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 57530702 410 ETVH-LFIPALAVGAIIGKQGQHIKQLSRFAGASIKIAPAeGPDAKLRMVIITGP--PEAQ-FKAQ 471
Cdd:cd22459   1 EVVFrLLCPVSKAGSVIGKGGEIIKQLRQETGARIKVEDG-VPGTEERVITISSSeaPEAPvSPAQ 65
RRM2_NsCP33_like cd21608
RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ...
3-70 6.42e-05

RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ribonucleoprotein (NsCP33) and similar proteins; The family includes NsCP33, Arabidopsis thaliana chloroplastic 31 kDa ribonucleoprotein (CP31A) and mitochondrial glycine-rich RNA-binding protein 2 (AtGR-RBP2). NsCP33 may be involved in splicing and/or processing of chloroplast RNA's. AtCP31A, also called RNA-binding protein 1/2/3 (AtRBP33), or RNA-binding protein CP31A, or RNA-binding protein RNP-T, or RNA-binding protein cp31, is required for specific RNA editing events in chloroplasts and stabilizes specific chloroplast mRNAs, as well as for normal chloroplast development under cold stress conditions by stabilizing transcripts of numerous mRNAs under these conditions. CP31A may modulate telomere replication through RNA binding domains. AtGR-RBP2, also called AtRBG2, or glycine-rich protein 2 (AtGRP2), or mitochondrial RNA-binding protein 1a (At-mRBP1a), plays a role in RNA transcription or processing during stress. It binds RNAs and DNAs sequence with a preference to single-stranded nucleic acids. AtGR-RBP2 displays strong affinity to poly(U) sequence. It exerts cold and freezing tolerance, probably by exhibiting an RNA chaperone activity during the cold and freezing adaptation process. Some members in this family contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the second RRM motif.


Pssm-ID: 410187 [Multi-domain]  Cd Length: 76  Bit Score: 41.39  E-value: 6.42e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 57530702   3 KLYIGNLGENVSPLDLESLF------KDSKI---PFSGQflvKTGYAFVDCPDESWAMKAIEALSGKvELHGKLIEV 70
Cdd:cd21608   1 KLYVGNLSWDTTEDDLRDLFsefgevESAKVitdRETGR---SRGFGFVTFSTAEAAEAAIDALNGK-ELDGRSIVV 73
KH-I_FUBP3_rpt3 cd22486
third type I K homology (KH) RNA-binding domain found in far upstream element-binding protein ...
411-465 7.11e-05

third type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 3 (FUBP3) and similar proteins; FUBP3, also called FUSE-binding protein 3, or MARTA2, was previously shown to mediate dendritic targeting of MAP2 mRNA in neurons. It may interact with single-stranded DNA from the far-upstream element (FUSE) and activate gene expression. It is required for beta-actin mRNA localization. It also interacts with fibroblast growth factor 9 (FGF9) 3'-UTR UG repeats and positively controls FGF9 expression through increasing translation of FGF9 mRNA. FUBP3 contains four K-homology (KH) RNA-binding domains. The model corresponds to the third one.


Pssm-ID: 411914  Cd Length: 70  Bit Score: 41.09  E-value: 7.11e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 57530702 411 TVHLFIPALAVGAIIGKQGQHIKQLSRFAGASIKIAPAEG--PDaklRMVIITGPPE 465
Cdd:cd22486   4 SIEVSVPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGisPE---RVAQVMGPPD 57
KH-I_FUBP_rpt4 cd22399
fourth type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding ...
201-263 7.17e-05

fourth type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding proteins; The far upstream element-binding protein (FUBP) family includes FUBP1-3. FUBP1, also called FBP, or FUSE-binding protein 1, or DNA helicase V, or DH V, binds RNA and single-stranded DNA (ssDNA) and may act both as activator and repressor of transcription. It regulates MYC expression by binding to a single-stranded far-upstream element (FUSE) upstream of the MYC promoter. FUBP2, also called FUSE-binding protein 2, or KH type-splicing regulatory protein (KSRP), or p75, is a single-strand nucleic acid binding protein implicated in a variety of cellular processes, including splicing in the nucleus, mRNA decay, maturation of miRNA, and transcriptional control of proto-oncogenes such as c-myc. It regulates the stability and/or translatability of many mRNA species, encoding immune-relevant proteins, either by binding to AU-rich elements (AREs) of mRNA 3'UTR or by facilitating miRNA biogenesis to target mRNA. FUBP3, also called FUSE-binding protein 3, or MARTA2, was previously shown to mediate dendritic targeting of MAP2 mRNA in neurons. It may interact with single-stranded DNA from the far-upstream element (FUSE) and activate gene expression. It is required for beta-actin mRNA localization. It also interacts with fibroblast growth factor 9 (FGF9) 3'-UTR UG repeats and positively controls FGF9 expression through increasing translation of FGF9 mRNA. FUBP proteins contain four K-homology (KH) RNA-binding domains. The model corresponds to the fourth one.


Pssm-ID: 411827 [Multi-domain]  Cd Length: 67  Bit Score: 41.06  E-value: 7.17e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 57530702 201 MLVPTQFVGAIIGKEGATIRNITKQTQSKIDIHRKENAGAAEKPITIHSTPEGCSTACKIIME 263
Cdd:cd22399   4 FLVPANKCGLVIGKGGETIRQINQQSGAHVELDRNPPPNPNEKLFIIRGNPQQIEHAKQLIRE 66
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
199-267 7.20e-05

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 45.81  E-value: 7.20e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57530702  199 LRMLVPTQFVGAIIGKEGATIRNITKQTQSKIDIhrkENAGAaekpITI-HSTPEGCSTACKIIMEIMQK 267
Cdd:PRK11824 556 ETIKIPPDKIRDVIGPGGKTIREITEETGAKIDI---EDDGT----VKIaATDGEAAEAAKERIEGITAE 618
RRM1_SRSF4_like cd12337
RNA recognition motif 1 (RRM1) found in serine/arginine-rich splicing factor 4 (SRSF4) and ...
3-73 8.47e-05

RNA recognition motif 1 (RRM1) found in serine/arginine-rich splicing factor 4 (SRSF4) and similar proteins; This subfamily corresponds to the RRM1 in three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 4 (SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5 or SRp40 or SFRS5 or HRS), serine/arginine-rich splicing factor 6 (SRSF6 or SRp55). SRSF4 plays an important role in both, constitutive and alternative, splicing of many pre-mRNAs. It can shuttle between the nucleus and cytoplasm. SRSF5 regulates both alternative splicing and basal splicing. It is the only SR protein efficiently selected from nuclear extracts (NE) by the splicing enhancer (ESE) and essential for enhancer activation. SRSF6 preferentially interacts with a number of purine-rich splicing enhancers (ESEs) to activate splicing of the ESE-containing exon. It is the only protein from HeLa nuclear extract or purified SR proteins that specifically binds B element RNA after UV irradiation. SRSF6 may also recognize different types of RNA sites. Members in this family contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides.


Pssm-ID: 409774 [Multi-domain]  Cd Length: 70  Bit Score: 40.77  E-value: 8.47e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 57530702   3 KLYIGNLGENVSPLDLESLFKD-SKIpfsGQFLVKTGYAFVDCPDESWAMKAIEALSGKvELHGKLIEVEHS 73
Cdd:cd12337   1 RVYIGRLPYRARERDVERFFRGyGRI---RDINLKNGFGFVEFEDPRDADDAVYELNGK-ELCGERVIVEHA 68
KH-I_IGF2BP_rpt4 cd22403
fourth type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 ...
201-247 8.67e-05

fourth type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 mRNA-binding protein (IGF2BP) family; The IGF2BP family includes three members: IGF2BP1/IMP-1/CRD-BP/VICKZ1, IGF2BP2/IMP-2/VICKZ2, and IGF2BP3/IMP-3/VICKZ3, which are RNA-binding factors that recruit target transcripts to cytoplasmic protein-RNA complexes (mRNPs). They function by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. IGF2BP proteins contain four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the fourth one.


Pssm-ID: 411831 [Multi-domain]  Cd Length: 66  Bit Score: 40.69  E-value: 8.67e-05
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 57530702 201 MLVPTQFVGAIIGKEGATIRNITKQTQSKIDIHRKENAGAAEK-PITI 247
Cdd:cd22403   4 IRVPSSMVGRIIGKGGQNVRELQRLTGAIIKLPRDQTPDEGDEvPVEI 51
RRM2_RBM40_like cd12239
RNA recognition motif 2 (RRM2) found in RNA-binding protein 40 (RBM40) and similar proteins; ...
2-71 9.58e-05

RNA recognition motif 2 (RRM2) found in RNA-binding protein 40 (RBM40) and similar proteins; This subfamily corresponds to the RRM2 of RBM40 and the RRM of RBM41. RBM40, also known as RNA-binding region-containing protein 3 (RNPC3) or U11/U12 small nuclear ribonucleoprotein 65 kDa protein (U11/U12-65K protein). It serves as a bridging factor between the U11 and U12 snRNPs. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), connected by a linker that includes a proline-rich region. It binds to the U11-associated 59K protein via its RRM1 and employs the RRM2 to bind hairpin III of the U12 small nuclear RNA (snRNA). The proline-rich region might be involved in protein-protein interactions. RBM41 contains only one RRM. Its biological function remains unclear.


Pssm-ID: 409685 [Multi-domain]  Cd Length: 82  Bit Score: 41.06  E-value: 9.58e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57530702   2 NKLYIGNLGENVSPLDLESLFK---DSKIPFSGQFLVK-------TGYAFVDCPDESWAMKAIEALSGkVELHGKLIEVE 71
Cdd:cd12239   2 NRLYVKNLSKRVSEKDLKYIFGrfvDSSSEEKNMFDIRlmtegrmKGQAFITFPSEELAEKALNLTNG-YVLHGKPMVVQ 80
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
71-151 1.00e-04

RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];


Pssm-ID: 223796 [Multi-domain]  Cd Length: 306  Bit Score: 44.55  E-value: 1.00e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57530702  71 EHSVPKRQRSRKLQIRNIPPHLQWEVLDSLLAQYGTVENCeQVNTDTETAVV----NVTYGNKDQARQAIEKLNGFQLEN 146
Cdd:COG0724 106 KSRQKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRV-RLVRDRETGKSrgfaFVEFESEESAEKAIEELNGKELEG 184

                ....*
gi 57530702 147 YSLKV 151
Cdd:COG0724 185 RPLRV 189
KH-I_Vigilin_rpt6 cd02394
sixth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, ...
421-475 1.13e-04

sixth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the sixth one.


Pssm-ID: 411804 [Multi-domain]  Cd Length: 68  Bit Score: 40.25  E-value: 1.13e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 57530702 421 VGAIIGKQGQHIKQLSRFAGASIKIapaEGPDAKLRMVIITGPPEAQFKAQGRIY 475
Cdd:cd02394  13 HGHIIGKGGANIKRIREESGVSIRI---PDDEANSDEIRIEGSPEGVKKAKAEIL 64
arCOG04150 TIGR03665
arCOG04150 universal archaeal KH domain protein; This family of proteins is universal among ...
413-527 1.14e-04

arCOG04150 universal archaeal KH domain protein; This family of proteins is universal among the 41 archaeal genomes analyzed, and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.


Pssm-ID: 274711 [Multi-domain]  Cd Length: 172  Bit Score: 42.94  E-value: 1.14e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57530702   413 HLFIPALAVGAIIGKQGQHIKQLSRFAGASIKIapaegpDAKLRMVII---TGPPEAQFKAQGRI----YGklkeenfFG 485
Cdd:TIGR03665   1 YVKIPKDRIGVLIGKGGETKKEIEERTGVKLDI------DSETGEVKIepeDEDPLAVMKAREVVkaigRG-------FS 67
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 57530702   486 PKEEVKLEAH------IKVPSYAA---------GRVIGKGGKTVNELQNLTSAEVVV 527
Cdd:TIGR03665  68 PEKALKLLDDdymlevIDLKEYGKspnalrrikGRIIGEGGKTRRIIEELTGVSISV 124
KH-I_TDRKH_rpt1 cd22428
first type I K homology (KH) RNA-binding domain found in tudor and KH domain-containing ...
289-348 1.16e-04

first type I K homology (KH) RNA-binding domain found in tudor and KH domain-containing protein (TDRKH) and similar proteins; TDRKH, also called tudor domain-containing protein 2 (TDRD2), is a mitochondria-anchored RNA-binding protein that is required for spermatogenesis and involved in piRNA biogenesis. It specifically recruits MIWI, but not MILI, to engage the piRNA pathway. TDRKH contains two K-homology (KH) RNA-binding domains and one tudor domain, which are involved in binding to RNA or single-strand DNA. The model corresponds to the first one.


Pssm-ID: 411856 [Multi-domain]  Cd Length: 74  Bit Score: 40.78  E-value: 1.16e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 57530702 289 VGRLIGKEGRNLKKIEQDTDTKITIsPLQDLTLYNPERTITVKGSIETCAKAEEEIMKKI 348
Cdd:cd22428  16 VGLIIGRQGATIKQIQKETGARIDF-KDEGSGGELPERVLLIQGNPVQAQRAEEAIHQII 74
KH-I_PCBP_rpt3 cd22439
third type I K homology (KH) RNA-binding domain found in the family of poly(C)-binding ...
201-257 1.16e-04

third type I K homology (KH) RNA-binding domain found in the family of poly(C)-binding proteins (PCBPs); The PCBP family, also known as hnRNP E family, comprises four members, PCBP1-4, which are RNA-binding proteins that interact in a sequence-specific manner with single-stranded poly(C) sequences. They are mainly involved in various posttranscriptional regulations, including mRNA stabilization or translational activation/silencing. Besides, PCBPs may share iron chaperone activity. PCBPs contain three K-homology (KH) RNA-binding domains. The model corresponds to the third one.


Pssm-ID: 411867 [Multi-domain]  Cd Length: 68  Bit Score: 40.29  E-value: 1.16e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 57530702 201 MLVPTQFVGAIIGKEGATIRNITKQTQSKIDIHRKENaGAAEKPITIHSTPEGCSTA 257
Cdd:cd22439   6 ITIPNDLIGCIIGKGGTKINEIRQLSGATIKIANSED-GSTERSVTITGTPEAVSLA 61
KH-I_PCBP3_rpt2 cd22519
second type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) ...
197-265 1.20e-04

second type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) and similar proteins; PCBP3, also called alpha-CP3, or PCBP3-overlapping transcript, or PCBP3-overlapping transcript 1, or heterogeneous nuclear ribonucleoprotein E3, or hnRNP E3, is a single-stranded nucleic acid binding protein that binds preferentially to oligo dC. It can function as a repressor dependent on binding to single-strand and double-stranded poly(C) sequences. PCBP3 contains three K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411947 [Multi-domain]  Cd Length: 79  Bit Score: 40.93  E-value: 1.20e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 57530702 197 VPLRMLVPTQFVGAIIGKEGATIRNITKQTQSKIDIHRKENAGAAEKPITIHSTPEGCSTACKIIMEIM 265
Cdd:cd22519   6 VTLRLVVPASQCGSLIGKGGSKIKEIRESTGAQVQVAGDMLPNSTERAVTISGTPDAIIQCVKQICVVM 74
KH-I_ScSCP160_rpt1 cd22446
first type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein ...
197-269 1.26e-04

first type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the first one.


Pssm-ID: 411874 [Multi-domain]  Cd Length: 86  Bit Score: 40.85  E-value: 1.26e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57530702 197 VPLRMLVPTQFVGAIIGKEGATIRNITKQTQSKIDIHRKENAGAAEK-------PITIHSTPEGCSTACKIIMEIMQKEA 269
Cdd:cd22446   7 VTITISVPSSVRGAIIGSRGKNLKSIQDKTGTKIQIPKRNEEGNYDEddddetvEISIEGDAEGVELAKKEIEAIVKERT 86
RRM_SRSF3_like cd12373
RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 3 (SRSF3) and ...
3-75 1.26e-04

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 3 (SRSF3) and similar proteins; This subfamily corresponds to the RRM of two serine/arginine (SR) proteins, serine/arginine-rich splicing factor 3 (SRSF3) and serine/arginine-rich splicing factor 7 (SRSF7). SRSF3, also termed pre-mRNA-splicing factor SRp20, modulates alternative splicing by interacting with RNA cis-elements in a concentration- and cell differentiation-dependent manner. It is also involved in termination of transcription, alternative RNA polyadenylation, RNA export, and protein translation. SRSF3 is critical for cell proliferation, and tumor induction and maintenance. It can shuttle between the nucleus and cytoplasm. SRSF7, also termed splicing factor 9G8, plays a crucial role in both constitutive splicing and alternative splicing of many pre-mRNAs. Its localization and functions are tightly regulated by phosphorylation. SRSF7 is predominantly present in the nuclear and can shuttle between nucleus and cytoplasm. It cooperates with the export protein, Tap/NXF1, helps mRNA export to the cytoplasm, and enhances the expression of unspliced mRNA. Moreover, SRSF7 inhibits tau E10 inclusion through directly interacting with the proximal downstream intron of E10, a clustering region for frontotemporal dementia with Parkinsonism (FTDP) mutations. Both SRSF3 and SRSF7 contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions.


Pssm-ID: 409808 [Multi-domain]  Cd Length: 73  Bit Score: 40.31  E-value: 1.26e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57530702   3 KLYIGNLGENVSPLDLESLFkdskipfsGQFLVKT---------GYAFVDCPDESWAMKAIEALSGKvELHGKLIEVEHS 73
Cdd:cd12373   1 KVYVGNLGPRVTKRELEDAF--------EKYGPLRnvwvarnppGFAFVEFEDPRDAEDAVRALDGR-RICGSRVRVELS 71

                ..
gi 57530702  74 VP 75
Cdd:cd12373  72 RG 73
RRM2_NsCP33_like cd21608
RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ...
82-151 1.30e-04

RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ribonucleoprotein (NsCP33) and similar proteins; The family includes NsCP33, Arabidopsis thaliana chloroplastic 31 kDa ribonucleoprotein (CP31A) and mitochondrial glycine-rich RNA-binding protein 2 (AtGR-RBP2). NsCP33 may be involved in splicing and/or processing of chloroplast RNA's. AtCP31A, also called RNA-binding protein 1/2/3 (AtRBP33), or RNA-binding protein CP31A, or RNA-binding protein RNP-T, or RNA-binding protein cp31, is required for specific RNA editing events in chloroplasts and stabilizes specific chloroplast mRNAs, as well as for normal chloroplast development under cold stress conditions by stabilizing transcripts of numerous mRNAs under these conditions. CP31A may modulate telomere replication through RNA binding domains. AtGR-RBP2, also called AtRBG2, or glycine-rich protein 2 (AtGRP2), or mitochondrial RNA-binding protein 1a (At-mRBP1a), plays a role in RNA transcription or processing during stress. It binds RNAs and DNAs sequence with a preference to single-stranded nucleic acids. AtGR-RBP2 displays strong affinity to poly(U) sequence. It exerts cold and freezing tolerance, probably by exhibiting an RNA chaperone activity during the cold and freezing adaptation process. Some members in this family contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the second RRM motif.


