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Conserved domains on  [gi|1034658956|ref|XP_016868477|]
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RNA-binding protein with multiple splicing isoform X9 [Homo sapiens]

Protein Classification

RNA-binding protein( domain architecture ID 106745)

RNA-binding protein containing an RNA recognition motif (RRM)

CATH:  3.30.70.330
Gene Ontology:  GO:0003723
PubMed:  15853797
SCOP:  3000110

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
RRM_SF super family cl17169
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
23-98 5.09e-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 cd12682:

Pssm-ID: 473069 [Multi-domain]  Cd Length: 76  Bit Score: 145.57  E-value: 5.09e-46
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1034658956  23 VRTLFVSGLPLDIKPRELYLLFRPFKGYEGSLIKLTSKQPVGFVSFDSRSEAEAAKNALNGIRFDPEIPQTLRLEF 98
Cdd:cd12682     1 VRTLFVSGLPLDIKPRELYLLFRPFKGYEGSLIKLTSKQPVGFVSFDSRSEAEAAKNALNGIRFDPEIPQTLRLEF 76
PABP-1234 super family cl31127
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
64-165 7.90e-04

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


The actual alignment was detected with superfamily member TIGR01628:

Pssm-ID: 130689 [Multi-domain]  Cd Length: 562  Bit Score: 39.02  E-value: 7.90e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034658956  64 GFVSFDSRSEAEAAKNALNGIRFDPEiP-------------QTLRLEFAKANTKMaknklvgtpnPSTPLPNTVPQFIAR 130
Cdd:TIGR01628 329 GFVCFSNPEEANRAVTEMHGRMLGGK-PlyvalaqrkeqrrAHLQDQFMQLQPRM----------RQLPMGSPMGGAMGQ 397
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1034658956 131 EPYELTVP-ALYPSSPEVWA-----PYPLYP-AELAPALPPP 165
Cdd:TIGR01628 398 PPYYGQGPqQQFNGQPLGWPrmsmmPTPMGPgGPLRPNGLAP 439
 
Name Accession Description Interval E-value
RRM_RBPMS cd12682
RNA recognition motif (RRM) found in vertebrate RNA-binding protein with multiple splicing ...
23-98 5.09e-46

RNA recognition motif (RRM) found in vertebrate RNA-binding protein with multiple splicing (RBP-MS); This subfamily corresponds to the RRM of RBP-MS, also termed heart and RRM expressed sequence (hermes), an RNA-binding proteins found in various vertebrate species. It contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). RBP-MS physically interacts with Smad2, Smad3 and Smad4 and plays a role in regulation of Smad-mediated transcriptional activity. In addition, RBP-MS may be involved in regulation of mRNA translation and localization during Xenopus laevis development.


Pssm-ID: 410083 [Multi-domain]  Cd Length: 76  Bit Score: 145.57  E-value: 5.09e-46
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1034658956  23 VRTLFVSGLPLDIKPRELYLLFRPFKGYEGSLIKLTSKQPVGFVSFDSRSEAEAAKNALNGIRFDPEIPQTLRLEF 98
Cdd:cd12682     1 VRTLFVSGLPLDIKPRELYLLFRPFKGYEGSLIKLTSKQPVGFVSFDSRSEAEAAKNALNGIRFDPEIPQTLRLEF 76
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
26-87 3.28e-12

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: 58.78  E-value: 3.28e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1034658956  26 LFVSGLPLDIKPRELYLLFRPFKGYEG-SLIKLTSKQP--VGFVSFDSRSEAEAAKNALNGIRFD 87
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFGPIKSiRLVRDETGRSkgFAFVEFEDEEDAEKAIEALNGKELG 65
RRM smart00360
RNA recognition motif;
25-87 5.73e-11

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 55.68  E-value: 5.73e-11
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1034658956   25 TLFVSGLPLDIKPRELYLLFRPFKGYEGSLI---KLTSK-QPVGFVSFDSRSEAEAAKNALNGIRFD 87
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLvrdKETGKsKGFAFVEFESEEDAEKALEALNGKELD 67
ELAV_HUD_SF TIGR01661
ELAV/HuD family splicing factor; This model describes the ELAV/HuD subfamily of splicing ...
26-120 8.39e-07

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


Pssm-ID: 273741 [Multi-domain]  Cd Length: 352  Bit Score: 47.63  E-value: 8.39e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034658956  26 LFVSGLPLDIKPRELYLLFRPFkgyeGSLIklTSK----------QPVGFVSFDSRSEAEAAKNALNGirfdpEIP---- 91
Cdd:TIGR01661  92 LYVSGLPKTMTQHELESIFSPF----GQII--TSRilsdnvtglsKGVGFIRFDKRDEADRAIKTLNG-----TTPsgct 160
                          90       100       110
                  ....*....|....*....|....*....|...
gi 1034658956  92 QTLRLEFA----KANTKMAKNKLVGTPNPSTPL 120
Cdd:TIGR01661 161 EPITVKFAnnpsSSNSKGLLSQLEAVQNPQTTR 193
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
25-87 6.93e-05

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


Pssm-ID: 440488 [Multi-domain]  Cd Length: 85  Bit Score: 39.70  E-value: 6.93e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034658956  25 TLFVSGLPLDIKPRELYLLFRPF-----------------KGYegslikltskqpvGFVSFDSRSEAEAAKNALNGIRFD 87
Cdd:COG0724     3 KIYVGNLPYSVTEEDLRELFSEYgevtsvklitdretgrsRGF-------------GFVEMPDDEEAQAAIEALNGAELM 69
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
64-165 7.90e-04

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


Pssm-ID: 130689 [Multi-domain]  Cd Length: 562  Bit Score: 39.02  E-value: 7.90e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034658956  64 GFVSFDSRSEAEAAKNALNGIRFDPEiP-------------QTLRLEFAKANTKMaknklvgtpnPSTPLPNTVPQFIAR 130
Cdd:TIGR01628 329 GFVCFSNPEEANRAVTEMHGRMLGGK-PlyvalaqrkeqrrAHLQDQFMQLQPRM----------RQLPMGSPMGGAMGQ 397
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1034658956 131 EPYELTVP-ALYPSSPEVWA-----PYPLYP-AELAPALPPP 165
Cdd:TIGR01628 398 PPYYGQGPqQQFNGQPLGWPrmsmmPTPMGPgGPLRPNGLAP 439
 
Name Accession Description Interval E-value
RRM_RBPMS cd12682
RNA recognition motif (RRM) found in vertebrate RNA-binding protein with multiple splicing ...
23-98 5.09e-46

RNA recognition motif (RRM) found in vertebrate RNA-binding protein with multiple splicing (RBP-MS); This subfamily corresponds to the RRM of RBP-MS, also termed heart and RRM expressed sequence (hermes), an RNA-binding proteins found in various vertebrate species. It contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). RBP-MS physically interacts with Smad2, Smad3 and Smad4 and plays a role in regulation of Smad-mediated transcriptional activity. In addition, RBP-MS may be involved in regulation of mRNA translation and localization during Xenopus laevis development.


Pssm-ID: 410083 [Multi-domain]  Cd Length: 76  Bit Score: 145.57  E-value: 5.09e-46
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1034658956  23 VRTLFVSGLPLDIKPRELYLLFRPFKGYEGSLIKLTSKQPVGFVSFDSRSEAEAAKNALNGIRFDPEIPQTLRLEF 98
Cdd:cd12682     1 VRTLFVSGLPLDIKPRELYLLFRPFKGYEGSLIKLTSKQPVGFVSFDSRSEAEAAKNALNGIRFDPEIPQTLRLEF 76
RRM_RBPMS2 cd12683
RNA recognition motif (RRM) found in vertebrate RNA-binding protein with multiple splicing 2 ...
23-98 4.42e-42

RNA recognition motif (RRM) found in vertebrate RNA-binding protein with multiple splicing 2 (RBP-MS2); This subfamily corresponds to the RRM of RBP-MS2, encoded by RBPMS2 gene, a paralog of RNA-binding protein with multiple splicing (RBP-MS). The biological function of RBP-MS2 remains unclear. Like RBP-MS, RBP-MS2 contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 410084 [Multi-domain]  Cd Length: 76  Bit Score: 135.55  E-value: 4.42e-42
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1034658956  23 VRTLFVSGLPLDIKPRELYLLFRPFKGYEGSLIKLTSKQPVGFVSFDSRSEAEAAKNALNGIRFDPEIPQTLRLEF 98
Cdd:cd12683     1 VRTLFVSGLPVDIKPRELYLLFRPFKGYEGSLIKLTSKQPVGFVTFDSRAGAEAAKNALNGIRFDPENPQTLRLEF 76
RRM_RBPMS_like cd12420
RNA recognition motif (RRM) found in RNA-binding protein with multiple splicing (RBP-MS)-like ...
24-97 7.88e-42

RNA recognition motif (RRM) found in RNA-binding protein with multiple splicing (RBP-MS)-like proteins; This subfamily corresponds to the RRM of RNA-binding proteins with multiple splicing (RBP-MS)-like proteins, including protein products of RBPMS genes (RBP-MS and its paralogue RBP-MS2), the Drosophila couch potato (cpo), and Caenorhabditis elegans Mec-8 genes. RBP-MS may be involved in regulation of mRNA translation and localization during Xenopus laevis development. It has also been shown to physically interact with Smad2, Smad3 and Smad4, and stimulates Smad-mediated transactivation. Cpo may play an important role in regulating normal function of the nervous system, whereas mutations in Mec-8 affect mechanosensory and chemosensory neuronal function. All members contain a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Some uncharacterized family members contain two RRMs; this subfamily includes their RRM1. Their RRM2 shows high sequence homology to the RRM of yeast proteins scw1, Whi3, and Whi4.


