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Conserved domains on  [gi|1331831441|gb|PNI90709|]
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TDRD10 isoform 3 [Pan troglodytes]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
Tudor_TDRD10 cd20432
Tudor domain found in Tudor domain-containing protein 10 (TDRD10) and similar proteins; TDRD10 ...
175-313 2.06e-91

Tudor domain found in Tudor domain-containing protein 10 (TDRD10) and similar proteins; TDRD10 is widely expressed and localized both to the nucleus and cytoplasm, and may play general roles like regulation of RNA metabolism. It contains a Tudor domain and an RNA recognition motif (RRM). The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.


:

Pssm-ID: 410503  Cd Length: 139  Bit Score: 270.07  E-value: 2.06e-91
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1331831441 175 LLRECFRDLSWLALIHSIRGEAGLLVTSIVPKTPFFWAMHITEALHQNMQALFSTLAQAEEQQPYLEGSTVTRGTRCLAE 254
Cdd:cd20432     1 MLKDCFGDLSWLASIMKVHGEVGLLVTDTFPHTPYFWAILLTEESQQNMQQLFSTLAEVESQQPFLAKEDVHRGRRCLAE 80
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1331831441 255 YHLGDYGHAWNRCWVLDRVDTWAVVMFIDFGQLATIPVQSLRSLDSDDFWTIPPLTQPF 313
Cdd:cd20432    81 CPLGEEGGAWNRCWVLDVVEDFAVVFFVDFGSTANIPLPSLRSLDEDEFWQIPPLAQPF 139
RRM_TDRD10 cd21617
RNA recognition motif (RRM) found in Tudor domain-containing protein 10 (TDRD10) and similar ...
35-103 9.76e-37

RNA recognition motif (RRM) found in Tudor domain-containing protein 10 (TDRD10) and similar proteins; TDRD10 is widely expressed and localized both to the nucleus and cytoplasm and may play general roles like regulation of RNA metabolism. It contains a Tudor domain and a RNA recognition motif (RRM).


:

Pssm-ID: 410196 [Multi-domain]  Cd Length: 69  Bit Score: 127.53  E-value: 9.76e-37
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1331831441  35 EVYVGNLPLDISKEEILYLLKDFNPLDVHKIQNGCKCFAFVDLGSMQKVTLAIQELNGKLFHKRKLFVN 103
Cdd:cd21617     1 EVYVGNLPLDISEEEILQLFKAFNPVLVKKIRSGFKCFAFVDLGSDENVKLAIQQLNGTLFGGRRLVVN 69
 
Name Accession Description Interval E-value
Tudor_TDRD10 cd20432
Tudor domain found in Tudor domain-containing protein 10 (TDRD10) and similar proteins; TDRD10 ...
175-313 2.06e-91

Tudor domain found in Tudor domain-containing protein 10 (TDRD10) and similar proteins; TDRD10 is widely expressed and localized both to the nucleus and cytoplasm, and may play general roles like regulation of RNA metabolism. It contains a Tudor domain and an RNA recognition motif (RRM). The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.


Pssm-ID: 410503  Cd Length: 139  Bit Score: 270.07  E-value: 2.06e-91
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1331831441 175 LLRECFRDLSWLALIHSIRGEAGLLVTSIVPKTPFFWAMHITEALHQNMQALFSTLAQAEEQQPYLEGSTVTRGTRCLAE 254
Cdd:cd20432     1 MLKDCFGDLSWLASIMKVHGEVGLLVTDTFPHTPYFWAILLTEESQQNMQQLFSTLAEVESQQPFLAKEDVHRGRRCLAE 80
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1331831441 255 YHLGDYGHAWNRCWVLDRVDTWAVVMFIDFGQLATIPVQSLRSLDSDDFWTIPPLTQPF 313
Cdd:cd20432    81 CPLGEEGGAWNRCWVLDVVEDFAVVFFVDFGSTANIPLPSLRSLDEDEFWQIPPLAQPF 139
RRM_TDRD10 cd21617
RNA recognition motif (RRM) found in Tudor domain-containing protein 10 (TDRD10) and similar ...
35-103 9.76e-37

RNA recognition motif (RRM) found in Tudor domain-containing protein 10 (TDRD10) and similar proteins; TDRD10 is widely expressed and localized both to the nucleus and cytoplasm and may play general roles like regulation of RNA metabolism. It contains a Tudor domain and a RNA recognition motif (RRM).


Pssm-ID: 410196 [Multi-domain]  Cd Length: 69  Bit Score: 127.53  E-value: 9.76e-37
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1331831441  35 EVYVGNLPLDISKEEILYLLKDFNPLDVHKIQNGCKCFAFVDLGSMQKVTLAIQELNGKLFHKRKLFVN 103
Cdd:cd21617     1 EVYVGNLPLDISEEEILQLFKAFNPVLVKKIRSGFKCFAFVDLGSDENVKLAIQQLNGTLFGGRRLVVN 69
RRM smart00360
RNA recognition motif;
36-102 6.67e-11

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 57.60  E-value: 6.67e-11
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1331831441   36 VYVGNLPLDISKEEILYLLKDFNPL-DVH----KIQNGCKCFAFVDLGSMQKVTLAIQELNGKLFHKRKLFV 102
Cdd:smart00360   2 LFVGNLPPDTTEEELRELFSKFGKVeSVRlvrdKETGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV 73
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
37-111 1.22e-09

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


Pssm-ID: 440488 [Multi-domain]  Cd Length: 85  Bit Score: 54.33  E-value: 1.22e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1331831441  37 YVGNLPLDISKEEILYLLKDFNplDVHKIQ-------NGCKCFAFVDLGSMQKVTLAIQELNGKLFHKRKLFVNTSKRPP 109
Cdd:COG0724     5 YVGNLPYSVTEEDLRELFSEYG--EVTSVKlitdretGRSRGFGFVEMPDDEEAQAAIEALNGAELMGRTLKVNEARPRE 82