Pssm-ID: 410187 [Multi-domain]  Cd Length: 76  Bit Score: 40.62  E-value: 1.30e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 57530702  82 KLQIRNIPPHLQWEVLDSLLAQYGTVENCeQVNTDTETAVVN----VTYGNKDQARQAIEKLNGFQLENYSLKV 151
Cdd:cd21608   1 KLYVGNLSWDTTEDDLRDLFSEFGEVESA-KVITDRETGRSRgfgfVTFSTAEAAEAAIDALNGKELDGRSIVV 73
KH-I_PCBP4_rpt2 cd22520
second type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 4 (PCBP4) ...
197-263 1.40e-04

second type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 4 (PCBP4) and similar proteins; PCBP4, also called alpha-CP4, or heterogeneous nuclear ribonucleoprotein E4, or hnRNP E4, is a single-stranded nucleic acid binding protein that binds preferentially to oligo dC. It regulates both basal and stress-induced p21 expression through binding p21 3'-UTR and modulating p21 mRNA stability. It also plays a role in the cell cycle and is implicated in lung tumor suppression. PCBP4 contains three K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411948 [Multi-domain]  Cd Length: 72  Bit Score: 40.39  E-value: 1.40e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 57530702 197 VPLRMLVPTQFVGAIIGKEGATIRNITKQTQSKIDIHRKENAGAAEKPITIHSTPEG----CSTACKIIME 263
Cdd:cd22520   2 VTLRLVIPASQCGSLIGKAGSKIKEIRESTGAQVQVAGDLLPNSTERAVTVSGVPDAiiqcVRQICAVILE 72
KH-I_BBP cd02395
type I K homology (KH) RNA-binding domain found in yeast branchpoint-bridging protein (BBP) ...
277-313 1.41e-04

type I K homology (KH) RNA-binding domain found in yeast branchpoint-bridging protein (BBP) and similar proteins; Yeast BBP, also called mud synthetic-lethal 5 protein, or splicing factor 1, or zinc finger protein BBP, is a mammalian splicing factor SF1 ortholog. It is involved in protein-protein interactions that bridge the 3' and 5' splice-site ends of the intron during the early steps of yeast pre-mRNA splicing. BBP interacts specifically with the pre-mRNA branchpoint sequence UACUAAC.


Pssm-ID: 411805 [Multi-domain]  Cd Length: 92  Bit Score: 41.05  E-value: 1.41e-04
                        10        20        30
                ....*....|....*....|....*....|....*..
gi 57530702 277 EIPLKILAHNNFVGRLIGKEGRNLKKIEQDTDTKITI 313
Cdd:cd02395   7 YIPVDEYPDYNFIGLIIGPRGNTQKRMEKESGAKIAI 43
KH-I_IGF2BP3_rpt1 cd22492
first type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 ...
279-354 1.65e-04

first type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3) and similar proteins; IGF2BP3, also called IGF2 mRNA-binding protein 3 (IMP-3), or hepatocellular carcinoma autoantigen p62, or IGF-II mRNA-binding protein 3, or VICKZ family member 3 (VICKZ3), or KH domain-containing protein overexpressed in cancer, or KOC, is primarily found in the nucleolus, where it can bind to the 5' UTR of the insulin-like growth factor II leader 3 mRNA and may repress translation of insulin-like growth factor II during late development. It acts as an RNA-binding factor that may recruit target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It also modulates the rate and location at which target transcripts encounter the translational apparatus and shields them from endonuclease attacks or microRNA-mediated degradation. IGF2BP3 binds to the 3'-UTR of CD44 mRNA and stabilizes it, hence promotes cell adhesion and invadopodia formation in cancer cells. It also binds to beta-actin/ACTB and MYC transcripts. IGF2BP3 can form homooligomers and heterooligomers with IGF2BP1 and IGF2BP2 in an RNA-dependent manner. IGF2BP3 contains four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the first one.


Pssm-ID: 411920  Cd Length: 76  Bit Score: 40.18  E-value: 1.65e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 57530702 279 PLKILAHNNFVGRLIGKEGRNLKKIEQDTDTKITISPLQDLTLynPERTITVKGSIETCAKAEEEIMKKIRESYEN 354
Cdd:cd22492   1 PLRLLVPTQFVGAIIGKEGATIRNITKQTQSKIDVHRKENAGA--AEKSITILSTPEGTSAACKSILEIMHKEAQD 74
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
4-153 1.80e-04

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.


Pssm-ID: 130689 [Multi-domain]  Cd Length: 562  Bit Score: 44.41  E-value: 1.80e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57530702     4 LYIGNLGENVSPLDLESLF------------KDSkipfSGQflvKTGYAFV--DCPDEswAMKAIEALSGK---VELHGK 66
Cdd:TIGR01628 181 LYVKNLDPSVNEDKLRELFakfgeitsaavmKDG----SGR---SRGFAFVnfEKHED--AAKAVEEMNGKkigLAKEGK 251
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57530702    67 LIEVEHSVPKRQRSRKLQ--------------------IRNIPPHLQWEVLDSLLAQYGTVENCeQVNTDtETAVVN--- 123
Cdd:TIGR01628 252 KLYVGRAQKRAEREAELRrkfeelqqerkmkaqgvnlyVKNLDDTVTDEKLRELFSECGEITSA-KVMLD-EKGVSRgfg 329
                         170       180       190
                  ....*....|....*....|....*....|.
gi 57530702   124 -VTYGNKDQARQAIEKLNGFQLENYSLKVAY 153
Cdd:TIGR01628 330 fVCFSNPEEANRAVTEMHGRMLGGKPLYVAL 360
KH-I_HEN4_like_rpt5 cd22462
fifth type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana KH ...
280-348 1.84e-04

fifth type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana KH domain-containing protein HEN4 and similar protein; HEN4, also called protein HUA ENHANCER 4, plays a role in floral reproductive organ identity in the third whorl and floral determinacy specification by specifically promoting the processing of AGAMOUS (AG) pre-mRNA. It functions in association with HUA1 and HUA2. HEN4 contains five K-homology (KH) RNA-binding domains. The model corresponds to the KH5 domain of HEN4.


Pssm-ID: 411890 [Multi-domain]  Cd Length: 66  Bit Score: 39.93  E-value: 1.84e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 57530702 280 LKILAHNNFVGRLIGKEGRNLKKIEQDTDTKITISPLQdltLYNPERTITVKGSIETCAKAEEEIMKKI 348
Cdd:cd22462   1 IEILIPAHAVGSVIGRGGSNINQIREISGAKVEVLKPD---SATGERIVLISGTPDQARHAQNLIEAFI 66
RRM1_MEI2_like cd12524
RNA recognition motif 1 (RRM1) found in plant Mei2-like proteins; This subgroup corresponds to ...
4-76 1.90e-04

RNA recognition motif 1 (RRM1) found in plant Mei2-like proteins; This subgroup corresponds to the RRM1 of Mei2-like proteins that represent an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and it is highly conserved between plants and fungi. Up to date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear.


Pssm-ID: 409944 [Multi-domain]  Cd Length: 77  Bit Score: 39.95  E-value: 1.90e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 57530702   4 LYIGNLGENVSPLDLESLFK---DSKIPFSGqfLVKTGYAFVDCPDESWAMKAIEALSGKvELHGKLIEVEHSVPK 76
Cdd:cd12524   4 LFVRNINSSVEDEELRALFEqfgEIRTLYTA--CKHRGFIMVSYYDIRAAQSAKRALQGT-ELGGRKLDIHFSIPK 76
MSL5 COG5176
Splicing factor (branch point binding protein) [RNA processing and modification];
272-313 1.94e-04

Splicing factor (branch point binding protein) [RNA processing and modification];


Pssm-ID: 227503 [Multi-domain]  Cd Length: 269  Bit Score: 43.42  E-value: 1.94e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
gi 57530702 272 TKFTEE--IPLKILAHNNFVGRLIGKEGRNLKKIEQDTDTKITI 313
Cdd:COG5176 146 SKYQNKiyIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAI 189
KH-I_FUBP3_rpt2 cd22483
second type I K homology (KH) RNA-binding domain found in far upstream element-binding protein ...
496-561 1.98e-04

second type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 3 (FUBP3) and similar proteins; FUBP3, also called FUSE-binding protein 3, or MARTA2, was previously shown to mediate dendritic targeting of MAP2 mRNA in neurons. It may interact with single-stranded DNA from the far-upstream element (FUSE) and activate gene expression. It is required for beta-actin mRNA localization. It also interacts with fibroblast growth factor 9 (FGF9) 3'-UTR UG repeats and positively controls FGF9 expression through increasing translation of FGF9 mRNA. FUBP3 contains four K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411911 [Multi-domain]  Cd Length: 83  Bit Score: 40.28  E-value: 1.98e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 57530702 496 IKVPSYAAGRVIGKGGKTVNELQNLTSAEVVVPRDQTPDENDQVVVKITGHFYACQLAQRKIQEIL 561
Cdd:cd22483   9 ILIPASKVGLVIGKGGETIKQLQERTGVKMIMIQDGPLPTGADKPLRITGDPFKVQQAREMVLEII 74
KH-I_AtC3H36_like cd22464
type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana zinc finger CCCH ...
416-474 2.13e-04

type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana zinc finger CCCH domain-containing proteins AtC3H36, AtC3H52 and similar proteins; The family corresponds to a group of plant CCCH family zinc finger proteins, such as AtC3H36 and AtC3H52, which contain one K homology (KH) RNA-binding domain. They may play important roles in RNA processing as RNA-binding proteins in animals. They may also have an effective role in stress tolerance.


Pssm-ID: 411892 [Multi-domain]  Cd Length: 66  Bit Score: 39.77  E-value: 2.13e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 57530702 416 IPALAVGAIIGKQGQHIKQLSRFAGASIKIAPAEGpDAKLRMVIITGPPEAQFKAQGRI 474
Cdd:cd22464   5 VDASLAGAIIGKGGVNSKQICRETGVKLSIRDHER-DPNLKNVELEGSFEQIKEASGMV 62
KH-I_Mextli_like cd22454
type I K homology (KH) RNA-binding domain found in Drosophila melanogaster eukaryotic ...
201-264 2.15e-04

type I K homology (KH) RNA-binding domain found in Drosophila melanogaster eukaryotic translation initiation factor 4E-binding protein Mextli and similar proteins; Mextli is a novel eukaryotic translation initiation factor 4E-binding protein that promotes translation in Drosophila melanogaster.


Pssm-ID: 411882 [Multi-domain]  Cd Length: 71  Bit Score: 39.61  E-value: 2.15e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 57530702 201 MLVPTQFVGAIIGKEGATIRNITKQTQSKIDIHRkENAGAAEKPITIHSTPEGCSTACKIIMEI 264
Cdd:cd22454   8 VVIPNADVGKVIGKGGETIKRIEALTDTVITFER-VNGGSPNREVQITGSPDNVAAAKRLIEDT 70
KH-I_FUBP2_rpt1 cd22479
first type I K homology (KH) RNA-binding domain found in far upstream element-binding protein ...
416-471 2.16e-04

first type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 2 (FUBP2) and similar proteins; FUBP2, also called FUSE-binding protein 2, or KH type-splicing regulatory protein (KSRP), or p75, is a single-strand nucleic acid binding protein implicated in a variety of cellular processes, including splicing in the nucleus, mRNA decay, maturation of miRNA, and transcriptional control of proto-oncogenes such as c-myc. It regulates the stability and/or translatability of many mRNA species, encoding immune-relevant proteins, either by binding to AU-rich elements (AREs) of mRNA 3'UTR or by facilitating miRNA biogenesis to target mRNA. FUBP2 contains four K-homology (KH) RNA-binding domains. The model corresponds to the first one.


Pssm-ID: 411907 [Multi-domain]  Cd Length: 71  Bit Score: 39.92  E-value: 2.16e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 57530702 416 IPALAVGAIIGKQGQHIKQLSRFAGASIKIAPAEG--PDaklRMVIITGPPEAQFKAQ 471
Cdd:cd22479   7 VPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGglPE---RSVSLTGSPEAVQKAK 61
KH-I_FUBP1_rpt4 cd22487
fourth type I K homology (KH) RNA-binding domain found in far upstream element-binding protein ...
203-263 2.30e-04

fourth type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 1 (FUBP1) and similar proteins; FUBP1, also called FBP, or FUSE-binding protein 1, or DNA helicase V, or DH V, binds RNA and single-stranded DNA (ssDNA) and may act both as activator and repressor of transcription. It regulates MYC expression by binding to a single-stranded far-upstream element (FUSE) upstream of the MYC promoter. FUBP1 contains four K-homology (KH) RNA-binding domains. The model corresponds to the fourth one.


Pssm-ID: 411915  Cd Length: 72  Bit Score: 39.94  E-value: 2.30e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 57530702 203 VPTQFVGAIIGKEGATIRNITKQTQSKIDIHRK--ENAGAAEKPITIHSTPEGCSTACKIIME 263
Cdd:cd22487   8 VPTGKTGLIIGKGGETIKSISQQSGARIELQRNppPNADPNMKLFTIRGSPQQIDYARQLIEE 70
KH-I_BTR1_rpt2 cd22437
second type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana protein BTR1 ...
498-561 2.37e-04

second type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana protein BTR1 and similar proteins; BTR1, also called Binding to ToMV RNA 1, is a negative regulator of tomato mosaic virus (ToMV) multiplication but has no effect on the multiplication of cucumber mosaic virus (CMV). BTR1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411865 [Multi-domain]  Cd Length: 69  Bit Score: 39.51  E-value: 2.37e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 57530702 498 VPSYAAGRVIGKGGKTVNELQNLTSAEV-VVPRDQTPDENDQVVVKITGHFYACQLAQRKIQEIL 561
Cdd:cd22437   5 VPNSSCGLIIGKGGSTIKELREDSNANIkISPKDQLLPGSSERIVTITGSFDQVVKAVALILEKL 69
KH-I_Rnc1_rpt2 cd22456
second type I K homology (KH) RNA-binding domain found in Schizosaccharomyces pombe ...
411-466 2.40e-04

second type I K homology (KH) RNA-binding domain found in Schizosaccharomyces pombe RNA-binding protein Rnc1 and similar proteins; Rnc1, also called RNA-binding protein that suppresses calcineurin deletion 1, is an RNA-binding protein that acts as an important regulator of the posttranscriptional expression of the MAPK phosphatase Pmp1 in fission yeast. It binds and stabilizes pmp1 mRNA and hence acts as a negative regulator of pmk1 signaling. Overexpression of Rnc1 suppresses the Cl(-) sensitivity of calcineurin deletion. The nuclear export of Rnc1 requires mRNA-binding ability and the mRNA export factor Rae1. Rnc1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411884 [Multi-domain]  Cd Length: 69  Bit Score: 39.59  E-value: 2.40e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 57530702 411 TVHLFIPALAVGAIIGKQGQHIKQLSRFAGASIKIAPAEGPDAKLRMVIITGPPEA 466
Cdd:cd22456   1 PIRLLIPHSLIGSIIGKGGARIKEIQDGSGARLVASKEFLPLSTERILEVQGTPDA 56
RRM2_SART3 cd12392
RNA recognition motif 2 (RRM2) found in squamous cell carcinoma antigen recognized by T-cells ...
81-152 2.48e-04

RNA recognition motif 2 (RRM2) found in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins; This subfamily corresponds to the RRM2 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), is an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409826 [Multi-domain]  Cd Length: 81  Bit Score: 40.01  E-value: 2.48e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 57530702  81 RKLQIRNIPPHLQWEVLDSLLAQYGTVENCEQVNTDT--ETAVVNVTYGNKDQARQAIEKLNGFQLENYSLKVA 152
Cdd:cd12392   3 NKLFVKGLPFSCTKEELEELFKQHGTVKDVRLVTYRNgkPKGLAYVEYENEADASQAVLKTDGTEIKDHTISVA 76
KH-I_Rnc1_rpt1 cd22455
first type I K homology (KH) RNA-binding domain found in Schizosaccharomyces pombe RNA-binding ...
199-265 2.49e-04

first type I K homology (KH) RNA-binding domain found in Schizosaccharomyces pombe RNA-binding protein Rnc1 and similar proteins; Rnc1, also called RNA-binding protein that suppresses calcineurin deletion 1, is an RNA-binding protein that acts as an important regulator of the posttranscriptional expression of the MAPK phosphatase Pmp1 in fission yeast. It binds and stabilizes pmp1 mRNA and hence acts as a negative regulator of pmk1 signaling. Overexpression of Rnc1 suppresses the Cl(-) sensitivity of calcineurin deletion. The nuclear export of Rnc1 requires mRNA-binding ability and the mRNA export factor Rae1. Rnc1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the first one.


Pssm-ID: 411883  Cd Length: 70  Bit Score: 39.59  E-value: 2.49e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 57530702 199 LRMLVPTQFVGAIIGKEGATIRNITKQTQSKIDIhRKENAGAAEKPITIHSTPEGCSTACKIIMEIM 265
Cdd:cd22455   3 LRALVSSKEAAVIIGKGGENIARLRATTGVKAGV-SKVVPGVHDRVLTVSGPLEGVAKAFGLIARTL 68
KH-I_NOVA_rpt2 cd22436
second type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ...
279-348 2.59e-04

second type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ventral antigen (Nova); The family includes two related neuronal RNA-binding proteins, Nova-1 and Nova-2. Nova-1, also called onconeural ventral antigen 1, or paraneoplastic Ri antigen, or ventral neuron-specific protein 1, may regulate RNA splicing or metabolism in a specific subset of developing neurons. It interacts with RNA containing repeats of the YCAY sequence. It is a brain-enriched splicing factor regulating neuronal alternative splicing. Nova-1 is involved in neurological disorders and carcinogenesis. Nova-2, also called astrocytic NOVA1-like RNA-binding protein, is a neuronal RNA-binding protein expressed in a broader central nervous system (CNS) distribution than Nova-1. It functions in neuronal RNA metabolism. NOVA family proteins contain three K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411864 [Multi-domain]  Cd Length: 70  Bit Score: 39.53  E-value: 2.59e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57530702 279 PLKILAHNNFVGRLIGKEGRNLKKIEQDTDTKITISPlQDLTLYNPERTITVKGSIETCAKAEEEIMKKI 348
Cdd:cd22436   2 QVKILVPNSTAGMIIGKGGATIKAIMEQSGARVQISQ-KPESINLQERVVTVTGEPEANRKAVSLILQKI 70
KH-I_PCBP3_rpt3 cd22522
third type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) ...
183-261 2.62e-04

third type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) and similar proteins; PCBP3, also called alpha-CP3, or PCBP3-overlapping transcript, or PCBP3-overlapping transcript 1, or heterogeneous nuclear ribonucleoprotein E3, or hnRNP E3, is a single-stranded nucleic acid binding protein that binds preferentially to oligo dC. It can function as a repressor dependent on binding to single-strand and double-stranded poly(C) sequences. PCBP3 contains three K-homology (KH) RNA-binding domains. The model corresponds to the third one.


Pssm-ID: 411950  Cd Length: 75  Bit Score: 39.71  E-value: 2.62e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 57530702 183 GSPSATTRQkpqsdvplrMLVPTQFVGAIIGKEGATIRNITKQTQSKIDIhRKENAGAAEKPITIHSTPEGCSTACKII 261
Cdd:cd22522   4 ASPPASTHE---------LTIPNDLIGCIIGRQGTKINEIRQMSGAQIKI-ANATEGSSERQITITGSPANISLAQYLI 72
KH-I_ScSCP160_rpt1 cd22446
first type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein ...
275-350 2.68e-04

first type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the first one.


