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Conserved domains on  [gi|944208227|gb|KQK75240|]
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putative RNA-binding protein 15 [Amazona aestiva]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
SPOC_RBM15 cd21549
SPOC (Spen paralog and ortholog C-terminal) domain found in vertebrate RNA binding motif ...
599-766 2.91e-112

SPOC (Spen paralog and ortholog C-terminal) domain found in vertebrate RNA binding motif protein 15 (RBM15); RBM15, also called one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possesses mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RBM15 belongs to the Spen (split end) protein family, which contain three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. The model corresponds to the SPOC domain that is involved in developmental signaling and has also been proposed to be a phosphorylation binding module.


:

Pssm-ID: 439212  Cd Length: 164  Bit Score: 337.25  E-value: 2.91e-112
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 944208227 599 AWQGMLLLKNSNFPSNMHLLQGDLGVASSLLVEGATGGKVAQLKITQRLRLDQPKLDEVNRRIKVAGPNGYAILLAVPGA 678
Cdd:cd21549    1 AWQGMLLLKNSNFPSNMHLLEGDLSVASSLLVDGSTGGKVAQLKITQRLRLDQPKLDEVTRRIKVAGPNGYAVLLAVPGS 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 944208227 679 SDNRSaagaSEAATTSTQRPLRNLVSYLKQKQAAGVISLPVGGNKDKENSGVLHAFPPCDFSQQFLDSTAKALAKSEDDY 758
Cdd:cd21549   81 SEVSS----VSDQATSTQRPLRNLVSYLKQKQAAGVISLPVGGSKDKDNTGVLHAFPPCDFSQQFLDSSAKALAKSEEDY 156

                 ....*...
gi 944208227 759 LVMIIVRG 766
Cdd:cd21549  157 LVMIIVRG 164
RRM_SF super family cl17169
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
14-97 3.26e-46

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).


The actual alignment was detected with superfamily member cd12553:

Pssm-ID: 473069 [Multi-domain]  Cd Length: 78  Bit Score: 158.96  E-value: 3.26e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 944208227  14 YKTLKISELGSALSDEAVEDGLFHEFKRFGDVSVKISRLppgtgaADERVAFVNFRRPEDARAAKHARGRLVLYDRPLKI 93
Cdd:cd12553    1 YKTLKISELGSQLSDEAVEDGLFHEFKKFGDVSVKISRL------GDERVAFVNFRRPEDARAAKHARGRLVLYDRPLKI 74

                 ....
gi 944208227  94 EAVY 97
Cdd:cd12553   75 EAVY 78
RRM_SF super family cl17169
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
278-332 1.86e-34

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).


The actual alignment was detected with superfamily member cd12557:

Pssm-ID: 473069 [Multi-domain]  Cd Length: 73  Bit Score: 125.82  E-value: 1.86e-34
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 944208227 278 EFDRFGTIRTIDYRKGDSWAYIQYESLDAAQAACTHMRGFPLGGPDRRLRVDFAD 332
Cdd:cd12557   19 EFDRFGTIRTIDYRKGDSWAYIQYESLDAAQAACTHMRGFPLGGPDRRLRVDFAD 73
RRM_SF super family cl17169
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
233-277 5.23e-18

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).


The actual alignment was detected with superfamily member cd12555:

Pssm-ID: 473069 [Multi-domain]  Cd Length: 87  Bit Score: 79.51  E-value: 5.23e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 944208227 233 EDDQRANRTLFLGNLDIT------------------------------------FENLDMAHRAKLAMSGKVLLRNPIKI 276
Cdd:cd12555    1 EDDQRANRTLFLGNLDITvtendlrrafdrfgvitevdikrpgrgqtstygflkFENLDMAHRAKLAMSGKVIGRNPIKI 80

                 .
gi 944208227 277 G 277
Cdd:cd12555   81 G 81
 
Name Accession Description Interval E-value
SPOC_RBM15 cd21549
SPOC (Spen paralog and ortholog C-terminal) domain found in vertebrate RNA binding motif ...
599-766 2.91e-112

SPOC (Spen paralog and ortholog C-terminal) domain found in vertebrate RNA binding motif protein 15 (RBM15); RBM15, also called one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possesses mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RBM15 belongs to the Spen (split end) protein family, which contain three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. The model corresponds to the SPOC domain that is involved in developmental signaling and has also been proposed to be a phosphorylation binding module.


Pssm-ID: 439212  Cd Length: 164  Bit Score: 337.25  E-value: 2.91e-112
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 944208227 599 AWQGMLLLKNSNFPSNMHLLQGDLGVASSLLVEGATGGKVAQLKITQRLRLDQPKLDEVNRRIKVAGPNGYAILLAVPGA 678
Cdd:cd21549    1 AWQGMLLLKNSNFPSNMHLLEGDLSVASSLLVDGSTGGKVAQLKITQRLRLDQPKLDEVTRRIKVAGPNGYAVLLAVPGS 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 944208227 679 SDNRSaagaSEAATTSTQRPLRNLVSYLKQKQAAGVISLPVGGNKDKENSGVLHAFPPCDFSQQFLDSTAKALAKSEDDY 758
Cdd:cd21549   81 SEVSS----VSDQATSTQRPLRNLVSYLKQKQAAGVISLPVGGSKDKDNTGVLHAFPPCDFSQQFLDSSAKALAKSEEDY 156

                 ....*...
gi 944208227 759 LVMIIVRG 766
Cdd:cd21549  157 LVMIIVRG 164
RRM1_RBM15 cd12553
RNA recognition motif 1 (RRM1) found in vertebrate RNA binding motif protein 15 (RBM15); This ...
14-97 3.26e-46

RNA recognition motif 1 (RRM1) found in vertebrate RNA binding motif protein 15 (RBM15); This subgroup corresponds to the RRM1 of RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possesses mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RBM15 belongs to the Spen (split end) protein family, which contains three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. This family also includes a RBM15-MKL1 (OTT-MAL) fusion protein that RBM15 is N-terminally fused to megakaryoblastic leukemia 1 protein (MKL1) at the C-terminus in a translocation involving chromosome 1 and 22, resulting in acute megakaryoblastic leukemia. The fusion protein could interact with the mRNA export machinery. Although it maintains the specific transactivator function of MKL1, the fusion protein cannot activate RTE-mediated mRNA expression and has lost the post-transcriptional activator function of RBM15. However, it has transdominant suppressor function contributing to its oncogenic properties.