                  ..
gi 1331831441 110 KR 111
Cdd:COG0724    83 ER 84
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
36-100 1.24e-08

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: 51.08  E-value: 1.24e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1331831441  36 VYVGNLPLDISKEEILYLLKDFNP---LDVHKIQNG-CKCFAFV---DLGSMQKvtlAIQELNGKLFHKRKL 100
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFGPiksIRLVRDETGrSKGFAFVefeDEEDAEK---AIEALNGKELGGREL 69
TUDOR pfam00567
Tudor domain;
219-315 1.34e-05

Tudor domain;


Pssm-ID: 425754 [Multi-domain]  Cd Length: 117  Bit Score: 43.88  E-value: 1.34e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1331831441 219 LHQNMQALFSTLAQaeeqqpylEGSTVTRGTRCLAEYHLGDyghAWNRCWVL-DRVDTWAVVMFIDFGQLATIPVQSLRS 297
Cdd:pfam00567  30 LTEELQEYYASKPP--------ESLPPAVGDGCVAAFSEDG---KWYRAKITeSLDDGLVEVLFIDYGNTETVPLSDLRP 98
                          90
                  ....*....|....*...
gi 1331831441 298 LDSdDFWTIPPLTQPFML 315
Cdd:pfam00567  99 LPP-ELESLPPQAIKCQL 115
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
36-122 2.06e-05

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: 46.34  E-value: 2.06e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1331831441  36 VYVGNLPLDISKEEILYLLKDFNPLDVHKI----QNGCKCFAFVDLGSMQKVTLAIQELNGKLFHKRKLFVNTSKRPPKR 111
Cdd:TIGR01628 288 LYVKNLDDTVTDEKLRELFSECGEITSAKVmldeKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQRKEQR 367
                          90
                  ....*....|....
gi 1331831441 112 TP---DMIQQPRAP 122
Cdd:TIGR01628 368 RAhlqDQFMQLQPR 381
 
Name Accession Description Interval E-value
Tudor_TDRD10 cd20432
Tudor domain found in Tudor domain-containing protein 10 (TDRD10) and similar proteins; TDRD10 ...
175-313 2.06e-91

Tudor domain found in Tudor domain-containing protein 10 (TDRD10) and similar proteins; TDRD10 is widely expressed and localized both to the nucleus and cytoplasm, and may play general roles like regulation of RNA metabolism. It contains a Tudor domain and an RNA recognition motif (RRM). The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.


Pssm-ID: 410503  Cd Length: 139  Bit Score: 270.07  E-value: 2.06e-91
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1331831441 175 LLRECFRDLSWLALIHSIRGEAGLLVTSIVPKTPFFWAMHITEALHQNMQALFSTLAQAEEQQPYLEGSTVTRGTRCLAE 254
Cdd:cd20432     1 MLKDCFGDLSWLASIMKVHGEVGLLVTDTFPHTPYFWAILLTEESQQNMQQLFSTLAEVESQQPFLAKEDVHRGRRCLAE 80
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1331831441 255 YHLGDYGHAWNRCWVLDRVDTWAVVMFIDFGQLATIPVQSLRSLDSDDFWTIPPLTQPF 313
Cdd:cd20432    81 CPLGEEGGAWNRCWVLDVVEDFAVVFFVDFGSTANIPLPSLRSLDEDEFWQIPPLAQPF 139
RRM_TDRD10 cd21617
RNA recognition motif (RRM) found in Tudor domain-containing protein 10 (TDRD10) and similar ...
35-103 9.76e-37

RNA recognition motif (RRM) found in Tudor domain-containing protein 10 (TDRD10) and similar proteins; TDRD10 is widely expressed and localized both to the nucleus and cytoplasm and may play general roles like regulation of RNA metabolism. It contains a Tudor domain and a RNA recognition motif (RRM).


Pssm-ID: 410196 [Multi-domain]  Cd Length: 69  Bit Score: 127.53  E-value: 9.76e-37
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1331831441  35 EVYVGNLPLDISKEEILYLLKDFNPLDVHKIQNGCKCFAFVDLGSMQKVTLAIQELNGKLFHKRKLFVN 103
Cdd:cd21617     1 EVYVGNLPLDISEEEILQLFKAFNPVLVKKIRSGFKCFAFVDLGSDENVKLAIQQLNGTLFGGRRLVVN 69
RRM smart00360
RNA recognition motif;
36-102 6.67e-11

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 57.60  E-value: 6.67e-11
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1331831441   36 VYVGNLPLDISKEEILYLLKDFNPL-DVH----KIQNGCKCFAFVDLGSMQKVTLAIQELNGKLFHKRKLFV 102
Cdd:smart00360   2 LFVGNLPPDTTEEELRELFSKFGKVeSVRlvrdKETGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV 73
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
36-103 1.05e-10

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


Pssm-ID: 409669 [Multi-domain]  Cd Length: 72  Bit Score: 56.91  E-value: 1.05e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1331831441  36 VYVGNLPLDISKEEILYLLKDFNPLD----VHKIQNGCKCFAFVDLGSMQKVTLAIQELNGKLFHKRKLFVN 103
Cdd:cd00590     1 LFVGNLPPDTTEEDLRELFSKFGEVVsvriVRDRDGKSKGFAFVEFESPEDAEKALEALNGTELGGRPLKVS 72
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
37-111 1.22e-09

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


Pssm-ID: 440488 [Multi-domain]  Cd Length: 85  Bit Score: 54.33  E-value: 1.22e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1331831441  37 YVGNLPLDISKEEILYLLKDFNplDVHKIQ-------NGCKCFAFVDLGSMQKVTLAIQELNGKLFHKRKLFVNTSKRPP 109
Cdd:COG0724     5 YVGNLPYSVTEEDLRELFSEYG--EVTSVKlitdretGRSRGFGFVEMPDDEEAQAAIEALNGAELMGRTLKVNEARPRE 82

