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Conserved domains on  [gi|12654891|gb|AAH01289|]
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Sjogren syndrome antigen B (autoantigen La) [Homo sapiens]

Protein Classification

LARP_3 and RRM2_La domain-containing protein( domain architecture ID 10168941)

protein containing domains LARP_3, RRM1_La, and RRM2_La

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
LARP_3 cd08028
La RNA-binding domain of La-related protein 3; This domain is found at the N-terminus of the ...
 10-91 3.42e-44

La RNA-binding domain of La-related protein 3; This domain is found at the N-terminus of the La autoantigen and similar proteins, and co-occurs with an RNA-recognition motif (RRM). Together these domains function to bind primary transcripts of RNA polymerase III at their 3' terminus and protect them from exonucleolytic degradation. Binding is specific for the 3'-terminal UUU-OH motif. The La autoantigen is also called Lupus La protein, LARP3, or Sjoegren syndrome type B antigen (SS-B).


:

Pssm-ID: 153397  Cd Length: 82  Bit Score: 148.22  E-value: 3.42e-44
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 12654891  10 MAALEAKICHQIEYYFGDFNLPRDKFLKEQIKLDEGWVPLEIMIKFNRLNRLTTDFNVIVEALSKSKAELMEISEDKTKI 89
Cdd:cd08028   1 MDDLEKKIIRQIEYYFGDFNLPRDKFLKEQIKEDDGWVPMEVMLKFNRLKSLSSDPEVIAKALKKSKSGLIEVSEDKTKI 80


                ..
gi 12654891  90 RR 91
Cdd:cd08028  81 RR 82
RRM_3 pfam08777
RNA binding motif; This domain is found in protein La which functions as an RNA chaperone ...
 231-334 2.16e-30

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: 112.46  E-value: 2.16e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 12654891   231 GCLLKFSGdLDDQTCREDLHILFSNHGEIKWIDFVRGAKEGIILFK--EKAKEALGKAKDANNgnlQLRNKEVTWEVLEG 308
Cdd:pfam08777   1 GVILKFSG-LGKPLSREDIKEAFSQLGEVAYVDYLEGDKEGHVRFKtdEAAKKAIEKATEAKT---IIKDAEVTAELLEG 76

                          90       100
                  ....*....|....*....|....*.
gi 12654891   309 EVEKEALKKIIEDQQESLNKWKSKGR 334
Cdd:pfam08777  77 EEEKEYWKKIIEDQQAKLNNPRNKGR 102
RRM1_La cd12291
RNA recognition motif 1 in La autoantigen (La or LARP3) and similar proteins; This subfamily ...
 112-183 5.27e-29

RNA recognition motif 1 in La autoantigen (La or LARP3) and similar proteins; This subfamily corresponds to the RRM1 of La autoantigen, also termed Lupus La protein, or La ribonucleoprotein, or Sjoegren syndrome type B antigen (SS-B), a highly abundant nuclear phosphoprotein and well conserved in eukaryotes. It specifically binds the 3'-terminal UUU-OH motif of nascent RNA polymerase III transcripts and protects them from exonucleolytic degradation by 3' exonucleases. In addition, La can directly facilitate the translation and/or metabolism of many UUU-3' OH-lacking cellular and viral mRNAs, through binding internal RNA sequences within the untranslated regions of target mRNAs. La contains an N-terminal La motif (LAM), followed by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It also possesses a short basic motif (SBM) and a nuclear localization signal (NLS) at the C-terminus.


:

Pssm-ID: 409733 [Multi-domain]  Cd Length: 73  Bit Score: 107.68  E-value: 5.27e-29
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 12654891 112 SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLIL 183
Cdd:cd12291   1 TVYVKGFPLDATLDDIQEFFEKKGKVENVRMRRDLDsKEFKGSVFVEFKTEEEAKKFLEKEKLKYKGKELTIM 73
 
Name Accession Description Interval E-value
LARP_3 cd08028
La RNA-binding domain of La-related protein 3; This domain is found at the N-terminus of the ...
 10-91 3.42e-44

La RNA-binding domain of La-related protein 3; This domain is found at the N-terminus of the La autoantigen and similar proteins, and co-occurs with an RNA-recognition motif (RRM). Together these domains function to bind primary transcripts of RNA polymerase III at their 3' terminus and protect them from exonucleolytic degradation. Binding is specific for the 3'-terminal UUU-OH motif. The La autoantigen is also called Lupus La protein, LARP3, or Sjoegren syndrome type B antigen (SS-B).