Pssm-ID: 409969 [Multi-domain]  Cd Length: 78  Bit Score: 158.96  E-value: 3.26e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 944208227  14 YKTLKISELGSALSDEAVEDGLFHEFKRFGDVSVKISRLppgtgaADERVAFVNFRRPEDARAAKHARGRLVLYDRPLKI 93
Cdd:cd12553    1 YKTLKISELGSQLSDEAVEDGLFHEFKKFGDVSVKISRL------GDERVAFVNFRRPEDARAAKHARGRLVLYDRPLKI 74

                 ....
gi 944208227  94 EAVY 97
Cdd:cd12553   75 EAVY 78
RRM3_RBM15 cd12557
RNA recognition motif 3 (RRM3) found in vertebrate RNA binding motif protein 15 (RBM15); This ...
278-332 1.86e-34

RNA recognition motif 3 (RRM3) found in vertebrate RNA binding motif protein 15 (RBM15); This subgroup corresponds to the RRM3 of RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, a novel mRNA export factor component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possesses mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RBM15 belongs to the Spen (split end) protein family, which contains three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralogue and ortholog C-terminal) domain. This family also includes a RBM15-MKL1 (OTT-MAL) fusion protein that RBM15 is N-terminally fused to megakaryoblastic leukemia 1 protein (MKL1) at the C-terminus in a translocation involving chromosome 1 and 22, resulting in acute megakaryoblastic leukemia. The fusion protein could interact with the mRNA export machinery. Although it maintains the specific transactivator function of MKL1, the fusion protein cannot activate RTE-mediated mRNA expression and has lost the post-transcriptional activator function of RBM15. However, it has transdominant suppressor function contributing to its oncogenic properties.


Pssm-ID: 409973 [Multi-domain]  Cd Length: 73  Bit Score: 125.82  E-value: 1.86e-34
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 944208227 278 EFDRFGTIRTIDYRKGDSWAYIQYESLDAAQAACTHMRGFPLGGPDRRLRVDFAD 332
Cdd:cd12557   19 EFDRFGTIRTIDYRKGDSWAYIQYESLDAAQAACTHMRGFPLGGPDRRLRVDFAD 73
SPOC pfam07744
SPOC domain; The SPOC (Spen paralogue and orthologue C-terminal) domain is involved in ...
593-765 5.00e-24

SPOC domain; The SPOC (Spen paralogue and orthologue C-terminal) domain is involved in developmental signalling.


Pssm-ID: 400205  Cd Length: 142  Bit Score: 98.58  E-value: 5.00e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 944208227  593 APKLCLAWQGMLLLKN-SNFPSNMHLLQGDLGVASSLLvegatggkvaqLKITQRLRLDQPK--LDEVNRRIkvagpngY 669
Cdd:pfam07744   2 LQDLEVIWQGTLAMKGvAEFSVRAHLVSGDIDSLLPSL-----------LRITGRIRLDAVWkyLDEVRRSI-------T 63
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 944208227  670 AILLAV---PGASDNRSAagaseaattstqrpLRNLVSYLKQKQAAGVISLPVGGNKDkensgvLHAFPPCDFSQQFLDS 746
Cdd:pfam07744  64 RDVLVVrffPSSESDESA--------------FDELIDYLQSKQRAGVIHAKSADVKD------LYLFPPCEFLELLLPV 123
                         170
                  ....*....|....*....
gi 944208227  747 TaKALAKSEDDYLVMIIVR 765
Cdd:pfam07744 124 G-LSLEVSEPNLLLGVVVR 141
RRM2_RBM15 cd12555
RNA recognition motif 2 (RRM2) found in vertebrate RNA binding motif protein 15 (RBM15); This ...
233-277 5.23e-18

RNA recognition motif 2 (RRM2) found in vertebrate RNA binding motif protein 15 (RBM15); This subgroup corresponds to the RRM2 of RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possesses mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RBM15 belongs to the Spen (split end) protein family, which contain three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. This family also includes a RBM15-MKL1 (OTT-MAL) fusion protein that RBM15 is N-terminally fused to megakaryoblastic leukemia 1 protein (MKL1) at the C-terminus in a translocation involving chromosome 1 and 22, resulting in acute megakaryoblastic leukemia. The fusion protein could interact with the mRNA export machinery. Although it maintains the specific transactivator function of MKL1, the fusion protein cannot activate RTE-mediated mRNA expression and has lost the post-transcriptional activator function of RBM15. However, it has transdominant suppressor function contributing to its oncogenic properties.


Pssm-ID: 409971 [Multi-domain]  Cd Length: 87  Bit Score: 79.51  E-value: 5.23e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 944208227 233 EDDQRANRTLFLGNLDIT------------------------------------FENLDMAHRAKLAMSGKVLLRNPIKI 276
Cdd:cd12555    1 EDDQRANRTLFLGNLDITvtendlrrafdrfgvitevdikrpgrgqtstygflkFENLDMAHRAKLAMSGKVIGRNPIKI 80

                 .
gi 944208227 277 G 277
Cdd:cd12555   81 G 81
RRM smart00360
RNA recognition motif;
26-93 8.43e-07

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 46.82  E-value: 8.43e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 944208227    26 LSDEAVEDGLFHEFKRFGDV-SVKISRlPPGTGAADeRVAFVNFRRPEDARAAKHARGRLVLYDRPLKI 93
Cdd:smart00360   7 LPPDTTEEELRELFSKFGKVeSVRLVR-DKETGKSK-GFAFVEFESEEDAEKALEALNGKELDGRPLKV 73
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
32-92 3.46e-04

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 characteriztic 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: 39.52  E-value: 3.46e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 944208227   32 EDGLFHEFKRFGDV-SVKISRlpPGTGAADeRVAFVNFRRPEDARAAKHARGRLVLYDRPLK 92
Cdd:pfam00076  12 EEDLKDLFSKFGPIkSIRLVR--DETGRSK-GFAFVEFEDEEDAEKAIEALNGKELGGRELK 70
RRM_3 pfam08777
RNA binding motif; This domain is found in protein La which functions as an RNA chaperone ...
261-311 6.37e-03

RNA binding motif; This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation. It contains a five stranded beta sheet which forms an atypical RNA recognition motif.