                  ..
gi 1331831441 110 KR 111
Cdd:COG0724    83 ER 84
RRM1_RRT5 cd12409
RNA recognition motif 1 (RRM1) found in yeast regulator of rDNA transcription protein 5 (RRT5) ...
36-102 3.81e-09

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


Pssm-ID: 409843 [Multi-domain]  Cd Length: 84  Bit Score: 53.05  E-value: 3.81e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1331831441  36 VYVGNLPLDISKEEILYLLKDFNPLDV----HKIQNGCKCF------AFVDLGSMQKVTLAIQELNGKLFHKRKLFV 102
Cdd:cd12409     2 VYISNLSYSTTEEELEELLKDYKPVSVlipsYTVRGFRSRKhrplgiAYAEFSSVEEAEKVVKDLNGKVFKGRKLFV 78
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
36-100 1.24e-08

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: 51.08  E-value: 1.24e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1331831441  36 VYVGNLPLDISKEEILYLLKDFNP---LDVHKIQNG-CKCFAFV---DLGSMQKvtlAIQELNGKLFHKRKL 100
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFGPiksIRLVRDETGrSKGFAFVefeDEEDAEK---AIEALNGKELGGREL 69
RRM1_CoAA cd12608
RNA recognition motif 1 (RRM1) found in vertebrate RRM-containing coactivator activator ...
35-105 9.49e-07

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


Pssm-ID: 410020 [Multi-domain]  Cd Length: 69  Bit Score: 45.95  E-value: 9.49e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1331831441  35 EVYVGNLPLDISKEEILYLlkdFNPldVHKIQNgC---KCFAFVDLGSMQKVTLAIQELNGKLFHKRKLFVNTS 105
Cdd:cd12608     2 KIFVGNVDEDTSQEELSAL---FEP--YGAVLS-CavmKQFAFVHMRGEAAADRAIRELNGRELHGRALVVEES 69
RRM_HP0827_like cd12399
RNA recognition motif (RRM) found in Helicobacter pylori HP0827 protein and similar proteins; ...
36-105 1.49e-06

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


Pssm-ID: 409833 [Multi-domain]  Cd Length: 75  Bit Score: 45.59  E-value: 1.49e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1331831441  36 VYVGNLPLDISKEEILYLLKDFNPL-DVHKIQN----GCKCFAFVDLGSMQKVTLAIQELNGKLFHKRKLFVNTS 105
Cdd:cd12399     1 LYVGNLPYSASEEQLKSLFGQFGAVfDVKLPMDretkRPRGFGFVELQEEESAEKAIAKLDGTDFMGRTIRVNEA 75
RRM3_I_PABPs cd12380
RNA recognition motif 3 (RRM3) found found in type I polyadenylate-binding proteins; This ...
34-102 4.88e-06

RNA recognition motif 3 (RRM3) found found in type I polyadenylate-binding proteins; This subfamily corresponds to the RRM3 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions.


Pssm-ID: 409814 [Multi-domain]  Cd Length: 80  Bit Score: 44.09  E-value: 4.88e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1331831441  34 TEVYVGNLPLDISKEEILYLLKDFNPLDVHKI---QNG-CKCFAFVDLGSMQKVTLAIQELNGKLFHKRKLFV 102
Cdd:cd12380     2 TNVYVKNFGEDVDDDELKELFEKYGKITSAKVmkdDSGkSKGFGFVNFENHEAAQKAVEELNGKELNGKKLYV 74
RRM3_PUB1 cd12622
RNA recognition motif 3 (RRM3) found in yeast nuclear and cytoplasmic polyadenylated ...
34-108 6.33e-06

RNA recognition motif 3 (RRM3) found in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins; This subfamily corresponds to the RRM3 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. PUB1 is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3.


Pssm-ID: 410033 [Multi-domain]  Cd Length: 74  Bit Score: 43.59  E-value: 6.33e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1331831441  34 TEVYVGNLPLDISKEEILYLLKDFNPLDVHKIQNGcKCFAFVDLGSMQKVTLAIQELNGKLFHKRKLFVNTSKRP 108
Cdd:cd12622     1 TTVYVGNLPPEVTQADLIPLFQNFGVIEEVRVQRD-KGFGFVKYDTHEEAALAIQQLNGQPFLGRPIKCSWGKKR 74
RRM1_PSRP2_like cd21609
RNA recognition motif 1 (RRM1) found in chloroplastic plastid-specific 30S ribosomal protein 2 ...
35-108 7.05e-06

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


Pssm-ID: 410188 [Multi-domain]  Cd Length: 80  Bit Score: 43.56  E-value: 7.05e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1331831441  35 EVYVGNLPLDISKEEILYLLKDFNplDVHKIQNGC-------KCFAFVDLGSMQKVTLAIQELNGKLFHKRKLFVNTSKR 107
Cdd:cd21609     1 RLYVGNIPRNVTSEELAKIFEEAG--TVEIAEVMYdrytgrsRGFGFVTMGSVEDAKAAIEKLNGTEVGGREIKVNITEK 78

                  .
gi 1331831441 108 P 108
Cdd:cd21609    79 P 79
Tudor_dTUD-like cd20379
Tudor domain found in Drosophila melanogaster maternal protein Tudor (dTUD) and similar ...
248-298 8.98e-06

Tudor domain found in Drosophila melanogaster maternal protein Tudor (dTUD) and similar proteins; dTUD is required during oogenesis for the formation of primordial germ cells and for normal abdominal segmentation. It contains 11 Tudor domains. The family also includes mitochondrial A-kinase anchor protein 1 (AKAP1) and Tudor domain-containing proteins (TDRDs). AKAP1, also called A-kinase anchor protein 149 kDa (AKAP 149), or dual specificity A-kinase-anchoring protein 1 (D-AKAP-1), or protein kinase A-anchoring protein 1 (PRKA1), or Spermatid A-kinase anchor protein 84 (S-AKAP84), is found in mitochondria and in the endoplasmic reticulum-nuclear envelope where it anchors protein kinases, phosphatases, and a phosphodiesterase. It regulates multiple cellular processes governing mitochondrial homeostasis and cell viability. AKAP1 binds to type I and II regulatory subunits of protein kinase A and anchors them to the cytoplasmic face of the mitochondrial outer membrane. TDRDs have diverse biological functions and may contain one or more copies of the Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.