Pssm-ID: 153397  Cd Length: 82  Bit Score: 148.22  E-value: 3.42e-44
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 12654891  10 MAALEAKICHQIEYYFGDFNLPRDKFLKEQIKLDEGWVPLEIMIKFNRLNRLTTDFNVIVEALSKSKAELMEISEDKTKI 89
Cdd:cd08028   1 MDDLEKKIIRQIEYYFGDFNLPRDKFLKEQIKEDDGWVPMEVMLKFNRLKSLSSDPEVIAKALKKSKSGLIEVSEDKTKI 80


                ..
gi 12654891  90 RR 91
Cdd:cd08028  81 RR 82
LA smart00715
Domain in the RNA-binding Lupus La protein; unknown function;
13-92 1.30e-31

Domain in the RNA-binding Lupus La protein; unknown function;


Pssm-ID: 128955 [Multi-domain]  Cd Length: 80  Bit Score: 115.02  E-value: 1.30e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 12654891     13 LEAKICHQIEYYFGDFNLPRDKFLKEQIKLDEGWVPLEIMIKFNRLNRLTTDFNVIVEALSKSkaELMEISEDKTKIRRS 92
Cdd:smart00715   3 LKQKIKKQVEYYFSDENLPRDKFLRKKMDKNDGYVPISTIASFKRVKSLTTDVNLIVEALRSS--PKLEVSEDGLKVRRR 80
RRM_3 pfam08777
RNA binding motif; This domain is found in protein La which functions as an RNA chaperone ...
 231-334 2.16e-30

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: 112.46  E-value: 2.16e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 12654891   231 GCLLKFSGdLDDQTCREDLHILFSNHGEIKWIDFVRGAKEGIILFK--EKAKEALGKAKDANNgnlQLRNKEVTWEVLEG 308
Cdd:pfam08777   1 GVILKFSG-LGKPLSREDIKEAFSQLGEVAYVDYLEGDKEGHVRFKtdEAAKKAIEKATEAKT---IIKDAEVTAELLEG 76

                          90       100
                  ....*....|....*....|....*.
gi 12654891   309 EVEKEALKKIIEDQQESLNKWKSKGR 334
Cdd:pfam08777  77 EEEKEYWKKIIEDQQAKLNNPRNKGR 102
RRM1_La cd12291
RNA recognition motif 1 in La autoantigen (La or LARP3) and similar proteins; This subfamily ...
 112-183 5.27e-29

RNA recognition motif 1 in La autoantigen (La or LARP3) and similar proteins; This subfamily corresponds to the RRM1 of La autoantigen, also termed Lupus La protein, or La ribonucleoprotein, or Sjoegren syndrome type B antigen (SS-B), a highly abundant nuclear phosphoprotein and well conserved in eukaryotes. It specifically binds the 3'-terminal UUU-OH motif of nascent RNA polymerase III transcripts and protects them from exonucleolytic degradation by 3' exonucleases. In addition, La can directly facilitate the translation and/or metabolism of many UUU-3' OH-lacking cellular and viral mRNAs, through binding internal RNA sequences within the untranslated regions of target mRNAs. La contains an N-terminal La motif (LAM), followed by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It also possesses a short basic motif (SBM) and a nuclear localization signal (NLS) at the C-terminus.


Pssm-ID: 409733 [Multi-domain]  Cd Length: 73  Bit Score: 107.68  E-value: 5.27e-29
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 12654891 112 SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLIL 183
Cdd:cd12291   1 TVYVKGFPLDATLDDIQEFFEKKGKVENVRMRRDLDsKEFKGSVFVEFKTEEEAKKFLEKEKLKYKGKELTIM 73
RRM2_La cd12541
RNA recognition motif 2 in La autoantigen (La or LARP3) and similar proteins; This subgroup ...
 231-307 3.35e-27

RNA recognition motif 2 in La autoantigen (La or LARP3) and similar proteins; This subgroup corresponds to the RRM2 of La autoantigen, also termed Lupus La protein, or La ribonucleoprotein, or Sjoegren syndrome type B antigen (SS-B), a highly abundant nuclear phosphoprotein and well conserved in eukaryotes. It specifically binds the 3'-terminal UUU-OH motif of nascent RNA polymerase III transcripts and protects them from exonucleolytic degradation by 3' exonucleases. In addition, La can directly facilitate the translation and/or metabolism of many UUU-3' OH-lacking cellular and viral mRNAs, through binding internal RNA sequences within the untranslated regions of target mRNAs. La contains an N-terminal La motif (LAM), followed by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In addition, it possesses a short basic motif (SBM) and a nuclear localization signal (NLS) at the C-terminus.


Pssm-ID: 409957 [Multi-domain]  Cd Length: 77  Bit Score: 103.12  E-value: 3.35e-27
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 12654891 231 GCLLKFSGDLDdQTCREDLHILFSNHGEIKWIDFVRGAKEGIILFKE--KAKEALGKAKDANNGnLQLRNKEVTWEVLE 307
Cdd:cd12541   1 GCILHFSGVGE-QTSREDLKEAFEKHGEVAWIDFARGQTEGYVRFKEedAAKEALEKAKEAKNG-LKIRGKEVTVKLLE 77
La pfam05383
La domain; This presumed domain is found at the N-terminus of La RNA-binding proteins as well ...
 17-74 1.07e-23

La domain; This presumed domain is found at the N-terminus of La RNA-binding proteins as well as other proteins. The function of this region is uncertain.