Pssm-ID: 400913 [Multi-domain]  Cd Length: 102  Bit Score: 36.96  E-value: 6.37e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 944208227  261 KLAMSGKVLLRNPIKIGeFDRFGTIRTIDYRKGDSWAYIQYESLDAAQAAC 311
Cdd:pfam08777   5 KFSGLGKPLSREDIKEA-FSQLGEVAYVDYLEGDKEGHVRFKTDEAAKKAI 54
 
Name Accession Description Interval E-value
SPOC_RBM15 cd21549
SPOC (Spen paralog and ortholog C-terminal) domain found in vertebrate RNA binding motif ...
599-766 2.91e-112

SPOC (Spen paralog and ortholog C-terminal) domain found in vertebrate RNA binding motif protein 15 (RBM15); RBM15, also called one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possesses mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RBM15 belongs to the Spen (split end) protein family, which contain three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. The model corresponds to the SPOC domain that is involved in developmental signaling and has also been proposed to be a phosphorylation binding module.


Pssm-ID: 439212  Cd Length: 164  Bit Score: 337.25  E-value: 2.91e-112
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 944208227 599 AWQGMLLLKNSNFPSNMHLLQGDLGVASSLLVEGATGGKVAQLKITQRLRLDQPKLDEVNRRIKVAGPNGYAILLAVPGA 678
Cdd:cd21549    1 AWQGMLLLKNSNFPSNMHLLEGDLSVASSLLVDGSTGGKVAQLKITQRLRLDQPKLDEVTRRIKVAGPNGYAVLLAVPGS 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 944208227 679 SDNRSaagaSEAATTSTQRPLRNLVSYLKQKQAAGVISLPVGGNKDKENSGVLHAFPPCDFSQQFLDSTAKALAKSEDDY 758
Cdd:cd21549   81 SEVSS----VSDQATSTQRPLRNLVSYLKQKQAAGVISLPVGGSKDKDNTGVLHAFPPCDFSQQFLDSSAKALAKSEEDY 156

                 ....*...
gi 944208227 759 LVMIIVRG 766
Cdd:cd21549  157 LVMIIVRG 164
SPOC_RBM15-like cd21544
SPOC (Spen paralog and ortholog C-terminal) domain found in RNA binding motif protein 15 ...
599-766 3.20e-76

SPOC (Spen paralog and ortholog C-terminal) domain found in RNA binding motif protein 15 (RBM15) and similar proteins; This subfamily includes RBM15, RBM15B, and similar proteins found in metazoans. RBM15, also called one-twenty two protein 1 (OTT1), is a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as a receptor for the RNA export element RTE. It also possesses mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also called one-twenty two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein that shares with RBM15, the association with the splicing factor compartment and the nuclear envelope, as well as the binding to mRNA export factors NXF1 and Aly/REF. Members of this family have a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC domain. This model corresponds to the SPOC domain that is involved in developmental signaling and has also been proposed to be a phosphorylation binding module.


Pssm-ID: 439207  Cd Length: 164  Bit Score: 243.34  E-value: 3.20e-76
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 944208227 599 AWQGMLLLKNSNFPSNMHLLQGDLGVASSLLVEGATGGKVaQLKITQRLRLDQPKLDEVNRRIKVAGPNGYAILLAVPGA 678
Cdd:cd21544    1 VWSGALVLKNSAFPVRMHLLRGDVQLADTLLPNPTSGEQP-VLRITQRLRLDPPKLDDVSRRISSAGSSGYCVLLAVPGS 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 944208227 679 SDNrsaagaSEAATTSTQRPLRNLVSYLKQKQAAGVISLPVGGNK-DKENSGVLHAFPPCDFSQQFLDSTAKAL--AKSE 755
Cdd:cd21544   80 GAN------SEADASTQQRPLRNLVSYLKQKEAAGVVSLPPNGSVgEKKVTGVLHAFPPCDFSQQLLRRLAPSLslESLK 153
                        170
                 ....*....|.
gi 944208227 756 DDYLVMIIVRG 766
Cdd:cd21544  154 DDHLVIVLVRG 164
SPOC_RBM15B cd21550
SPOC (Spen paralog and ortholog C-terminal) domain found in putative RNA binding motif protein ...
599-765 1.75e-70

SPOC (Spen paralog and ortholog C-terminal) domain found in putative RNA binding motif protein 15B (RBM15B); RBM15B, also called one-twenty two 3 (OTT3), is a paralog of RNA binding motif protein 15 (RBM15), which is also known as one-twenty two protein 1 (OTT1). Like RBM15, RBM15B has post-transcriptional regulatory activity. It is a nuclear protein that shares with RBM15, the association with the splicing factor compartment and the nuclear envelope, as well as the binding to mRNA export factors NXF1 and Aly/REF. RBM15B belongs to the Spen (split end) protein family, which contains a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC domain. This model corresponds to the SPOC domain that is involved in developmental signaling and has also been proposed to be a phosphorylation binding module.


Pssm-ID: 439213  Cd Length: 167  Bit Score: 228.20  E-value: 1.75e-70
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 944208227 599 AWQGMLLLKNSNFPSNMHLLQGDLGVASSLLVEGATGGKVAQLKITQRLRLDQPKLDEVNRRIKVAGPNGYAILLAVPgA 678
Cdd:cd21550    1 AWNGVLVLKNSCFPTNMHILEGDLGVVNILLKDYTSGGKLTQLKIAQRLRLDQPKLDEVTRRIKQGSPDGYAVLLATQ-A 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 944208227 679 SDNRSAAGASEAATTSTQRPLRNLVSYLKQKQAAGVISLPVGGNKDKENSGVLHAFPPCDFSQQFLDSTAKALAKSEDDY 758
Cdd:cd21550   80 PQGGEGGGAPPVEPGLQRRLLRNLVSYLKQKQAAGVISLPVGGSKDRDNTGMLYAFPPCDFSQQYLQSALRTLGKLEEEH 159

                 ....*..
gi 944208227 759 LVMIIVR 765
Cdd:cd21550  160 MVIVIVK 166
SPOC_Spen cd21539
SPOC (Spen paralog and ortholog C-terminal) domain found in the Spen (split end) protein ...
599-764 3.05e-47