Pssm-ID: 409854 [Multi-domain]  Cd Length: 76  Bit Score: 134.76  E-value: 7.88e-42
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1034658956  24 RTLFVSGLPLDIKPRELYLLFRPFKGYEGSLIKLTSK--QPVGFVSFDSRSEAEAAKNALNGIRFDPEIPQTLRLE 97
Cdd:cd12420     1 RTLFVSGLPLDVKERELYNLFRPLPGYEASQLKFTGKntQPVGFVTFESRAAAEAAKDALQGMRFDPDTPQVLRLE 76
RRM_cpo cd12684
RNA recognition motif (RRM) found in Drosophila couch potato (cpo) coding RNA-binding protein ...
23-100 6.20e-39

RNA recognition motif (RRM) found in Drosophila couch potato (cpo) coding RNA-binding protein and similar proteins; This subfamily corresponds to the RRM of Cpo, an RNA-binding protein encoded by Drosophila couch potato (cpo) gene. Cpo contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It may control the processing of RNA molecules required for the proper functioning of the peripheral nervous system (PNS).


Pssm-ID: 410085 [Multi-domain]  Cd Length: 83  Bit Score: 127.72  E-value: 6.20e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034658956  23 VRTLFVSGLPLDIKPRELYLLFRPFKGYEGSLIKLTSKQ-----PVGFVSFDSRSEAEAAKNALNGIRFDPEIPQTLRLE 97
Cdd:cd12684     1 VRTLFVSGLPMDAKPRELYLLFRAYKGYEGSLLKVTSKNgkttsPVGFVTFLSRQAAEAAKQDLQGVRFDPDLPQTLRLE 80

                  ...
gi 1034658956  98 FAK 100
Cdd:cd12684    81 FAK 83
RRM_AtNSRA_like cd21618
RNA recognition motif (RRM) found in Arabidopsis thaliana nuclear speckle RNA-binding protein ...
24-100 2.42e-17

RNA recognition motif (RRM) found in Arabidopsis thaliana nuclear speckle RNA-binding protein A (AtNSRA) and similar protein; AtNSRA is an alternative splicing (AS) regulator that binds to specific mRNAs and modulates auxin effects on the transcriptome. It can be displaced from its targets upon binding to AS competitor long non-coding RNA (ASCO-RNA). Members in this family contain an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 410197 [Multi-domain]  Cd Length: 87  Bit Score: 72.68  E-value: 2.42e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034658956  24 RTLFVSGLPLDIKPRELYLLFRPFKGYEG-SLI----KLTSKQPVGFVSFDSRSEAEAAKNALNGIRFDPEIPQ--TLRL 96
Cdd:cd21618     4 STLYVEGLPLDATEREVAHIFRPFPGFKSvRLVpkegKRGRKLVLCFVDFADAQQAAAALETLQGYRLDEDDSDskGLRI 83

                  ....
gi 1034658956  97 EFAK 100
Cdd:cd21618    84 SFAR 87
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
26-87 3.28e-12

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: 58.78  E-value: 3.28e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1034658956  26 LFVSGLPLDIKPRELYLLFRPFKGYEG-SLIKLTSKQP--VGFVSFDSRSEAEAAKNALNGIRFD 87
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFGPIKSiRLVRDETGRSkgFAFVEFEDEEDAEKAIEALNGKELG 65
RRM smart00360
RNA recognition motif;
25-87 5.73e-11

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 55.68  E-value: 5.73e-11
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1034658956   25 TLFVSGLPLDIKPRELYLLFRPFKGYEGSLI---KLTSK-QPVGFVSFDSRSEAEAAKNALNGIRFD 87
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLvrdKETGKsKGFAFVEFESEEDAEKALEALNGKELD 67
RRM2_Hu cd12652
RNA recognition motif 2 (RRM2) found in the Hu proteins family; This subfamily corresponds to ...
26-83 2.87e-10

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


Pssm-ID: 410055 [Multi-domain]  Cd Length: 79  Bit Score: 53.87  E-value: 2.87e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1034658956  26 LFVSGLPLDIKPRELYLLFRPFkgyeGSLIklTSK----------QPVGFVSFDSRSEAEAAKNALNG 83
Cdd:cd12652     3 LYVSGLPKTMTQKELEQLFSQF----GRII--TSRilcdnvtglsRGVGFIRFDKRVEAERAIKALNG 64
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
26-87 1.85e-09

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


Pssm-ID: 409669 [Multi-domain]  Cd Length: 72  Bit Score: 51.51  E-value: 1.85e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1034658956  26 LFVSGLPLDIKPRELYLLFRPFKGYEGSLIKLTSKQP---VGFVSFDSRSEAEAAKNALNGIRFD 87
Cdd:cd00590     1 LFVGNLPPDTTEEDLRELFSKFGEVVSVRIVRDRDGKskgFAFVEFESPEDAEKALEALNGTELG 65
RRM2_U1A_like cd12247
RNA recognition motif 2 (RRM2) found in the U1A/U2B"/SNF protein family; This subfamily ...
24-91 1.12e-07

RNA recognition motif 2 (RRM2) found in the U1A/U2B"/SNF protein family; This subfamily corresponds to the RRM2 of U1A/U2B"/SNF protein family, containing Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which consist of two RNA recognition motifs (RRMs) connected by a variable, flexible linker. SNF is an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila where it is essential in sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). U1A is an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. Moreover, U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins. U2B", initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a unique protein that comprises of the U2 snRNP. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. U2B" does not require an auxiliary protein for binding to RNA and its nuclear transport is independent on U2 snRNA binding.


Pssm-ID: 409693 [Multi-domain]  Cd Length: 72  Bit Score: 46.79  E-value: 1.12e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1034658956  24 RTLFVSGLPLDIKPRELYLLFRPFKGYEGslIKLTSKQPVGFVSFDSRSEAEAAKNALNGIRFDPEIP 91
Cdd:cd12247     3 KILFLQNLPEETTKEMLEMLFNQFPGFKE--VRLVPRRGIAFVEFETEEQATVALQALQGFKITPGHA 68
RRM_Srp1p_AtRSp31_like cd12233
RNA recognition motif (RRM) found in fission yeast pre-mRNA-splicing factor Srp1p, Arabidopsis ...
25-100 1.32e-07

RNA recognition motif (RRM) found in fission yeast pre-mRNA-splicing factor Srp1p, Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins; This subfamily corresponds to the RRM of Srp1p and RRM2 of plant SR splicing factors. Srp1p is encoded by gene srp1 from fission yeast Schizosaccharomyces pombe. It plays a role in the pre-mRNA splicing process, but is not essential for growth. Srp1p is closely related to the SR protein family found in Metazoa. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine hinge and a RS domain in the middle, and a C-terminal domain. The family also includes a novel group of arginine/serine (RS) or serine/arginine (SR) splicing factors existing in plants, such as A. thaliana RSp31, RSp35, RSp41 and similar proteins. Like vertebrate RS splicing factors, these proteins function as plant splicing factors and play crucial roles in constitutive and alternative splicing in plants. They all contain two RRMs at their N-terminus and an RS domain at their C-terminus.