Pssm-ID: 461635  Cd Length: 59  Bit Score: 92.87  E-value: 1.07e-23
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 12654891    17 ICHQIEYYFGDFNLPRDKFLKEQIKLD-EGWVPLEIMIKFNRLNRLTTDFNVIVEALSK 74
Cdd:pfam05383   1 IKKQVEYYFSDENLPKDKFLRKQMDKDpDGYVPISVIASFKRMKKLTTDIDLIAEALRE 59
LHP1 COG5193
La protein, small RNA-binding pol III transcript stabilizing protein and related ...
 20-285 3.85e-11

La protein, small RNA-binding pol III transcript stabilizing protein and related La-motif-containing proteins involved in translation [Posttranslational modification, protein turnover, chaperones / Translation, ribosomal structure and biogenesis];


Pssm-ID: 227520 [Multi-domain]  Cd Length: 438  Bit Score: 64.30  E-value: 3.85e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 12654891  20 QIEYYFG-----DFNLPRDKFLKEQ---IKLDEGWVPLEIMIKFNRLNRLTTDFNVIVEALSKSK-AELMEISEDKTKIR 90
Cdd:COG5193  78 QVEFYFSgskdtDSNFPKDKFLKTTapkNKKRDKWVPIKTIATFNRMKNSGSPVSAVSGALRKSLdARVLEVSSSGSNKN 157

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 12654891  91 RspSKPLPEVTDEyKNDVKNRSVYIKGFPTDATLD--------DIKEWLEDKGQ--VLNIQMRRTLH-KAFKGSIFVVFD 159
Cdd:COG5193 158 R--TEKLISNNNK-STSQMQRDVYQNGFGKEDVNNasrpeqqeDLEIQFPPHYHapPSQIRNRRDWLnKNFRGSVFVEFK 234

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 12654891 160 SIESAKKF--------------VETPGQKYKETDLLILFKDD----YFAKKNEerkqnkveaklrAKQEQEAKQKLEEDA 221
Cdd:COG5193 235 YFREAQRFnngfyrnkkypndpETVYYYSVEPILLSIMAKKEqieyYFSEENL------------KSDEFLRKKFKKAGF 302

                       250       260       270       280       290       300
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 12654891 222 EMKSLEEKIGCLLKFSGD--LDDQTCREDLHILFSNHGEIkwidfVRGAKEGIILFKEKAKEALGK 285
Cdd:COG5193 303 IPLSFIGKFYRNLSFGGDknLILAAMKEVVQNKATNHLEI-----ALGSIEDAQKNEAKDFSPGKK 363
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 113-181 4.50e-11

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: 58.01  E-value: 4.50e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 12654891   113 VYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVET-PGQKYKETDLL 181
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFGPIKSIRLVRDETGRSKGFAFVEFEDEEDAEKAIEAlNGKELGGRELK 70
RRM smart00360
RNA recognition motif;
112-169 3.38e-08

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 50.28  E-value: 3.38e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 12654891    112 SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRR-TLHKAFKGSIFVVFDSIESAKKFVE 169
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRdKETGKSKGFAFVEFESEEDAEKALE 59
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
 103-283 9.57e-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: 47.49  E-value: 9.57e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 12654891   103 EYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPGQkyKETDLLI 182
Cdd:TIGR01628 171 EAAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMNG--KKIGLAK 248

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 12654891   183 LFKDDYF--AKKNEERkqnkvEAKLRAKQEQEaKQKLEEDAEMKSLEEKigcllkfsgDLDDQTCREDLHILFSNHGEIK 260
Cdd:TIGR01628 249 EGKKLYVgrAQKRAER-----EAELRRKFEEL-QQERKMKAQGVNLYVK---------NLDDTVTDEKLRELFSECGEIT 313

                         170       180       190
                  ....*....|....*....|....*....|
gi 12654891   261 WIDFVRGAKE-----GIILFK--EKAKEAL 283
Cdd:TIGR01628 314 SAKVMLDEKGvsrgfGFVCFSnpEEANRAV 343
 
Name Accession Description Interval E-value
LARP_3 cd08028
La RNA-binding domain of La-related protein 3; This domain is found at the N-terminus of the ...
 10-91 3.42e-44

La RNA-binding domain of La-related protein 3; This domain is found at the N-terminus of the La autoantigen and similar proteins, and co-occurs with an RNA-recognition motif (RRM). Together these domains function to bind primary transcripts of RNA polymerase III at their 3' terminus and protect them from exonucleolytic degradation. Binding is specific for the 3'-terminal UUU-OH motif. The La autoantigen is also called Lupus La protein, LARP3, or Sjoegren syndrome type B antigen (SS-B).