SPOC (Spen paralog and ortholog C-terminal) domain found in the Spen (split end) protein family; The Spen protein family includes a group of proteins characterized by containing RNA recognition motifs (RRMs) and a SPOC domain, such as SMART/HDAC1-associated repressor protein (SHARP) and RNA binding motif protein 15 (RBM15)-like proteins from metazoans, as well as plant flowering time control protein FPA and yeast chromo domain-containing protein 1 (Chp1p). SHARP, also called Msx2-interacting protein (MINT), or Spen homolog, is an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs), and components of the NuRD complex. RBM15, also called one-twenty two protein 1 (OTT1), is a novel mRNA export factor and component of the NXF1 pathway. RNA-binding protein 15B (RBM15B), also called one-twenty two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. Chp1p is a component of the kinetochore which plays a role in stabilizing microtubules and thus, allowing accurate chromosome segregation. It has a role in the RNA interference (RNAi) pathway which is important for heterochromatin formation and accurate chromosome segregation. FPA plays a role in the regulation of flowering time in the autonomous flowering pathway by decreasing FLOWERING LOCUS C mRNA levels. It is required for RNA-mediated chromatin silencing of a range of loci in the genome. This model corresponds to the SPOC domain that is involved in developmental signaling and has also been proposed to be a phosphorylation binding module.


Pssm-ID: 439202  Cd Length: 148  Bit Score: 164.60  E-value: 3.05e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 944208227 599 AWQGMLLLKNSNFPSNMHLLQGDLGVASSllVEGATGGKVAQLKITQRLRLDQPKLDEvnrrIKVAGPNGYAILLAVPGA 678
Cdd:cd21539    1 IWRGVLLVKNSAFLFRCHLAKGDAEIASQ--QLLRETVSCPQVDIVQRMRLDELALFE----RSGAVATGLAILLALPCG 74
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 944208227 679 SDNRSAAgaseaatTSTQRPLRNLVSYLKQKQAAGVISLPVGgnkdkENSGVLHAFPPCDFSQQFLDSTAKALAKSEDDY 758
Cdd:cd21539   75 DDSISSA-------SITEAPLTNFVSYLKAKQAAGVVLLSDD-----HENYVLLLFPPSEFSLSLLKRSLNSEQATSDSY 142

                 ....*.
gi 944208227 759 LVMIIV 764
Cdd:cd21539  143 LVMVVV 148
RRM1_RBM15 cd12553
RNA recognition motif 1 (RRM1) found in vertebrate RNA binding motif protein 15 (RBM15); This ...
14-97 3.26e-46

RNA recognition motif 1 (RRM1) found in vertebrate RNA binding motif protein 15 (RBM15); This subgroup corresponds to the RRM1 of RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possesses mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RBM15 belongs to the Spen (split end) protein family, which contains three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. This family also includes a RBM15-MKL1 (OTT-MAL) fusion protein that RBM15 is N-terminally fused to megakaryoblastic leukemia 1 protein (MKL1) at the C-terminus in a translocation involving chromosome 1 and 22, resulting in acute megakaryoblastic leukemia. The fusion protein could interact with the mRNA export machinery. Although it maintains the specific transactivator function of MKL1, the fusion protein cannot activate RTE-mediated mRNA expression and has lost the post-transcriptional activator function of RBM15. However, it has transdominant suppressor function contributing to its oncogenic properties.


Pssm-ID: 409969 [Multi-domain]  Cd Length: 78  Bit Score: 158.96  E-value: 3.26e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 944208227  14 YKTLKISELGSALSDEAVEDGLFHEFKRFGDVSVKISRLppgtgaADERVAFVNFRRPEDARAAKHARGRLVLYDRPLKI 93
Cdd:cd12553    1 YKTLKISELGSQLSDEAVEDGLFHEFKKFGDVSVKISRL------GDERVAFVNFRRPEDARAAKHARGRLVLYDRPLKI 74

                 ....
gi 944208227  94 EAVY 97
Cdd:cd12553   75 EAVY 78
RRM1_RBM15B cd12554
RNA recognition motif 1 (RRM1) found in putative RNA binding motif protein 15B (RBM15B) from ...
14-97 9.05e-35

RNA recognition motif 1 (RRM1) found in putative RNA binding motif protein 15B (RBM15B) from vertebrate; This subfamily corresponds to the RRM1 of RBM15B, also termed one twenty-two 3 (OTT3), a paralog of RNA binding motif protein 15 (RBM15), also known as One-twenty two protein 1 (OTT1). Like RBM15, RBM15B has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. RBM15B belongs to the Spen (split end) protein family, which shares a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain.


Pssm-ID: 409970 [Multi-domain]  Cd Length: 80  Bit Score: 126.86  E-value: 9.05e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 944208227  14 YKTLKISELGSALSDEAVEDGLFHEFKRFGDVSVKISRLPPGTgaadeRVAFVNFRRPEDARAAKHARGRLVLYDRPLKI 93
Cdd:cd12554    2 YKTLLVSNLGSQLPDELLEDGLFHEFKKFGEVSVKLSHTPELG-----RVAYVNFRHPEDAKEARHAKGRLVLYDRPLKV 76

                 ....
gi 944208227  94 EAVY 97
Cdd:cd12554   77 EPVY 80
RRM3_RBM15 cd12557
RNA recognition motif 3 (RRM3) found in vertebrate RNA binding motif protein 15 (RBM15); This ...
278-332 1.86e-34

RNA recognition motif 3 (RRM3) found in vertebrate RNA binding motif protein 15 (RBM15); This subgroup corresponds to the RRM3 of RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, a novel mRNA export factor component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possesses mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RBM15 belongs to the Spen (split end) protein family, which contains three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralogue and ortholog C-terminal) domain. This family also includes a RBM15-MKL1 (OTT-MAL) fusion protein that RBM15 is N-terminally fused to megakaryoblastic leukemia 1 protein (MKL1) at the C-terminus in a translocation involving chromosome 1 and 22, resulting in acute megakaryoblastic leukemia. The fusion protein could interact with the mRNA export machinery. Although it maintains the specific transactivator function of MKL1, the fusion protein cannot activate RTE-mediated mRNA expression and has lost the post-transcriptional activator function of RBM15. However, it has transdominant suppressor function contributing to its oncogenic properties.