Pssm-ID: 410450  Cd Length: 50  Bit Score: 42.50  E-value: 8.98e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1331831441 248 GTRCLAEYHLGDyghAWNRCWVLDRV-DTWAVVMFIDFGQLATIPVQSLRSL 298
Cdd:cd20379     2 GDLCAAKYEEDG---KWYRARVLEVLsNDKVEVFFVDYGNTETVPLSDLRPL 50
TUDOR pfam00567
Tudor domain;
219-315 1.34e-05

Tudor domain;


Pssm-ID: 425754 [Multi-domain]  Cd Length: 117  Bit Score: 43.88  E-value: 1.34e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1331831441 219 LHQNMQALFSTLAQaeeqqpylEGSTVTRGTRCLAEYHLGDyghAWNRCWVL-DRVDTWAVVMFIDFGQLATIPVQSLRS 297
Cdd:pfam00567  30 LTEELQEYYASKPP--------ESLPPAVGDGCVAAFSEDG---KWYRAKITeSLDDGLVEVLFIDYGNTETVPLSDLRP 98
                          90
                  ....*....|....*...
gi 1331831441 298 LDSdDFWTIPPLTQPFML 315
Cdd:pfam00567  99 LPP-ELESLPPQAIKCQL 115
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
36-122 2.06e-05

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: 46.34  E-value: 2.06e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1331831441  36 VYVGNLPLDISKEEILYLLKDFNPLDVHKI----QNGCKCFAFVDLGSMQKVTLAIQELNGKLFHKRKLFVNTSKRPPKR 111
Cdd:TIGR01628 288 LYVKNLDDTVTDEKLRELFSECGEITSAKVmldeKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQRKEQR 367
                          90
                  ....*....|....
gi 1331831441 112 TP---DMIQQPRAP 122
Cdd:TIGR01628 368 RAhlqDQFMQLQPR 381
RRM3_PES4_MIP6 cd21603
RNA recognition motif 3 (RRM3) found in Saccharomyces cerevisiae protein PES4, protein MIP6 ...
36-102 2.55e-05

RNA recognition motif 3 (RRM3) found in Saccharomyces cerevisiae protein PES4, protein MIP6 and similar proteins; The family includes PES4 (also called DNA polymerase epsilon suppressor 4) and MIP6 (also called MEX67-interacting protein 6), both of which are predicted RNA binding proteins that may act as regulators of late translation, protection, and mRNA localization. MIP6 acts as a novel factor for nuclear mRNA export, binds to both poly(A)+ RNA and nuclear pores. It interacts with MEX67. Members in this family contain four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the third RRM motif.


Pssm-ID: 410182 [Multi-domain]  Cd Length: 73  Bit Score: 41.89  E-value: 2.55e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1331831441  36 VYVGNLPLDISKEEILYLLKDFNPL------DVHKIQNgckCFAFVDLGSMQKVTLAIQELNGKLFHKRKLFV 102
Cdd:cd21603     3 IFVKNLPLDTNNDEILDFFSKVGPIksvftsPKYKYNS---LWAFVTYKKGSDTEKAIKLLNGTLFKGRTIEV 72
RBD_RRM1_NPL3 cd12340
RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 3 (Npl3p) and similar proteins; ...
37-102 4.52e-05

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: 41.23  E-value: 4.52e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1331831441  37 YVGNLPLDISKEEILYLLKDFNPLDVHKIQNGcKCFAFVDLGSMQKVTLAIQELNGKLFHKRKLFV 102
Cdd:cd12340     3 FVRPFPPDTSESAIREIFSPYGPVKEVKMLSD-SNFAFVEFEELEDAIRAKDSVHGRVLNNEPLYV 67
RRM2_RBM34 cd12395
RNA recognition motif 2 (RRM2) found in RNA-binding protein 34 (RBM34) and similar proteins; ...
36-102 5.04e-05

RNA recognition motif 2 (RRM2) found in RNA-binding protein 34 (RBM34) and similar proteins; This subfamily corresponds to the RRM2 of RBM34, a putative RNA-binding protein containing two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Although the function of RBM34 remains unclear currently, its RRM domains may participate in mRNA processing. RBM34 may act as an mRNA processing-related protein.


Pssm-ID: 409829 [Multi-domain]  Cd Length: 73  Bit Score: 40.94  E-value: 5.04e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1331831441  36 VYVGNLPLDISKEEILYLLKDFNPLDVHKI----QNG-CKCFAFVDLGSMQKVTLAIQeLNGKLFHKRKLFV 102
Cdd:cd12395     2 VFVGNLPFDIEEEELRKHFEDCGDVEAVRIvrdrETGiGKGFGYVLFKDKDSVDLALK-LNGSKLRGRKLRV 72
RRM2_RBMS3 cd12475
RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding motif, ...
34-130 1.01e-04

RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding motif, single-stranded-interacting protein 3 (RBMS3); This subgroup corresponds to the RRM2 of RBMS3, a new member of the c-myc gene single-strand binding proteins (MSSP) family of DNA regulators. Unlike other MSSP proteins, RBMS3 is not a transcriptional regulator. It 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. RBMS3 contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and its C-terminal region is acidic and enriched in prolines, glutamines and threonines.