Pssm-ID: 153397  Cd Length: 82  Bit Score: 148.22  E-value: 3.42e-44
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 12654891  10 MAALEAKICHQIEYYFGDFNLPRDKFLKEQIKLDEGWVPLEIMIKFNRLNRLTTDFNVIVEALSKSKAELMEISEDKTKI 89
Cdd:cd08028   1 MDDLEKKIIRQIEYYFGDFNLPRDKFLKEQIKEDDGWVPMEVMLKFNRLKSLSSDPEVIAKALKKSKSGLIEVSEDKTKI 80


                ..
gi 12654891  90 RR 91
Cdd:cd08028  81 RR 82
LA smart00715
Domain in the RNA-binding Lupus La protein; unknown function;
13-92 1.30e-31

Domain in the RNA-binding Lupus La protein; unknown function;


Pssm-ID: 128955 [Multi-domain]  Cd Length: 80  Bit Score: 115.02  E-value: 1.30e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 12654891     13 LEAKICHQIEYYFGDFNLPRDKFLKEQIKLDEGWVPLEIMIKFNRLNRLTTDFNVIVEALSKSkaELMEISEDKTKIRRS 92
Cdd:smart00715   3 LKQKIKKQVEYYFSDENLPRDKFLRKKMDKNDGYVPISTIASFKRVKSLTTDVNLIVEALRSS--PKLEVSEDGLKVRRR 80
RRM_3 pfam08777
RNA binding motif; This domain is found in protein La which functions as an RNA chaperone ...
 231-334 2.16e-30

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: 112.46  E-value: 2.16e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 12654891   231 GCLLKFSGdLDDQTCREDLHILFSNHGEIKWIDFVRGAKEGIILFK--EKAKEALGKAKDANNgnlQLRNKEVTWEVLEG 308
Cdd:pfam08777   1 GVILKFSG-LGKPLSREDIKEAFSQLGEVAYVDYLEGDKEGHVRFKtdEAAKKAIEKATEAKT---IIKDAEVTAELLEG 76

                          90       100
                  ....*....|....*....|....*.
gi 12654891   309 EVEKEALKKIIEDQQESLNKWKSKGR 334
Cdd:pfam08777  77 EEEKEYWKKIIEDQQAKLNNPRNKGR 102
RRM1_La cd12291
RNA recognition motif 1 in La autoantigen (La or LARP3) and similar proteins; This subfamily ...
 112-183 5.27e-29

RNA recognition motif 1 in La autoantigen (La or LARP3) and similar proteins; This subfamily corresponds to the RRM1 of La autoantigen, also termed Lupus La protein, or La ribonucleoprotein, or Sjoegren syndrome type B antigen (SS-B), a highly abundant nuclear phosphoprotein and well conserved in eukaryotes. It specifically binds the 3'-terminal UUU-OH motif of nascent RNA polymerase III transcripts and protects them from exonucleolytic degradation by 3' exonucleases. In addition, La can directly facilitate the translation and/or metabolism of many UUU-3' OH-lacking cellular and viral mRNAs, through binding internal RNA sequences within the untranslated regions of target mRNAs. La contains an N-terminal La motif (LAM), followed by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It also possesses a short basic motif (SBM) and a nuclear localization signal (NLS) at the C-terminus.


Pssm-ID: 409733 [Multi-domain]  Cd Length: 73  Bit Score: 107.68  E-value: 5.27e-29
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 12654891 112 SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLIL 183
Cdd:cd12291   1 TVYVKGFPLDATLDDIQEFFEKKGKVENVRMRRDLDsKEFKGSVFVEFKTEEEAKKFLEKEKLKYKGKELTIM 73
LAM cd07323
LA motif RNA-binding domain; This domain is found at the N-terminus of La RNA-binding proteins ...
 15-91 8.94e-28

LA motif RNA-binding domain; This domain is found at the N-terminus of La RNA-binding proteins as well as in other related proteins. Typically, the domain co-occurs with an RNA-recognition motif (RRM), and together these domains function to bind primary transcripts of RNA polymerase III in the La autoantigen (Lupus La protein, LARP3, or Sjoegren syndrome type B antigen, SS-B). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.


Pssm-ID: 153396  Cd Length: 75  Bit Score: 104.54  E-value: 8.94e-28
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 12654891  15 AKICHQIEYYFGDFNLPRDKFLKEQIKlDEGWVPLEIMIKFNRLNRLTTDFNVIVEALSKSKaeLMEISEDKTKIRR 91
Cdd:cd07323   2 EKIKKQVEYYFSDENLCKDRFLRSLMD-DDGWVPLSLLASFNRVKKLTTDVELILEALRDSS--VVEVSEDGTKVRR 75
RRM2_La cd12541
RNA recognition motif 2 in La autoantigen (La or LARP3) and similar proteins; This subgroup ...
 231-307 3.35e-27

RNA recognition motif 2 in La autoantigen (La or LARP3) and similar proteins; This subgroup corresponds to the RRM2 of La autoantigen, also termed Lupus La protein, or La ribonucleoprotein, or Sjoegren syndrome type B antigen (SS-B), a highly abundant nuclear phosphoprotein and well conserved in eukaryotes. It specifically binds the 3'-terminal UUU-OH motif of nascent RNA polymerase III transcripts and protects them from exonucleolytic degradation by 3' exonucleases. In addition, La can directly facilitate the translation and/or metabolism of many UUU-3' OH-lacking cellular and viral mRNAs, through binding internal RNA sequences within the untranslated regions of target mRNAs. La contains an N-terminal La motif (LAM), followed by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In addition, it possesses a short basic motif (SBM) and a nuclear localization signal (NLS) at the C-terminus.