Pssm-ID: 409973 [Multi-domain]  Cd Length: 73  Bit Score: 125.82  E-value: 1.86e-34
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 944208227 278 EFDRFGTIRTIDYRKGDSWAYIQYESLDAAQAACTHMRGFPLGGPDRRLRVDFAD 332
Cdd:cd12557   19 EFDRFGTIRTIDYRKGDSWAYIQYESLDAAQAACTHMRGFPLGGPDRRLRVDFAD 73
RRM1_Spen cd12308
RNA recognition motif 1 (RRM1) found in the Spen (split end) protein family; This subfamily ...
14-97 7.09e-33

RNA recognition motif 1 (RRM1) found in the Spen (split end) protein family; This subfamily corresponds to the RRM1 domain in the Spen (split end) family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B), and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possesses mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also known as one twenty-two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. Members in this family belong- to the Spen (split end) protein family, which share a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain.


Pssm-ID: 409749 [Multi-domain]  Cd Length: 78  Bit Score: 121.19  E-value: 7.09e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 944208227  14 YKTLKISELGSALSDEAVEDGLFHEFKRFGDVSVKISrlppgtGAADERVAFVNFRRPEDARAAKHARGRLVLYDRPLKI 93
Cdd:cd12308    1 YKTLCVSNLPAKLSDEEIEDVLYHEFKKFGDVSVRLQ------HDGDERVAYVNFRHPEDAREAKHAKLRLVLFDRPLNV 74

                 ....
gi 944208227  94 EAVY 97
Cdd:cd12308   75 EPVY 78
SPOC_SHARP cd21543
SPOC (Spen paralog and ortholog C-terminal) domain found in SMART/HDAC1-associated repressor ...
600-764 7.02e-32

SPOC (Spen paralog and ortholog C-terminal) domain found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins; SHARP, also called Msx2-interacting protein (MINT), or Spen homolog, is an estrogen-inducible transcriptional repressor that interacts directly with transcriptional corepressors silencing mediator for retinoid and thyroid receptor (SMRT)/nuclear receptor corepressor (NCoR), histone deacetylases (HDACs), and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also called RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain that binds to SMRT/NcoR. This model corresponds to the SPOC domain that is involved in developmental signaling and has also been proposed to be a phosphorylation binding module.


Pssm-ID: 439206  Cd Length: 163  Bit Score: 121.55  E-value: 7.02e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 944208227 600 WQGMLLLKNSNFPSNMHLLQGDLGVASSLLVEGATGGKVAQLKITQRLRLDQPKLDEVNRRIKVagPNGYAILLAVPgas 679
Cdd:cd21543    6 WQGLLALKNDEAAVQMHYVSGNQDLAKRSLPRHLTNGNLPPLRIAQRMRLEPSQLEGVARKMQD--ESEYCLLLALP--- 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 944208227 680 dnrsaAGASEAATTSTQRPLRN-LVSYLKQKQAAGVISLPVGGNKDkeNSGVLHAFPPCDFSQQFLDSTAKALAKS--ED 756
Cdd:cd21543   81 -----CGRDQEDVLKQTNNLKNgFITYLQQKQAAGIVNVPNPGSQQ--PAYVVHIFPPCEFSNSHLSRLAPDLLNSiaDI 153

                 ....*...
gi 944208227 757 DYLVMIIV 764
Cdd:cd21543  154 PHLMIVIA 161
RRM3_Spen cd12310
RNA recognition motif 3 (RRM3) found in the Spen (split end) protein family; This subfamily ...
278-332 1.70e-28

RNA recognition motif 3 (RRM3) found in the Spen (split end) protein family; This subfamily corresponds to the RRM3 domain in the Spen (split end) protein family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B) and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and is a novel component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possess mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also termed one twenty-two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. Members in this family belong to the Spen (split end) protein family, which shares a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain.


Pssm-ID: 409750 [Multi-domain]  Cd Length: 72  Bit Score: 108.52  E-value: 1.70e-28
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 944208227 278 EFDRFGTIRTIDYRKGDSWAYIQYESLDAAQAACTHMRGFPLGGPDRRLRVDFAD 332
Cdd:cd12310   18 EFDRFGAIRKIDYRKGDDYAYILYESLDAAQAAVRALRGFPLGGPDRRLRVDFAD 72
RRM3_RBM15B cd12558
RNA recognition motif 3 (RRM3) found in putative RNA-binding protein 15B (RBM15B) from ...
278-331 1.06e-25

RNA recognition motif 3 (RRM3) found in putative RNA-binding protein 15B (RBM15B) from vertebrate; This subgroup corresponds to the RRM3 of RBM15B, also termed one twenty-two 3 (OTT3), a paralog of RNA binding motif protein 15 (RBM15), also known as One-twenty two protein 1 (OTT1). Like RBM15, RBM15B has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. RBM15B belongs to the Spen (split end) protein family, which shares a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain.


Pssm-ID: 409974 [Multi-domain]  Cd Length: 76  Bit Score: 100.86  E-value: 1.06e-25
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 944208227 278 EFDRFGTIRTIDYRKGDSWAYIQYESLDAAQAACTHMRGFPLGGPDRRLRVDFA 331
Cdd:cd12558   22 EFDRFGSIRTIDYVKGDSFAYIQYESLDAAQAACAQMRGFPLGGPDRRLRVDFA 75
SPOC pfam07744
SPOC domain; The SPOC (Spen paralogue and orthologue C-terminal) domain is involved in ...
593-765 5.00e-24

SPOC domain; The SPOC (Spen paralogue and orthologue C-terminal) domain is involved in developmental signalling.