Pssm-ID: 240919 [Multi-domain]  Cd Length: 88  Bit Score: 40.86  E-value: 1.01e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1331831441  34 TEVYVGNLPLDISKEEILYLLKDFNPLDVHKI---QNGC-KCFAFVDLGSMQKVTLAIQELNGKLFhkrklfvntskrpp 109
Cdd:cd12475     2 TNLYISNLPISMDEQELENMLKPFGHVISTRIlrdANGVsRGVGFARMESTEKCEVVIQHFNGKYL-------------- 67
                          90       100
                  ....*....|....*....|.
gi 1331831441 110 kRTPDMIQQPRAPLVLEKASG 130
Cdd:cd12475    68 -KTPPGVPAPTEPLLCKFADG 87
RRM2_4_MRN1 cd12262
RNA recognition motif 2 (RRM2) and 4 (RRM4) found in RNA-binding protein MRN1 and similar ...
36-101 1.22e-04

RNA recognition motif 2 (RRM2) and 4 (RRM4) found in RNA-binding protein MRN1 and similar proteins; This subgroup corresponds to the RRM2 and RRM4 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, and is an RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409706 [Multi-domain]  Cd Length: 78  Bit Score: 40.07  E-value: 1.22e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1331831441  36 VYVGNLPLDISKEEILYLLKDFNPLDVHKIQNGCKCfAFVDLGSMQKVTLAIQELNGK--LFHKRKLF 101
Cdd:cd12262     6 VYVGNLDDSLTEEEIRGILEKYGEIESIKILKEKNC-AFVNYLNIANAIKAVQELPIKnpKFKKVRIN 72
RRM1_Mug28 cd21620
RNA recognition motif 1 (RRM1) found in Schizosaccharomyces pombe meiotically up-regulated ...
33-102 1.58e-04

RNA recognition motif 1 (RRM1) found in Schizosaccharomyces pombe meiotically up-regulated gene 28 protein (Mug28) and similar proteins; Mug28 is a meiosis-specific protein that regulates spore wall formation. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the first RRM motif.


Pssm-ID: 410199 [Multi-domain]  Cd Length: 84  Bit Score: 39.80  E-value: 1.58e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1331831441  33 ETEVYVGNLPLDISKEEILYLLK------DFNPLDVHKIQN----GCKCFAFVDLGSMQKVTLAIQELNGKLFHKRKLFV 102
Cdd:cd21620     1 ERSLYVGNLPQTCQSEDLIILFEpygnvcGAHIASRKKVKVswvkPSKLFAFVEFETKEAATTAIVLLNGITYMGCQLKV 80
U2AF_lg TIGR01642
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
13-102 2.19e-04

U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi.


Pssm-ID: 273727 [Multi-domain]  Cd Length: 509  Bit Score: 42.96  E-value: 2.19e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1331831441  13 KLLGKNGVLEEqkspgfkkrETEVYVGNLPLDISKEEILYLLKDFNPLD----VHKIQNG-CKCFAFVDLGSMQKVTLAI 87
Cdd:TIGR01642 284 KLVNSTTVLDS---------KDRIYIGNLPLYLGEDQIKELLESFGDLKafnlIKDIATGlSKGYAFCEYKDPSVTDVAI 354
                          90
                  ....*....|....*
gi 1331831441  88 QELNGKLFHKRKLFV 102
Cdd:TIGR01642 355 AALNGKDTGDNKLHV 369
RRM1_VICKZ cd12358
RNA recognition motif 1 (RRM1) found in the VICKZ family proteins; Thid subfamily corresponds ...
37-96 2.39e-04

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


Pssm-ID: 240804 [Multi-domain]  Cd Length: 73  Bit Score: 39.28  E-value: 2.39e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1331831441  37 YVGNLPLDISKEEILYLLKDfNPLDVHKI---QNGckcFAFVDLGSMQKVTLAIQELNGKLFH 96
Cdd:cd12358     2 YIGNLSSDVNESDLRQLFEE-HKIPVSSVlvkKGG---YAFVDCPDQSWADKAIEKLNGKILQ 60
RRM1_2_CoAA_like cd12343
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in RRM-containing coactivator activator ...
36-102 3.12e-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: 38.75  E-value: 3.12e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1331831441  36 VYVGNLPLDISKEEILYLLKDFNPL---DVhkIQNgckcFAFVDLGSMQKVTLAIQELNGKLFHKRKLFV 102
Cdd:cd12343     2 IFVGNLPDAATSEELRALFEKYGKVtecDI--VKN----YAFVHMEKEEDAEDAIKALNGYEFMGSRINV 65
RRM1_SRSF1_like cd12338
RNA recognition motif 1 (RRM1) found in serine/arginine-rich splicing factor 1 (SRSF1) and ...
36-102 3.95e-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: 38.50  E-value: 3.95e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1331831441  36 VYVGNLPLDISKEEILYLLKDFNPL---DVHKIQNGCKcFAFVDLGSMQKVTLAIQELNGKLFHKRKLFV 102
Cdd:cd12338     2 IYVGNLPGDIRERDIEDLFYKYGPIlaiDLKNRRRGPP-FAFVEFEDPRDAEDAIRGRDGYDFDGYRLRV 70
RRM2_MRN1 cd12523
RNA recognition motif 2 (RRM2) found in RNA-binding protein MRN1 and similar proteins; This ...
36-101 4.87e-04

RNA recognition motif 2 (RRM2) found in RNA-binding protein MRN1 and similar proteins; This subgroup corresponds to the RRM2 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, which is a RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409943 [Multi-domain]  Cd Length: 78  Bit Score: 38.57  E-value: 4.87e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1331831441  36 VYVGNLPLDISKEEILYLLKDFNPLDVHKIQNGcKCFAFVDLGSMQKVTLAIQELN-GKLFHKRKLF 101
Cdd:cd12523     6 VYLGNLPESITEEELREDLEKFGPIDQIKIVKE-KNIAFVHFLSIANAIKVVTTLPlNPKWAKRRIY 71
RRM_scw1_like cd12245
RNA recognition motif (RRM) found in yeast cell wall integrity protein scw1 and similar ...
37-96 5.23e-04