Pssm-ID: 411874 [Multi-domain]  Cd Length: 86  Bit Score: 40.08  E-value: 2.68e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57530702 275 TEEIPLKILAHnnfvgrLIGKEGRNLKKIEQDTDTKITISPLQDLTLYNPER-----TITVKGSIETCAKAEEEIMKKIR 349
Cdd:cd22446  10 TISVPSSVRGA------IIGSRGKNLKSIQDKTGTKIQIPKRNEEGNYDEDDddetvEISIEGDAEGVELAKKEIEAIVK 83

                .
gi 57530702 350 E 350
Cdd:cd22446  84 E 84
KH-I_PCBP1_2_rpt2 cd22518
second type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 1 (PCBP1) ...
411-466 2.78e-04

second type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 1 (PCBP1) and similar proteins; The family includes PCBP1 (also called alpha-CP1, or heterogeneous nuclear ribonucleoprotein E1, or hnRNP E1, or nucleic acid-binding protein SUB2.3) and PCBP2 (also called alpha-CP2, or heterogeneous nuclear ribonucleoprotein E2, or hnRNP E2). They are single-stranded nucleic acid binding proteins that bind preferentially to oligo dC. They act as iron chaperones for ferritin. In case of infection by poliovirus, PCBP1 plays a role in initiation of viral RNA replication in concert with the viral protein 3CD. PCBP2 is a major cellular poly(rC)-binding protein. It also binds poly(rU). PCBP2 negatively regulates cellular antiviral responses mediated by MAVS signaling. It acts as an adapter between MAVS and the E3 ubiquitin ligase ITCH, therefore triggering MAVS ubiquitination and degradation. PCBP2 forms a metabolon with the heme oxygenase 1/cytochrome P450 reductase complex for heme catabolism and iron transfer. Both PCBP1 and PCBP2 contain three K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411946 [Multi-domain]  Cd Length: 78  Bit Score: 39.72  E-value: 2.78e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 57530702 411 TVHLFIPALAVGAIIGKQGQHIKQLSRFAGASIKIAPAEGPDAKLRMVIITGPPEA 466
Cdd:cd22518   8 TLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPNSTERAITIAGIPQS 63
KH-I_MASK cd22404
type I K homology (KH) RNA-binding domain found in Mask family proteins; The Mask family ...
496-559 2.78e-04

type I K homology (KH) RNA-binding domain found in Mask family proteins; The Mask family includes Drosophila melanogaster ankyrin repeat and KH domain-containing protein Mask, and its mammalian homologues Mask1/ANKHD1 and Mask2/ANKRD17. Mask, also called multiple ankyrin repeat single KH domain-containing protein, is a large ankyrin repeat and KH domain-containing protein involved in Drosophila receptor tyrosine kinase signaling. It acts as a mediator of receptor tyrosine kinase (RTK) signaling and may act either downstream of MAPK or transduce signaling through a parallel branch of the RTK pathway. Mask is required for the development and organization of indirect flight muscle sarcomeres by regulating the formation of M line and H zone and the correct assembly of thick and thin filaments in the sarcomere. Mask1/ANKHD1, also called HIV-1 Vpr-binding ankyrin repeat protein, or multiple ankyrin repeats single KH domain, or Hmask, is highly expressed in various cancer tissues and is involved in cancer progression, including proliferation and invasion. Mask2/ANKRD17, also called ankyrin repeat protein 17, or gene trap ankyrin repeat protein (GTAR), or serologically defined breast cancer antigen NY-BR-16, is a ubiquitously expressed ankyrin factor essential for the vascular integrity during embryogenesis. It may be directly involved in the DNA replication process and play pivotal roles in cell cycle and DNA regulation. It is also involved in innate immune defense against bacteria and viruses.


Pssm-ID: 411832 [Multi-domain]  Cd Length: 71  Bit Score: 39.50  E-value: 2.78e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 57530702 496 IKVPSYAAGRVIGKGGKTVNELQNLTSAEVVVPRDQTPDENDQVVVKITGH--FYACQLAQRKIQE 559
Cdd:cd22404   5 VTVPNSAISRVIGRGGCNINAIREVSGAHIEIDKQKGEQGDRRITIKGSADatRQAAQLINALIKD 70
KH-I_IGF2BP_rpt1 cd22400
first type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 ...
496-561 2.98e-04

first type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 mRNA-binding protein (IGF2BP) family; The IGF2BP family includes three members: IGF2BP1/IMP-1/ CRD-BP/ VICKZ1, IGF2BP2/IMP-2/ VICKZ2, and IGF2BP3/IMP-3/VICKZ3, which are RNA-binding factors that recruit target transcripts to cytoplasmic protein-RNA complexes (mRNPs). They function by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. IGF2BP proteins contain four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the first one.


Pssm-ID: 411828 [Multi-domain]  Cd Length: 68  Bit Score: 39.18  E-value: 2.98e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 57530702 496 IKVPSYAAGRVIGKGGKTVNELQNLTSAEVVVPRDQTPDENDQVVVkITGHFYACQLAQRKIQEIL 561
Cdd:cd22400   4 ILVPSEFVGAIIGKGGATIRQITQQTGARIDIHRKENAGAAEKAIT-IYGTPEGCSSACKQILEIM 68
KH-I_Vigilin_rpt8 cd22411
eighth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; ...
504-558 3.03e-04

eighth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the eighth one.


Pssm-ID: 411839 [Multi-domain]  Cd Length: 62  Bit Score: 39.11  E-value: 3.03e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 57530702 504 GRVIGKGGKTVNELQNLTSAEVVVPRdqtpDENDQVVVKITGHFYACQLAQRKIQ 558
Cdd:cd22411  12 KNIIGKGGATIKKIREETNTRIDLPE----ENSDSDVITITGKKEDVEKARERIL 62
KH-I_PCBP3_rpt1 cd22516
first type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) ...
278-350 3.06e-04

first type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) and similar proteins; PCBP3, also called alpha-CP3, or PCBP3-overlapping transcript, or PCBP3-overlapping transcript 1, or heterogeneous nuclear ribonucleoprotein E3, or hnRNP E3, is a single-stranded nucleic acid binding protein that binds preferentially to oligo dC. It can function as a repressor dependent on binding to single-strand and double-stranded poly(C) sequences. PCBP3 contains three K-homology (KH) RNA-binding domains. The model corresponds to the first one.


Pssm-ID: 411944  Cd Length: 77  Bit Score: 39.70  E-value: 3.06e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 57530702 278 IPLKILAHNNFVGRLIGKEGRNLKKIEQDTDTKITISPLQdltlyNPERTITVKGSIETCAKAEEEIMKKIRE 350
Cdd:cd22516   9 LTIRLLMHGKEVGSIIGKKGETVKKMREESGARINISEGN-----CPERIVTITGPTDAIFKAFAMIAYKFEE 76
KH-I_Rnc1_rpt1 cd22455
first type I K homology (KH) RNA-binding domain found in Schizosaccharomyces pombe RNA-binding ...
290-340 3.09e-04

first type I K homology (KH) RNA-binding domain found in Schizosaccharomyces pombe RNA-binding protein Rnc1 and similar proteins; Rnc1, also called RNA-binding protein that suppresses calcineurin deletion 1, is an RNA-binding protein that acts as an important regulator of the posttranscriptional expression of the MAPK phosphatase Pmp1 in fission yeast. It binds and stabilizes pmp1 mRNA and hence acts as a negative regulator of pmk1 signaling. Overexpression of Rnc1 suppresses the Cl(-) sensitivity of calcineurin deletion. The nuclear export of Rnc1 requires mRNA-binding ability and the mRNA export factor Rae1. Rnc1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the first one.


Pssm-ID: 411883  Cd Length: 70  Bit Score: 39.20  E-value: 3.09e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 57530702 290 GRLIGKEGRNLKKIEQDTDTKITISplqDLTLYNPERTITVKGSIETCAKA 340
Cdd:cd22455  13 AVIIGKGGENIARLRATTGVKAGVS---KVVPGVHDRVLTVSGPLEGVAKA 60
KH-I_DDX43_DDX53 cd22430
type I K homology (KH) RNA-binding domain found in DEAD box protein 43 (DDX43), DEAD box ...
412-474 3.11e-04

type I K homology (KH) RNA-binding domain found in DEAD box protein 43 (DDX43), DEAD box protein 53 (DDX53) and similar proteins; DDX43 (also called cancer/testis antigen 13, or DEAD box protein HAGE, or helical antigen) displays tumor-specific expression. Diseases associated with DDX43 include rheumatoid lung disease. DDX53 (also called cancer-associated gene protein, or cancer/testis antigen 26, or DEAD box protein CAGE) shows high expression level in various tumors and is involved in anti-cancer drug resistance. Both DDX46 and DDX53 are members of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation.


Pssm-ID: 411858 [Multi-domain]  Cd Length: 66  Bit Score: 39.19  E-value: 3.11e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 57530702 412 VHLFIPALAVGAIIGKQGQHIKQLSRFAGASIKIApAEGPDAKlrmVIITGPPEAQFKAQGRI 474
Cdd:cd22430   2 LCFKIDSSLVGAVIGRGGSKIRELEESTGSKIKII-KGGQEAE---VKIFGSDEAQQKAKELI 60
KH-I_IGF2BP2_rpt3 cd22497
third type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 ...
201-253 3.27e-04

third type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2) and similar proteins; IGF2BP2, also called IGF2 mRNA-binding protein 2 (IMP-2), or hepatocellular carcinoma autoantigen p62, or IGF-II mRNA-binding protein 2, or VICKZ family member 2 (VICKZ2), is an RNA-binding factor that recruits target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It functions by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. It also binds to beta-actin/ACTB and MYC transcripts. IGF2BP2 can form homooligomers and heterooligomers with IGF2BP1 and IGF2BP3 in an RNA-dependent manner. It contains four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the third one.


Pssm-ID: 411925  Cd Length: 77  Bit Score: 39.31  E-value: 3.27e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 57530702 201 MLVPTQFVGAIIGKEGATIRNITKQTQSKIDIHRKENAGAAEKPITIHSTPEG 253
Cdd:cd22497   7 LFIPTQAVGAIIGKKGQHIKQLARFAGASIKIAPAEGPDVSERMVIITGPPEA 59
RRM2_CoAA cd12609
RNA recognition motif 2 (RRM2) found in vertebrate RRM-containing coactivator activator ...
3-71 4.05e-04

RNA recognition motif 2 (RRM2) found in vertebrate RRM-containing coactivator activator/modulator (CoAA); This subgroup corresponds to the RRM2 of CoAA, also termed RNA-binding protein 14 (RBM14), or paraspeckle protein 2 (PSP2), or synaptotagmin-interacting protein (SYT-interacting protein), a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. It stimulates transcription through its interactions with coactivators, such as TRBP and CREB-binding protein CBP/p300, via the TRBP-interacting domain and interaction with an RNA-containing complex, such as DNA-dependent protein kinase-poly(ADP-ribose) polymerase complexes, via the RRMs.


Pssm-ID: 410021 [Multi-domain]  Cd Length: 68  Bit Score: 39.06  E-value: 4.05e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 57530702   3 KLYIGNLGENVSPLDLESLFKDSkipfsGQFL---VKTGYAFVDCPDESWAMKAIEALSGKvELHGKLIEVE 71
Cdd:cd12609   2 KIFVGNVSATCTSDELRGLFEEF-----GRVVecdKVKDYAFVHMEREEEALAAIEALNGK-EVKGRRINVE 67
KH-I_HEN4_like_rpt5 cd22462
fifth type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana KH ...
494-561 4.07e-04

fifth type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana KH domain-containing protein HEN4 and similar protein; HEN4, also called protein HUA ENHANCER 4, plays a role in floral reproductive organ identity in the third whorl and floral determinacy specification by specifically promoting the processing of AGAMOUS (AG) pre-mRNA. It functions in association with HUA1 and HUA2. HEN4 contains five K-homology (KH) RNA-binding domains. The model corresponds to the KH5 domain of HEN4.


Pssm-ID: 411890 [Multi-domain]  Cd Length: 66  Bit Score: 38.77  E-value: 4.07e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 57530702 494 AHIKVPSYAAGRVIGKGGKTVNELQNLTSAEVVVpRDQTPDENDQvVVKITGHFYACQLAQRKIQEIL 561
Cdd:cd22462   1 IEILIPAHAVGSVIGRGGSNINQIREISGAKVEV-LKPDSATGER-IVLISGTPDQARHAQNLIEAFI 66
KH-I_PCBP4_rpt3 cd22523
third type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 4 (PCBP4) ...
414-471 4.12e-04

third type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 4 (PCBP4) and similar proteins; PCBP4, also called alpha-CP4, or heterogeneous nuclear ribonucleoprotein E4, or hnRNP E4, is a single-stranded nucleic acid binding protein that binds preferentially to oligo dC. It regulates both basal and stress-induced p21 expression through binding p21 3'-UTR and modulating p21 mRNA stability. It also plays a role in the cell cycle and is implicated in lung tumor suppression. PCBP4 contains three K-homology (KH) RNA-binding domains. The model corresponds to the third one.


Pssm-ID: 411951  Cd Length: 68  Bit Score: 38.72  E-value: 4.12e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 57530702 414 LFIPALAVGAIIGKQGQHIKQLSRFAGASIKIA-PAEGpdAKLRMVIITGPPEAQFKAQ 471
Cdd:cd22523   6 FLIPNDLIGCVIGRQGSKISEIRQMSGAHIKIGnQTEG--TSERHVTITGSPVSITLAQ 62
RRM1_SXL cd12649
RNA recognition motif 1 (RRM1) found in Drosophila sex-lethal (SXL) and similar proteins; This ...
83-153 4.26e-04

RNA recognition motif 1 (RRM1) found in Drosophila sex-lethal (SXL) and similar proteins; This subfamily corresponds to the RRM1 of SXL which governs sexual differentiation and X chromosome dosage compensation in Drosophila melanogaster. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that show high preference to bind single-stranded, uridine-rich target RNA transcripts.


Pssm-ID: 241093 [Multi-domain]  Cd Length: 81  Bit Score: 39.31  E-value: 4.26e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 57530702  83 LQIRNIPPHLQWEVLDSLLAQYGTVENCEQVNtDTETAVVN----VTYGNKDQARQAIEKLNGFQLENYSLKVAY 153
Cdd:cd12649   3 LIVNYLPQDLTDREFRALFRAIGPVNTCKIVR-DKKTGYSYgfgfVDFTSEEDAQRAIKTLNGLQLQNKRLKVAY 76
KH-I_FUBP3_rpt1 cd22480
first type I K homology (KH) RNA-binding domain found in far upstream element-binding protein ...
203-267 4.52e-04

first type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 3 (FUBP3) and similar proteins; FUBP3, also called FUSE-binding protein 3, or MARTA2, was previously shown to mediate dendritic targeting of MAP2 mRNA in neurons. It may interact with single-stranded DNA from the far-upstream element (FUSE) and activate gene expression. It is required for beta-actin mRNA localization. It also interacts with fibroblast growth factor 9 (FGF9) 3'-UTR UG repeats and positively controls FGF9 expression through increasing translation of FGF9 mRNA. FUBP3 contains four K-homology (KH) RNA-binding domains. The model corresponds to the first one.


Pssm-ID: 411908 [Multi-domain]  Cd Length: 71  Bit Score: 38.72  E-value: 4.52e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 57530702 203 VPTQFVGAIIGKEGATIRNITKQTQSKIDIhRKENAGAAEKPITIHSTPEGCSTACKIIMEIMQK 267
Cdd:cd22480   7 VPDKMVGFIIGRGGEQISRIQLESGCKIQI-APDSGGMPERPCVLTGTPESIEQAKRLLGQIVDR 70
KH-I_MER1_like cd22458
type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae meiotic ...
289-340 4.74e-04

type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae meiotic recombination 1 protein (MER1) and similar proteins; MER1 is required for chromosome pairing and genetic recombination. It may function to bring the axial elements of the synaptonemal complex corresponding to homologous chromosomes together by initiating recombination. MER1 might be responsible for regulating the MER2 gene and/or gene product.


Pssm-ID: 411886  Cd Length: 65  Bit Score: 38.58  E-value: 4.74e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 57530702 289 VGRLIGKEGRNLKKIEQDTDTKITISPLQDltlyNPERTITVKGSIETCAKA 340
Cdd:cd22458  12 CGRLIGAKGKNIKALSEKSGASIRLIPISN----SSQQTIHLSGTDKQIALA 59
KH-I_RCF3_like_rpt5 cd22463
fifth type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH ...
199-265 4.85e-04

fifth type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH domain-containing protein RCF3 and similar protein; RCF3, also called protein ENHANCED STRESS RESPONSE 1 (ESR1), or protein HIGH OSMOTIC STRESS GENE EXPRESSION 5 (HOS5), or protein REGULATOR OF CBF GENE EXPRESSION 3, or protein SHINY 1 (SHI1), acts as negative regulator of osmotic stress-induced gene expression. It is involved in the regulation of thermotolerance responses under heat stress. It functions as an upstream regulator of heat stress transcription factor (HSF) genes. HEN4, also called protein HUA ENHANCER 4, plays a role in floral reproductive organ identity in the third whorl and floral determinacy specification by specifically promoting the processing of AGAMOUS (AG) pre-mRNA. It functions in association with HUA1 and HUA2. RCF3 contains five K-homology (KH) RNA-binding domains. The model corresponds to the KH5 domain of RCF3.


Pssm-ID: 411891  Cd Length: 71  Bit Score: 38.95  E-value: 4.85e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 57530702 199 LRMLVPTQFVGAIIGKEGATIRNITKQTQSKIDIHRKENAG-AAEKPITIHSTPEGCSTACKIIMEIM 265
Cdd:cd22463   4 IEFQIPEAVVGLIIGKSGNTIKQISERSGAFVAIVQDRYPLeETQKILRISGTEEQLKRAQSLVEGLI 71
KH-I_PCBP_rpt2 cd02396
second type I K homology (KH) RNA-binding domain found in the family of poly(C)-binding ...
278-350 4.89e-04

second type I K homology (KH) RNA-binding domain found in the family of poly(C)-binding proteins (PCBPs); The PCBP family, also known as hnRNP E family, comprises four members, PCBP1-4, which are RNA-binding proteins that interact in a sequence-specific manner with single-stranded poly(C) sequences. They are mainly involved in various posttranscriptional regulations, including mRNA stabilization or translational activation/silencing. Besides, PCBPs may share iron chaperone activity. PCBPs contain three K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411806 [Multi-domain]  Cd Length: 72  Bit Score: 38.79  E-value: 4.89e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 57530702 278 IPLKILAHNNFVGRLIGKEGRNLKKIEQDTDTKITISPlqDLTLYNPERTITVKGSIETCAKAEEEIMKKIRE 350
Cdd:cd02396   2 ITLRLLVPASQCGSLIGKGGSKIKEIRESTGASVQVAS--EMLPNSTERAVTISGSPEAITKCVEQICCVMLE 72
KH-I_Hqk_like cd22383
type I K homology (KH) RNA-binding domain found in protein quaking (Hqk) family; The Hqk ...
278-313 5.03e-04

type I K homology (KH) RNA-binding domain found in protein quaking (Hqk) family; The Hqk family includes Hqk and protein held out wings (how) found in Drosophila. Hqk, also called HqkI, is an RNA-binding protein that plays a central role in myelinization. It binds to the 5'-NACUAAY-N(1,20)-UAAY-3' RNA core sequence and regulates target mRNA stability. It acts by regulating pre-mRNA splicing, mRNA export and protein translation. Hqk is a regulator of oligodendrocyte differentiation and maturation in the brain that may play a role in myelin and oligodendrocyte dysfunction in schizophrenia. How, also called KH domain protein KH93F, or protein muscle-specific, or protein Struthio, or protein wings held out (who), or Quaking-related 93F (qkr93F), is an RNA-binding protein involved in the control of muscular and cardiac activity. It is required for integrin-mediated cell-adhesion in wing blade. It plays essential roles during embryogenesis, in late stages of somatic muscle development, for myotube migration and during metamorphosis for muscle reorganization.