Pssm-ID: 409957 [Multi-domain]  Cd Length: 77  Bit Score: 103.12  E-value: 3.35e-27
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 12654891 231 GCLLKFSGDLDdQTCREDLHILFSNHGEIKWIDFVRGAKEGIILFKE--KAKEALGKAKDANNGnLQLRNKEVTWEVLE 307
Cdd:cd12541   1 GCILHFSGVGE-QTSREDLKEAFEKHGEVAWIDFARGQTEGYVRFKEedAAKEALEKAKEAKNG-LKIRGKEVTVKLLE 77
La pfam05383
La domain; This presumed domain is found at the N-terminus of La RNA-binding proteins as well ...
 17-74 1.07e-23

La domain; This presumed domain is found at the N-terminus of La RNA-binding proteins as well as other proteins. The function of this region is uncertain.


Pssm-ID: 461635  Cd Length: 59  Bit Score: 92.87  E-value: 1.07e-23
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 12654891    17 ICHQIEYYFGDFNLPRDKFLKEQIKLD-EGWVPLEIMIKFNRLNRLTTDFNVIVEALSK 74
Cdd:pfam05383   1 IKKQVEYYFSDENLPKDKFLRKQMDKDpDGYVPISVIASFKRMKKLTTDIDLIAEALRE 59
RRM2_La_like cd12292
RNA recognition motif 2 in La autoantigen (La or SS-B or LARP3), La-related protein 7 (LARP7 ...
 231-307 1.41e-19

RNA recognition motif 2 in La autoantigen (La or SS-B or LARP3), La-related protein 7 (LARP7 or PIP7S) and similar proteins; This subfamily corresponds to the RRM2 of La and LARP7. La is a highly abundant nuclear phosphoprotein and well conserved in eukaryotes. It specifically binds the 3'-terminal UUU-OH motif of nascent RNA polymerase III transcripts and protects them from exonucleolytic degradation by 3' exonucleases. In addition, La can directly facilitate the translation and/or metabolism of many UUU-3' OH-lacking cellular and viral mRNAs, through binding internal RNA sequences within the untranslated regions of target mRNAs. LARP7 is an oligopyrimidine-binding protein that binds to the highly conserved 3'-terminal U-rich stretch (3' -UUU-OH) of 7SK RNA. It is a stable component of the 7SK small nuclear ribonucleoprotein (7SK snRNP), intimately associates with all the nuclear 7SK and is required for 7SK stability. LARP7 also acts as a negative transcriptional regulator of cellular and viral polymerase II genes, acting by means of the 7SK snRNP system. LARP7 plays an essential role in the inhibition of positive transcription elongation factor b (P-TEFb)-dependent transcription, which has been linked to the global control of cell growth and tumorigenesis. Both La and LARP7 contain an N-terminal La motif (LAM), followed by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409734 [Multi-domain]  Cd Length: 74  Bit Score: 82.37  E-value: 1.41e-19
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 12654891 231 GCLLKFSGDLDdQTCREDLHILFSNHGEIKWIDFVRGAKEGIILFKEkaKEALGKAKDANNGNLQLRNKEVTWEVLE 307
Cdd:cd12292   1 GLILKITGIGP-SVSRDDLKELFKQFGEVEYVDFTPGDDEGHVRFKT--SEAAQKARDAYTGKLELNGKEWKLEILE 74
LA_like_fungal cd08029
La-motif domain of fungal proteins similar to the La autoantigen; This domain is found in ...
 14-91 2.64e-15

La-motif domain of fungal proteins similar to the La autoantigen; This domain is found in fungal proteins related to the La autoantigen. A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.


Pssm-ID: 153398  Cd Length: 76  Bit Score: 70.41  E-value: 2.64e-15
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 12654891  14 EAKICHQIEYYFGDFNLPRDKFLKEQI-KLDEGWVPLEIMIKFNRLNRLtTDFNVIVEALSKSkaELMEISEDKTKIRR 91
Cdd:cd08029   1 PEEIRKQVEFYFSDSNLPTDKFLWTLTgGSNNGWVPIKTIASFKRMRRF-QPLEAVVEALRES--ELLEVSEDGENVRR 76
LARP_6 cd08033
La RNA-binding domain of La-related protein 6; This domain is found in animal and plant ...
 15-91 8.28e-15

La RNA-binding domain of La-related protein 6; This domain is found in animal and plant proteins related to the La autoantigen. A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.


Pssm-ID: 153402  Cd Length: 77  Bit Score: 68.85  E-value: 8.28e-15
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 12654891  15 AKICHQIEYYFGDFNLPRDKFLKEQIKLD-EGWVPLEIMIKFNRLNRLTTDFNVIVEALSKSkaELMEISEDKTKIRR 91
Cdd:cd08033   2 QKIVKQVEYYFSDENLLKDAFLLKHVRRNkEGYVPIKLIASFKKVKALTRDWRVVAAALRRS--SKLVVSEDGKKVRR 77
LARP_7 cd08032
La RNA-binding domain of La-related protein 7; LARP7 is a component of the 7SK snRNP, a key ...
 9-91 3.22e-13

La RNA-binding domain of La-related protein 7; LARP7 is a component of the 7SK snRNP, a key factor in the regulation of RNA polymerase II transcription. 7SK functionality is dependent on the presence of LARP7, which is thought to stabilize the 7SK RNA by interacting with its 3' end. The release of 7SK RNA from P-TEFb/HEXIM/7SK complexes activates the cyclin-dependent kinase P-TEFb, which in turn phosphorylates the C-terminal domain of RNA pol II and mediates a transition into productive transcription elongation.