Pssm-ID: 400205  Cd Length: 142  Bit Score: 98.58  E-value: 5.00e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 944208227  593 APKLCLAWQGMLLLKN-SNFPSNMHLLQGDLGVASSLLvegatggkvaqLKITQRLRLDQPK--LDEVNRRIkvagpngY 669
Cdd:pfam07744   2 LQDLEVIWQGTLAMKGvAEFSVRAHLVSGDIDSLLPSL-----------LRITGRIRLDAVWkyLDEVRRSI-------T 63
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 944208227  670 AILLAV---PGASDNRSAagaseaattstqrpLRNLVSYLKQKQAAGVISLPVGGNKDkensgvLHAFPPCDFSQQFLDS 746
Cdd:pfam07744  64 RDVLVVrffPSSESDESA--------------FDELIDYLQSKQRAGVIHAKSADVKD------LYLFPPCEFLELLLPV 123
                         170
                  ....*....|....*....
gi 944208227  747 TaKALAKSEDDYLVMIIVR 765
Cdd:pfam07744 124 G-LSLEVSEPNLLLGVVVR 141
RRM2_RBM15 cd12555
RNA recognition motif 2 (RRM2) found in vertebrate RNA binding motif protein 15 (RBM15); This ...
233-277 5.23e-18

RNA recognition motif 2 (RRM2) found in vertebrate RNA binding motif protein 15 (RBM15); This subgroup corresponds to the RRM2 of RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possesses mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RBM15 belongs to the Spen (split end) protein family, which contain three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. This family also includes a RBM15-MKL1 (OTT-MAL) fusion protein that RBM15 is N-terminally fused to megakaryoblastic leukemia 1 protein (MKL1) at the C-terminus in a translocation involving chromosome 1 and 22, resulting in acute megakaryoblastic leukemia. The fusion protein could interact with the mRNA export machinery. Although it maintains the specific transactivator function of MKL1, the fusion protein cannot activate RTE-mediated mRNA expression and has lost the post-transcriptional activator function of RBM15. However, it has transdominant suppressor function contributing to its oncogenic properties.


Pssm-ID: 409971 [Multi-domain]  Cd Length: 87  Bit Score: 79.51  E-value: 5.23e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 944208227 233 EDDQRANRTLFLGNLDIT------------------------------------FENLDMAHRAKLAMSGKVLLRNPIKI 276
Cdd:cd12555    1 EDDQRANRTLFLGNLDITvtendlrrafdrfgvitevdikrpgrgqtstygflkFENLDMAHRAKLAMSGKVIGRNPIKI 80

                 .
gi 944208227 277 G 277
Cdd:cd12555   81 G 81
RRM2_Spen cd12309
RNA recognition motif 2 (RRM2) found in the Spen (split end) protein family; This subfamily ...
238-277 5.19e-13

RNA recognition motif 2 (RRM2) found in the Spen (split end) protein family; This subfamily corresponds to the RRM2 domain in the Spen (split end) protein family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B), and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possess mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also termed one twenty-two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. Members in this family belong to the Spen (split end) protein family, which share a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain.


Pssm-ID: 240755 [Multi-domain]  Cd Length: 79  Bit Score: 64.73  E-value: 5.19e-13
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 944208227 238 ANRTLFLGNLDIT------------------------------------FENLDMAHRAKLAMSGKVLLRNPIKIG 277
Cdd:cd12309    1 ATRTLFVGNLEITiteeelrraferygvvedvdikrpprgqgnayafvkFLNLDMAHRAKVAMSGQYIGRNQIKIG 76
RRM2_RBM15B cd12556
RNA recognition motif 2 (RRM2) found in putative RNA binding motif protein 15B (RBM15B) from ...
232-277 1.90e-12

RNA recognition motif 2 (RRM2) found in putative RNA binding motif protein 15B (RBM15B) from vertebrate; This subgroup corresponds to the RRM2 of RBM15B, also termed one twenty-two 3 (OTT3), a paralog of RNA binding motif protein 15 (RBM15), also known as One-twenty two protein 1 (OTT1). Like RBM15, RBM15B has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. RBM15B belongs to the Spen (split end) protein family, which shares a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain.


Pssm-ID: 409972 [Multi-domain]  Cd Length: 85  Bit Score: 63.40  E-value: 1.90e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 944208227 232 PEDDQRANRTLFLGNLD------------------------------------ITFENLDMAHRAKLAMSGKVLLRNPIK 275
Cdd:cd12556    1 PEDDQRATRNLFIGNLDhnvsevelrrafekygiieevvikrpargqggayafLKFQNLDMAHRAKVAMSGRVIGRNPIK 80

                 ..
gi 944208227 276 IG 277
Cdd:cd12556   81 IG 82
RRM2_SHARP cd12349
RNA recognition motif 2 (RRM2) found in SMART/HDAC1-associated repressor protein (SHARP) and ...
17-77 4.02e-11

RNA recognition motif 2 (RRM2) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins; This subfamily corresponds to the RRM2 of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins.


Pssm-ID: 409785 [Multi-domain]  Cd Length: 74  Bit Score: 59.34  E-value: 4.02e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 944208227  17 LKISELGSALSDEAVEDGLFHEFKRFGDV-SVKIsrlppgTGAADERVAFVNFRRPEDARAA 77
Cdd:cd12349    2 IKVRNLPVRSSDTSLKDGLFHEFKKHGKVtSVKV------HGQGEERYAIVFFRRPEDAEKA 57
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
26-94 4.34e-08

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: 50.74  E-value: 4.34e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 944208227  26 LSDEAVEDGLFHEFKRFGDV-SVKISRLPPGtgaADERVAFVNFRRPEDARAAKHARGRLVLYDRPLKIE 94
Cdd:cd00590    6 LPPDTTEEDLRELFSKFGEVvSVRIVRDRDG---KSKGFAFVEFESPEDAEKALEALNGTELGGRPLKVS 72
SPOC_SF cd21520
SPOC (Spen paralog and ortholog C-terminal) domain superfamily; The SPOC domain is involved in ...
600-755 4.96e-07

SPOC (Spen paralog and ortholog C-terminal) domain superfamily; The SPOC domain is involved in developmental signalling and has also been proposed to be a phosphorylation binding module. It has been found mainly in two protein families: transcription factor S-II (TFIIS) and Spen (split end). The TFIIS family includes SPOC domain-containing protein 1 (SPOCD1), yeast bypass of ESS1 protein 1 (Bye1p), PHD finger protein 3 (PHF3), and death-inducer obliterator (Dido) splicing variants, among others. They are characterized by having both a central RNA polymerase II (Pol II)-binding TFIIS-like domain (TLD) domain, and a C-terminal SPOC domain. The Spen protein family includes SMART/HDAC1-associated repressor protein (SHARP) and RNA binding motif protein 15 (RBM15)-like proteins from metazoans, as well as plant flowering time control protein FPA and yeast chromo domain-containing protein 1 (Chp1p). They are characterized by containing RNA recognition motifs (RRMs) and a SPOC domain.