Pssm-ID: 411811 [Multi-domain]  Cd Length: 101  Bit Score: 39.65  E-value: 5.03e-04
                        10        20        30
                ....*....|....*....|....*....|....*.
gi 57530702 278 IPLKILAHNNFVGRLIGKEGRNLKKIEQDTDTKITI 313
Cdd:cd22383   8 VPVDEYPDYNFVGRILGPRGMTAKQLEQDTGCKIMI 43
KH-I_PCBP1_2_rpt2 cd22518
second type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 1 (PCBP1) ...
197-265 5.63e-04

second type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 1 (PCBP1) and similar proteins; The family includes PCBP1 (also called alpha-CP1, or heterogeneous nuclear ribonucleoprotein E1, or hnRNP E1, or nucleic acid-binding protein SUB2.3) and PCBP2 (also called alpha-CP2, or heterogeneous nuclear ribonucleoprotein E2, or hnRNP E2). They are single-stranded nucleic acid binding proteins that bind preferentially to oligo dC. They act as iron chaperones for ferritin. In case of infection by poliovirus, PCBP1 plays a role in initiation of viral RNA replication in concert with the viral protein 3CD. PCBP2 is a major cellular poly(rC)-binding protein. It also binds poly(rU). PCBP2 negatively regulates cellular antiviral responses mediated by MAVS signaling. It acts as an adapter between MAVS and the E3 ubiquitin ligase ITCH, therefore triggering MAVS ubiquitination and degradation. PCBP2 forms a metabolon with the heme oxygenase 1/cytochrome P450 reductase complex for heme catabolism and iron transfer. Both PCBP1 and PCBP2 contain three K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411946 [Multi-domain]  Cd Length: 78  Bit Score: 38.95  E-value: 5.63e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 57530702 197 VPLRMLVPTQFVGAIIGKEGATIRNITKQTQSKIDIHRKENAGAAEKPITIHSTPEGCSTACKIIMEIM 265
Cdd:cd22518   7 VTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPNSTERAITIAGIPQSIIECVKQICVVM 75
KH-I_ASCC1 cd22419
type I K homology (KH) RNA-binding domain found in activating signal cointegrator 1 complex ...
199-265 5.69e-04

type I K homology (KH) RNA-binding domain found in activating signal cointegrator 1 complex subunit 1 (ASCC1) and similar proteins; ASCC1, also called ASC-1 complex subunit p50, or Trip4 complex subunit p50, plays a role in DNA damage repair as component of the ASCC complex. It is part of the ASC-1 complex that enhances NF-kappa-B, SRF and AP1 transactivation. In cells responding to gastrin-activated paracrine signals, it is involved in the induction of SERPINB2 expression by gastrin. ASCC1 may also play a role in the development of neuromuscular junction.


Pssm-ID: 411847 [Multi-domain]  Cd Length: 66  Bit Score: 38.33  E-value: 5.69e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 57530702 199 LRMLVPTQFVGAIIGKEGATIRNITKQTQSKIDIHRKEnagaAEKPITIHSTPE-GCSTACKIIMEIM 265
Cdd:cd22419   3 LSLDVPSALFKFIIGKKGETKKRLESETKTQIRIPRQG----KEGDIVITGKDRsGVDSARTRIEVLV 66
KH-I_FUBP1_rpt1 cd22478
first type I K homology (KH) RNA-binding domain found in far upstream element-binding protein ...
416-481 5.89e-04

first type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 1 (FUBP1) and similar proteins; FUBP1, also called FBP, or FUSE-binding protein 1, or DNA helicase V, or DH V, binds RNA and single-stranded DNA (ssDNA) and may act both as activator and repressor of transcription. It regulates MYC expression by binding to a single-stranded far-upstream element (FUSE) upstream of the MYC promoter. FUBP1 contains four K-homology (KH) RNA-binding domains. The model corresponds to the first one.


Pssm-ID: 411906 [Multi-domain]  Cd Length: 75  Bit Score: 38.85  E-value: 5.89e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 57530702 416 IPALAVGAIIGKQGQHIKQLSRFAGASIKIAPAEG--PDaklRMVIITGPPEAqFKAQGRIYGKLKEE 481
Cdd:cd22478  10 VPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGglPE---RSCMLTGTPES-VQSAKRLLDQIVEK 73
KH-I_Vigilin_rpt14 cd22417
fourteenth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; ...
288-350 6.40e-04

fourteenth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the fourteenth one.


Pssm-ID: 411845 [Multi-domain]  Cd Length: 72  Bit Score: 38.34  E-value: 6.40e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 57530702 288 FVGRLIGKEGRNLKKIEQDTDTKITISPLQDltlyNPERTITVKGSIETCAKAEEEIMKKIRE 350
Cdd:cd22417  11 YHPKIIGRKGAVITKLRDDHDVNIQFPDKGD----ENDDEITITGYEKNAEAAKDAILKIVQE 69
KH-I_MASK cd22404
type I K homology (KH) RNA-binding domain found in Mask family proteins; The Mask family ...
416-480 6.87e-04

type I K homology (KH) RNA-binding domain found in Mask family proteins; The Mask family includes Drosophila melanogaster ankyrin repeat and KH domain-containing protein Mask, and its mammalian homologues Mask1/ANKHD1 and Mask2/ANKRD17. Mask, also called multiple ankyrin repeat single KH domain-containing protein, is a large ankyrin repeat and KH domain-containing protein involved in Drosophila receptor tyrosine kinase signaling. It acts as a mediator of receptor tyrosine kinase (RTK) signaling and may act either downstream of MAPK or transduce signaling through a parallel branch of the RTK pathway. Mask is required for the development and organization of indirect flight muscle sarcomeres by regulating the formation of M line and H zone and the correct assembly of thick and thin filaments in the sarcomere. Mask1/ANKHD1, also called HIV-1 Vpr-binding ankyrin repeat protein, or multiple ankyrin repeats single KH domain, or Hmask, is highly expressed in various cancer tissues and is involved in cancer progression, including proliferation and invasion. Mask2/ANKRD17, also called ankyrin repeat protein 17, or gene trap ankyrin repeat protein (GTAR), or serologically defined breast cancer antigen NY-BR-16, is a ubiquitously expressed ankyrin factor essential for the vascular integrity during embryogenesis. It may be directly involved in the DNA replication process and play pivotal roles in cell cycle and DNA regulation. It is also involved in innate immune defense against bacteria and viruses.


Pssm-ID: 411832 [Multi-domain]  Cd Length: 71  Bit Score: 38.35  E-value: 6.87e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 57530702 416 IPALAVGAIIGKQGQHIKQLSRFAGASIKIAPAEGPDAkLRMVIITGPPEAQFKAQGRIYGKLKE 480
Cdd:cd22404   7 VPNSAISRVIGRGGCNINAIREVSGAHIEIDKQKGEQG-DRRITIKGSADATRQAAQLINALIKD 70
KH-I_SF1 cd22382
type I K homology (KH) RNA-binding domain found in splicing factor 1 (SF1) and similar ...
287-313 6.96e-04

type I K homology (KH) RNA-binding domain found in splicing factor 1 (SF1) and similar proteins; SF1, also called branch point-binding protein, or BBP, or transcription factor ZFM1, or zinc finger gene in MEN1 locus, or zinc finger protein 162, is necessary for the ATP-dependent first step of spliceosome assembly. Binds to the intron branch point sequence (BPS) 5'-UACUAAC-3' of the pre-mRNA. It may act as transcription repressor.


Pssm-ID: 411810 [Multi-domain]  Cd Length: 93  Bit Score: 38.83  E-value: 6.96e-04
                        10        20
                ....*....|....*....|....*..
gi 57530702 287 NFVGRLIGKEGRNLKKIEQDTDTKITI 313
Cdd:cd22382  17 NFVGLLIGPRGNTLKKIEKETGAKIMI 43
KH-I_HNRNPK_rpt1 cd22432
first type I K homology (KH) RNA-binding domain found in heterogeneous nuclear ...
196-233 7.33e-04

first type I K homology (KH) RNA-binding domain found in heterogeneous nuclear ribonucleoprotein K (hnRNP K) and similar proteins; hnRNP K, also called transformation up-regulated nuclear protein (TUNP), is a pre-mRNA binding protein that binds tenaciously to poly(C) sequences. It may be involved in the nuclear metabolism of hnRNAs, particularly for pre-mRNAs that contain cytidine-rich sequences. It can also bind poly(C) single-stranded DNA. hnRNP K plays an important role in p53/TP53 response to DNA damage, acting at the level of both transcription activation and repression. hnRNP K contains three K-homology (KH) RNA-binding domains. The model corresponds to the first one.


Pssm-ID: 411860 [Multi-domain]  Cd Length: 64  Bit Score: 37.93  E-value: 7.33e-04
                        10        20        30
                ....*....|....*....|....*....|....*...
gi 57530702 196 DVPLRMLVPTQFVGAIIGKEGATIRNItkQTQSKIDIH 233
Cdd:cd22432   1 VVELRLLIPSKAAGAIIGKGGENIKRL--RTEYNASVS 36
KH-I_MASK cd22404
type I K homology (KH) RNA-binding domain found in Mask family proteins; The Mask family ...
200-262 7.36e-04

type I K homology (KH) RNA-binding domain found in Mask family proteins; The Mask family includes Drosophila melanogaster ankyrin repeat and KH domain-containing protein Mask, and its mammalian homologues Mask1/ANKHD1 and Mask2/ANKRD17. Mask, also called multiple ankyrin repeat single KH domain-containing protein, is a large ankyrin repeat and KH domain-containing protein involved in Drosophila receptor tyrosine kinase signaling. It acts as a mediator of receptor tyrosine kinase (RTK) signaling and may act either downstream of MAPK or transduce signaling through a parallel branch of the RTK pathway. Mask is required for the development and organization of indirect flight muscle sarcomeres by regulating the formation of M line and H zone and the correct assembly of thick and thin filaments in the sarcomere. Mask1/ANKHD1, also called HIV-1 Vpr-binding ankyrin repeat protein, or multiple ankyrin repeats single KH domain, or Hmask, is highly expressed in various cancer tissues and is involved in cancer progression, including proliferation and invasion. Mask2/ANKRD17, also called ankyrin repeat protein 17, or gene trap ankyrin repeat protein (GTAR), or serologically defined breast cancer antigen NY-BR-16, is a ubiquitously expressed ankyrin factor essential for the vascular integrity during embryogenesis. It may be directly involved in the DNA replication process and play pivotal roles in cell cycle and DNA regulation. It is also involved in innate immune defense against bacteria and viruses.


Pssm-ID: 411832 [Multi-domain]  Cd Length: 71  Bit Score: 38.35  E-value: 7.36e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 57530702 200 RMLVPTQFVGAIIGKEGATIRNITKQTQSKIDIHrKENAGAAEKPITIHSTPEGCSTACKIIM 262
Cdd:cd22404   4 KVTVPNSAISRVIGRGGCNINAIREVSGAHIEID-KQKGEQGDRRITIKGSADATRQAAQLIN 65
KH-I_HNRNPK_rpt2 cd22433
second type I K homology (KH) RNA-binding domain found in heterogeneous nuclear ...
280-346 7.62e-04

second type I K homology (KH) RNA-binding domain found in heterogeneous nuclear ribonucleoprotein K (hnRNP K) and similar proteins; hnRNP K, also called transformation up-regulated nuclear protein (TUNP), is a pre-mRNA binding protein that binds tenaciously to poly(C) sequences. It may be involved in the nuclear metabolism of hnRNAs, particularly for pre-mRNAs that contain cytidine-rich sequences. It can also bind poly(C) single-stranded DNA. hnRNP K plays an important role in p53/TP53 response to DNA damage, acting at the level of both transcription activation and repression. hnRNP K contains three K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411861 [Multi-domain]  Cd Length: 70  Bit Score: 38.00  E-value: 7.62e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 57530702 280 LKILAHNNFVGRLIGKEGRNLKKIEQDTDTKITISplQDLTLYNPERTITVKGSIETCAKAEEEIMK 346
Cdd:cd22433   4 LRLLVHQSQAGCIIGRAGFKIKELREKTGATIKVY--SECCPRSTDRVVQIGGKPDKVVECIREILE 68
RRM1_SRSF4 cd12594
RNA recognition motif 1 (RRM1) found in vertebrate serine/arginine-rich splicing factor 4 ...
1-77 7.70e-04

RNA recognition motif 1 (RRM1) found in vertebrate serine/arginine-rich splicing factor 4 (SRSF4); This subgroup corresponds to the RRM1 of SRSF4, also termed pre-mRNA-splicing factor SRp75, or SRP001LB, or splicing factor, arginine/serine-rich 4 (SFRS4). SRSF4 is a splicing regulatory serine/arginine (SR) protein that plays an important role in both constitutive splicing and alternative splicing of many pre-mRNAs. For instance, it interacts with heterogeneous nuclear ribonucleoproteins, hnRNP G and hnRNP E2, and further regulates the 5' splice site of tau exon 10, whose misregulation causes frontotemporal dementia. SFSF4 also induces production of HIV-1 vpr mRNA through the inhibition of the 5'-splice site of exon 3. In addition, it activates splicing of the cardiac troponin T (cTNT) alternative exon by direct interactions with the cTNT exon 5 enhancer RNA. SRSF4 can shuttle between the nucleus and cytoplasm. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine-rich region, an internal region homologous to the RRM, and a very long, highly phosphorylated C-terminal SR domains rich in serine-arginine dipeptides.


Pssm-ID: 410007 [Multi-domain]  Cd Length: 87  Bit Score: 38.86  E-value: 7.70e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57530702   1 MNKLYIGNLGENVSPLDLESLFKDSkipfsGQFL---VKTGYAFVDCPDESWAMKAIEALSGKvELHGKLIEVEHSV-PK 76
Cdd:cd12594   1 MPRVYIGRLSYQARERDVERFFKGY-----GKILevdLKNGYGFVEFDDLRDADDAVYELNGK-DLCGERVIVEHARgPR 74

                .
gi 57530702  77 R 77
Cdd:cd12594  75 R 75
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
3-72 7.79e-04

splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed.


Pssm-ID: 273721 [Multi-domain]  Cd Length: 494  Bit Score: 42.21  E-value: 7.79e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57530702     3 KLYIGNLGENVSPLDLESLFKdskiPFSGQFLVK----------TGYAFVDCPDESWAMKAIEALSGkVELHGKLIEVEH 72
Cdd:TIGR01622 216 RLYVGNLHFNITEQDLRQIFE----PFGEIEFVQlqkdpetgrsKGYGFIQFRDAEQAKEALEKMNG-FELAGRPIKVGL 290
RRM1_HuC cd12772
RNA recognition motif 1 (RRM1) found in vertebrate Hu-antigen C (HuC); This subgroup ...
83-153 8.10e-04

RNA recognition motif 1 (RRM1) found in vertebrate Hu-antigen C (HuC); This subgroup corresponds to the RRM1 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 410165 [Multi-domain]  Cd Length: 85  Bit Score: 38.56  E-value: 8.10e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 57530702  83 LQIRNIPPHLQWEVLDSLLAQYGTVENCEQVN---TDTETAVVNVTYGNKDQARQAIEKLNGFQLENYSLKVAY 153
Cdd:cd12772   7 LIVNYLPQNMTQEEFKSLFGSIGDIESCKLVRdkiTGQSLGYGFVNYVDPNDADKAINTLNGLKLQTKTIKVSY 80
KH-I_FUBP_rpt4 cd22399
fourth type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding ...
498-559 8.79e-04

fourth type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding proteins; The far upstream element-binding protein (FUBP) family includes FUBP1-3. FUBP1, also called FBP, or FUSE-binding protein 1, or DNA helicase V, or DH V, binds RNA and single-stranded DNA (ssDNA) and may act both as activator and repressor of transcription. It regulates MYC expression by binding to a single-stranded far-upstream element (FUSE) upstream of the MYC promoter. FUBP2, also called FUSE-binding protein 2, or KH type-splicing regulatory protein (KSRP), or p75, is a single-strand nucleic acid binding protein implicated in a variety of cellular processes, including splicing in the nucleus, mRNA decay, maturation of miRNA, and transcriptional control of proto-oncogenes such as c-myc. It regulates the stability and/or translatability of many mRNA species, encoding immune-relevant proteins, either by binding to AU-rich elements (AREs) of mRNA 3'UTR or by facilitating miRNA biogenesis to target mRNA. FUBP3, also called FUSE-binding protein 3, or MARTA2, was previously shown to mediate dendritic targeting of MAP2 mRNA in neurons. It may interact with single-stranded DNA from the far-upstream element (FUSE) and activate gene expression. It is required for beta-actin mRNA localization. It also interacts with fibroblast growth factor 9 (FGF9) 3'-UTR UG repeats and positively controls FGF9 expression through increasing translation of FGF9 mRNA. FUBP proteins contain four K-homology (KH) RNA-binding domains. The model corresponds to the fourth one.


Pssm-ID: 411827 [Multi-domain]  Cd Length: 67  Bit Score: 37.97  E-value: 8.79e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 57530702 498 VPSYAAGRVIGKGGKTVNELQNLTSAEVVVPRDQTPDENDQVVVkITGHFYACQLAQRKIQE 559
Cdd:cd22399   6 VPANKCGLVIGKGGETIRQINQQSGAHVELDRNPPPNPNEKLFI-IRGNPQQIEHAKQLIRE 66
RRM1_HuB cd12771
RNA recognition motif 1 (RRM1) found in vertebrate Hu-antigen B (HuB); This subgroup ...
83-153 8.83e-04

RNA recognition motif 1 (RRM1) found in vertebrate Hu-antigen B (HuB); This subgroup corresponds to the RRM1 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads and is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 410164 [Multi-domain]  Cd Length: 83  Bit Score: 38.55  E-value: 8.83e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 57530702  83 LQIRNIPPHLQWEVLDSLLAQYGTVENCEQVN---TDTETAVVNVTYGNKDQARQAIEKLNGFQLENYSLKVAY 153
Cdd:cd12771   7 LIVNYLPQNMTQEELKSLFGSIGEIESCKLVRdkiTGQSLGYGFVNYIEPKDAEKAINTLNGLRLQTKTIKVSY 80
RRM1_Hu cd12650
RNA recognition motif 1 (RRM1) found in the Hu proteins family; This subfamily corresponds to ...
83-153 9.43e-04

RNA recognition motif 1 (RRM1) found in the Hu proteins family; This subfamily corresponds to the RRM1 of the Hu proteins family which represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 410053 [Multi-domain]  Cd Length: 77  Bit Score: 38.15  E-value: 9.43e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 57530702  83 LQIRNIPPHLQWEVLDSLLAQYGTVENCEQVNtDTET------AVVNvtYGNKDQARQAIEKLNGFQLENYSLKVAY 153
Cdd:cd12650   3 LIVNYLPQNMTQDEIRSLFSSIGEIESCKLIR-DKVTgqslgyGFVN--YVDPSDAEKAINTLNGLRLQNKTIKVSY 76
KH-I_FUBP2_rpt3 cd22485
third type I K homology (KH) RNA-binding domain found in far upstream element-binding protein ...
416-465 9.74e-04

third type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 2 (FUBP2) and similar proteins; FUBP2, also called FUSE-binding protein 2, or KH type-splicing regulatory protein (KSRP), or p75, is a single-strand nucleic acid binding protein implicated in a variety of cellular processes, including splicing in the nucleus, mRNA decay, maturation of miRNA, and transcriptional control of proto-oncogenes such as c-myc. It regulates the stability and/or translatability of many mRNA species, encoding immune-relevant proteins, either by binding to AU-rich elements (AREs) of mRNA 3'UTR or by facilitating miRNA biogenesis to target mRNA. FUBP2 contains four K-homology (KH) RNA-binding domains. The model corresponds to the third one.


Pssm-ID: 411913  Cd Length: 68  Bit Score: 38.02  E-value: 9.74e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 57530702 416 IPALAVGAIIGKQGQHIKQLSRFAGASIKIAPAEG--PDaklRMVIITGPPE 465
Cdd:cd22485   7 VPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGtgPE---KIAHIMGPPD 55
KH-I_KHDRBS1 cd22468
type I K homology (KH) RNA-binding domain found in KH domain-containing, RNA-binding, signal ...
278-365 1.01e-03

type I K homology (KH) RNA-binding domain found in KH domain-containing, RNA-binding, signal transduction-associated protein 1 (KHDRBS1) and similar proteins; KHDRBS1, also called GAP-associated tyrosine phosphoprotein p62, or Src-associated in mitosis 68 kDa protein, or Sam68, or p21 Ras GTPase-activating protein-associated p62, or p68, is an RNA-binding protein that plays a role in the regulation of alternative splicing and influences mRNA splice site selection and exon inclusion. It binds to RNA containing 5'-[AU]UAA-3' as a bipartite motif spaced by more than 15 nucleotides. It also binds poly(A). KHDRBS1 acts as a putative regulator of mRNA stability and/or translation rates and mediates mRNA nuclear export. It is recruited and tyrosine phosphorylated by several receptor systems, for example the T-cell, leptin and insulin receptors.