Pssm-ID: 240679 [Multi-domain]  Cd Length: 70  Bit Score: 46.67  E-value: 1.32e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1034658956  25 TLFVSGL-PLDIKPRELYLLFRPFkgyeGSLIKLTSKQPVGFVSFDSRSEAEAAKNALNGIRFDPEIpqtLRLEFAK 100
Cdd:cd12233     1 TLFVVGFdPGTTREEDIEKLFEPF----GPLVRCDIRKTFAFVEFEDSEDATKALEALHGSRIDGSV---LTVEFVK 70
RRM_eIF3G_like cd12408
RNA recognition motif (RRM) found in eukaryotic translation initiation factor 3 subunit G ...
25-99 1.53e-07

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


Pssm-ID: 409842 [Multi-domain]  Cd Length: 76  Bit Score: 46.73  E-value: 1.53e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034658956  25 TLFVSGLPLDIKPRELYLLFRPFkgyeGSLIKLT------SKQPVGF--VSFDSRSEAEAAKNALNGIRFDPEIpqtLRL 96
Cdd:cd12408     1 TIRVTNLSEDATEEDLRELFRPF----GPISRVYlakdkeTGQSKGFafVTFETREDAERAIEKLNGFGYDNLI---LSV 73

                  ...
gi 1034658956  97 EFA 99
Cdd:cd12408    74 EWA 76
RRM_scw1_like cd12245
RNA recognition motif (RRM) found in yeast cell wall integrity protein scw1 and similar ...
25-100 2.37e-07

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


Pssm-ID: 409691 [Multi-domain]  Cd Length: 79  Bit Score: 46.08  E-value: 2.37e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1034658956  25 TLFVSGLPLDIKPRELYLLFRPFKGYEGSLIKLTSKQPVGFVSFDSRSEAEAAKNALNGIRFDPEIPQTLRLEFAK 100
Cdd:cd12245     4 TLFVANLGPNVSEQELRQLFSRQPGFRRLRMHNKGGGPVCFVEFEDVPFATQALNHLQGAILSSSDRGGIRIEYAK 79
ELAV_HUD_SF TIGR01661
ELAV/HuD family splicing factor; This model describes the ELAV/HuD subfamily of splicing ...
26-120 8.39e-07

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


Pssm-ID: 273741 [Multi-domain]  Cd Length: 352  Bit Score: 47.63  E-value: 8.39e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034658956  26 LFVSGLPLDIKPRELYLLFRPFkgyeGSLIklTSK----------QPVGFVSFDSRSEAEAAKNALNGirfdpEIP---- 91
Cdd:TIGR01661  92 LYVSGLPKTMTQHELESIFSPF----GQII--TSRilsdnvtglsKGVGFIRFDKRDEADRAIKTLNG-----TTPsgct 160
                          90       100       110
                  ....*....|....*....|....*....|...
gi 1034658956  92 QTLRLEFA----KANTKMAKNKLVGTPNPSTPL 120
Cdd:TIGR01661 161 EPITVKFAnnpsSSNSKGLLSQLEAVQNPQTTR 193
RRM1_p54nrb_like cd12332
RNA recognition motif 1 (RRM1) found in the p54nrb/PSF/PSP1 family; This subfamily corresponds ...
26-98 9.52e-07

RNA recognition motif 1 (RRM1) found in the p54nrb/PSF/PSP1 family; This subfamily corresponds to the RRM1 of the p54nrb/PSF/PSP1 family, including 54 kDa nuclear RNA- and DNA-binding protein (p54nrb or NonO or NMT55), polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF or POMp100), paraspeckle protein 1 (PSP1 or PSPC1), which are ubiquitously expressed and are conserved in vertebrates. p54nrb is a multi-functional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. PSF is also a multi-functional protein that binds RNA, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and many factors, and mediates diverse activities in the cell. PSP1 is a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. The cellular function of PSP1 remains unknown currently. This subfamily also includes some p54nrb/PSF/PSP1 homologs from invertebrate species, such as the Drosophila melanogaster gene no-ontransient A (nonA) encoding puff-specific protein Bj6 (also termed NONA) and Chironomus tentans hrp65 gene encoding protein Hrp65. D. melanogaster NONA is involved in eye development and behavior, and may play a role in circadian rhythm maintenance, similar to vertebrate p54nrb. C. tentans Hrp65 is a component of nuclear fibers associated with ribonucleoprotein particles in transit from the gene to the nuclear pore. All family members contain a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction module. PSF has an additional large N-terminal domain that differentiates it from other family members.


Pssm-ID: 409769 [Multi-domain]  Cd Length: 71  Bit Score: 44.59  E-value: 9.52e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1034658956  26 LFVSGLPLDIKPRELYLLFRPFKgyEGSLIKLTSKQPVGFVSFDSRSEAEAAKNALNGIrfdPEIPQTLRLEF 98
Cdd:cd12332     4 LFVGNLPNDITEEEFKELFQKYG--EVSEVFLNKGKGFGFIRLDTRANAEAAKAELDGT---PRKGRQLRVRF 71
RRM3_CELF1-6 cd12362
RNA recognition motif 3 (RRM3) found in CELF/Bruno-like family of RNA binding proteins CELF1, ...
26-83 1.64e-06

RNA recognition motif 3 (RRM3) found in CELF/Bruno-like family of RNA binding proteins CELF1, CELF2, CELF3, CELF4, CELF5, CELF6 and similar proteins; This subgroup corresponds to the RRM3 of the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) proteins, a family of structurally related RNA-binding proteins involved in the regulation of pre-mRNA splicing in the nucleus and in the control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also termed BRUNOL-2, or CUG-BP1, or NAPOR, or EDEN-BP), CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR-2), CELF-3 (also termed BRUNOL-1, or TNRC4, or ETR-1, or CAGH4, or ER DA4), CELF-4 (also termed BRUNOL-4), CELF-5 (also termed BRUNOL-5), CELF-6 (also termed BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts.


Pssm-ID: 409797 [Multi-domain]  Cd Length: 73  Bit Score: 43.76  E-value: 1.64e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1034658956  26 LFVSGLPLDIKPRELYLLFRPFkGYEGSLIKLTSKQP-----VGFVSFDSRSEAEAAKNALNG 83
Cdd:cd12362     1 LFVYHLPNEFTDQDLYQLFAPF-GNVVSAKVFVDKNTgrskgFGFVSYDNPLSAQAAIKAMNG 62
RRM1_U1A_like cd12246
RNA recognition motif 1 (RRM1) found in the U1A/U2B"/SNF protein family; This subfamily ...
25-100 3.38e-06

RNA recognition motif 1 (RRM1) found in the U1A/U2B"/SNF protein family; This subfamily corresponds to the RRM1 of U1A/U2B"/SNF protein family which contains Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which consist of two RNA recognition motifs (RRMs), connected by a variable, flexible linker. SNF is an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila where it is essential in sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). U1A is an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. Moreover, U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins. U2B", initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a unique protein that comprises of the U2 snRNP. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. Moreover, U2B" does not require an auxiliary protein for binding to RNA, and its nuclear transport is independent of U2 snRNA binding.


Pssm-ID: 409692 [Multi-domain]  Cd Length: 78  Bit Score: 42.91  E-value: 3.38e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034658956  25 TLFVSGLPLDIKPRE----LYLLFRPFkgyeGSLIK---LTSKQPVG--FVSFDSRSEAEAAKNALNGIRFdpeIPQTLR 95
Cdd:cd12246     1 TLYINNLNEKIKKDElkrsLYALFSQF----GPVLDivaSKSLKMRGqaFVVFKDVESATNALRALQGFPF---YGKPMR 73

                  ....*
gi 1034658956  96 LEFAK 100
Cdd:cd12246    74 IQYAK 78
RRM_ACINU cd12432
RNA recognition motif (RRM) found in apoptotic chromatin condensation inducer in the nucleus ...
65-99 3.73e-06

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: 43.35  E-value: 3.73e-06
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1034658956  65 FVSFDSRSEAEAAKNALNGIRFDPEIPQTLRLEFA 99
Cdd:cd12432    43 YVTYSSEEEAVATREALHGVVWPSSNGKRLKVEFV 77
RBD_RRM1_NPL3 cd12340
RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 3 (Npl3p) and similar proteins; ...
26-83 7.13e-06

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


Pssm-ID: 409777 [Multi-domain]  Cd Length: 69  Bit Score: 42.00  E-value: 7.13e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1034658956  26 LFVSGLPLDIKPRELYLLFRPFKGYEGslIKLTSKQPVGFVSFDSRSEAEAAKNALNG 83
Cdd:cd12340     2 LFVRPFPPDTSESAIREIFSPYGPVKE--VKMLSDSNFAFVEFEELEDAIRAKDSVHG 57
RRM2_Hu_like cd12376
RNA recognition motif 2 (RRM2) found in the Hu proteins family, Drosophila sex-lethal (SXL), ...
26-85 8.59e-06

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


Pssm-ID: 240822 [Multi-domain]  Cd Length: 79  Bit Score: 42.23  E-value: 8.59e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1034658956  26 LFVSGLPLDIKPRELYLLFRPFkgyeGSLI-------KLTSK-QPVGFVSFDSRSEAEAAKNALNGIR 85
Cdd:cd12376     3 LYVSGLPKTMTQKELEQLFSQY----GRIItsrilrdQLTGVsRGVGFIRFDKRIEAEEAIKGLNGQK 66
RRM2_U2B cd12481
RNA recognition motif 2 (RRM2) found in vertebrate U2 small nuclear ribonucleoprotein B" (U2B") ...
26-100 1.38e-05

RNA recognition motif 2 (RRM2) found in vertebrate U2 small nuclear ribonucleoprotein B" (U2B"); This subgroup corresponds to the RRM1 of U2B" (also termed U2 snRNP B"), a unique protein that comprises the U2 snRNP. It was initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. U2B" does not require an auxiliary protein for binding to RNA and its nuclear transport is independent of U2 snRNA binding. U2B" contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It also contains a nuclear localization signal (NLS) in the central domain. However, nuclear import of U2B'' does not depend on this NLS. The N-terminal RRM is sufficient to direct U2B" to the nucleus.