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: 38.37  E-value: 5.23e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1331831441  37 YVGNLPLDISKEEILYLLKD---FNPLDVHKIQNGCKCfaFVDLGSMQKVTLAIQELNGKLFH 96
Cdd:cd12245     6 FVANLGPNVSEQELRQLFSRqpgFRRLRMHNKGGGPVC--FVEFEDVPFATQALNHLQGAILS 66
RRM4_RBM12_like cd12514
RNA recognition motif 4 (RRM4) found in RNA-binding protein RBM12, RBM12B and similar proteins; ...
36-102 7.12e-04

RNA recognition motif 4 (RRM4) found in RNA-binding protein RBM12, RBM12B and similar proteins; This subfamily corresponds to the RRM4 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: 409936 [Multi-domain]  Cd Length: 73  Bit Score: 37.78  E-value: 7.12e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1331831441  36 VYVGNLPLDISKEEILYLLKD--FNPLDVHKIQNG---CKCFAFVDLGSMQKVtLAIQELNGKLFHKRKLFV 102
Cdd:cd12514     2 IRITNLPYDATPVDIQRFFEDhgVRPEDVHLLRNKkgrGNGEALVTFKSEGDA-REVLKLNGKKLGKREAVV 72
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
31-93 7.73e-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: 41.33  E-value: 7.73e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1331831441  31 KRETEVYVGNLPLDISKEEilyLLKDFNP------LDVHKIQNG-CKCFAFVDLGSMQKVTLAIQELNGK 93
Cdd:TIGR01628 176 KKFTNLYVKNLDPSVNEDK---LRELFAKfgeitsAAVMKDGSGrSRGFAFVNFEKHEDAAKAVEEMNGK 242
Tudor_TDRD11 cd20433
Tudor domain found in Tudor domain-containing protein 11 (TDRD11) and similar proteins; TDRD11, ...
230-300 8.06e-04

Tudor domain found in Tudor domain-containing protein 11 (TDRD11) and similar proteins; TDRD11, also called Staphylococcal nuclease domain-containing protein 1 (SND1), 100 kDa coactivator, EBNA2 coactivator p100, or p100 co-activator, is a multifunctional protein that is reportedly associated with different types of RNA molecules, including mRNA, miRNA, pre-miRNA, and dsRNA. It has been implicated in a number of biological processes in eukaryotic cells, including the cell cycle, DNA damage repair, proliferation, and apoptosis. TDRD11 is overexpressed in multiple cancers and functions as an oncogene. It contains multiple Staphylococcal nuclease (SN) domains and a C-terminal Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.


Pssm-ID: 410504 [Multi-domain]  Cd Length: 84  Bit Score: 38.05  E-value: 8.06e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1331831441 230 LAQAEEQQPYLEGS-TVTRGTRCLAEYHLGDyghAWNRCWVLD-RVDTWAVVMFIDFGQLATIPVQSLRSLDS 300
Cdd:cd20433    12 LRFEIASNPPLPGSyTPRKGDLCAAKFVEDG---EWYRAKVEKvEGDKKVHVLYIDYGNREVLPSTRLAALPP 81
RRM1_TIA1_like cd12352
RNA recognition motif 1 (RRM1) found in granule-associated RNA binding proteins p40-TIA-1 and ...
37-103 9.42e-04

RNA recognition motif 1 (RRM1) found in granule-associated RNA binding proteins p40-TIA-1 and TIAR; This subfamily corresponds to the RRM1 of nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR), both of which are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. TIA-1 and TIAR share high sequence similarity. They are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis.TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both, TIA-1 and TIAR, bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains.


Pssm-ID: 409788 [Multi-domain]  Cd Length: 73  Bit Score: 37.39  E-value: 9.42e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1331831441  37 YVGNLPLDISKEEILYLLKDFNPLDVHKI---QNGCKCFAFVDLGSMQKVTLAIQELNGKLFHKRKLFVN 103
Cdd:cd12352     2 YVGNLDRQVTEDLILQLFSQIGPCKSCKMiteHGGNDPYCFVEFYEHNHAAAALQAMNGRKILGKEVKVN 71
RRM3_Hu cd12377
RNA recognition motif 3 (RRM3) found in the Hu proteins family; This subfamily corresponds to ...
36-102 1.95e-03

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


Pssm-ID: 409811 [Multi-domain]  Cd Length: 76  Bit Score: 36.53  E-value: 1.95e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1331831441  36 VYVGNLPLDISkEEILYLLkdFNP----------LDVHKiqNGCKCFAFVDLGSMQKVTLAIQELNGKLFHKRKLFV 102
Cdd:cd12377     2 IFVYNLAPDAD-ESLLWQL--FGPfgavqnvkiiRDFTT--NKCKGYGFVTMTNYDEAAVAIASLNGYRLGGRVLQV 73
Tudor_TDRD1_rpt1 cd20408
first Tudor domain found in Tudor domain-containing protein 1 (TDRD1) and similar proteins; ...
217-308 2.02e-03

first Tudor domain found in Tudor domain-containing protein 1 (TDRD1) and similar proteins; TDRD1, also called cancer/testis antigen 41.1 (CT41.1), plays a central role during spermatogenesis by participating in the repression transposable elements and preventing their mobilization, which is essential for germline integrity. It acts via the piRNA metabolic process, which mediates the repression of transposable elements during meiosis by forming complexes composed of piRNAs and Piwi proteins, and governs the methylation and subsequent repression of transposons. TDRD1 contains four Tudor domains. This model corresponds to the first one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.