Pssm-ID: 439200  Cd Length: 138  Bit Score: 49.59  E-value: 4.96e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 944208227 600 WQGMLLLKNSN-FPSNMHLLQGDLGVASSLLVEgatggkvaQLKITQRLRLDQPKLDEVNRRIKVAgpNGYAILLAVPGA 678
Cdd:cd21520    2 WQGLLALKNDPtAAARLHFVSGNNVLALSELPP--------VLRIAQRMRLNATQLEGVARRMAVA--TDYCLVLALPCG 71
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 944208227 679 SDNRSAAgaseaattstqrplRNLVSYLKQKQAAGVISLpvggnkdkENSGVLHAFPPCDFSQQFLDSTAKALAKSE 755
Cdd:cd21520   72 RDDESLK--------------AAFITYLQAKQRAGIASN--------QPAYVLQLFPPCEFSESHLSRLAPDLLASI 126
RRM smart00360
RNA recognition motif;
26-93 8.43e-07

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 46.82  E-value: 8.43e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 944208227    26 LSDEAVEDGLFHEFKRFGDV-SVKISRlPPGTGAADeRVAFVNFRRPEDARAAKHARGRLVLYDRPLKI 93
Cdd:smart00360   7 LPPDTTEEELRELFSKFGKVeSVRLVR-DKETGKSK-GFAFVEFESEEDAEKALEALNGKELDGRPLKV 73
RRM_RDM1 cd12364
RNA recognition motif (RRM) found in RAD52 motif-containing protein 1 (RDM1) and similar ...
15-93 1.13e-06

RNA recognition motif (RRM) found in RAD52 motif-containing protein 1 (RDM1) and similar proteins; This subfamily corresponds to the RRM of RDM1, also termed RAD52 homolog B, a novel factor involved in the cellular response to the anti-cancer drug cisplatin in vertebrates. RDM1 contains a small RD motif that shares with the recombination and repair protein RAD52, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The RD motif is responsible for the acidic pH-dependent DNA-binding properties of RDM1. It interacts with ss- and dsDNA, and may act as a DNA-damage recognition factor by recognizing the distortions of the double helix caused by cisplatin-DNA adducts in vitro. In addition, due to the presence of RRM, RDM1 can bind to RNA as well as DNA.


Pssm-ID: 409799 [Multi-domain]  Cd Length: 81  Bit Score: 46.98  E-value: 1.13e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 944208227  15 KTLKISELGSALSDEAVEDGLFHEFKRFGDV-SVKIsrLPPGTGAADERVAFVNFRRPEDARAAKHA-RGRLVLYDRPLK 92
Cdd:cd12364    1 KTLFVWNISPKLTEEEIYESLCKAFSAFGLLySVRV--FPNAAVATPGFYAFVKFYSARDASRAQKAlNGKWLFQGSPLK 78

                 .
gi 944208227  93 I 93
Cdd:cd12364   79 V 79
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
279-329 4.69e-06

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: 44.97  E-value: 4.69e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 944208227 279 FDRFGTIRTIDYRKGDS-----WAYIQYESLDAAQAACTHMRGFPLGGpdRRLRVD 329
Cdd:cd00590   19 FSKFGEVVSVRIVRDRDgkskgFAFVEFESPEDAEKALEALNGTELGG--RPLKVS 72
RRM4_SHARP cd12351
RNA recognition motif 4 (RRM4) found in SMART/HDAC1-associated repressor protein (SHARP) and ...
279-330 2.16e-05

RNA recognition motif 4 (RRM4) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins; This subfamily corresponds to the RRM of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, is an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins.


Pssm-ID: 409787 [Multi-domain]  Cd Length: 77  Bit Score: 43.13  E-value: 2.16e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 944208227 279 FDRFGTIR--TIDYRKGDswAYIQYESLDAAQAACTHMRGFPLGGpdRRLRVDF 330
Cdd:cd12351   28 FCRYGPVVkvVIDRQKGM--ALVLYDEVECAQAAVKETKGRKIGG--RKIQVDF 77
RRM3_SHARP cd12350
RNA recognition motif 3 (RRM3) found in SMART/HDAC1-associated repressor protein (SHARP) and ...
238-321 4.31e-05

RNA recognition motif 3 (RRM3) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins; This subfamily corresponds to the RRM3 of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins.


Pssm-ID: 409786 [Multi-domain]  Cd Length: 74  Bit Score: 42.40  E-value: 4.31e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 944208227 238 ANRTLFLGNLDITFENLDmahraklamsgkvlLRNpikigEFDRFGTIRTIDYRK---GDSWAYIQYESLDAAQAACTHM 314
Cdd:cd12350    1 ATRTLFIGNLEKTTTYGD--------------LRN-----IFERFGEIIDIDIKKqngNPQYAFLQYCDIASVVKAIKKM 61

                 ....*..
gi 944208227 315 RGFPLGG 321
Cdd:cd12350   62 DGEYLGN 68
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
32-92 3.46e-04

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 characteriztic 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: 39.52  E-value: 3.46e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 944208227   32 EDGLFHEFKRFGDV-SVKISRlpPGTGAADeRVAFVNFRRPEDARAAKHARGRLVLYDRPLK 92
Cdd:pfam00076  12 EEDLKDLFSKFGPIkSIRLVR--DETGRSK-GFAFVEFEDEEDAEKAIEALNGKELGGRELK 70
RRM1_PUF60 cd12370
RNA recognition motif 1 (RRM1) found in (U)-binding-splicing factor PUF60 and similar proteins; ...
279-328 1.84e-03

RNA recognition motif 1 (RRM1) found in (U)-binding-splicing factor PUF60 and similar proteins; This subfamily corresponds to the RRM1 of PUF60, also termed FUSE-binding protein-interacting repressor (FBP-interacting repressor or FIR), or Ro-binding protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1). PUF60 is an essential splicing factor that functions as a poly-U RNA-binding protein required to reconstitute splicing in depleted nuclear extracts. Its function is enhanced through interaction with U2 auxiliary factor U2AF65. PUF60 also controls human c-myc gene expression by binding and inhibiting the transcription factor far upstream sequence element (FUSE)-binding-protein (FBP), an activator of c-myc promoters. PUF60 contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors another RRM and binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) in several nuclear proteins. Research indicates that PUF60 binds FUSE as a dimer, and only the first two RRM domains participate in the single-stranded DNA recognition.