Pssm-ID: 153401  Cd Length: 82  Bit Score: 64.58  E-value: 3.22e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 12654891   9 KMAALEAKICHQIEYYFGDFNLPRDKFLKEQI-KLDEGWVPLEIMIKFNRLNRLTTDFNVIVEALSKSKaeLMEISEDKT 87
Cdd:cd08032   1 RVKQLLADIAKQVDFWFGDVNLHKDRFLREQIeKSRDGYIDISLLVSFNKMKKLTTDGKLIARALKNSS--VVELNLEGT 78


                ....
gi 12654891  88 KIRR 91
Cdd:cd08032  79 RIRR 82
LA_like_plant cd08030
La-motif domain of plant proteins similar to the La autoantigen; This domain is found in plant ...
 15-91 1.17e-12

La-motif domain of plant proteins similar to the La autoantigen; This domain is found in plant proteins related to the La autoantigen. A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.


Pssm-ID: 153399  Cd Length: 90  Bit Score: 63.18  E-value: 1.17e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 12654891  15 AKICHQIEYYFGDFNLPRDKFLKEQIKLD-EGWVPLEIMIKFNRLNRL-------TTDFNV-----IVEALSKSkaELME 81
Cdd:cd08030   3 EKVLRQVEFYFSDSNLPRDDFLLEEVEEDpDGMVSLALICSFSRMRSLlglgggkPEDVPEdtlkaVAEALRTS--TLLK 80

                        90
                ....*....|
gi 12654891  82 ISEDKTKIRR 91
Cdd:cd08030  81 VSEDGKRVGR 90
LARP_1_2 cd08034
La RNA-binding domain proteins similar to La-related proteins 1 and 2; This domain is found in ...
 17-86 1.24e-12

La RNA-binding domain proteins similar to La-related proteins 1 and 2; This domain is found in proteins similar to vertebrate La-related proteins 1 and 2 (LARP1, LARP2). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.


Pssm-ID: 153403  Cd Length: 73  Bit Score: 62.83  E-value: 1.24e-12
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 12654891  17 ICHQIEYYFGDFNLPRDKFLKEQIKlDEGWVPLEIMIKFNRLNRLTTDFNVIVEALSKSkaELMEISEDK 86
Cdd:cd08034   4 IKKQIEYYFSVDNLEKDFFLRRKMD-PEGYLPIALIASFHRVQALTTDVNLILEALKDS--TVVELVDEK 70
LARP_4_5_like cd08031
La RNA-binding domain of proteins similar to La-related proteins 4 and 5; This domain is found ...
 19-90 3.04e-12

La RNA-binding domain of proteins similar to La-related proteins 4 and 5; This domain is found in proteins similar to La-related proteins 4 and 5 (LARP4, LARP5). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.


Pssm-ID: 153400  Cd Length: 75  Bit Score: 61.69  E-value: 3.04e-12
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 12654891  19 HQIEYYFGDFNLPRDKFLKEQIKLDEgWVPLEIMIKFNRLNRLTTDFNVIVEALSKSkaELMEISEDKTKIR 90
Cdd:cd08031   6 RQLEYYFSRENLANDAYLLSQMDSDQ-YVPIWTIANFNKIKKLTTDIDLIVEALRES--PNVQVDEKGEKVR 74
LHP1 COG5193
La protein, small RNA-binding pol III transcript stabilizing protein and related ...
 20-285 3.85e-11

La protein, small RNA-binding pol III transcript stabilizing protein and related La-motif-containing proteins involved in translation [Posttranslational modification, protein turnover, chaperones / Translation, ribosomal structure and biogenesis];


Pssm-ID: 227520 [Multi-domain]  Cd Length: 438  Bit Score: 64.30  E-value: 3.85e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 12654891  20 QIEYYFG-----DFNLPRDKFLKEQ---IKLDEGWVPLEIMIKFNRLNRLTTDFNVIVEALSKSK-AELMEISEDKTKIR 90
Cdd:COG5193  78 QVEFYFSgskdtDSNFPKDKFLKTTapkNKKRDKWVPIKTIATFNRMKNSGSPVSAVSGALRKSLdARVLEVSSSGSNKN 157

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 12654891  91 RspSKPLPEVTDEyKNDVKNRSVYIKGFPTDATLD--------DIKEWLEDKGQ--VLNIQMRRTLH-KAFKGSIFVVFD 159
Cdd:COG5193 158 R--TEKLISNNNK-STSQMQRDVYQNGFGKEDVNNasrpeqqeDLEIQFPPHYHapPSQIRNRRDWLnKNFRGSVFVEFK 234

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 12654891 160 SIESAKKF--------------VETPGQKYKETDLLILFKDD----YFAKKNEerkqnkveaklrAKQEQEAKQKLEEDA 221
Cdd:COG5193 235 YFREAQRFnngfyrnkkypndpETVYYYSVEPILLSIMAKKEqieyYFSEENL------------KSDEFLRKKFKKAGF 302