Pssm-ID: 240925 [Multi-domain]  Cd Length: 80  Bit Score: 41.54  E-value: 1.38e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1034658956  26 LFVSGLPLDIKPRELYLLFRPFKGYEGSLIkLTSKQPVGFVSFDSRSEAEAAKNALNGIRFDPEipQTLRLEFAK 100
Cdd:cd12481     8 LFLNNLPEETNEMMLSMLFNQFPGFKEVRL-VPGRHDIAFVEFENEAQAGAARDALQGFKITPS--HAMKITYAK 79
RRM3_NGR1_NAM8_like cd12346
RNA recognition motif 3 (RRM3) found in yeast negative growth regulatory protein NGR1 (RBP1), ...
25-83 2.13e-05

RNA recognition motif 3 (RRM3) found in yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8 and similar proteins; This subfamily corresponds to the RRM3 of NGR1 and NAM8. NGR1, also termed RNA-binding protein RBP1, is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA) in yeast. It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the carboxyl terminus which also harbors a methionine-rich region. The family also includes protein NAM8, which is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. Like NGR1, NAM8 contains two RRMs.


Pssm-ID: 409782 [Multi-domain]  Cd Length: 72  Bit Score: 40.77  E-value: 2.13e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1034658956  25 TLFVSGLPLDIKPRELYLLFRPFkgyeGSL--IKLTSKQPVGFVSFDSRSEAEAAKNALNG 83
Cdd:cd12346     3 TVFVGGLDPNVTEEDLRVLFGPF----GEIvyVKIPPGKGCGFVQFVNRASAEAAIQKLQG 59
RRM_NRD1_SEB1_like cd12331
RNA recognition motif (RRM) found in Saccharomyces cerevisiae protein Nrd1, ...
24-86 2.38e-05

RNA recognition motif (RRM) found in Saccharomyces cerevisiae protein Nrd1, Schizosaccharomyces pombe Rpb7-binding protein seb1 and similar proteins; This subfamily corresponds to the RRM of Nrd1 and Seb1. Nrd1 is a novel heterogeneous nuclear ribonucleoprotein (hnRNP)-like RNA-binding protein encoded by gene NRD1 (for nuclear pre-mRNA down-regulation) from yeast S. cerevisiae. It is implicated in 3' end formation of small nucleolar and small nuclear RNAs transcribed by polymerase II, and plays a critical role in pre-mRNA metabolism. Nrd1 contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a short arginine-, serine-, and glutamate-rich segment similar to the regions rich in RE and RS dipeptides (RE/RS domains) in many metazoan splicing factors, and a proline- and glutamine-rich C-terminal domain (P+Q domain) similar to domains found in several yeast hnRNPs. Disruption of NRD1 gene is lethal to yeast cells. Its N-terminal domain is sufficient for viability, which may facilitate interactions with RNA polymerase II where Nrd1 may function as an auxiliary factor. By contrast, the RRM, RE/RS domains, and P+Q domain are dispensable. Seb1 is an RNA-binding protein encoded by gene seb1 (for seven binding) from fission yeast S. pombe. It is essential for cell viability and bound directly to Rpb7 subunit of RNA polymerase II. Seb1 is involved in processing of polymerase II transcripts. It also contains one RRM motif and a region rich in arginine-serine dipeptides (RS domain).


Pssm-ID: 409768 [Multi-domain]  Cd Length: 79  Bit Score: 41.01  E-value: 2.38e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1034658956  24 RTLFVSGLPLDIKPRELYLLFRPFkGYEGSLIkLTSKQPVGFVSFDSRSEAEAAKNALNGIRF 86
Cdd:cd12331     4 RTLFIGGVTLNMKEWDLRSVFKRF-GEVQSVI-LNNSRRHAFVKMYSRHEAENALQAMEKVPD 64
RRM2_HuC cd12776
RNA recognition motif 2 (RRM2) found in vertebrate Hu-antigen C (HuC); This subgroup ...
26-83 4.90e-05

RNA recognition motif 2 (RRM2) found in vertebrate Hu-antigen C (HuC); This subgroup corresponds to the RRM2 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 241220 [Multi-domain]  Cd Length: 81  Bit Score: 39.98  E-value: 4.90e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1034658956  26 LFVSGLPLDIKPRELYLLFRPFKGYEGSLIKLTS----KQPVGFVSFDSRSEAEAAKNALNG 83
Cdd:cd12776     4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQvtgvSRGVGFIRFDKRIEAEEAIKGLNG 65
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
25-87 6.93e-05

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


Pssm-ID: 440488 [Multi-domain]  Cd Length: 85  Bit Score: 39.70  E-value: 6.93e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034658956  25 TLFVSGLPLDIKPRELYLLFRPF-----------------KGYegslikltskqpvGFVSFDSRSEAEAAKNALNGIRFD 87
Cdd:COG0724     3 KIYVGNLPYSVTEEDLRELFSEYgevtsvklitdretgrsRGF-------------GFVEMPDDEEAQAAIEALNGAELM 69
RRM2_MSSP cd12244
RNA recognition motif 2 (RRM2) found in the c-myc gene single-strand binding proteins (MSSP) ...
26-99 7.18e-05

RNA recognition motif 2 (RRM2) found in the c-myc gene single-strand binding proteins (MSSP) family; This subfamily corresponds to the RRM2 of c-myc gene single-strand binding proteins (MSSP) family, including single-stranded DNA-binding protein MSSP-1 (also termed RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3). All MSSP family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity. Both, MSSP-1 and -2, have been identified as protein factors binding to a putative DNA replication origin/transcriptional enhancer sequence present upstream from the human c-myc gene in both single- and double-stranded forms. Thus they have been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. Moreover, they family includes a new member termed RNA-binding motif, single-stranded-interacting protein 3 (RBMS3), which is not a transcriptional regulator. RBMS3 binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. In addition, a putative meiosis-specific RNA-binding protein termed sporulation-specific protein 5 (SPO5, or meiotic RNA-binding protein 1, or meiotically up-regulated gene 12 protein), encoded by Schizosaccharomyces pombe Spo5/Mug12 gene, is also included in this family. SPO5 is a novel meiosis I regulator that may function in the vicinity of the Mei2 dot.


Pssm-ID: 409690 [Multi-domain]  Cd Length: 82  Bit Score: 39.67  E-value: 7.18e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034658956  26 LFVSGLPLDIKPRELYLLFRPFkgyeGSLI--------KLTSKQpVGFVSFDSRSEAEAAKNALNGIRFDPEIPQT--LR 95
Cdd:cd12244     3 LYISNLPLDMDEQDLENMLKPF----GQVIstrilrdsKGQSRG-VGFARMESREKCEDVISKFNGKVLKTPSASGepLL 77

                  ....
gi 1034658956  96 LEFA 99
Cdd:cd12244    78 VKFA 81
RRM2_HuB cd12775
RNA recognition motif 2 (RRM2) found in vertebrate Hu-antigen B (HuB); This subgroup ...
26-99 8.06e-05

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


Pssm-ID: 410168 [Multi-domain]  Cd Length: 84  Bit Score: 39.70  E-value: 8.06e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1034658956  26 LFVSGLPLDIKPRELYLLFRPFKGYEGSLIKLTS----KQPVGFVSFDSRSEAEAAKNALNGIRfDPEIPQTLRLEFA 99
Cdd:cd12775     8 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQvtgvSRGVGFIRFDKRIEAEEAIKGLNGQK-PPGATEPITVKFA 84
RRM2_HuD cd12774
RNA recognition motif 2 (RRM2) found in vertebrate Hu-antigen D (HuD); This subgroup ...
26-83 1.00e-04

RNA recognition motif 2 (RRM2) found in vertebrate Hu-antigen D (HuD); This subgroup corresponds to the RRM2 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells and also regulates the neurite elongation and morphological differentiation. HuD specifically binds poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 410167 [Multi-domain]  Cd Length: 84  Bit Score: 39.32  E-value: 1.00e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1034658956  26 LFVSGLPLDIKPRELYLLFRPFKGYEGSLIKLTS----KQPVGFVSFDSRSEAEAAKNALNG 83
Cdd:cd12774     8 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQvtgvSRGVGFIRFDKRIEAEEAIKGLNG 69
RRM3_Hu cd12377
RNA recognition motif 3 (RRM3) found in the Hu proteins family; This subfamily corresponds to ...
25-92 1.16e-04

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


Pssm-ID: 409811 [Multi-domain]  Cd Length: 76  Bit Score: 38.84  E-value: 1.16e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1034658956  25 TLFVSGLPLDIKPRELYLLFRPFKGYEG-SLIKLTSKQP---VGFVSFDSRSEAEAAKNALNGIRFDPEIPQ 92
Cdd:cd12377     1 CIFVYNLAPDADESLLWQLFGPFGAVQNvKIIRDFTTNKckgYGFVTMTNYDEAAVAIASLNGYRLGGRVLQ 72
RRM1_SRSF1_like cd12338
RNA recognition motif 1 (RRM1) found in serine/arginine-rich splicing factor 1 (SRSF1) and ...
25-98 1.18e-04

RNA recognition motif 1 (RRM1) found in serine/arginine-rich splicing factor 1 (SRSF1) and similar proteins; This subgroup corresponds to the RRM1 in three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 1 (SRSF1 or ASF-1), serine/arginine-rich splicing factor 9 (SRSF9 or SRp30C), and plant pre-mRNA-splicing factor SF2 (SR1). SRSF1 is a shuttling SR protein involved in constitutive and alternative splicing, nonsense-mediated mRNA decay (NMD), mRNA export and translation. It also functions as a splicing-factor oncoprotein that regulates apoptosis and proliferation to promote mammary epithelial cell transformation. SRSF9 has been implicated in the activity of many elements that control splice site selection, the alternative splicing of the glucocorticoid receptor beta in neutrophils and in the gonadotropin-releasing hormone pre-mRNA. It can also interact with other proteins implicated in alternative splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. Both, SRSF1 and SRSF9, contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RS domains rich in serine-arginine dipeptides. In contrast, SF2 contains two N-terminal RRMs and a C-terminal PSK domain rich in proline, serine and lysine residues.