Pssm-ID: 411896 [Multi-domain]  Cd Length: 106  Bit Score: 38.84  E-value: 1.01e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57530702 278 IPLKILAHNNFVGRLIGKEGRNLKKIEQDTDTKItisplqdltlynperTITVKGSIETCAKAEEeimkkIRESYENDIA 357
Cdd:cd22468  11 IPVKQYPKFNFVGKILGPQGNTIKRLQEETGAKI---------------SVLGKGSMRDKAKEEE-----LRKGGDPKYA 70

                ....*...
gi 57530702 358 AMNLQAHL 365
Cdd:cd22468  71 HLNMDLHV 78
KH-I_ScSCP160_rpt2 cd22447
second type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein ...
287-315 1.06e-03

second type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411875 [Multi-domain]  Cd Length: 80  Bit Score: 38.17  E-value: 1.06e-03
                        10        20
                ....*....|....*....|....*....
gi 57530702 287 NFVGRLIGKEGRNLKKIEQDTDTKITISP 315
Cdd:cd22447  13 STRARIIGKKGANLKQIREKTGVRIDIPP 41
KH-I_KHDC4_rpt2 cd22386
first type I K homology (KH) RNA-binding domain found in KH homology domain-containing protein ...
273-313 1.07e-03

first type I K homology (KH) RNA-binding domain found in KH homology domain-containing protein 4 (KHDC4) and similar proteins; KHDC4, also called Brings lots of money 7 (Blom7), or pre-mRNA splicing factor protein KHDC4, is an RNA-binding protein involved in pre-mRNA splicing. It interacts with the PRP19C/Prp19 complex/NTC/Nineteen complex which is part of the spliceosome. KHDC4 binds preferentially RNA with A/C rich sequences and poly-C stretches. KHDC4 contains two type I K homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411814 [Multi-domain]  Cd Length: 102  Bit Score: 38.69  E-value: 1.07e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
gi 57530702 273 KFTEEIPLKI-LAHNNF--VGRLIGKEGRNLKKIEQDTDTKITI 313
Cdd:cd22386   2 YYQEKVFVGLeHAPPGFnvRGKLIGPGGSNVKHIQQETGAKVQL 45
KH-I_ScSCP160_rpt7 cd22452
seventh type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein ...
493-559 1.07e-03

seventh type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the seventh one.


Pssm-ID: 411880 [Multi-domain]  Cd Length: 65  Bit Score: 37.69  E-value: 1.07e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 57530702 493 EAHIKVPSYAAGRVIGKGGKTVNELQNLTSAEVVVPRdqTPDENDqvVVKITGHFYACQLAQRKIQE 559
Cdd:cd22452   3 RGWIKVSPRYFGRIIGPGGSNINQIREKSGCFINVPK--KNKESD--VITLRGTKEGVEKAEEMIKK 65
KH-I_Vigilin_rpt3 cd22407
third type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, ...
287-345 1.16e-03

third type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the third one.


Pssm-ID: 411835 [Multi-domain]  Cd Length: 62  Bit Score: 37.57  E-value: 1.16e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 57530702 287 NFVGRLIGKEGRNLKKIEQDTDTKITISPLQdltlyNPERTITVKGSIETCAKAEEEIM 345
Cdd:cd22407   9 VYHPFIAGPNNENVKELQEETGVRINIPPPS-----VNKDEIVVSGEKEGVAQAVAKIK 62
RRM_HP0827_like cd12399
RNA recognition motif (RRM) found in Helicobacter pylori HP0827 protein and similar proteins; ...
4-73 1.20e-03

RNA recognition motif (RRM) found in Helicobacter pylori HP0827 protein and similar proteins; This subfamily corresponds to the RRM of H. pylori HP0827, a putative ssDNA-binding protein 12rnp2 precursor, containing one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The ssDNA binding may be important in activation of HP0827.


Pssm-ID: 409833 [Multi-domain]  Cd Length: 75  Bit Score: 37.88  E-value: 1.20e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 57530702   4 LYIGNLGENVSPLDLESLF------KDSKIPFSGQFLVKTGYAFVDCPDESWAMKAIEALSGKvELHGKLIEVEHS 73
Cdd:cd12399   1 LYVGNLPYSASEEQLKSLFgqfgavFDVKLPMDRETKRPRGFGFVELQEEESAEKAIAKLDGT-DFMGRTIRVNEA 75
RRM1_RRT5 cd12409
RNA recognition motif 1 (RRM1) found in yeast regulator of rDNA transcription protein 5 (RRT5) ...
3-75 1.26e-03

RNA recognition motif 1 (RRM1) found in yeast regulator of rDNA transcription protein 5 (RRT5) and similar proteins; This subfamily corresponds to the RRM1 of the lineage specific family containing a group of uncharacterized yeast regulators of rDNA transcription protein 5 (RRT5), which may play roles in the modulation of rDNA transcription. RRT5 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409843 [Multi-domain]  Cd Length: 84  Bit Score: 38.03  E-value: 1.26e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57530702   3 KLYIGNLGENVSPLDLESLFKDSK-----IP-----FSGQFLVKT-GYAFVDCPDESWAMKAIEALSGKVeLHGKLIEVE 71
Cdd:cd12409   1 RVYISNLSYSTTEEELEELLKDYKpvsvlIPsytvrGFRSRKHRPlGIAYAEFSSVEEAEKVVKDLNGKV-FKGRKLFVK 79

                ....
gi 57530702  72 HSVP 75
Cdd:cd12409  80 LHVP 83
KH-I_FUBP_rpt2 cd22397
second type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding ...
411-471 1.31e-03

second type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding proteins; The far upstream element-binding protein (FUBP) family includes FUBP1-3. FUBP1, also called FBP, or FUSE-binding protein 1, or DNA helicase V, or DH V, binds RNA and single-stranded DNA (ssDNA) and may act both as activator and repressor of transcription. It regulates MYC expression by binding to a single-stranded far-upstream element (FUSE) upstream of the MYC promoter. FUBP2, also called FUSE-binding protein 2, or KH type-splicing regulatory protein (KSRP), or p75, is a single-strand nucleic acid binding protein implicated in a variety of cellular processes, including splicing in the nucleus, mRNA decay, maturation of miRNA, and transcriptional control of proto-oncogenes such as c-myc. It regulates the stability and/or translatability of many mRNA species, encoding immune-relevant proteins, either by binding to AU-rich elements (AREs) of mRNA 3'UTR or by facilitating miRNA biogenesis to target mRNA. FUBP3, also called FUSE-binding protein 3, or MARTA2, was previously shown to mediate dendritic targeting of MAP2 mRNA in neurons. It may interact with single-stranded DNA from the far-upstream element (FUSE) and activate gene expression. It is required for beta-actin mRNA localization. It also interacts with fibroblast growth factor 9 (FGF9) 3'-UTR UG repeats and positively controls FGF9 expression through increasing translation of FGF9 mRNA. FUBP proteins contain four K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411825 [Multi-domain]  Cd Length: 69  Bit Score: 37.61  E-value: 1.31e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 57530702 411 TVHLFIPALAVGAIIGKQGQHIKQLSRFAGAS---IKIAP-AEGPDAKLRmviITGPPEAQFKAQ 471
Cdd:cd22397   1 TIEIMIPGNKVGLIIGKGGETIKQLQERAGVKmvmIQDGPqPTGQDKPLR---ITGDPQKVQRAK 62
KH-I_HNRNPK_rpt3 cd22434
third type I K homology (KH) RNA-binding domain found in heterogeneous nuclear ...
203-252 1.40e-03

third type I K homology (KH) RNA-binding domain found in heterogeneous nuclear ribonucleoprotein K (hnRNP K) and similar proteins; hnRNP K, also called transformation up-regulated nuclear protein (TUNP), is a pre-mRNA binding protein that binds tenaciously to poly(C) sequences. It may be involved in the nuclear metabolism of hnRNAs, particularly for pre-mRNAs that contain cytidine-rich sequences. It can also bind poly(C) single-stranded DNA. hnRNP K plays an important role in p53/TP53 response to DNA damage, acting at the level of both transcription activation and repression. hnRNP K contains three K-homology (KH) RNA-binding domains. The model corresponds to the third one.


Pssm-ID: 411862 [Multi-domain]  Cd Length: 74  Bit Score: 37.68  E-value: 1.40e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 57530702 203 VPTQFVGAIIGKEGATIRNITKQTQSKIDIHrKENAGAAEKPITIHSTPE 252
Cdd:cd22434   8 IPKDLAGSIIGKGGQRIRQIRHESGASIKID-EPLPGSEDRIITITGTQD 56
KH-I_RCF3_like_rpt5 cd22463
fifth type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH ...
409-471 1.43e-03

fifth type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH domain-containing protein RCF3 and similar protein; RCF3, also called protein ENHANCED STRESS RESPONSE 1 (ESR1), or protein HIGH OSMOTIC STRESS GENE EXPRESSION 5 (HOS5), or protein REGULATOR OF CBF GENE EXPRESSION 3, or protein SHINY 1 (SHI1), acts as negative regulator of osmotic stress-induced gene expression. It is involved in the regulation of thermotolerance responses under heat stress. It functions as an upstream regulator of heat stress transcription factor (HSF) genes. HEN4, also called protein HUA ENHANCER 4, plays a role in floral reproductive organ identity in the third whorl and floral determinacy specification by specifically promoting the processing of AGAMOUS (AG) pre-mRNA. It functions in association with HUA1 and HUA2. RCF3 contains five K-homology (KH) RNA-binding domains. The model corresponds to the KH5 domain of RCF3.


Pssm-ID: 411891  Cd Length: 71  Bit Score: 37.41  E-value: 1.43e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 57530702 409 SETVHLFIPALAVGAIIGKQGQHIKQLSRFAGASIKI---APAEGPDAKLrmVIITGPPEAQFKAQ 471
Cdd:cd22463   1 RSKIEFQIPEAVVGLIIGKSGNTIKQISERSGAFVAIvqdRYPLEETQKI--LRISGTEEQLKRAQ 64
KH-I_IGF2BP1_rpt3 cd22496
third type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 ...
495-561 1.44e-03

third type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1) and similar proteins; IGF2BP1, also called IGF2 mRNA-binding protein 1 (IMP-1), or coding region determinant-binding protein (CRD-BP), or IGF-II mRNA-binding protein 1, or VICKZ family member 1 (VICKZ1), or zipcode-binding protein 1 (ZBP-1), is an RNA-binding factor that recruits target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It functions by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. It regulates localized beta-actin/ACTB mRNA translation, a crucial process for cell polarity, cell migration and neurite outgrowth. IGF2BP1 can form homodimers and heterodimers with IGF2BP1 and IGF2BP3. It contains four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the third one.


Pssm-ID: 411924  Cd Length: 76  Bit Score: 37.69  E-value: 1.44e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 57530702 495 HIKVPSYAAGRVIGKGGKTVNELQNLTSAEVVVPRDQTPDENDQVVVkITGHFYACQLAQRKIQEIL 561
Cdd:cd22496   6 HVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVI-ITGPPEAQFKAQGRIYGKL 71
KH-I_FUBP2_rpt1 cd22479
first type I K homology (KH) RNA-binding domain found in far upstream element-binding protein ...
286-341 1.47e-03

first type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 2 (FUBP2) and similar proteins; FUBP2, also called FUSE-binding protein 2, or KH type-splicing regulatory protein (KSRP), or p75, is a single-strand nucleic acid binding protein implicated in a variety of cellular processes, including splicing in the nucleus, mRNA decay, maturation of miRNA, and transcriptional control of proto-oncogenes such as c-myc. It regulates the stability and/or translatability of many mRNA species, encoding immune-relevant proteins, either by binding to AU-rich elements (AREs) of mRNA 3'UTR or by facilitating miRNA biogenesis to target mRNA. FUBP2 contains four K-homology (KH) RNA-binding domains. The model corresponds to the first one.


Pssm-ID: 411907 [Multi-domain]  Cd Length: 71  Bit Score: 37.61  E-value: 1.47e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 57530702 286 NNFVGRLIGKEGRNLKKIEQDTDTKITISPLQDLTlynPERTITVKGSIETCAKAE 341
Cdd:cd22479   9 DGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGGL---PERSVSLTGSPEAVQKAK 61
RRM_II_PABPs cd12306
RNA recognition motif in type II polyadenylate-binding proteins; This subfamily corresponds to ...
5-70 1.47e-03

RNA recognition motif in type II polyadenylate-binding proteins; This subfamily corresponds to the RRM of type II polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 2 (PABP-2 or PABPN1), embryonic polyadenylate-binding protein 2 (ePABP-2 or PABPN1L) and similar proteins. PABPs are highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. ePABP-2 is predominantly located in the cytoplasm and PABP-2 is located in the nucleus. In contrast to the type I PABPs containing four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), the type II PABPs contains a single highly-conserved RRM. This subfamily also includes Saccharomyces cerevisiae RBP29 (SGN1, YIR001C) gene encoding cytoplasmic mRNA-binding protein Rbp29 that binds preferentially to poly(A). Although not essential for cell viability, Rbp29 plays a role in modulating the expression of cytoplasmic mRNA. Like other type II PABPs, Rbp29 contains one RRM only.


Pssm-ID: 409747 [Multi-domain]  Cd Length: 73  Bit Score: 37.28  E-value: 1.47e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 57530702   5 YIGNLGENVSPLDLESLFKD----SKI-----PFSGQflvKTGYAFVDCPDESWAMKAIeALSGKvELHGKLIEV 70
Cdd:cd12306   3 YVGNVDYGTTPEELQAHFKScgtiNRVtilcdKFTGQ---PKGFAYIEFVDKSSVENAL-LLNES-EFRGRQIKV 72
KH-I_IGF2BP_rpt3 cd22402
third type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 ...
494-554 1.69e-03

third type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 mRNA-binding protein (IGF2BP) family; The IGF2BP family includes three members: IGF2BP1/IMP-1/ CRD-BP/ VICKZ1, IGF2BP2/IMP-2/ VICKZ2, and IGF2BP3/IMP-3/VICKZ3, which are RNA-binding factors that recruit target transcripts to cytoplasmic protein-RNA complexes (mRNPs). They function by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. IGF2BP proteins contain four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the third one.


Pssm-ID: 411830  Cd Length: 66  Bit Score: 37.23  E-value: 1.69e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 57530702 494 AHIKVPSYAAGRVIGKGGKTVNELQNLTSAEV-VVPRDQTPDENDQVVvkITGHFYACQLAQ 554
Cdd:cd22402   3 TYLYIPNKAVGAIIGTKGSHIRYIKRFSGASIkIAPADSPDAPERKVT--ITGPPEAQWKAQ 62
KH-I_BTR1_rpt3 cd22514
third type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana protein BTR1 and ...
496-554 1.70e-03

third type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana protein BTR1 and similar proteins; BTR1, also called Binding to ToMV RNA 1, is a negative regulator of tomato mosaic virus (ToMV) multiplication but has no effect on the multiplication of cucumber mosaic virus (CMV). BTR1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the third one.


Pssm-ID: 411942 [Multi-domain]  Cd Length: 71  Bit Score: 37.40  E-value: 1.70e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 57530702 496 IKVPSYAAGRVIGKGGKTVNELQNLTSAEVVVPR--DQTPDENDQVVVkITGHFYACQLAQ 554
Cdd:cd22514   5 IGVPDEHIGAILGRGGRTINEIQQHSGARIKISDrgDFVSGTRNRKVT-ITGPQDAVQMAQ 64
KH-I_IGF2BP2_rpt2 cd22494
second type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 ...
421-480 1.71e-03

second type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2) and similar proteins; IGF2BP2, also called IGF2 mRNA-binding protein 2 (IMP-2), or hepatocellular carcinoma autoantigen p62, or IGF-II mRNA-binding protein 2, or VICKZ family member 2 (VICKZ2), is an RNA-binding factor that recruits target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It functions by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. It also binds to beta-actin/ACTB and MYC transcripts. IGF2BP2 can form homooligomers and heterooligomers with IGF2BP1 and IGF2BP3 in an RNA-dependent manner. It contains four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the second one.


Pssm-ID: 411922  Cd Length: 77  Bit Score: 37.31  E-value: 1.71e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 57530702 421 VGAIIGKQGQHIKQLSRFAGASIKIAPAE-----GPDaklRMVIITGPPEAQFKAQGRIYGKLKE 480
Cdd:cd22494  11 VGRLIGKEGRNLKKIEQDTGTKITISSLQdltiyNPE---RTITVKGSIEACSSAEVEIMKKLRE 72
KH-I_ScSCP160_rpt6 cd22451
sixth type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein ...
290-350 1.73e-03

sixth type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the sixth one.


Pssm-ID: 411879 [Multi-domain]  Cd Length: 69  Bit Score: 37.05  E-value: 1.73e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 57530702 290 GRLIGKEGRNLKKIEQDTDTKITIsPLQDltlyNPERTITVKGSIETCAKAEEEIMKKIRE 350
Cdd:cd22451  13 RAIIGKGGAVLRELEAETGCRIQV-PKKD----DPSGKIRITGARDGVEAATAKILNISDE 68
KH-I_FUBP_rpt3 cd22398
third type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding ...
201-264 1.74e-03

third type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding proteins; The far upstream element-binding protein (FUBP) family includes FUBP1-3. FUBP1, also called FBP, or FUSE-binding protein 1, or DNA helicase V, or DH V, binds RNA and single-stranded DNA (ssDNA) and may act both as activator and repressor of transcription. It regulates MYC expression by binding to a single-stranded far-upstream element (FUSE) upstream of the MYC promoter. FUBP2, also called FUSE-binding protein 2, or KH type-splicing regulatory protein (KSRP), or p75, is a single-strand nucleic acid binding protein implicated in a variety of cellular processes, including splicing in the nucleus, mRNA decay, maturation of miRNA, and transcriptional control of proto-oncogenes such as c-myc. It regulates the stability and/or translatability of many mRNA species, encoding immune-relevant proteins, either by binding to AU-rich elements (AREs) of mRNA 3'UTR or by facilitating miRNA biogenesis to target mRNA. FUBP3, also called FUSE-binding protein 3, or MARTA2, was previously shown to mediate dendritic targeting of MAP2 mRNA in neurons. It may interact with single-stranded DNA from the far-upstream element (FUSE) and activate gene expression. It is required for beta-actin mRNA localization. It also interacts with fibroblast growth factor 9 (FGF9) 3'-UTR UG repeats and positively controls FGF9 expression through increasing translation of FGF9 mRNA. FUBP proteins contain four K-homology (KH) RNA-binding domains. The model corresponds to the third one.


Pssm-ID: 411826 [Multi-domain]  Cd Length: 67  Bit Score: 37.24  E-value: 1.74e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 57530702 201 MLVPTQFVGAIIGKEGATIRNITKQTQSKIDIhRKENAGAAEKPITIHSTPEGCSTACKIIMEI 264
Cdd:cd22398   4 VPVPRFAVGVVIGKGGEMIKKIQNETGARVQF-KPDDGNSPDRICVITGPPDQVQHAARMIQEL 66
KH-I_HNRNPK_rpt2 cd22433
second type I K homology (KH) RNA-binding domain found in heterogeneous nuclear ...
421-465 1.83e-03

second type I K homology (KH) RNA-binding domain found in heterogeneous nuclear ribonucleoprotein K (hnRNP K) and similar proteins; hnRNP K, also called transformation up-regulated nuclear protein (TUNP), is a pre-mRNA binding protein that binds tenaciously to poly(C) sequences. It may be involved in the nuclear metabolism of hnRNAs, particularly for pre-mRNAs that contain cytidine-rich sequences. It can also bind poly(C) single-stranded DNA. hnRNP K plays an important role in p53/TP53 response to DNA damage, acting at the level of both transcription activation and repression. hnRNP K contains three K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411861 [Multi-domain]  Cd Length: 70  Bit Score: 37.23  E-value: 1.83e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 57530702 421 VGAIIGKQGQHIKQLSRFAGASIKIAPAEGPDAKLRMVIITGPPE 465
Cdd:cd22433  13 AGCIIGRAGFKIKELREKTGATIKVYSECCPRSTDRVVQIGGKPD 57
KH-I_PCBP4_rpt1 cd22517
first type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 4 (PCBP4) ...
199-261 1.90e-03

first type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 4 (PCBP4) and similar proteins; PCBP4, also called alpha-CP4, or heterogeneous nuclear ribonucleoprotein E4, or hnRNP E4, is a single-stranded nucleic acid binding protein that binds preferentially to oligo dC. It regulates both basal and stress-induced p21 expression through binding p21 3'-UTR and modulating p21 mRNA stability. It also plays a role in the cell cycle and is implicated in lung tumor suppression. PCBP4 contains three K-homology (KH) RNA-binding domains. The model corresponds to the first one.