                       250       260       270       280       290       300
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 12654891 222 EMKSLEEKIGCLLKFSGD--LDDQTCREDLHILFSNHGEIkwidfVRGAKEGIILFKEKAKEALGK 285
Cdd:COG5193 303 IPLSFIGKFYRNLSFGGDknLILAAMKEVVQNKATNHLEI-----ALGSIEDAQKNEAKDFSPGKK 363
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 113-181 4.50e-11

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: 58.01  E-value: 4.50e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 12654891   113 VYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVET-PGQKYKETDLL 181
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFGPIKSIRLVRDETGRSKGFAFVEFEDEEDAEKAIEAlNGKELGGRELK 70
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 113-169 8.97e-10

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: 54.60  E-value: 8.97e-10
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 12654891 113 VYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE 169
Cdd:cd00590   1 LFVGNLPPDTTEEDLRELFSKFGEVVSVRIVRDRDGKSKGFAFVEFESPEDAEKALE 57
LARP_1 cd08037
La RNA-binding domain of La-related protein 1; This domain is found in vertebrate La-related ...
 17-91 3.24e-09

La RNA-binding domain of La-related protein 1; This domain is found in vertebrate La-related protein 1 (LARP1). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.


Pssm-ID: 153406  Cd Length: 73  Bit Score: 52.98  E-value: 3.24e-09
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 12654891  17 ICHQIEYYFGDFNLPRDKFLKEQIKlDEGWVPLEIMIKFNRLNRLTTDFNVIVEALSKSKaeLMEISEDktKIRR 91
Cdd:cd08037   4 IKRQIEYYFSVDNLERDFFLRRKMD-EDGFLPVTLIASFHRVQALTTDISLIIKALKDSK--VVEIIDM--KIRR 73
LARP_2 cd08038
La RNA-binding domain of La-related protein 2; This domain is found in vertebrate La-related ...
 17-91 1.32e-08

La RNA-binding domain of La-related protein 2; This domain is found in vertebrate La-related protein 2 (LARP2). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.


Pssm-ID: 153407  Cd Length: 73  Bit Score: 51.49  E-value: 1.32e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 12654891  17 ICHQIEYYFGDFNLPRDKFLKEQIKLdEGWVPLEIMIKFNRLNRLTTDFNVIVEALSKSkaelMEISEDKTKIRR 91
Cdd:cd08038   4 IKRQIEYYFSTENLERDFFLRRKMDL-QGFLPISLIAGFYRVQALTTNVDLILEALKDS----TEVEIVDQKIRR 73
RRM smart00360
RNA recognition motif;
112-169 3.38e-08

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 50.28  E-value: 3.38e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 12654891    112 SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRR-TLHKAFKGSIFVVFDSIESAKKFVE 169
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRdKETGKSKGFAFVEFESEEDAEKALE 59
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
 103-283 9.57e-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: 47.49  E-value: 9.57e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 12654891   103 EYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPGQkyKETDLLI 182
Cdd:TIGR01628 171 EAAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMNG--KKIGLAK 248

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 12654891   183 LFKDDYF--AKKNEERkqnkvEAKLRAKQEQEaKQKLEEDAEMKSLEEKigcllkfsgDLDDQTCREDLHILFSNHGEIK 260
Cdd:TIGR01628 249 EGKKLYVgrAQKRAER-----EAELRRKFEEL-QQERKMKAQGVNLYVK---------NLDDTVTDEKLRELFSECGEIT 313

                         170       180       190
                  ....*....|....*....|....*....|
gi 12654891   261 WIDFVRGAKE-----GIILFK--EKAKEAL 283
Cdd:TIGR01628 314 SAKVMLDEKGvsrgfGFVCFSnpEEANRAV 343
RRM_hnRNPH_ESRPs_RBM12_like cd12254
RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein ...
 113-166 4.82e-05

RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein family, epithelial splicing regulatory proteins (ESRPs), Drosophila RNA-binding protein Fusilli, RNA-binding protein 12 (RBM12) and similar proteins; The family includes RRM domains in the hnRNP H protein family, G-rich sequence factor 1 (GRSF-1), ESRPs (also termed RBM35), Drosophila Fusilli, RBM12 (also termed SWAN), RBM12B, RBM19 (also termed RBD-1) and similar proteins. The hnRNP H protein family includes hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H'), hnRNP F and hnRNP H3 (also termed hnRNP 2H9), which represent a group of nuclear RNA binding proteins that are involved in pre-mRNA processing. GRSF-1 is a cytoplasmic poly(A)+ mRNA binding protein which interacts with RNA in a G-rich element-dependent manner. It may function in RNA packaging, stabilization of RNA secondary structure, or other macromolecular interactions. ESRP1 (also termed RBM35A) and ESRP2 (also termed RBM35B) are epithelial-specific RNA binding proteins that promote splicing of the epithelial variant of fibroblast growth factor receptor 2 (FGFR2), ENAH (also termed hMena), CD44 and CTNND1 (also termed p120-Catenin) transcripts. Fusilli shows high sequence homology to ESRPs. It can regulate endogenous FGFR2 splicing and functions as a splicing factor. The biological roles of both, RBM12 and RBM12B, remain unclear. RBM19 is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. Members in this family contain 2~6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409699 [Multi-domain]  Cd Length: 73  Bit Score: 41.39  E-value: 4.82e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 12654891 113 VYIKGFPTDATLDDIKEWLED-KGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKK 166
Cdd:cd12254   2 VRLRGLPFSATEEDIRDFFSGlDIPPDGIHIVYDDDGRPTGEAYVEFASEEDAQR 56
RRM1_PHIP1 cd12271
RNA recognition motif 1 (RRM1) found in Arabidopsis thaliana phragmoplastin interacting ...
 113-174 2.82e-04