Pssm-ID: 409775 [Multi-domain]  Cd Length: 72  Bit Score: 38.89  E-value: 1.18e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1034658956  25 TLFVSGLPLDIKPRELYLLFRPFkgyeGSLIKLTSKQPVG-----FVSFDSRSEAEAAKNALNGIRFDpeiPQTLRLEF 98
Cdd:cd12338     1 RIYVGNLPGDIRERDIEDLFYKY----GPILAIDLKNRRRgppfaFVEFEDPRDAEDAIRGRDGYDFD---GYRLRVEF 72
RRM_Srp1p_like cd12467
RNA recognition motif 1 (RRM1) found in fission yeast pre-mRNA-splicing factor Srp1p and ...
25-100 1.63e-04

RNA recognition motif 1 (RRM1) found in fission yeast pre-mRNA-splicing factor Srp1p and similar proteins; This subgroup corresponds to the RRM domain in Srp1p encoded by gene srp1 from fission yeast Schizosaccharomyces pombe. It plays a role in the pre-mRNA splicing process, but not essential for growth. Srp1p is closely related to the SR protein family found in metazoa. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine hinge and a RS domain in the middle, and a C-terminal domain. Some family members also contain another RRM domain.


Pssm-ID: 240913 [Multi-domain]  Cd Length: 78  Bit Score: 38.63  E-value: 1.63e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034658956  25 TLFVSGLPLDIKPRELYLLFRPFkgyeGSLIKL-------TSKQPVGFVSFDSRSEAEAAKNALNGIRFdPEIPQTLRLE 97
Cdd:cd12467     1 TLYVTGFGAETRARDLAYEFERY----GRLVRCdippprtFQSRPFAFVEYESHRDAEDAYEEMHGRRF-PDTGDTLHVQ 75

                  ...
gi 1034658956  98 FAK 100
Cdd:cd12467    76 WAK 78
RRM1_SF2_plant_like cd12599
RNA recognition motif 1 (RRM1) found in plant pre-mRNA-splicing factor SF2 and similar ...
25-97 2.10e-04

RNA recognition motif 1 (RRM1) found in plant pre-mRNA-splicing factor SF2 and similar proteins; This subgroup corresponds to the RRM1 of SF2, also termed SR1 protein, a plant serine/arginine (SR)-rich phosphoprotein similar to the mammalian splicing factor SF2/ASF. It promotes splice site switching in mammalian nuclear extracts. SF2 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal domain rich in proline, serine and lysine residues (PSK domain), a composition reminiscent of histones. This PSK domain harbors a putative phosphorylation site for the mitotic kinase cyclin/p34cdc2.


Pssm-ID: 410011 [Multi-domain]  Cd Length: 72  Bit Score: 38.19  E-value: 2.10e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1034658956  25 TLFVSGLPLDIKPRELYLLFRPFkgyeGSLIKLTSKQPV-----GFVSFDSRSEAEAAKNALNGIRFDpeiPQTLRLE 97
Cdd:cd12599     1 RVYVGNLPMDIREREVEDLFSKY----GPVVSIDLKIPPrppayAFVEFEDARDAEDAIRGRDGYDFD---GHRLRVE 71
RRM2_NsCP33_like cd21608
RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ...
25-87 2.91e-04

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


Pssm-ID: 410187 [Multi-domain]  Cd Length: 76  Bit Score: 37.92  E-value: 2.91e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1034658956  25 TLFVSGLPLDIKPRELYLLFRPFKG-YEGSLI--KLTSKQPV-GFVSFDSRSEAEAAKNALNGIRFD 87
Cdd:cd21608     1 KLYVGNLSWDTTEDDLRDLFSEFGEvESAKVItdRETGRSRGfGFVTFSTAEAAEAAIDALNGKELD 67
RRM1_Nop4p cd12674
RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; ...
24-101 3.97e-04

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


Pssm-ID: 410075 [Multi-domain]  Cd Length: 80  Bit Score: 37.44  E-value: 3.97e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034658956  24 RTLFVSGLPLDIKPRELYLLFRPFKGYEGSLIKLTSK----QPVGFVSFDSRSEAEAAKNALNGIRFDPEIpqtLRLEFA 99
Cdd:cd12674     1 TTLFVRNLPFDVTLESLTDFFSDIGPVKHAVVVTDPEtkksRGYGFVSFSTHDDAEEALAKLKNRKLSGHI---LKLDFA 77

                  ..
gi 1034658956 100 KA 101
Cdd:cd12674    78 KP 79
RRM1_MEI2_like cd12524
RNA recognition motif 1 (RRM1) found in plant Mei2-like proteins; This subgroup corresponds to ...
24-83 5.53e-04

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


Pssm-ID: 409944 [Multi-domain]  Cd Length: 77  Bit Score: 37.26  E-value: 5.53e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1034658956  24 RTLFVSGLPLDIKPRELYLLFRPFkgyeGSLIKL-TSKQPVGF--VSF-DSRSeAEAAKNALNG 83
Cdd:cd12524     2 RTLFVRNINSSVEDEELRALFEQF----GEIRTLyTACKHRGFimVSYyDIRA-AQSAKRALQG 60
RRM2_CELF3_4_5_6 cd12635
RNA recognition motif 2 (RRM2) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, ...
24-99 6.05e-04

RNA recognition motif 2 (RRM2) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins; This subgroup corresponds to the RRM2 of CELF-3, CELF-4, CELF-5, and CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, being highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contain three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. On the other hand, both RRM1 and RRM2 of CELF-4 can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, being strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in a muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In addition to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region.


Pssm-ID: 410043 [Multi-domain]  Cd Length: 81  Bit Score: 37.01  E-value: 6.05e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034658956  24 RTLFVSGLPLDIKPRELYLLFRPFkgyeGSLIKLT-------SKQPVGFVSFDSRSEAEAAKNALNGIRFDPEIPQTLRL 96
Cdd:cd12635     2 RKLFVGMLGKQQSEDDVRRLFEPF----GSIEECTilrgpdgNSKGCAFVKFSSHAEAQAAINALHGSQTMPGASSSLVV 77

                  ...
gi 1034658956  97 EFA 99
Cdd:cd12635    78 KFA 80
RRM2_SNF cd12479
RNA recognition motif 2 (RRM2) found in Drosophila melanogaster sex determination protein SNF ...
24-100 6.13e-04

RNA recognition motif 2 (RRM2) found in Drosophila melanogaster sex determination protein SNF and similar proteins; This subgroup corresponds to the RRM2 of SNF (Sans fille), also termed U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A), an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila. It is essential in Drosophila sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). SNF contains two RNA recognition motifs (RRMs); it can self-associate through RRM1, and each RRM can recognize poly(U) RNA binding independently.


Pssm-ID: 240923 [Multi-domain]  Cd Length: 80  Bit Score: 36.99  E-value: 6.13e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1034658956  24 RTLFVSGLPLDIKPRELYLLFRPFKGYEGSLIkLTSKQPVGFVSFDSRSEAEAAKNALNGIRFDPEipQTLRLEFAK 100
Cdd:cd12479     6 QILFLTNLPEETNEMMLSMLFNQFPGFKEVRL-VPGRHDIAFVEFENEVQSAAAKEALQGFKITPT--HAMKITFAK 79
RRM1_2_CoAA_like cd12343
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in RRM-containing coactivator activator ...
26-88 6.79e-04

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


Pssm-ID: 409779 [Multi-domain]  Cd Length: 66  Bit Score: 36.44  E-value: 6.79e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1034658956  26 LFVSGLPLDIKPRELYLLFRPF-KGYEGSLIKltskqPVGFVSFDSRSEAEAAKNALNGIRFDP 88
Cdd:cd12343     2 IFVGNLPDAATSEELRALFEKYgKVTECDIVK-----NYAFVHMEKEEDAEDAIKALNGYEFMG 60
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
64-165 7.90e-04

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


Pssm-ID: 130689 [Multi-domain]  Cd Length: 562  Bit Score: 39.02  E-value: 7.90e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034658956  64 GFVSFDSRSEAEAAKNALNGIRFDPEiP-------------QTLRLEFAKANTKMaknklvgtpnPSTPLPNTVPQFIAR 130
Cdd:TIGR01628 329 GFVCFSNPEEANRAVTEMHGRMLGGK-PlyvalaqrkeqrrAHLQDQFMQLQPRM----------RQLPMGSPMGGAMGQ 397
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1034658956 131 EPYELTVP-ALYPSSPEVWA-----PYPLYP-AELAPALPPP 165
Cdd:TIGR01628 398 PPYYGQGPqQQFNGQPLGWPrmsmmPTPMGPgGPLRPNGLAP 439
RRM1_RBM28_like cd12413
RNA recognition motif 1 (RRM1) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
25-100 8.11e-04

RNA recognition motif 1 (RRM1) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM1 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs.