Pssm-ID: 411945  Cd Length: 70  Bit Score: 36.93  E-value: 1.90e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 57530702 199 LRMLVPTQFVGAIIGKEGATIRNITKQTQSKIDIhrkENAGAAEKPITIHSTPEGCSTACKII 261
Cdd:cd22517   4 LRLLMHGKEVGSIIGKKGETVKRIREESSARITI---SEGSCPERITTITGSTDAVFRAFSMI 63
RRM_RBM18 cd12355
RNA recognition motif (RRM) found in eukaryotic RNA-binding protein 18 and similar proteins; ...
3-68 1.96e-03

RNA recognition motif (RRM) found in eukaryotic RNA-binding protein 18 and similar proteins; This subfamily corresponds to the RRM of RBM18, a putative RNA-binding protein containing a well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The biological role of RBM18 remains unclear.


Pssm-ID: 409791 [Multi-domain]  Cd Length: 80  Bit Score: 37.28  E-value: 1.96e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 57530702   3 KLYIGNLGENVSPLDLESLF-KDSKI-----------PFSGQflvKTGYAFVDCPDESWAMKAIEALSGKVELHGKLI 68
Cdd:cd12355   1 RLWIGNLDPRLTEYHLLKLLsKYGKIkkfdflfhktgPLKGQ---PRGYCFVTFETKEEAEKAIECLNGKLALGKKLV 75
KH-I_FUBP_rpt4 cd22399
fourth type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding ...
411-465 2.11e-03

fourth type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding proteins; The far upstream element-binding protein (FUBP) family includes FUBP1-3. FUBP1, also called FBP, or FUSE-binding protein 1, or DNA helicase V, or DH V, binds RNA and single-stranded DNA (ssDNA) and may act both as activator and repressor of transcription. It regulates MYC expression by binding to a single-stranded far-upstream element (FUSE) upstream of the MYC promoter. FUBP2, also called FUSE-binding protein 2, or KH type-splicing regulatory protein (KSRP), or p75, is a single-strand nucleic acid binding protein implicated in a variety of cellular processes, including splicing in the nucleus, mRNA decay, maturation of miRNA, and transcriptional control of proto-oncogenes such as c-myc. It regulates the stability and/or translatability of many mRNA species, encoding immune-relevant proteins, either by binding to AU-rich elements (AREs) of mRNA 3'UTR or by facilitating miRNA biogenesis to target mRNA. FUBP3, also called FUSE-binding protein 3, or MARTA2, was previously shown to mediate dendritic targeting of MAP2 mRNA in neurons. It may interact with single-stranded DNA from the far-upstream element (FUSE) and activate gene expression. It is required for beta-actin mRNA localization. It also interacts with fibroblast growth factor 9 (FGF9) 3'-UTR UG repeats and positively controls FGF9 expression through increasing translation of FGF9 mRNA. FUBP proteins contain four K-homology (KH) RNA-binding domains. The model corresponds to the fourth one.


Pssm-ID: 411827 [Multi-domain]  Cd Length: 67  Bit Score: 36.82  E-value: 2.11e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 57530702 411 TVHLFIPALAVGAIIGKQGQHIKQLSRFAGASIKIAPAEGPDAKLRMVIITGPPE 465
Cdd:cd22399   1 EVTFLVPANKCGLVIGKGGETIRQINQQSGAHVELDRNPPPNPNEKLFIIRGNPQ 55
RRM1_HuD cd12770
RNA recognition motif 1 (RRM1) found in vertebrate Hu-antigen D (HuD); This subgroup ...
83-153 2.23e-03

RNA recognition motif 1 (RRM1) found in vertebrate Hu-antigen D (HuD); This subgroup corresponds to the RRM1 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells, as well as the neurite elongation and morphological differentiation. HuD specifically binds poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 410163 [Multi-domain]  Cd Length: 81  Bit Score: 37.40  E-value: 2.23e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 57530702  83 LQIRNIPPHLQWEVLDSLLAQYGTVENCEQVN---TDTETAVVNVTYGNKDQARQAIEKLNGFQLENYSLKVAY 153
Cdd:cd12770   4 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRdkiTGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSY 77
RRM1_MEI2_like cd12524
RNA recognition motif 1 (RRM1) found in plant Mei2-like proteins; This subgroup corresponds to ...
80-157 2.23e-03

RNA recognition motif 1 (RRM1) found in plant Mei2-like proteins; This subgroup corresponds to the RRM1 of Mei2-like proteins that represent an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and it is highly conserved between plants and fungi. Up to date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear.


Pssm-ID: 409944 [Multi-domain]  Cd Length: 77  Bit Score: 36.87  E-value: 2.23e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57530702  80 SRKLQIRNIPPHLQWEVLDSLLAQYGTVencEQVNTDTET-AVVNVTYGNKDQARQAIEKLNGFQLENYSLKVAY-IPDE 157
Cdd:cd12524   1 SRTLFVRNINSSVEDEELRALFEQFGEI---RTLYTACKHrGFIMVSYYDIRAAQSAKRALQGTELGGRKLDIHFsIPKD 77
KH-I_Vigilin_rpt10 cd22413
tenth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, ...
274-344 2.24e-03

tenth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the tenth one.


Pssm-ID: 411841 [Multi-domain]  Cd Length: 66  Bit Score: 36.85  E-value: 2.24e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 57530702 274 FTEEIPLKiLAHNNFvgrLIGKEGRNLKKIEQDTDTKITISPLQDltlyNPERTITVKGSIETCAKAEEEI 344
Cdd:cd22413   3 FTVEIRAK-PEYHRF---LIGRGGANIRKIRDNTGARIIFPTARD----EDQELITIIGTKEAVEKAKEEL 65
KH-I_Vigilin_rpt14 cd22417
fourteenth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; ...
495-562 2.27e-03

fourteenth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the fourteenth one.


Pssm-ID: 411845 [Multi-domain]  Cd Length: 72  Bit Score: 36.80  E-value: 2.27e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 57530702 495 HIKVPSYAAGRVIGKGGKTVNELQNLTSAEVVVPRDQtpDENDQVVVkITGHFYACQLAQRKIQEILA 562
Cdd:cd22417   4 TVEVDPKYHPKIIGRKGAVITKLRDDHDVNIQFPDKG--DENDDEIT-ITGYEKNAEAAKDAILKIVQ 68
KH-I_Mextli_like cd22454
type I K homology (KH) RNA-binding domain found in Drosophila melanogaster eukaryotic ...
489-545 2.36e-03

type I K homology (KH) RNA-binding domain found in Drosophila melanogaster eukaryotic translation initiation factor 4E-binding protein Mextli and similar proteins; Mextli is a novel eukaryotic translation initiation factor 4E-binding protein that promotes translation in Drosophila melanogaster.


Pssm-ID: 411882 [Multi-domain]  Cd Length: 71  Bit Score: 36.91  E-value: 2.36e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 57530702 489 EVKLEAHIkvPSYAAGRVIGKGGKTVNELQNLTSAEVVVPRDqTPDENDQVVVkITG 545
Cdd:cd22454   3 QTTIEVVI--PNADVGKVIGKGGETIKRIEALTDTVITFERV-NGGSPNREVQ-ITG 55
KH-I_PNPase cd02393
type I K homology (KH) RNA-binding domain found in polyribonucleotide nucleotidyltransferase ...
496-562 2.37e-03

type I K homology (KH) RNA-binding domain found in polyribonucleotide nucleotidyltransferase (PNPase) and similar proteins; PNPase, also called polynucleotide phosphorylase, is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. It catalyzes the phosphorolysis of single-stranded polyribonucleotides processively in the 3'- to 5'-direction. It is also involved, along with RNase II, in tRNA processing. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. The model corresponds to the KH domain.


Pssm-ID: 411803 [Multi-domain]  Cd Length: 70  Bit Score: 36.69  E-value: 2.37e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 57530702 496 IKVPSYAAGRVIGKGGKTVNELQNLTSAEVvvprdqtpDENDQVVVKITGHFY-ACQLAQRKIQEILA 562
Cdd:cd02393   8 IKIPPDKIGDVIGPGGKTIRAIIEETGAKI--------DIEDDGTVTIFATDKeSAEAAKAMIEDIVA 67
KH-I_HNRNPK_rpt1 cd22432
first type I K homology (KH) RNA-binding domain found in heterogeneous nuclear ...
277-345 2.39e-03

first type I K homology (KH) RNA-binding domain found in heterogeneous nuclear ribonucleoprotein K (hnRNP K) and similar proteins; hnRNP K, also called transformation up-regulated nuclear protein (TUNP), is a pre-mRNA binding protein that binds tenaciously to poly(C) sequences. It may be involved in the nuclear metabolism of hnRNAs, particularly for pre-mRNAs that contain cytidine-rich sequences. It can also bind poly(C) single-stranded DNA. hnRNP K plays an important role in p53/TP53 response to DNA damage, acting at the level of both transcription activation and repression. hnRNP K contains three K-homology (KH) RNA-binding domains. The model corresponds to the first one.


Pssm-ID: 411860 [Multi-domain]  Cd Length: 64  Bit Score: 36.39  E-value: 2.39e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 57530702 277 EIPLKILAHNNFVGRLIGKEGRNLKKIEQDTDTKITISPLQdltlyNPERTITVKGSIETCAKAEEEIM 345
Cdd:cd22432   1 VVELRLLIPSKAAGAIIGKGGENIKRLRTEYNASVSVPDSS-----GPERILTISADRETVLGILTEIL 64
KH-I_MASK cd22404
type I K homology (KH) RNA-binding domain found in Mask family proteins; The Mask family ...
281-351 2.39e-03

type I K homology (KH) RNA-binding domain found in Mask family proteins; The Mask family includes Drosophila melanogaster ankyrin repeat and KH domain-containing protein Mask, and its mammalian homologues Mask1/ANKHD1 and Mask2/ANKRD17. Mask, also called multiple ankyrin repeat single KH domain-containing protein, is a large ankyrin repeat and KH domain-containing protein involved in Drosophila receptor tyrosine kinase signaling. It acts as a mediator of receptor tyrosine kinase (RTK) signaling and may act either downstream of MAPK or transduce signaling through a parallel branch of the RTK pathway. Mask is required for the development and organization of indirect flight muscle sarcomeres by regulating the formation of M line and H zone and the correct assembly of thick and thin filaments in the sarcomere. Mask1/ANKHD1, also called HIV-1 Vpr-binding ankyrin repeat protein, or multiple ankyrin repeats single KH domain, or Hmask, is highly expressed in various cancer tissues and is involved in cancer progression, including proliferation and invasion. Mask2/ANKRD17, also called ankyrin repeat protein 17, or gene trap ankyrin repeat protein (GTAR), or serologically defined breast cancer antigen NY-BR-16, is a ubiquitously expressed ankyrin factor essential for the vascular integrity during embryogenesis. It may be directly involved in the DNA replication process and play pivotal roles in cell cycle and DNA regulation. It is also involved in innate immune defense against bacteria and viruses.


Pssm-ID: 411832 [Multi-domain]  Cd Length: 71  Bit Score: 36.80  E-value: 2.39e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 57530702 281 KILAHNNFVGRLIGKEGRNLKKIEQDTDTKITISPLQDLTlynPERTITVKGSIETCAKAEEEIMKKIRES 351
Cdd:cd22404   4 KVTVPNSAISRVIGRGGCNINAIREVSGAHIEIDKQKGEQ---GDRRITIKGSADATRQAAQLINALIKDP 71
RRM2_HRB1_GBP2 cd21606
RNA recognition motif 2 (RRM2) found in Saccharomyces cerevisiae protein HRB1, ...
85-151 2.42e-03

RNA recognition motif 2 (RRM2) found in Saccharomyces cerevisiae protein HRB1, G-strand-binding protein 2 (GBP2) and similar proteins; The family includes Saccharomyces cerevisiae protein HRB1 (also called protein TOM34) and GBP2, both of which are SR-like mRNA-binding proteins which shuttle from the nucleus to the cytoplasm when bound to the mature mRNA molecules. They act as quality control factors for spliced mRNAs. GBP2, also called RAP1 localization factor 6, is a single-strand telomeric DNA-binding protein that binds single-stranded telomeric sequences of the type (TG[1-3])n in vitro. It also binds to RNA. GBP2 influences the localization of RAP1 in the nuclei and plays a role in modulating telomere length. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the second RRM motif.


Pssm-ID: 410185 [Multi-domain]  Cd Length: 75  Bit Score: 36.96  E-value: 2.42e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57530702  85 IRNIPPHLQWEVLDSLLAQYGTVENCEqVNTDTE---TAVVNVTYGNKDQARQAIEKLNGFQLENYSLKV 151
Cdd:cd21606   6 IANLPYSINWQALKDMFKECGDVLRAD-VELDYNgrsRGFGTVIYATEEEMHRAIDTFNGYELEGRVLEV 74
RRM_eIF3G_like cd12408
RNA recognition motif (RRM) found in eukaryotic translation initiation factor 3 subunit G ...
83-151 2.45e-03

RNA recognition motif (RRM) found in eukaryotic translation initiation factor 3 subunit G (eIF-3G) and similar proteins; This subfamily corresponds to the RRM of eIF-3G and similar proteins. eIF-3G, also termed eIF-3 subunit 4, or eIF-3-delta, or eIF3-p42, or eIF3-p44, is the RNA-binding subunit of eIF3, a large multisubunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3G binds 18 S rRNA and beta-globin mRNA, and therefore appears to be a nonspecific RNA-binding protein. eIF-3G is one of the cytosolic targets and interacts with mature apoptosis-inducing factor (AIF). eIF-3G contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). This family also includes yeast eIF3-p33, a homolog of vertebrate eIF-3G, plays an important role in the initiation phase of protein synthesis in yeast. It binds both, mRNA and rRNA, fragments due to an RRM near its C-terminus.


Pssm-ID: 409842 [Multi-domain]  Cd Length: 76  Bit Score: 36.72  E-value: 2.45e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 57530702  83 LQIRNIPPHLQWEVLDSLLAQYGTVENCeQVNTDTETAVVN----VTYGNKDQARQAIEKLNGFQLENYSLKV 151
Cdd:cd12408   2 IRVTNLSEDATEEDLRELFRPFGPISRV-YLAKDKETGQSKgfafVTFETREDAERAIEKLNGFGYDNLILSV 73
KH-I_BICC1_rpt3 cd22422
third type I K homology (KH) RNA-binding domain found in protein bicaudal C homolog 1 (BICC1) ...
285-345 2.78e-03

third type I K homology (KH) RNA-binding domain found in protein bicaudal C homolog 1 (BICC1) and similar proteins; BICC1, also called Bic-C, is a mammalian homologue of Drosophila Bicaudal-C (dBic-C). BICC1 functions as an RNA-binding protein that represses the translation of selected mRNAs to control development. It regulates gene expression and modulates cell proliferation and apoptosis. BICC1 is a negative regulator of Wnt signaling. Increased levels of BICC1 may be associated with depression. Besides, BICC1 is a genetic determinant of osteoblastogenesis and bone mineral density. BICC1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the third one.


Pssm-ID: 411850  Cd Length: 67  Bit Score: 36.55  E-value: 2.78e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 57530702 285 HNNFVgrlIGKEGRNLKKIEQDTDTKITispLQDLTLYNPER-TITVKGSIETCAKAEEEIM 345
Cdd:cd22422  12 HHLFM---LGRNGSNIKHIMQRTGAQIH---FPDPNNPPQRKsTVFISGSIDSVYLARQQLM 67
KH-I_DDX43_DDX53 cd22430
type I K homology (KH) RNA-binding domain found in DEAD box protein 43 (DDX43), DEAD box ...
198-234 3.16e-03

type I K homology (KH) RNA-binding domain found in DEAD box protein 43 (DDX43), DEAD box protein 53 (DDX53) and similar proteins; DDX43 (also called cancer/testis antigen 13, or DEAD box protein HAGE, or helical antigen) displays tumor-specific expression. Diseases associated with DDX43 include rheumatoid lung disease. DDX53 (also called cancer-associated gene protein, or cancer/testis antigen 26, or DEAD box protein CAGE) shows high expression level in various tumors and is involved in anti-cancer drug resistance. Both DDX46 and DDX53 are members of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation.


Pssm-ID: 411858 [Multi-domain]  Cd Length: 66  Bit Score: 36.49  E-value: 3.16e-03
                        10        20        30
                ....*....|....*....|....*....|....*..
gi 57530702 198 PLRMLVPTQFVGAIIGKEGATIRNITKQTQSKIDIHR 234
Cdd:cd22430   1 PLCFKIDSSLVGAVIGRGGSKIRELEESTGSKIKIIK 37
KH-I_FUBP2_rpt3 cd22485
third type I K homology (KH) RNA-binding domain found in far upstream element-binding protein ...
196-265 3.20e-03

third type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 2 (FUBP2) and similar proteins; FUBP2, also called FUSE-binding protein 2, or KH type-splicing regulatory protein (KSRP), or p75, is a single-strand nucleic acid binding protein implicated in a variety of cellular processes, including splicing in the nucleus, mRNA decay, maturation of miRNA, and transcriptional control of proto-oncogenes such as c-myc. It regulates the stability and/or translatability of many mRNA species, encoding immune-relevant proteins, either by binding to AU-rich elements (AREs) of mRNA 3'UTR or by facilitating miRNA biogenesis to target mRNA. FUBP2 contains four K-homology (KH) RNA-binding domains. The model corresponds to the third one.


Pssm-ID: 411913  Cd Length: 68  Bit Score: 36.48  E-value: 3.20e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 57530702 196 DVPlrmlVPTQFVGAIIGKEGATIRNItkQTQSKIDIHRKENAGAA-EKPITIHSTPEGCSTACKIIMEIM 265
Cdd:cd22485   4 DVP----VPRHSVGVVIGRSGEMIKKI--QNDAGVRIQFKQDDGTGpEKIAHIMGPPDRCEHAARIINDLL 68
KH-I_PCBP4_rpt3 cd22523
third type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 4 (PCBP4) ...
201-261 3.28e-03

third type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 4 (PCBP4) and similar proteins; PCBP4, also called alpha-CP4, or heterogeneous nuclear ribonucleoprotein E4, or hnRNP E4, is a single-stranded nucleic acid binding protein that binds preferentially to oligo dC. It regulates both basal and stress-induced p21 expression through binding p21 3'-UTR and modulating p21 mRNA stability. It also plays a role in the cell cycle and is implicated in lung tumor suppression. PCBP4 contains three K-homology (KH) RNA-binding domains. The model corresponds to the third one.