RNA recognition motif 1 (RRM1) found in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins; This subfamily corresponds to the RRM1 of PHIP1. A. thaliana PHIP1 and its homologs represent a novel class of plant-specific RNA-binding proteins that may play a unique role in the polarized mRNA transport to the vicinity of the cell plate. The family members consist of multiple functional domains, including a lysine-rich domain (KRD domain) that contains three nuclear localization motifs (KKKR/NK), two RNA recognition motifs (RRMs), and three CCHC-type zinc fingers. PHIP1 is a peripheral membrane protein and is localized at the cell plate during cytokinesis in plants. In addition to phragmoplastin, PHIP1 interacts with two Arabidopsis small GTP-binding proteins, Rop1 and Ran2. However, PHIP1 interacted only with the GTP-bound form of Rop1 but not the GDP-bound form. It also binds specifically to Ran2 mRNA.


Pssm-ID: 409714 [Multi-domain]  Cd Length: 72  Bit Score: 39.23  E-value: 2.82e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 12654891 113 VYIKGFPTDATLDDIKEWLEDKGQVLNIQ-MRRTLHKAFKGSIFVVFDSIESAKKFVETPGQK 174
Cdd:cd12271   1 VYVGGIPYYSTEAEIRSYFSSCGEVRSVDlMRFPDSGNFRGIAFITFKTEEAAKRALALDGEM 63
LARP_4 cd08035
La RNA-binding domain of La-related protein 4; This domain is found in vertebrate La-related ...
 20-90 3.90e-04

La RNA-binding domain of La-related protein 4; This domain is found in vertebrate La-related protein 4 (LARP4), also known as c-MPL binding protein. La-type domains often co-occur with RNA-recognition motifs (RRMs). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.


Pssm-ID: 153404  Cd Length: 75  Bit Score: 38.87  E-value: 3.90e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 12654891  20 QIEYYFGDFNLPRDKFLKEQIKLDEgWVPLEIMIKFNRLNRLTTDFNVIVEALSKSKaeLMEISEDKTKIR 90
Cdd:cd08035   7 QLEFCFSRENLSKDLYLISQMDSDQ-FVPIWTVANMEGIKKLTTDMDLILDVLRSSP--MVQVDETGEKVR 74
RRM_SF3B14 cd12241
RNA recognition motif (RRM) found in pre-mRNA branch site protein p14 (SF3B14) and similar ...
 110-169 1.13e-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: 37.60  E-value: 1.13e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 12654891 110 NRSVYIKGFPTDATLDDIKEWLEDKGQVlnIQMRRTLHKAFKGSIFVVFDSIESAKKFVE 169
Cdd:cd12241   2 NRILYVRNLPYKISSEELYDLFGKYGAI--RQIRIGNTKETRGTAFVVYEDIFDAKNACD 59
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 238-304 5.81e-03

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: 35.34  E-value: 5.81e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 12654891 238 GDLDDQTCREDLHILFSNHGEIKWIDFVRGAKE-----GIILFKEkaKEALGKAKDANNGNlQLRNKEVTWE 304
Cdd:cd00590   4 GNLPPDTTEEDLRELFSKFGEVVSVRIVRDRDGkskgfAFVEFES--PEDAEKALEALNGT-ELGGRPLKVS 72
RRM2_MSI cd12323
RNA recognition motif 2 (RRM2) found in RNA-binding protein Musashi homologs Musashi-1, ...
 113-170 9.98e-03

RNA recognition motif 2 (RRM2) found in RNA-binding protein Musashi homologs Musashi-1, Musashi-2 and similar proteins; This subfamily corresponds to the RRM2.in Musashi-1 (also termed Msi1), a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. It is evolutionarily conserved from invertebrates to vertebrates. Musashi-1 is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). It has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, Musashi-1 represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-2 (also termed Msi2) has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Both, Musashi-1 and Musashi-2, contain two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function.


Pssm-ID: 240769 [Multi-domain]  Cd Length: 74  Bit Score: 34.72  E-value: 9.98e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 12654891 113 VYIKGFPTDATLDDIKEWLEDKGQVLNIQ-MRRTLHKAFKGSIFVVFDSIESAKKFVET 170
Cdd:cd12323   2 IFVGGLSANTTEDDVKKYFSQFGKVEDAMlMFDKQTNRHRGFGFVTFESEDVVDKVCEI 60
 
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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