Pssm-ID: 409847 [Multi-domain]  Cd Length: 79  Bit Score: 36.80  E-value: 8.11e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034658956  25 TLFVSGLPLDIKPRELYLLF-------RPFkgyegsLIKLTSKQP---VGFVSFDSRSEAEAAKNALNGIRFDPEIpqtL 94
Cdd:cd12413     1 TLFVRNLPYDTTDEQLEELFsdvgpvkRCF------VVKDKGKDKcrgFGYVTFALAEDAQRALEEVKGKKFGGRK---I 71

                  ....*.
gi 1034658956  95 RLEFAK 100
Cdd:cd12413    72 KVELAK 77
RRM4_MRD1 cd12319
RNA recognition motif 4 (RRM4) found in yeast multiple RNA-binding domain-containing protein 1 ...
25-87 8.53e-04

RNA recognition motif 4 (RRM4) found in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins; This subfamily corresponds to the RRM4 of MRD1which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 409758 [Multi-domain]  Cd Length: 84  Bit Score: 36.69  E-value: 8.53e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1034658956  25 TLFVSGLPLDIKPRELYLLFRPFKGYEGSLIKLTS--KQP-------VGFVSFDSRSEAEAAKNALNGIRFD 87
Cdd:cd12319     2 TLFVKNLNFSTTNQHLTDVFKHLDGFVFARVKTKPdpKRPgktlsmgFGFVGFKTKEQAQAALKAMDGFVLD 73
RRM2_HuR cd12773
RNA recognition motif 2 (RRM2) found in vertebrate Hu-antigen R (HuR); This subgroup ...
26-83 1.18e-03

RNA recognition motif 2 (RRM2) found in vertebrate Hu-antigen R (HuR); This subgroup corresponds to the RRM2 of HuR, also termed ELAV-like protein 1 (ELAV-1), the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Like other Hu proteins, HuR contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 410166 [Multi-domain]  Cd Length: 84  Bit Score: 36.43  E-value: 1.18e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1034658956  26 LFVSGLPLDIKPRELYLLFRPFKGYEGS--LIKLTS--KQPVGFVSFDSRSEAEAAKNALNG 83
Cdd:cd12773     3 LYISGLPRTMTQKDVEDMFSRFGRIINSrvLVDQATglSRGVAFIRFDKRSEAEEAITNFNG 64
RRM_RBM22 cd12224
RNA recognition motif (RRM) found in Pre-mRNA-splicing factor RBM22 and similar proteins; This ...
23-77 1.21e-03

RNA recognition motif (RRM) found in Pre-mRNA-splicing factor RBM22 and similar proteins; This subgroup corresponds to the RRM of RBM22 (also known as RNA-binding motif protein 22, or Zinc finger CCCH domain-containing protein 16), a newly discovered RNA-binding motif protein which belongs to the SLT11 gene family. SLT11 gene encoding protein (Slt11p) is a splicing factor in yeast, which is required for spliceosome assembly. Slt11p has two distinct biochemical properties: RNA-annealing and RNA-binding activities. RBM22 is the homolog of SLT11 in vertebrate. It has been reported to be involved in pre-splicesome assembly and to interact with the Ca2+-signaling protein ALG-2. It also plays an important role in embryogenesis. RBM22 contains a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a zinc finger of the unusual type C-x8-C-x5-C-x3-H, and a C-terminus that is unusually rich in the amino acids Gly and Pro, including sequences of tetraprolines.


Pssm-ID: 409671 [Multi-domain]  Cd Length: 74  Bit Score: 36.11  E-value: 1.21e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1034658956  23 VRTLFVSGLPLDIKPRELYLLFRPFkgyeGSL--IKLTSKQPVGFVSFDSRSEAEAA 77
Cdd:cd12224     1 ITTLYVGGLGDKITEKDLRDHFYQF----GEIrsITVVARQQCAFVQFTTRQAAERA 53
sex-lethal TIGR01659
sex-lethal family splicing factor; This model describes the sex-lethal family of splicing ...
26-84 1.26e-03

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


Pssm-ID: 273740 [Multi-domain]  Cd Length: 346  Bit Score: 38.46  E-value: 1.26e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1034658956  26 LFVSGLPLDIKPRELYLLFRPFKGYEGSLIKLTSKQ----PVGFVSFDSRSEAEAAKNALNGI 84
Cdd:TIGR01659 110 LIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTgysfGYAFVDFGSEADSQRAIKNLNGI 172
RRM4_NCL cd12406
RNA recognition motif 4 (RRM4) found in vertebrate nucleolin; This subfamily corresponds to ...
24-100 2.10e-03

RNA recognition motif 4 (RRM4) found in vertebrate nucleolin; This subfamily corresponds to the RRM4 of ubiquitously expressed protein nucleolin, also termed protein C23, is a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines.


Pssm-ID: 409840 [Multi-domain]  Cd Length: 78  Bit Score: 35.66  E-value: 2.10e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034658956  24 RTLFVSGLPLDIKPRELYllfRPFKGYEGSLI----KLTSKQPVGFVSFDSRSEAEAAKNALNgirfDPEIP-QTLRLEF 98
Cdd:cd12406     1 KTLFVKGLSEDTTEETLK---EAFEGAISARIatdrDTGSSKGFGFVDFSSEEDAKAAKEAME----DGEIDgNKVTLDF 73

                  ..
gi 1034658956  99 AK 100
Cdd:cd12406    74 AK 75
RRM1_PSP1 cd12586
RNA recognition motif 1 (RRM1) found in vertebrate paraspeckle protein 1 (PSP1); This subgroup ...
26-83 2.90e-03

RNA recognition motif 1 (RRM1) found in vertebrate paraspeckle protein 1 (PSP1); This subgroup corresponds to the RRM1 of PSPC1, also termed paraspeckle component 1 (PSPC1), a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. It is ubiquitously expressed and highly conserved in vertebrates. Its cellular function remains unknown currently, however, PSPC1 forms a novel heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO), which localizes to paraspeckles in an RNA-dependent manner. PSPC1 contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus.


Pssm-ID: 409999 [Multi-domain]  Cd Length: 71  Bit Score: 34.90  E-value: 2.90e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1034658956  26 LFVSGLPLDIKPRELYLLFrpFKGYEGSLIKLTSKQPVGFVSFDSRSEAEAAKNALNG 83
Cdd:cd12586     4 LFVGNLPTDITEEDFKRLF--ERYGEPSEVFINRDRGFGFIRLESRTLAEIAKAELDG 59
RRM_ALKBH8 cd12431
RNA recognition motif (RRM) found in alkylated DNA repair protein alkB homolog 8 (ALKBH8) and ...
24-101 3.09e-03

RNA recognition motif (RRM) found in alkylated DNA repair protein alkB homolog 8 (ALKBH8) and similar proteins; This subfamily corresponds to the RRM of ALKBH8, also termed alpha-ketoglutarate-dependent dioxygenase ABH8, or S-adenosyl-L-methionine-dependent tRNA methyltransferase ABH8, expressed in various types of human cancers. It is essential in urothelial carcinoma cell survival mediated by NOX-1-dependent ROS signals. ALKBH8 has also been identified as a tRNA methyltransferase that catalyzes methylation of tRNA to yield 5-methylcarboxymethyl uridine (mcm5U) at the wobble position of the anticodon loop. Thus, ALKBH8 plays a crucial role in the DNA damage survival pathway through a distinct mechanism involving the regulation of tRNA modification. ALKBH8 localizes to the cytoplasm. It contains the characteristic AlkB domain that is composed of a tRNA methyltransferase motif, a motif homologous to the bacterial AlkB DNA/RNA repair enzyme, and a dioxygenase catalytic core domain encompassing cofactor-binding sites for iron and 2-oxoglutarate. In addition, unlike other AlkB homologs, ALKBH8 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal S-adenosylmethionine (SAM)-dependent methyltransferase (MT) domain.