Pssm-ID: 411951  Cd Length: 68  Bit Score: 36.41  E-value: 3.28e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 57530702 201 MLVPTQFVGAIIGKEGATIRNITKQTQSKIDIHRKENaGAAEKPITIHSTPEGCSTACKII 261
Cdd:cd22523   6 FLIPNDLIGCVIGRQGSKISEIRQMSGAHIKIGNQTE-GTSERHVTITGSPVSITLAQYLI 65
RRM3_hnRNPR_like cd12251
RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein R (hnRNP R) ...
83-151 3.45e-03

RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins; This subfamily corresponds to the RRM3 in hnRNP R, hnRNP Q, and APOBEC-1 complementation factor (ACF). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches and has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone and play a key role in cell growth and differentiation. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members contain three conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409697 [Multi-domain]  Cd Length: 72  Bit Score: 36.45  E-value: 3.45e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 57530702  83 LQIRNIPPHLQWEVLDSLLAQYGTVENCEQVNtdtETAVVNvtYGNKDQARQAIEKLNGFQLENYSLKV 151
Cdd:cd12251   4 LYVRNLMLSTTEEKLRELFSEYGKVERVKKIK---DYAFVH--FEERDDAVKAMEEMNGKELEGSEIEV 67
RRM2_SRSF1_4_like cd12339
RNA recognition motif 2 (RRM2) found in serine/arginine-rich splicing factor SRSF1, SRSF4 and ...
82-151 3.51e-03

RNA recognition motif 2 (RRM2) found in serine/arginine-rich splicing factor SRSF1, SRSF4 and similar proteins; This subfamily corresponds to the RRM2 of several serine/arginine (SR) proteins that have been classified into two subgroups. The first subgroup consists of serine/arginine-rich splicing factor 4 (SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5 or SRp40 or SFRS5 or HRS) and serine/arginine-rich splicing factor 6 (SRSF6 or SRp55). The second subgroup is composed of serine/arginine-rich splicing factor 1 (SRSF1 or ASF-1), serine/arginine-rich splicing factor 9 (SRSF9 or SRp30C) and plant pre-mRNA-splicing factor SF2 (SR1). These SR proteins are mainly involved in regulating constitutive and alternative pre-mRNA splicing. They also have been implicated in transcription, genomic stability, mRNA export and translation. All SR proteins in this family, except SRSF5, undergo nucleocytoplasmic shuttling, suggesting their widespread roles in gene expression. These SR proteins share a common domain architecture comprising two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. Both domains can directly contact with RNA. The RRMs appear to determine the binding specificity and the SR domain also mediates protein-protein interactions. In addition, this subfamily includes the yeast nucleolar protein 3 (Npl3p), also termed mitochondrial targeting suppressor 1 protein, or nuclear polyadenylated RNA-binding protein 1. It is a major yeast RNA-binding protein that competes with 3'-end processing factors, such as Rna15, for binding to the nascent RNA, protecting the transcript from premature termination and coordinating transcription termination and the packaging of the fully processed transcript for export. It specifically recognizes a class of G/U-rich RNAs. Npl3p is a multi-domain protein with two RRMs, separated by a short linker and a C-terminal domain rich in glycine, arginine and serine residues.


Pssm-ID: 409776 [Multi-domain]  Cd Length: 70  Bit Score: 36.41  E-value: 3.51e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57530702  82 KLQIRNIPPHLQWEVLDSLLAQYGTVENCEQVNTDTETAVVNvtYGNKDQARQAIEKLNGFQLENYSLKV 151
Cdd:cd12339   2 RVVVSNLPERASWQDLKDFMRKAGEVTYADVHRDREGEGVVE--FTSEEDMKRAIEKLDGTEFNGRRIRV 69
KH-I_FUBP3_rpt1 cd22480
first type I K homology (KH) RNA-binding domain found in far upstream element-binding protein ...
416-478 3.63e-03

first type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 3 (FUBP3) and similar proteins; FUBP3, also called FUSE-binding protein 3, or MARTA2, was previously shown to mediate dendritic targeting of MAP2 mRNA in neurons. It may interact with single-stranded DNA from the far-upstream element (FUSE) and activate gene expression. It is required for beta-actin mRNA localization. It also interacts with fibroblast growth factor 9 (FGF9) 3'-UTR UG repeats and positively controls FGF9 expression through increasing translation of FGF9 mRNA. FUBP3 contains four K-homology (KH) RNA-binding domains. The model corresponds to the first one.


Pssm-ID: 411908 [Multi-domain]  Cd Length: 71  Bit Score: 36.41  E-value: 3.63e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 57530702 416 IPALAVGAIIGKQGQHIKQLSRFAGASIKIAPAEG--PDaklRMVIITGPPEAQFKAQgRIYGKL 478
Cdd:cd22480   7 VPDKMVGFIIGRGGEQISRIQLESGCKIQIAPDSGgmPE---RPCVLTGTPESIEQAK-RLLGQI 67
PRK12705 PRK12705
hypothetical protein; Provisional
214-369 3.73e-03

hypothetical protein; Provisional


Pssm-ID: 237178 [Multi-domain]  Cd Length: 508  Bit Score: 40.08  E-value: 3.73e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57530702  214 KEGATIRNITKQTQSKIDIHRKENAGAAEKPITIHSTPEGCSTACKIIMEIMQKEAQDTKFTEEIPLKILAHNNFVGRLI 293
Cdd:PRK12705 135 VAGLTPEQARKLLLKLLDAELEEEKAQRVKKIEEEADLEAERKAQNILAQAMQRIASETASDLSVSVVPIPSDAMKGRII 214
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57530702  294 GKEGRNLKKIEQDTDTKITISPLQD---LTLYNP-ERTITV--------KGSI------ETCAKAEEEIMKKIRESYENd 355
Cdd:PRK12705 215 GREGRNIRAFEGLTGVDLIIDDTPEavvISSFNPiRREIARltlekllaDGRIhparieEYVQKANEEFKQKIYEIGEE- 293
                        170
                 ....*....|....*
gi 57530702  356 iAAMNLQAH-LIPGL 369
Cdd:PRK12705 294 -VLEELGIFdLKPGL 307
KH-I_MEX3_rpt2 cd22424
second type I K homology (KH) RNA-binding domain found in the family of MEX-3 RNA-binding ...
194-230 3.82e-03

second type I K homology (KH) RNA-binding domain found in the family of MEX-3 RNA-binding proteins; The MEX-3 protein family includes four members, MEX3A/RKHD4, MEX3B/RKHD3/RNF195, MEX3C/ RKHD2/RNF194, and MEX3D/RKHD1/RNF193/TINO. They are homologous of Caenorhabditis elegans MEX-3 protein, a translational regulator that specifies the posterior blastomere identity in the early embryo and contributes to the maintenance of the germline totipotency. Mex-3 proteins are RNA-binding phosphoproteins involved in post-transcriptional regulatory mechanisms. They are characterized by containing two K-homology (KH) RNA-binding domains and a C-terminal RING finger. They bind RNA through their KH domains and shuttle between the nucleus and the cytoplasm via the CRM1-dependent export pathway. The model corresponds to the second KH domain.


Pssm-ID: 411852 [Multi-domain]  Cd Length: 72  Bit Score: 36.16  E-value: 3.82e-03
                        10        20        30
                ....*....|....*....|....*....|....*..
gi 57530702 194 QSDVPLRMLVPTQFVGAIIGKEGATIRNITKQTQSKI 230
Cdd:cd22424   1 PGQTTIQVRVPYRVVGLVVGPKGATIKRIQQQTHTYI 37
RRM_SF3B14 cd12241
RNA recognition motif (RRM) found in pre-mRNA branch site protein p14 (SF3B14) and similar ...
81-153 4.02e-03

RNA recognition motif (RRM) found in pre-mRNA branch site protein p14 (SF3B14) and similar proteins; This subfamily corresponds to the RRM of SF3B14 (also termed p14), a 14 kDa protein subunit of SF3B which is a multiprotein complex that is an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA and has been involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B14 associates directly with another SF3B subunit called SF3B155. It is also present in both U2- and U12-dependent spliceosomes and may contribute to branch site positioning in both the major and minor spliceosome. Moreover, SF3B14 interacts directly with the pre-mRNA branch adenosine early in spliceosome assembly and within the fully assembled spliceosome. SF3B14 contains one well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409687 [Multi-domain]  Cd Length: 77  Bit Score: 36.45  E-value: 4.02e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 57530702  81 RKLQIRNIPPHLQWEVLDSLLAQYGTVENCEQVNTDTETAVVNVTYGNKDQARQAIEKLNGFQLENYSLKVAY 153
Cdd:cd12241   3 RILYVRNLPYKISSEELYDLFGKYGAIRQIRIGNTKETRGTAFVVYEDIFDAKNACDHLSGFNVCNRYLVVLY 75
RRM1_Nop4p cd12674
RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; ...
81-151 4.11e-03

RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; This subgroup corresponds to the RRM1 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 410075 [Multi-domain]  Cd Length: 80  Bit Score: 36.29  E-value: 4.11e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 57530702  81 RKLQIRNIPPHLQWEVLDSLLAQYGTVENCEQVnTDTETAVVN----VTYGNKDQARQAIEKLNGFQLENYSLKV 151
Cdd:cd12674   1 TTLFVRNLPFDVTLESLTDFFSDIGPVKHAVVV-TDPETKKSRgygfVSFSTHDDAEEALAKLKNRKLSGHILKL 74
RRM_FOX1_like cd12407
RNA recognition motif (RRM) found in vertebrate RNA binding protein fox-1 homologs and similar ...
81-151 4.45e-03

RNA recognition motif (RRM) found in vertebrate RNA binding protein fox-1 homologs and similar proteins; This subfamily corresponds to the RRM of several tissue-specific alternative splicing isoforms of vertebrate RNA binding protein Fox-1 homologs, which show high sequence similarity to the Caenorhabditis elegans feminizing locus on X (Fox-1) gene encoding Fox-1 protein. RNA binding protein Fox-1 homolog 1 (RBFOX1), also termed ataxin-2-binding protein 1 (A2BP1), or Fox-1 homolog A, or hexaribonucleotide-binding protein 1 (HRNBP1), is predominantly expressed in neurons, skeletal muscle and heart. It regulates alternative splicing of tissue-specific exons by binding to UGCAUG elements. Moreover, RBFOX1 binds to the C-terminus of ataxin-2 and forms an ataxin-2/A2BP1 complex involved in RNA processing. RNA binding protein fox-1 homolog 2 (RBFOX2), also termed Fox-1 homolog B, or hexaribonucleotide-binding protein 2 (HRNBP2), or RNA-binding motif protein 9 (RBM9), or repressor of tamoxifen transcriptional activity, is expressed in ovary, whole embryo, and human embryonic cell lines in addition to neurons and muscle. RBFOX2 activates splicing of neuron-specific exons through binding to downstream UGCAUG elements. RBFOX2 also functions as a repressor of tamoxifen activation of the estrogen receptor. RNA binding protein Fox-1 homolog 3 (RBFOX3 or NeuN or HRNBP3), also termed Fox-1 homolog C, is a nuclear RNA-binding protein that regulates alternative splicing of the RBFOX2 pre-mRNA, producing a message encoding a dominant negative form of the RBFOX2 protein. Its message is detected exclusively in post-mitotic regions of embryonic brain. Like RBFOX1, both RBFOX2 and RBFOX3 bind to the hexanucleotide UGCAUG elements and modulate brain and muscle-specific splicing of exon EIIIB of fibronectin, exon N1 of c-src, and calcitonin/CGRP. Members in this family also harbor one RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409841 [Multi-domain]  Cd Length: 76  Bit Score: 36.22  E-value: 4.45e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 57530702  81 RKLQIRNIPPHLQWEVLDSLLAQYGTVENCEQV-NTDTETAVVNVTYGNKDQARQAIEKLNGFQLENYSLKV 151
Cdd:cd12407   1 KRLHVSNIPFRFRDPDLRQMFGQFGTILDVEIIfNERGSKGFGFVTFANSADADRAREKLNGTVVEGRKIEV 72
KH-I_Vigilin_rpt2 cd22406
second type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; ...
496-560 4.48e-03

second type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the second one.


Pssm-ID: 411834 [Multi-domain]  Cd Length: 75  Bit Score: 36.13  E-value: 4.48e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 57530702 496 IKVPSYAAGRVIGKGGKTVNELQNLTSAEVVVPRdqtPDENDQvVVKITGHFYACQLAQRKIQEI 560
Cdd:cd22406   9 VNIPKEHHRFILGKKGKKLQELELKTATKIVIPR---QEDNSD-EIKITGTKEGIEKARHEIQLI 69
PRK00106 PRK00106
ribonuclease Y;
256-366 4.81e-03

ribonuclease Y;


Pssm-ID: 178867 [Multi-domain]  Cd Length: 535  Bit Score: 39.85  E-value: 4.81e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57530702  256 TACKIIMEIMQKEAQDTKFTEEIPLKILAHNNFVGRLIGKEGRNLKKIEQDTDTKITISPLQD---LTLYNPERTITVKG 332
Cdd:PRK00106 204 MAKDLLAQAMQRLAGEYVTEQTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDDTPEvvvLSGFDPIRREIARM 283
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 57530702  333 SIETC--------AKAEE-------EIMKKIRESYEN---DIAAMNLQAHLI 366
Cdd:PRK00106 284 TLESLikdgrihpARIEElveknrlEMDNRIREYGEAaayEIGAPNLHPDLI 335
RBD_RRM1_NPL3 cd12340
RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 3 (Npl3p) and similar proteins; ...
3-67 4.99e-03

RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 3 (Npl3p) and similar proteins; This subfamily corresponds to the RRM1 of Npl3p, also termed mitochondrial targeting suppressor 1 protein, or nuclear polyadenylated RNA-binding protein 1. Npl3p is a major yeast RNA-binding protein that competes with 3'-end processing factors, such as Rna15, for binding to the nascent RNA, protecting the transcript from premature termination and coordinating transcription termination and the packaging of the fully processed transcript for export. It specifically recognizes a class of G/U-rich RNAs. Npl3p is a multi-domain protein containing two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), separated by a short linker and a C-terminal domain rich in glycine, arginine and serine residues.


Pssm-ID: 409777 [Multi-domain]  Cd Length: 69  Bit Score: 35.84  E-value: 4.99e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 57530702   3 KLYIGNLGENVSPLDLESLF------KDSKIpfsgqfLVKTGYAFVDCPDESWAMKAIEALSGKVELHGKL 67
Cdd:cd12340   1 RLFVRPFPPDTSESAIREIFspygpvKEVKM------LSDSNFAFVEFEELEDAIRAKDSVHGRVLNNEPL 65
KH-I_FUBP1_rpt4 cd22487
fourth type I K homology (KH) RNA-binding domain found in far upstream element-binding protein ...
416-465 5.13e-03

fourth type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 1 (FUBP1) and similar proteins; FUBP1, also called FBP, or FUSE-binding protein 1, or DNA helicase V, or DH V, binds RNA and single-stranded DNA (ssDNA) and may act both as activator and repressor of transcription. It regulates MYC expression by binding to a single-stranded far-upstream element (FUSE) upstream of the MYC promoter. FUBP1 contains four K-homology (KH) RNA-binding domains. The model corresponds to the fourth one.


Pssm-ID: 411915  Cd Length: 72  Bit Score: 36.09  E-value: 5.13e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 57530702 416 IPALAVGAIIGKQGQHIKQLSRFAGASIKIA--PAEGPDAKLRMVIITGPPE 465
Cdd:cd22487   8 VPTGKTGLIIGKGGETIKSISQQSGARIELQrnPPPNADPNMKLFTIRGSPQ 59
RRM3_HuD cd12656
RNA recognition motif 3 (RRM3) found in vertebrate Hu-antigen D (HuD); This subgroup ...
85-153 5.49e-03

RNA recognition motif 3 (RRM3) found in vertebrate Hu-antigen D (HuD); This subgroup corresponds to the RRM3 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells. And it also regulates the neurite elongation and morphological differentiation. HuD specifically bound poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 241100 [Multi-domain]  Cd Length: 86  Bit Score: 36.22  E-value: 5.49e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 57530702  85 IRNIPPHLQWEVLDSLLAQYGTVENCEQV---NTDTETAVVNVTYGNKDQARQAIEKLNGFQLENYSLKVAY 153
Cdd:cd12656   8 VYNLSPDSDESVLWQLFGPFGAVNNVKVIrdfNTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSF 79
KH-I_MEX3_rpt2 cd22424
second type I K homology (KH) RNA-binding domain found in the family of MEX-3 RNA-binding ...
289-348 5.84e-03

second type I K homology (KH) RNA-binding domain found in the family of MEX-3 RNA-binding proteins; The MEX-3 protein family includes four members, MEX3A/RKHD4, MEX3B/RKHD3/RNF195, MEX3C/ RKHD2/RNF194, and MEX3D/RKHD1/RNF193/TINO. They are homologous of Caenorhabditis elegans MEX-3 protein, a translational regulator that specifies the posterior blastomere identity in the early embryo and contributes to the maintenance of the germline totipotency. Mex-3 proteins are RNA-binding phosphoproteins involved in post-transcriptional regulatory mechanisms. They are characterized by containing two K-homology (KH) RNA-binding domains and a C-terminal RING finger. They bind RNA through their KH domains and shuttle between the nucleus and the cytoplasm via the CRM1-dependent export pathway. The model corresponds to the second KH domain.


Pssm-ID: 411852 [Multi-domain]  Cd Length: 72  Bit Score: 35.77  E-value: 5.84e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 57530702 289 VGRLIGKEGRNLKKIEQDTDTKItISPLQDLtlynpERTITVKGSIETCAKAEEEIMKKI 348
Cdd:cd22424  15 VGLVVGPKGATIKRIQQQTHTYI-VTPSRDK-----EPVFEVTGMPENVERAREEIEAHI 68
KH-I_PCBP_rpt2 cd02396
second type I K homology (KH) RNA-binding domain found in the family of poly(C)-binding ...
498-545 5.88e-03

second type I K homology (KH) RNA-binding domain found in the family of poly(C)-binding proteins (PCBPs); The PCBP family, also known as hnRNP E family, comprises four members, PCBP1-4, which are RNA-binding proteins that interact in a sequence-specific manner with single-stranded poly(C) sequences. They are mainly involved in various posttranscriptional regulations, including mRNA stabilization or translational activation/silencing. Besides, PCBPs may share iron chaperone activity. PCBPs contain three K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411806 [Multi-domain]  Cd Length: 72  Bit Score: 35.71  E-value: 5.88e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 57530702 498 VPSYAAGRVIGKGGKTVNELQNLTSAEVVVPRDQTPDENDQVVVkITG 545
Cdd:cd02396   8 VPASQCGSLIGKGGSKIKEIRESTGASVQVASEMLPNSTERAVT-ISG 54
KH-I_BTR1_rpt3 cd22514
third type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana protein BTR1 and ...
411-471 6.23e-03

third type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana protein BTR1 and similar proteins; BTR1, also called Binding to ToMV RNA 1, is a negative regulator of tomato mosaic virus (ToMV) multiplication but has no effect on the multiplication of cucumber mosaic virus (CMV). BTR1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the third one.


Pssm-ID: 411942 [Multi-domain]  Cd Length: 71  Bit Score: 35.47  E-value: 6.23e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 57530702 411 TVHLFIPALAVGAIIGKQGQHIKQLSRFAGASIKIApAEG---PDAKLRMVIITGPPEAQFKAQ 471
Cdd:cd22514   2 SVTIGVPDEHIGAILGRGGRTINEIQQHSGARIKIS-DRGdfvSGTRNRKVTITGPQDAVQMAQ 64
KH-I_ANKHD1 cd22503
type I K homology (KH) RNA-binding domain found in ankyrin repeat and KH domain-containing ...
496-559 6.61e-03

type I K homology (KH) RNA-binding domain found in ankyrin repeat and KH domain-containing protein 1 (ANKHD1) and similar proteins; ANKHD1, also called HIV-1 Vpr-binding ankyrin repeat protein, or multiple ankyrin repeats single KH domain, or Hmask, is highly expressed in various cancer tissues and is involved in cancer progression, including proliferation and invasion. It acts as a scaffolding protein that may be associated with the abnormal phenotype of leukemia cells. It may play might have a role in MM cell proliferation and cell cycle progression by regulating expression of p21. It also regulates cell cycle progression and proliferation in multiple myeloma cells. ANKHD1 is a component of Hippo signaling pathway. It functions as a positive regulator of YAP1 and promotes cell growth and cell cycle progression through Cyclin A upregulation in prostate cancer cells.