Pssm-ID: 409805 [Multi-domain]  Cd Length: 76  Bit Score: 37.78  E-value: 1.84e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 944208227 279 FDRFGTIRTIDY------RKGDSWAYIQYESLDAAQAACTHMRGFPLGGpdRRLRV 328
Cdd:cd12370   21 FAPFGPIKSIDMswdpvtMKHKGFAFVEYEVPEAAQLALEQMNGVMLGG--RNIKV 74
RRM1_RIM4_like cd12453
RNA recognition motif 1 (RRM1) found in yeast meiotic activator RIM4 and similar proteins; ...
19-98 2.19e-03

RNA recognition motif 1 (RRM1) found in yeast meiotic activator RIM4 and similar proteins; This subfamily corresponds to the RRM1 of RIM4, also termed regulator of IME2 protein 4, a putative RNA binding protein that is expressed at elevated levels early in meiosis. It functions as a meiotic activator required for both the IME1- and IME2-dependent pathways of meiotic gene expression, as well as early events of meiosis, such as meiotic division and recombination, in Saccharomyces cerevisiae. RIM4 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes a putative RNA-binding protein termed multicopy suppressor of sporulation protein Msa1. It is a putative RNA-binding protein encoded by a novel gene, msa1, from the fission yeast Schizosaccharomyces pombe. Msa1 may be involved in the inhibition of sexual differentiation by controlling the expression of Ste11-regulated genes, possibly through the pheromone-signaling pathway. Like RIM4, Msa1 also contains two RRMs, both of which are essential for the function of Msa1.


Pssm-ID: 409887 [Multi-domain]  Cd Length: 86  Bit Score: 37.77  E-value: 2.19e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 944208227  19 ISELGSALSDEAVEDGLFHEFKRFGDV-SVKISRLPpgtgaADERVAFVNFRRPEDA-RAAKHARGRLVLyDRPLKIEAV 96
Cdd:cd12453    7 VASLSSARSDEELCAAVTNHFSKWGELlNVKVLKDW-----SNRPYAFVQYTNTEDAkNALVNGHNTLLD-GRHLRVEKA 80

                 ..
gi 944208227  97 YV 98
Cdd:cd12453   81 KV 82
RRM_PPIL4 cd12235
RNA recognition motif (RRM) found in peptidyl-prolyl cis-trans isomerase-like 4 (PPIase) and ...
272-330 2.48e-03

RNA recognition motif (RRM) found in peptidyl-prolyl cis-trans isomerase-like 4 (PPIase) and similar proteins; This subfamily corresponds to the RRM of PPIase, also termed cyclophilin-like protein PPIL4, or rotamase PPIL4, a novel nuclear RNA-binding protein encoded by cyclophilin-like PPIL4 gene. The precise role of PPIase remains unclear. PPIase contains a conserved N-terminal peptidyl-prolyl cistrans isomerase (PPIase) motif, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a lysine rich domain, and a pair of bipartite nuclear targeting sequences (NLS) at the C-terminus.


Pssm-ID: 409681 [Multi-domain]  Cd Length: 83  Bit Score: 37.64  E-value: 2.48e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 944208227 272 NPIKIGE-----FDRFGTIRTI----DYRKGDS--WAYIQYESLDAAQAACTHMRGFPLGgpDRRLRVDF 330
Cdd:cd12235   12 NPVTTDEdleiiFSRFGKIKSCevirDKKTGDSlqYAFIEFETKESCEEAYFKMDNVLID--DRRIHVDF 79
RRM_3 pfam08777
RNA binding motif; This domain is found in protein La which functions as an RNA chaperone ...
261-311 6.37e-03

RNA binding motif; This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation. It contains a five stranded beta sheet which forms an atypical RNA recognition motif.


Pssm-ID: 400913 [Multi-domain]  Cd Length: 102  Bit Score: 36.96  E-value: 6.37e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 944208227  261 KLAMSGKVLLRNPIKIGeFDRFGTIRTIDYRKGDSWAYIQYESLDAAQAAC 311
Cdd:pfam08777   5 KFSGLGKPLSREDIKEA-FSQLGEVAYVDYLEGDKEGHVRFKTDEAAKKAI 54
RRM_ACINU cd12432
RNA recognition motif (RRM) found in apoptotic chromatin condensation inducer in the nucleus ...
295-334 7.15e-03

RNA recognition motif (RRM) found in apoptotic chromatin condensation inducer in the nucleus (acinus) and similar proteins; This subfamily corresponds to the RRM of Acinus, a caspase-3-activated nuclear factor that induces apoptotic chromatin condensation after cleavage by caspase-3 without inducing DNA fragmentation. It is essential for apoptotic chromatin condensation and may also participate in nuclear structural changes occurring in normal cells. Acinus contains a P-loop motif and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which indicates Acinus might have ATPase and DNA/RNA-binding activity.


Pssm-ID: 409866 [Multi-domain]  Cd Length: 90  Bit Score: 36.41  E-value: 7.15e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 944208227 295 SWAYIQYESLDAAQAACTHMRG--FPLGGPdRRLRVDFADTE 334
Cdd:cd12432   40 SHCYVTYSSEEEAVATREALHGvvWPSSNG-KRLKVEFVTEE 80
RRM_SF3B14 cd12241
RNA recognition motif (RRM) found in pre-mRNA branch site protein p14 (SF3B14) and similar ...
239-321 8.60e-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: 35.68  E-value: 8.60e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 944208227 239 NRTLFLGNL--DITFENL-DMahraklamsgkvllrnpikigeFDRFGTIRTIdyRKGDS-----WAYIQYESLDAAQAA 310
Cdd:cd12241    2 NRILYVRNLpyKISSEELyDL----------------------FGKYGAIRQI--RIGNTketrgTAFVVYEDIFDAKNA 57
                         90
                 ....*....|.
gi 944208227 311 CTHMRGFPLGG 321
Cdd:cd12241   58 CDHLSGFNVCN 68
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
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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