Pssm-ID: 409865 [Multi-domain]  Cd Length: 80  Bit Score: 35.25  E-value: 3.09e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034658956  24 RTLFVS--GLPLDIKPRELYLLFRPFKGYEgSLIKLTSKqPVGFVSFDSRSEAEAAKNALNGIR-FDPEIPQTLRLEFAK 100
Cdd:cd12431     2 QHLVVAngGLGNGVSREQLLEVFEKYGTVE-DIVMLPGK-PYSFVSFKSVEEAAKAYNALNGKElELPQQNVPLYLSFVE 79

                  .
gi 1034658956 101 A 101
Cdd:cd12431    80 K 80
RRM1_SECp43_like cd12344
RNA recognition motif 1 (RRM1) found in tRNA selenocysteine-associated protein 1 (SECp43) and ...
56-102 3.09e-03

RNA recognition motif 1 (RRM1) found in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins; This subfamily corresponds to the RRM1 in tRNA selenocysteine-associated protein 1 (SECp43), yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8, and similar proteins. SECp43 is an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. Yeast proteins, NGR1 and NAM8, show high sequence similarity with SECp43. NGR1 is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA). It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains three RRMs, two of which are followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the C-terminus which also harbors a methionine-rich region. NAM8 is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. NAM8 also contains three RRMs.


Pssm-ID: 409780 [Multi-domain]  Cd Length: 82  Bit Score: 34.97  E-value: 3.09e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1034658956  56 KLTSKQP-VGFVSFDSRSEAEAAKNALNGIRFdPEIPQTLRLEFAKAN 102
Cdd:cd12344    36 KQTGKSAgYCFVEFATQEAAEQALEHLNGKPI-PNTQQRFRLNWASFS 82
RRM2_SXL cd12651
RNA recognition motif 2 (RRM2) found in Drosophila sex-lethal (SXL) and similar proteins; This ...
26-86 3.24e-03

RNA recognition motif 2 (RRM2) found in Drosophila sex-lethal (SXL) and similar proteins; This subfamily corresponds to the RRM2 of the sex-lethal protein (SXL) which governs sexual differentiation and X chromosome dosage compensation in Drosophila melanogaster. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that show high preference to bind single-stranded, uridine-rich target RNA transcripts.


Pssm-ID: 410054 [Multi-domain]  Cd Length: 81  Bit Score: 35.25  E-value: 3.24e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1034658956  26 LFVSGLPLDIKPRELYLLFrpfkGYEGSLI-------KLTSK-QPVGFVSFDSRSEAEAAKNALNGIRF 86
Cdd:cd12651     5 LYVTNLPRTITEDELDTIF----GAYGNIVqknllrdKLTGRpRGVAFVRYDKREEAQAAISALNGTIP 69
RRM_TRA2 cd12363
RNA recognition motif (RRM) found in transformer-2 protein homolog TRA2-alpha, TRA2-beta and ...
23-87 4.41e-03

RNA recognition motif (RRM) found in transformer-2 protein homolog TRA2-alpha, TRA2-beta and similar proteins; This subfamily corresponds to the RRM of two mammalian homologs of Drosophila transformer-2 (Tra2), TRA2-alpha, TRA2-beta (also termed SFRS10), and similar proteins found in eukaryotes. TRA2-alpha is a 40-kDa serine/arginine-rich (SR) protein that specifically binds to gonadotropin-releasing hormone (GnRH) exonic splicing enhancer on exon 4 (ESE4) and is necessary for enhanced GnRH pre-mRNA splicing. It strongly stimulates GnRH intron A excision in a dose-dependent manner. In addition, TRA2-alpha can interact with either 9G8 or SRp30c, which may also be crucial for ESE-dependent GnRH pre-mRNA splicing. TRA2-beta is a serine/arginine-rich (SR) protein that controls the pre-mRNA alternative splicing of the calcitonin/calcitonin gene-related peptide (CGRP), the survival motor neuron 1 (SMN1) protein and the tau protein. Both, TRA2-alpha and TRA2-beta, contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions.


Pssm-ID: 409798 [Multi-domain]  Cd Length: 80  Bit Score: 34.51  E-value: 4.41e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1034658956  23 VRTLFVSGLPLDIKPRELYLLFRPFkgyeGSLIKLtskQPV-----------GFVSFDSRSEAEAAKNALNGIRFD 87
Cdd:cd12363     1 SRCLGVFGLSLYTTERDLREVFSRY----GPIEKV---QVVydqqtgrsrgfGFVYFESVEDAKEAKERLNGQEID 69
RRM3_Nop4p cd12676
RNA recognition motif 3 (RRM3) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; ...
24-100 4.71e-03

RNA recognition motif 3 (RRM3) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; This subgroup corresponds to the RRM3 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 410077 [Multi-domain]  Cd Length: 107  Bit Score: 35.09  E-value: 4.71e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034658956  24 RTLFVSGLPLDIKPRELYLLFRPFKGYEGSLI---KLT--SKQpVGFVSFDSRSEAEAAknalngIRFDPEIPQTLRLEF 98
Cdd:cd12676     2 RTLFVRNLPFDATEDELYSHFSQFGPLKYARVvkdPATgrSKG-TAFVKFKNKEDADNC------LSAAPEAQSTSLLEK 74

                  ..
gi 1034658956  99 AK 100
Cdd:cd12676    75 YS 76
RRM_RBMX_like cd12382
RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein G (hnRNP G), Y ...
26-87 4.77e-03

RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein G (hnRNP G), Y chromosome RNA recognition motif 1 (hRBMY), testis-specific heterogeneous nuclear ribonucleoprotein G-T (hnRNP G-T) and similar proteins; This subfamily corresponds to the RRM domain of hnRNP G, also termed glycoprotein p43 or RBMX, an RNA-binding motif protein located on the X chromosome. It is expressed ubiquitously and has been implicated in the splicing control of several pre-mRNAs. Moreover, hnRNP G may function as a regulator of transcription for SREBP-1c and GnRH1. Research has shown that hnRNP G may also act as a tumor-suppressor since it upregulates the Txnip gene and promotes the fidelity of DNA end-joining activity. In addition, hnRNP G appears to play a critical role in proper neural development of zebrafish and frog embryos. The family also includes several paralogs of hnRNP G, such as hRBMY and hnRNP G-T (also termed RNA-binding motif protein, X-linked-like-2). Both, hRBMY and hnRNP G-T, are exclusively expressed in testis and critical for male fertility. Like hnRNP G, hRBMY and hnRNP G-T interact with factors implicated in the regulation of pre-mRNA splicing, such as hTra2-beta1 and T-STAR. Although members in this family share a high conserved N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), they appear to recognize different RNA targets. For instance, hRBMY interacts specifically with a stem-loop structure in which the loop is formed by the sequence CA/UCAA. In contrast, hnRNP G associates with single stranded RNA sequences containing a CCA/C motif. In addition to the RRM, hnRNP G contains a nascent transcripts targeting domain (NTD) in the middle region and a novel auxiliary RNA-binding domain (RBD) in its C-terminal region. The C-terminal RBD exhibits distinct RNA binding specificity, and would play a critical role in the regulation of alternative splicing by hnRNP G.


Pssm-ID: 409816 [Multi-domain]  Cd Length: 80  Bit Score: 34.69  E-value: 4.77e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1034658956  26 LFVSGLPLDIKPRELYLLFRPF-KGYEGSLIK--LTSK-QPVGFVSFDSRSEAEAAKNALNGIRFD 87
Cdd:cd12382     4 LFIGGLNTETNEKALEAVFGKYgRIVEVLLMKdrETNKsRGFAFVTFESPADAKDAARDMNGKELD 69
RRM3_CELF3_4_5_6 cd12639
RNA recognition motif 2 (RRM2) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, ...
26-85 5.17e-03

RNA recognition motif 2 (RRM2) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins; This subgroup corresponds to the RRM3 of CELF-3, CELF-4, CELF-5, and CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein.The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contains three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. Both, RRM1 and RRM2 of CELF-4, can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in an muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In addition to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region.


Pssm-ID: 241083 [Multi-domain]  Cd Length: 79  Bit Score: 34.45  E-value: 5.17e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1034658956  26 LFVSGLPLDIKPRELYLLFRPFkgyeGSLI-------KLTSKQPV-GFVSFDSRSEAEAAKNALNGIR 85
Cdd:cd12639     7 LFIYHLPQEFGDAELMQMFLPF----GNVIsakvfvdRATNQSKCfGFVSFDNPASAQAAIQAMNGFQ 70
RRM3_hnRNPR_like cd12251
RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein R (hnRNP R) ...
23-101 5.60e-03

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


Pssm-ID: 409697 [Multi-domain]  Cd Length: 72  Bit Score: 34.14  E-value: 5.60e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1034658956  23 VRTLFVSGLPLDIKPRELYLLFRPFkgyeGSLIKLTSKQPVGFVSFDSRSEAEAAKNALNGIRFDpeiPQTLRLEFAKA 101
Cdd:cd12251     1 VKVLYVRNLMLSTTEEKLRELFSEY----GKVERVKKIKDYAFVHFEERDDAVKAMEEMNGKELE---GSEIEVSLAKP 72
RRM_SR140 cd12223
RNA recognition motif (RRM) found in U2-associated protein SR140 and similar proteins; This ...
26-101 7.37e-03

RNA recognition motif (RRM) found in U2-associated protein SR140 and similar proteins; This subgroup corresponds to the RRM of SR140 (also termed U2 snRNP-associated SURP motif-containing protein orU2SURP, or 140 kDa Ser/Arg-rich domain protein) which is a putative splicing factor mainly found in higher eukaryotes. Although it is initially identified as one of the 17S U2 snRNP-associated proteins, the molecular and physiological function of SR140 remains unclear. SR140 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a SWAP/SURP domain that is found in a number of pre-mRNA splicing factors in the middle region, and a C-terminal arginine/serine-rich domain (RS domain).