Pssm-ID: 410479  Cd Length: 130  Bit Score: 37.73  E-value: 2.02e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1331831441 217 EALHQNMQALFSTLAQAEEQQPYlegsTVTRGTRCLAEYHLGdygHAWNRCWV--LDRVDTWAVVMFIDFGQLATIPVQS 294
Cdd:cd20408    23 ESLVKLTSQLKKTYASVNNHKEY----IPEVGEVCVAKYSED---QNWYRALVqtVDVQQKKAGVFYIDYGNEETVPLNR 95
                          90
                  ....*....|....
gi 1331831441 295 LRSLDsDDFWTIPP 308
Cdd:cd20408    96 IQPLK-KDIELFPP 108
RRM2_U2AF65 cd12231
RNA recognition motif 2 (RRM2) found in U2 large nuclear ribonucleoprotein auxiliary factor ...
36-102 2.40e-03

RNA recognition motif 2 (RRM2) found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins; This subfamily corresponds to the RRM2 of U2AF65 and dU2AF50. U2AF65, also termed U2AF2, is the large subunit of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF), which has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF65 specifically recognizes the intron polypyrimidine tract upstream of the 3' splice site and promotes binding of U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays an important role in the nuclear export of mRNA. It facilitates the formation of a messenger ribonucleoprotein export complex, containing both the NXF1 receptor and the RNA substrate. Moreover, U2AF65 interacts directly and specifically with expanded CAG RNA, and serves as an adaptor to link expanded CAG RNA to NXF1 for RNA export. U2AF65 contains an N-terminal RS domain rich in arginine and serine, followed by a proline-rich segment and three C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The N-terminal RS domain stabilizes the interaction of U2 snRNP with the branch point (BP) by contacting the branch region, and further promotes base pair interactions between U2 snRNA and the BP. The proline-rich segment mediates protein-protein interactions with the RRM domain of the small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are sufficient for specific RNA binding, while RRM3 is responsible for protein-protein interactions. The family also includes Splicing factor U2AF 50 kDa subunit (dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50 functions as an essential pre-mRNA splicing factor in flies. It associates with intronless mRNAs and plays a significant and unexpected role in the nuclear export of a large number of intronless mRNAs.


Pssm-ID: 409678 [Multi-domain]  Cd Length: 77  Bit Score: 36.48  E-value: 2.40e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1331831441  36 VYVGNLPLDISKEEILYLLKDFNPLD----VHKIQNG-CKCFAFVDLGSMQKVTLAIQELNGKLFHKRKLFV 102
Cdd:cd12231     3 LFIGGLPNYLNEDQVKELLQSFGKLKafnlVKDSATGlSKGYAFCEYVDDNVTDQAIAGLNGMQLGDKKLLV 74
RRM_RBM18 cd12355
RNA recognition motif (RRM) found in eukaryotic RNA-binding protein 18 and similar proteins; ...
36-102 2.53e-03

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


Pssm-ID: 409791 [Multi-domain]  Cd Length: 80  Bit Score: 36.51  E-value: 2.53e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1331831441  36 VYVGNLPLDISKEEILYLLKDFNPLDVHKI---QNGCKC-----FAFVDLGSMQKVTLAIQELNGKLFHKRKLFV 102
Cdd:cd12355     2 LWIGNLDPRLTEYHLLKLLSKYGKIKKFDFlfhKTGPLKgqprgYCFVTFETKEEAEKAIECLNGKLALGKKLVV 76
RRM1_Crp79 cd21619
RNA recognition motif 1 (RRM1) found in Schizosaccharomyces pombe mRNA export factor Crp79 and ...
35-102 2.60e-03

RNA recognition motif 1 (RRM1) found in Schizosaccharomyces pombe mRNA export factor Crp79 and similar proteins; Crp79, also called meiotic expression up-regulated protein 5 (Mug5), or polyadenylate-binding protein crp79, or PABP, or poly(A)-binding protein, is an auxiliary mRNA export factor that binds the poly(A) tail of mRNA and is involved in the export of mRNA from the nucleus to the cytoplasm. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the first RRM motif.


Pssm-ID: 410198 [Multi-domain]  Cd Length: 78  Bit Score: 36.35  E-value: 2.60e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1331831441  35 EVYVGNLPLDISKEEILYLLKDFN--------PLDVHKIQNGcKCFAFVDLGSMQKVTLAIQELNGKLFHKRKLFV 102
Cdd:cd21619     3 TIYVGNIDMTINEDALEKIFSRYGqvesvrrpPIHTDKADRT-TGFGFIKYTDAESAERAMQQADGILLGRRRLVV 77
RRM2_RRT5 cd12410
RNA recognition motif 2 (RRM2) found in yeast regulator of rDNA transcription protein 5 (RRT5) ...
33-102 3.14e-03

RNA recognition motif 2 (RRM2) found in yeast regulator of rDNA transcription protein 5 (RRT5) and similar proteins; This subfamily corresponds to the RRM2 of the lineage specific family containing a group of uncharacterized yeast regulators of rDNA transcription protein 5 (RRT5), which may play roles in the modulation of rDNA transcription. RRT5 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409844 [Multi-domain]  Cd Length: 93  Bit Score: 36.52  E-value: 3.14e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1331831441  33 ETEVYVGNLPLDISKEEILYLLKDFNPLDV----HKIQNGCKCF-------AFVDLGSMQKVTLAIQELNGKLFHKRKLF 101
Cdd:cd12410     2 KDTVYIGNLPGNTTDNDLREFFKDYNPQEIwifrTKKSRRNPMYlhrhftaALVTLPDEERLDEAIESLKSKKLNGKKIS 81

                  .
gi 1331831441 102 V 102
Cdd:cd12410    82 L 82
RRM_FOX1_like cd12407
RNA recognition motif (RRM) found in vertebrate RNA binding protein fox-1 homologs and similar ...
36-103 3.27e-03

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


Pssm-ID: 409841 [Multi-domain]  Cd Length: 76  Bit Score: 35.84  E-value: 3.27e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1331831441  36 VYVGNLPLDISKEEILYLLKDFNP-LDVHKIQN--GCKCFAFVDLGSMQKVTLAIQELNGKLFHKRKLFVN 103
Cdd:cd12407     3 LHVSNIPFRFRDPDLRQMFGQFGTiLDVEIIFNerGSKGFGFVTFANSADADRAREKLNGTVVEGRKIEVN 73
RRM3_hnRNPR_like cd12251
RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein R (hnRNP R) ...
36-106 3.38e-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: 35.68  E-value: 3.38e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1331831441  36 VYVGNLPLDISKEEILYLLKDFNPLD-VHKIqngcKCFAFVDLGSMQKVTLAIQELNGKLFHKRKLFVNTSK 106
Cdd:cd12251     4 LYVRNLMLSTTEEKLRELFSEYGKVErVKKI----KDYAFVHFEERDDAVKAMEEMNGKELEGSEIEVSLAK 71
RRM1_MEI2_like cd12524
RNA recognition motif 1 (RRM1) found in plant Mei2-like proteins; This subgroup corresponds to ...
37-102 3.93e-03