Pssm-ID: 411931  Cd Length: 83  Bit Score: 35.88  E-value: 6.61e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 57530702 496 IKVPSYAAGRVIGKGGKTVNELQNLTSAEVVVprDQTPDENDQVVVKITGHF----YACQLAQRKIQE 559
Cdd:cd22503   5 LSVPASVVSRIMGRGGCNITAIQDVTGAHIDV--DKQKDKNGERMITIRGGTestrYAVQLINALIQD 70
KH-I_FUBP1_rpt1 cd22478
first type I K homology (KH) RNA-binding domain found in far upstream element-binding protein ...
203-267 6.93e-03

first type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 1 (FUBP1) and similar proteins; FUBP1, also called FBP, or FUSE-binding protein 1, or DNA helicase V, or DH V, binds RNA and single-stranded DNA (ssDNA) and may act both as activator and repressor of transcription. It regulates MYC expression by binding to a single-stranded far-upstream element (FUSE) upstream of the MYC promoter. FUBP1 contains four K-homology (KH) RNA-binding domains. The model corresponds to the first one.


Pssm-ID: 411906 [Multi-domain]  Cd Length: 75  Bit Score: 35.77  E-value: 6.93e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 57530702 203 VPTQFVGAIIGKEGATIRNITKQTQSKIDIhRKENAGAAEKPITIHSTPEGCSTACKIIMEIMQK 267
Cdd:cd22478  10 VPDGMVGFIIGRGGEQISRIQQESGCKIQI-APDSGGLPERSCMLTGTPESVQSAKRLLDQIVEK 73
RRM_RBM8 cd12324
RNA recognition motif (RRM) found in RNA-binding protein RBM8A, RBM8B nd similar proteins; ...
85-151 7.14e-03

RNA recognition motif (RRM) found in RNA-binding protein RBM8A, RBM8B nd similar proteins; This subfamily corresponds to the RRM of RBM8, also termed binder of OVCA1-1 (BOV-1), or RNA-binding protein Y14, which is one of the components of the exon-exon junction complex (EJC). It has two isoforms, RBM8A and RBM8B, both of which are identical except that RBM8B is 16 amino acids shorter at its N-terminus. RBM8, together with other EJC components (such as Magoh, Aly/REF, RNPS1, Srm160, and Upf3), plays critical roles in postsplicing processing, including nuclear export and cytoplasmic localization of the mRNA, and the nonsense-mediated mRNA decay (NMD) surveillance process. RBM8 binds to mRNA 20-24 nucleotides upstream of a spliced exon-exon junction. It is also involved in spliced mRNA nuclear export, and the process of nonsense-mediated decay of mRNAs with premature stop codons. RBM8 forms a specific heterodimer complex with the EJC protein Magoh which then associates with Aly/REF, RNPS1, DEK, and SRm160 on the spliced mRNA, and inhibits ATP turnover by eIF4AIII, thereby trapping the EJC core onto RNA. RBM8 contains an N-terminal putative bipartite nuclear localization signal, one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), in the central region, and a C-terminal serine-arginine rich region (SR domain) and glycine-arginine rich region (RG domain).


Pssm-ID: 409762 [Multi-domain]  Cd Length: 88  Bit Score: 36.05  E-value: 7.14e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 57530702  85 IRNIPPHLQWEVLDSLLAQYGTVENCeQVNTDTETAVVN----VTYGNKDQARQAIEKLNGFQLENYSLKV 151
Cdd:cd12324  11 VTGVHEEAQEEDIHDKFAEFGEIKNL-HLNLDRRTGFVKgyalVEYETKKEAQAAIEGLNGKELLGQTISV 80
RRM_scw1_like cd12245
RNA recognition motif (RRM) found in yeast cell wall integrity protein scw1 and similar ...
2-60 7.16e-03

RNA recognition motif (RRM) found in yeast cell wall integrity protein scw1 and similar proteins; This subfamily corresponds to the RRM of the family including yeast cell wall integrity protein scw1, yeast Whi3 protein, yeast Whi4 protein and similar proteins. The strong cell wall protein 1, scw1, is a nonessential cytoplasmic RNA-binding protein that regulates septation and cell-wall structure in fission yeast. It may function as an inhibitor of septum formation, such that its loss of function allows weak SIN signaling to promote septum formation. It's RRM domain shows high homology to two budding yeast proteins, Whi3 and Whi4. Whi3 is a dose-dependent modulator of cell size and has been implicated in cell cycle control in the yeast Saccharomyces cerevisiae. It functions as a negative regulator of ceroid-lipofuscinosis, neuronal 3 (Cln3), a G1 cyclin that promotes transcription of many genes to trigger the G1/S transition in budding yeast. It specifically binds the CLN3 mRNA and localizes it into discrete cytoplasmic loci that may locally restrict Cln3 synthesis to modulate cell cycle progression. Moreover, Whi3 plays a key role in cell fate determination in budding yeast. The RRM domain is essential for Whi3 function. Whi4 is a partially redundant homolog of Whi3, also containing one RRM. Some uncharacterized family members of this subfamily contain two RRMs; their RRM1 shows high sequence homology to the RRM of RNA-binding protein with multiple splicing (RBP-MS)-like proteins.


Pssm-ID: 409691 [Multi-domain]  Cd Length: 79  Bit Score: 35.68  E-value: 7.16e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 57530702   2 NKLYIGNLGENVSPLDLESLFKDskipFSG----QFLVKTG--YAFVDCPDESWAMKAIEALSGK 60
Cdd:cd12245   3 NTLFVANLGPNVSEQELRQLFSR----QPGfrrlRMHNKGGgpVCFVEFEDVPFATQALNHLQGA 63
KH-I_NOVA_rpt3 cd09031
third type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ...
287-348 7.30e-03

third type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ventral antigen (Nova); The family includes two related neuronal RNA-binding proteins, Nova-1 and Nova-2. Nova-1, also called onconeural ventral antigen 1, or paraneoplastic Ri antigen, or ventral neuron-specific protein 1, may regulate RNA splicing or metabolism in a specific subset of developing neurons. It interacts with RNA containing repeats of the YCAY sequence. It is a brain-enriched splicing factor regulating neuronal alternative splicing. Nova-1 is involved in neurological disorders and carcinogenesis. Nova-2, also called astrocytic NOVA1-like RNA-binding protein, is a neuronal RNA-binding protein expressed in a broader central nervous system (CNS) distribution than Nova-1. It functions in neuronal RNA metabolism. NOVA family proteins contain three K-homology (KH) RNA-binding domains. The model corresponds to the third one.


Pssm-ID: 411807 [Multi-domain]  Cd Length: 71  Bit Score: 35.25  E-value: 7.30e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 57530702 287 NFVGRLIGKEGRNLKKIEQDTDTKITISPLQDLTLYNPERTITVKGSIETCAKAEEEIMKKI 348
Cdd:cd09031  10 NLVGAILGKGGKTLVEIQELTGARIQISKKGEFVPGTRNRKVTITGTPAAVQAAQYLIEQRI 71
RRM2_RAVER cd12389
RNA recognition motif 2 (RRM2) found in ribonucleoprotein PTB-binding raver-1, raver-2 and ...
83-154 7.35e-03

RNA recognition motif 2 (RRM2) found in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins; This subfamily corresponds to the RRM2 of raver-1 and raver-2. Raver-1 is a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-2 is a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It shows high sequence homology to raver-1. Raver-2 exerts a spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Both, raver-1 and raver-2, contain three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. They binds to RNA through the RRMs. In addition, the two [SG][IL]LGxxP motifs serve as the PTB-binding motifs in raver1. However, raver-2 interacts with PTB through the SLLGEPP motif only.


Pssm-ID: 409823 [Multi-domain]  Cd Length: 77  Bit Score: 35.75  E-value: 7.35e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 57530702  83 LQIRNIPPHLQWEVLDSLLAQYGTVENCEQV---NTDTETAVVNVTYGNKDQARQAIEKLNGFQLENYSLKVAYI 154
Cdd:cd12389   2 LCVTNLPLSFTEEQFEELVRPYGNVERCFLVyseVTGESKGYGFVEYTSKESAIRAKNQLHGRQIGGRALQVDWL 76
KH-I_Vigilin_rpt4 cd22408
fourth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; ...
504-557 7.53e-03

fourth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the fourth one.


Pssm-ID: 411836 [Multi-domain]  Cd Length: 62  Bit Score: 35.22  E-value: 7.53e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 57530702 504 GRVIGKGGKTVNELQNLTSAEVVVPRDQTPDENdqvvVKITGHFYACQLAQRKI 557
Cdd:cd22408  12 RFVIGPRGSTIQEILEETGCSVEVPPNDSDSET----ITLRGPADKLGAALTLV 61
RRM1_2_CoAA_like cd12343
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in RRM-containing coactivator activator ...
82-151 7.67e-03

RNA recognition motif 1 (RRM1) and 2 (RRM2) found in RRM-containing coactivator activator/modulator (CoAA) and similar proteins; This subfamily corresponds to the RRM in CoAA (also known as RBM14 or PSP2) and RNA-binding protein 4 (RBM4). CoAA is a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner, and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. RBM4 is a ubiquitously expressed splicing factor with two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may also function as a translational regulator of stress-associated mRNAs as well as play a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RRMs, a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. This family also includes Drosophila RNA-binding protein lark (Dlark), a homolog of human RBM4. It plays an important role in embryonic development and in the circadian regulation of adult eclosion. Dlark shares high sequence similarity with RBM4 at the N-terminal region. However, Dlark has three proline-rich segments instead of three alanine-rich segments within the C-terminal region.


Pssm-ID: 409779 [Multi-domain]  Cd Length: 66  Bit Score: 35.28  E-value: 7.67e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 57530702  82 KLQIRNIPPHLQWEVLDSLLAQYGTVenceqvntdTETAVVN----VTYGNKDQARQAIEKLNGFQLENYSLKV 151
Cdd:cd12343   1 KIFVGNLPDAATSEELRALFEKYGKV---------TECDIVKnyafVHMEKEEDAEDAIKALNGYEFMGSRINV 65
KH-I_MER1_like cd22458
type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae meiotic ...
496-559 7.68e-03

type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae meiotic recombination 1 protein (MER1) and similar proteins; MER1 is required for chromosome pairing and genetic recombination. It may function to bring the axial elements of the synaptonemal complex corresponding to homologous chromosomes together by initiating recombination. MER1 might be responsible for regulating the MER2 gene and/or gene product.


Pssm-ID: 411886  Cd Length: 65  Bit Score: 35.12  E-value: 7.68e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 57530702 496 IKVPSYAAGRVIGKGGKTVNELQNLTSAEVVVprdqTP-DENDQVVVKITGHFYACQLAQRKIQE 559
Cdd:cd22458   5 IKLPQALCGRLIGAKGKNIKALSEKSGASIRL----IPiSNSSQQTIHLSGTDKQIALAISSIEE 65
KH-I_BTR1_rpt3 cd22514
third type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana protein BTR1 and ...
281-348 7.89e-03

third type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana protein BTR1 and similar proteins; BTR1, also called Binding to ToMV RNA 1, is a negative regulator of tomato mosaic virus (ToMV) multiplication but has no effect on the multiplication of cucumber mosaic virus (CMV). BTR1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the third one.


Pssm-ID: 411942 [Multi-domain]  Cd Length: 71  Bit Score: 35.47  E-value: 7.89e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 57530702 281 KILAHNNFVGRLIGKEGRNLKKIEQDTDTKITISPLQDLTLYNPERTITVKGSIETCAKAEEEIMKKI 348
Cdd:cd22514   4 TIGVPDEHIGAILGRGGRTINEIQQHSGARIKISDRGDFVSGTRNRKVTITGPQDAVQMAQYLLEQKL 71
KH-I_FUBP3_rpt4 cd22489
fourth type I K homology (KH) RNA-binding domain found in far upstream element-binding protein ...
416-465 8.61e-03

fourth type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 3 (FUBP3) and similar proteins; FUBP3, also called FUSE-binding protein 3, or MARTA2, was previously shown to mediate dendritic targeting of MAP2 mRNA in neurons. It may interact with single-stranded DNA from the far-upstream element (FUSE) and activate gene expression. It is required for beta-actin mRNA localization. It also interacts with fibroblast growth factor 9 (FGF9) 3'-UTR UG repeats and positively controls FGF9 expression through increasing translation of FGF9 mRNA. FUBP3 contains four K-homology (KH) RNA-binding domains. The model corresponds to the fourth one.


Pssm-ID: 411917 [Multi-domain]  Cd Length: 69  Bit Score: 35.29  E-value: 8.61e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 57530702 416 IPALAVGAIIGKQGQHIKQLSRFAGASIKIA--PAEGPDAKLRMVIITGPPE 465
Cdd:cd22489   6 IPADKCGLVIGKGGENIKSINQQSGAHVELQrnPPPNTDPNVRIFTIRGVPQ 57
RRM3_Hu cd12377
RNA recognition motif 3 (RRM3) found in the Hu proteins family; This subfamily corresponds to ...
85-153 8.63e-03

RNA recognition motif 3 (RRM3) found in the Hu proteins family; This subfamily corresponds to the RRM3 of the Hu proteins family which represent a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 409811 [Multi-domain]  Cd Length: 76  Bit Score: 35.37  E-value: 8.63e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 57530702  85 IRNIPPHLQWEVLDSLLAQYGTVENCEqVNTDTETAVVN----VTYGNKDQARQAIEKLNGFQLENYSLKVAY 153
Cdd:cd12377   4 VYNLAPDADESLLWQLFGPFGAVQNVK-IIRDFTTNKCKgygfVTMTNYDEAAVAIASLNGYRLGGRVLQVSF 75
KH-I_FUBP_rpt3 cd22398
third type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding ...
289-344 8.84e-03

third type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding proteins; The far upstream element-binding protein (FUBP) family includes FUBP1-3. FUBP1, also called FBP, or FUSE-binding protein 1, or DNA helicase V, or DH V, binds RNA and single-stranded DNA (ssDNA) and may act both as activator and repressor of transcription. It regulates MYC expression by binding to a single-stranded far-upstream element (FUSE) upstream of the MYC promoter. FUBP2, also called FUSE-binding protein 2, or KH type-splicing regulatory protein (KSRP), or p75, is a single-strand nucleic acid binding protein implicated in a variety of cellular processes, including splicing in the nucleus, mRNA decay, maturation of miRNA, and transcriptional control of proto-oncogenes such as c-myc. It regulates the stability and/or translatability of many mRNA species, encoding immune-relevant proteins, either by binding to AU-rich elements (AREs) of mRNA 3'UTR or by facilitating miRNA biogenesis to target mRNA. FUBP3, also called FUSE-binding protein 3, or MARTA2, was previously shown to mediate dendritic targeting of MAP2 mRNA in neurons. It may interact with single-stranded DNA from the far-upstream element (FUSE) and activate gene expression. It is required for beta-actin mRNA localization. It also interacts with fibroblast growth factor 9 (FGF9) 3'-UTR UG repeats and positively controls FGF9 expression through increasing translation of FGF9 mRNA. FUBP proteins contain four K-homology (KH) RNA-binding domains. The model corresponds to the third one.


Pssm-ID: 411826 [Multi-domain]  Cd Length: 67  Bit Score: 34.93  E-value: 8.84e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 57530702 289 VGRLIGKEGRNLKKIEQDTDTKITISPLQDltlYNPERTITVKGSIETCAKAEEEI 344
Cdd:cd22398  11 VGVVIGKGGEMIKKIQNETGARVQFKPDDG---NSPDRICVITGPPDQVQHAARMI 63
Pnp COG1185
Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ...
201-297 8.84e-03

Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis];


Pssm-ID: 224106 [Multi-domain]  Cd Length: 692  Bit Score: 39.10  E-value: 8.84e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57530702 201 MLVPTQFVGAIIGKEGATIRNITKQTQSKIDIhrkENAGAaekpITIHSTPEGCSTACKIIMEIMQKEAQDTKFTEEIPL 280
Cdd:COG1185 556 IKIDPDKIRDVIGPGGKTIKAITEETGVKIDI---EDDGT----VKIAASDGESAKKAKERIEAITREVEVGEVYEGTVV 628
                        90
                ....*....|....*..
gi 57530702 281 KILAHNNFVGRLIGKEG 297
Cdd:COG1185 629 RIVDFGAFVELLPGKDG 645
KH-I_PCBP3_rpt2 cd22519
second type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) ...
498-540 8.95e-03

second type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) and similar proteins; PCBP3, also called alpha-CP3, or PCBP3-overlapping transcript, or PCBP3-overlapping transcript 1, or heterogeneous nuclear ribonucleoprotein E3, or hnRNP E3, is a single-stranded nucleic acid binding protein that binds preferentially to oligo dC. It can function as a repressor dependent on binding to single-strand and double-stranded poly(C) sequences. PCBP3 contains three K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411947 [Multi-domain]  Cd Length: 79  Bit Score: 35.53  E-value: 8.95e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|...
gi 57530702 498 VPSYAAGRVIGKGGKTVNELQNLTSAEVVVPRDQTPDENDQVV 540
Cdd:cd22519  12 VPASQCGSLIGKGGSKIKEIRESTGAQVQVAGDMLPNSTERAV 54
KH-I_Hqk cd22465
type I K homology (KH) RNA-binding domain found in protein quaking (Hqk) and similar proteins; ...
278-313 9.20e-03

type I K homology (KH) RNA-binding domain found in protein quaking (Hqk) and similar proteins; Hqk, also called HqkI, is an RNA-binding protein that plays a central role in myelinization. It binds to the 5'-NACUAAY-N(1,20)-UAAY-3' RNA core sequence and regulates target mRNA stability. It acts by regulating pre-mRNA splicing, mRNA export and protein translation. Hqk is a regulator of oligodendrocyte differentiation and maturation in the brain that may play a role in myelin and oligodendrocyte dysfunction in schizophrenia.


Pssm-ID: 411893 [Multi-domain]  Cd Length: 103  Bit Score: 36.07  E-value: 9.20e-03
                        10        20        30
                ....*....|....*....|....*....|....*.
gi 57530702 278 IPLKILAHNNFVGRLIGKEGRNLKKIEQDTDTKITI 313
Cdd:cd22465   8 VPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMV 43
KH-I_Vigilin_rpt1 cd22405
first type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, ...
300-345 9.22e-03

first type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the first one.


Pssm-ID: 411833  Cd Length: 69  Bit Score: 34.96  E-value: 9.22e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*.
gi 57530702 300 LKKIEQDTDTKITISPLQDLTLynperTITVKGSIETCAKAEEEIM 345
Cdd:cd22405  29 CKDIMQKTGATIELSSAKDQSL-----TIMVTGKQSAVMKARREVL 69
KH-I_FUBP3_rpt2 cd22483
second type I K homology (KH) RNA-binding domain found in far upstream element-binding protein ...
201-270 9.22e-03

second type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 3 (FUBP3) and similar proteins; FUBP3, also called FUSE-binding protein 3, or MARTA2, was previously shown to mediate dendritic targeting of MAP2 mRNA in neurons. It may interact with single-stranded DNA from the far-upstream element (FUSE) and activate gene expression. It is required for beta-actin mRNA localization. It also interacts with fibroblast growth factor 9 (FGF9) 3'-UTR UG repeats and positively controls FGF9 expression through increasing translation of FGF9 mRNA. FUBP3 contains four K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411911 [Multi-domain]  Cd Length: 83  Bit Score: 35.65  E-value: 9.22e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 57530702 201 MLVPTQFVGAIIGKEGATIRNITKQTQSK-IDIHRKENAGAAEKPITIHSTPEGCSTACKIIMEIMQKEAQ 270
Cdd:cd22483   9 ILIPASKVGLVIGKGGETIKQLQERTGVKmIMIQDGPLPTGADKPLRITGDPFKVQQAREMVLEIIREKDQ 79
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.20
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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