Pssm-ID: 409670 [Multi-domain]  Cd Length: 84  Bit Score: 34.19  E-value: 7.37e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034658956  26 LFVSGLPLDIKPRELYLLFRPFkgyeGSLIKLTSKQP-----------VGFVSFDSRSEAEAAKNALNGIRFDPEipqTL 94
Cdd:cd12223     4 LYVGNLPPSVTEEVLLREFGRF----GPLASVKIMWPrteeerrrnrnCGFVAFMSRADAERAMRELNGKDVMGY---EL 76

                  ....*..
gi 1034658956  95 RLEFAKA 101
Cdd:cd12223    77 KLGWGKA 83
RRM1_2_CELF1-6_like cd12361
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in CELF/Bruno-like family of RNA binding ...
17-84 7.39e-03

RNA recognition motif 1 (RRM1) and 2 (RRM2) found in CELF/Bruno-like family of RNA binding proteins and plant flowering time control protein FCA; This subfamily corresponds to the RRM1 and RRM2 domains of the CUGBP1 and ETR-3-like factors (CELF) as well as plant flowering time control protein FCA. CELF, also termed BRUNOL (Bruno-like) proteins, is a family of structurally related RNA-binding proteins involved in regulation of pre-mRNA splicing in the nucleus, and control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also known as BRUNOL-2, CUG-BP1, NAPOR, EDEN-BP), CELF-2 (also known as BRUNOL-3, ETR-3, CUG-BP2, NAPOR-2), CELF-3 (also known as BRUNOL-1, TNRC4, ETR-1, CAGH4, ER DA4), CELF-4 (BRUNOL-4), CELF-5 (BRUNOL-5) and CELF-6 (BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both, sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts. This subfamily also includes plant flowering time control protein FCA that functions in the posttranscriptional regulation of transcripts involved in the flowering process. FCA contains two RRMs, and a WW protein interaction domain.


Pssm-ID: 409796 [Multi-domain]  Cd Length: 77  Bit Score: 34.13  E-value: 7.39e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1034658956  17 NLQEEEVRTLFVSGLPLDikprELYLLFRPFKGyegsliklTSKQpVGFVSFDSRSEAEAAKNALNGI 84
Cdd:cd12361    10 TASEEDVRPLFEQFGNIE----EVQILRDKQTG--------QSKG-CAFVTFSTREEALRAIEALHNK 64
RRM1_PSF cd12587
RNA recognition motif 1 (RRM1) found in vertebrate polypyrimidine tract-binding protein (PTB) ...
26-98 8.41e-03

RNA recognition motif 1 (RRM1) found in vertebrate polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF); This subgroup corresponds to the RRM1 of PSF, also termed proline- and glutamine-rich splicing factor, or 100 kDa DNA-pairing protein (POMp100), or 100 kDa subunit of DNA-binding p52/p100 complex, a multifunctional protein that mediates diverse activities in the cell. It is ubiquitously expressed and highly conserved in vertebrates. PSF binds not only RNA but also both single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) and facilitates the renaturation of complementary ssDNAs. Besides, it promotes the formation of D-loops in superhelical duplex DNA, and is involved in cell proliferation. PSF can also interact with multiple factors. It is an RNA-binding component of spliceosomes and binds to insulin-like growth factor response element (IGFRE). PSF functions as a transcriptional repressor interacting with Sin3A and mediating silencing through the recruitment of histone deacetylases (HDACs) to the DNA binding domain (DBD) of nuclear hormone receptors. Additionally, PSF is an essential pre-mRNA splicing factor and is dissociated from PTB and binds to U1-70K and serine-arginine (SR) proteins during apoptosis. PSF forms a heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO). The PSF/p54nrb complex displays a variety of functions, such as DNA recombination and RNA synthesis, processing, and transport. PSF contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which are responsible for interactions with RNA and for the localization of the protein in speckles. It also contains an N-terminal region rich in proline, glycine, and glutamine residues, which may play a role in interactions recruiting other molecules.


Pssm-ID: 410000 [Multi-domain]  Cd Length: 71  Bit Score: 33.68  E-value: 8.41e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1034658956  26 LFVSGLPLDIKPRELYLLFRPFKgyEGSLIKLTSKQPVGFVSFDSRSEAEAAKNALNGIrfdPEIPQTLRLEF 98
Cdd:cd12587     4 LFVGNLPADITEDEFKRLFAKYG--EPGEVFINKGKGFGFIKLESRALAEIAKAELDDT---PMRGRQLRVRF 71
RRM_Nab3p cd12342
RNA recognition motif (RRM) found in yeast nuclear polyadenylated RNA-binding protein 3 (Nab3p) ...
26-83 8.73e-03

RNA recognition motif (RRM) found in yeast nuclear polyadenylated RNA-binding protein 3 (Nab3p) and similar proteins; This subfamily corresponds to the RRM of Nab3p, an acidic nuclear polyadenylated RNA-binding protein encoded by Saccharomyces cerevisiae NAB3 gene that is essential for cell viability. Nab3p is predominantly localized within the nucleoplasm and essential for growth in yeast. It may play an important role in packaging pre-mRNAs into ribonucleoprotein structures amenable to efficient nuclear RNA processing. Nab3p contains an N-terminal aspartic/glutamic acid-rich region, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal region rich in glutamine and proline residues.


Pssm-ID: 240788 [Multi-domain]  Cd Length: 71  Bit Score: 33.57  E-value: 8.73e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1034658956  26 LFVSGLPLD-IKPRELYLLFRPFkgyeGSLIKLTSKQPVGFVSFDSrseAEAAKNALNG 83
Cdd:cd12342     2 LFIGNLPTKrVSKEDLFRIFSPY----GHLMQIVIKNAFGFVQFDS---PQSCRNAIEC 53
RRM_SF3B14 cd12241
RNA recognition motif (RRM) found in pre-mRNA branch site protein p14 (SF3B14) and similar ...
24-87 9.11e-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: 33.75  E-value: 9.11e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1034658956  24 RTLFVSGLPLDIKPRELYLLFRPFkgyeGSL--IKL-TSKQPVG--FVSFDSRSEAEAAKNALNGIRFD 87
Cdd:cd12241     3 RILYVRNLPYKISSEELYDLFGKY----GAIrqIRIgNTKETRGtaFVVYEDIFDAKNACDHLSGFNVC 67
RRM1_SRSF4_like cd12337
RNA recognition motif 1 (RRM1) found in serine/arginine-rich splicing factor 4 (SRSF4) and ...
26-83 9.23e-03

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


Pssm-ID: 409774 [Multi-domain]  Cd Length: 70  Bit Score: 33.45  E-value: 9.23e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1034658956  26 LFVSGLPLDIKPRELYllfRPFKGYeGSLIKLTSKQPVGFVSFDSRSEAEAAKNALNG 83
Cdd:cd12337     2 VYIGRLPYRARERDVE---RFFRGY-GRIRDINLKNGFGFVEFEDPRDADDAVYELNG 55
RRM5_RBM12_like cd12515
RNA recognition motif 5 (RRM5) found in RNA-binding protein RBM12, RBM12B and similar proteins; ...
28-84 9.78e-03

RNA recognition motif 5 (RRM5) found in RNA-binding protein RBM12, RBM12B and similar proteins; This subfamily corresponds to the RRM5 of RBM12 and RBM12B. RBM12, also termed SH3/WW domain anchor protein in the nucleus (SWAN), is ubiquitously expressed. It contains five distinct RNA binding motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two proline-rich regions, and several putative transmembrane domains. RBM12B show high sequence semilarity with RBM12. It contains five distinct RRMs as well. The biological roles of both RBM12 and RBM12B remain unclear.


Pssm-ID: 409937 [Multi-domain]  Cd Length: 75  Bit Score: 33.73  E-value: 9.78e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1034658956  28 VSGLPLDIKPRELYLLFRPFKGYEGSLIKLTSK--QPVG--FVSFDSRSEAEAAKNALNGI 84
Cdd:cd12515     5 MRNLPFKATIEDILDFFYGYRVIPDSVSIRYNDdgQPTGdaRVAFPSPREARRAVRELNNR 65
 
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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