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


Pssm-ID: 409944 [Multi-domain]  Cd Length: 77  Bit Score: 35.72  E-value: 3.93e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1331831441  37 YVGNLPLDISKEEILYLLKDFNplDVHKIQNGCKCFAFV-----DLGSMQKvtlAIQELNGKLFHKRKLFV 102
Cdd:cd12524     5 FVRNINSSVEDEELRALFEQFG--EIRTLYTACKHRGFImvsyyDIRAAQS---AKRALQGTELGGRKLDI 70
RRM1_U2AF65 cd12230
RNA recognition motif 1 (RRM1) found in U2 large nuclear ribonucleoprotein auxiliary factor ...
35-108 3.95e-03

RNA recognition motif 1 (RRM1) found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins; The subfamily corresponds to the RRM1 of U2AF65 and dU2AF50. U2AF65, also termed U2AF2, is the large subunit of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF), which has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF65 specifically recognizes the intron polypyrimidine tract upstream of the 3' splice site and promotes binding of U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays an important role in the nuclear export of mRNA. It facilitates the formation of a messenger ribonucleoprotein export complex, containing both the NXF1 receptor and the RNA substrate. Moreover, U2AF65 interacts directly and specifically with expanded CAG RNA, and serves as an adaptor to link expanded CAG RNA to NXF1 for RNA export. U2AF65 contains an N-terminal RS domain rich in arginine and serine, followed by a proline-rich segment and three C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The N-terminal RS domain stabilizes the interaction of U2 snRNP with the branch point (BP) by contacting the branch region, and further promotes base pair interactions between U2 snRNA and the BP. The proline-rich segment mediates protein-protein interactions with the RRM domain of the small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are sufficient for specific RNA binding, while RRM3 is responsible for protein-protein interactions. The family also includes Splicing factor U2AF 50 kDa subunit (dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50 functions as an essential pre-mRNA splicing factor in flies. It associates with intronless mRNAs and plays a significant and unexpected role in the nuclear export of a large number of intronless mRNAs.


Pssm-ID: 409677 [Multi-domain]  Cd Length: 82  Bit Score: 35.99  E-value: 3.95e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1331831441  35 EVYVGNLPLDISKEEILyllkDF---------------NPldVHKIQ-NGCKCFAFVDLGSMQKVTLAIQeLNGKLFHKR 98
Cdd:cd12230     3 RLYVGNIPPGITEEELM----DFfnqamraagltqapgNP--VLAVQiNPDKNFAFVEFRSVEETTAALA-LDGIIFKGQ 75
                          90
                  ....*....|
gi 1331831441  99 KLFVntsKRP 108
Cdd:cd12230    76 PLKI---RRP 82
RRM1_CPEB2_like cd12724
RNA recognition motif 1 (RRM1) found in cytoplasmic polyadenylation element-binding protein ...
36-95 4.15e-03

RNA recognition motif 1 (RRM1) found in cytoplasmic polyadenylation element-binding protein CPEB-2, CPEB-3, CPEB-4 and similar protiens; This subgroup corresponds to the RRM1 of the paralog proteins CPEB-2, CPEB-3 and CPEB-4, all well-conserved in both, vertebrates and invertebrates. Due to the high sequence similarity, members in this family may share similar expression patterns and functions. CPEB-2 is an RNA-binding protein that is abundantly expressed in testis and localized in cytoplasm in transfected HeLa cells. It preferentially binds to poly(U) RNA oligomers and may regulate the translation of stored mRNAs during spermiogenesis. Moreover, CPEB-2 impedes target RNA translation at elongation; it directly interacts with the elongation factor, eEF2, to reduce eEF2/ribosome-activated GTP hydrolysis in vitro and inhibit peptide elongation of CPEB2-bound RNA in vivo. CPEB-3 is a sequence-specific translational regulatory protein that regulates translation in a polyadenylation-independent manner. It functions as a translational repressor that governs the synthesis of the AMPA receptor GluR2 through binding GluR2 mRNA. It also represses translation of a reporter RNA in transfected neurons and stimulates translation in response to NMDA. CPEB-4 is an RNA-binding protein that mediates meiotic mRNA cytoplasmic polyadenylation and translation. It is essential for neuron survival and present on the endoplasmic reticulum (ER). It is accumulated in the nucleus upon ischemia or the depletion of ER calcium. CPEB-4 is overexpressed in a large variety of tumors and is associated with many mRNAs in cancer cells. All family members contain an N-terminal unstructured region, two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a Zn-finger motif. In addition, they do have conserved nuclear export signals that are not present in CPEB-1.


Pssm-ID: 410123 [Multi-domain]  Cd Length: 92  Bit Score: 36.21  E-value: 4.15e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1331831441  36 VYVGNLPLDISKEEILYLLKDFNPLDV---HKIQNgCKCFA--------FVDLGSMQKVTLAIQELNGKLF 95
Cdd:cd12724     3 VFVGGLPPDIDEDEITASFRRFGPLVVdwpHKAES-KSYFPpkgyafllFQDERSVQALIDACIEEDDKLY 72
RRM_PIN4_like cd12253
RNA recognition motif (RRM) found in yeast RNA-binding protein PIN4, fission yeast RNA-binding ...
34-102 4.27e-03

RNA recognition motif (RRM) found in yeast RNA-binding protein PIN4, fission yeast RNA-binding post-transcriptional regulators cip1, cip2 and similar proteins; This subfamily corresponds to the RRM in PIN4, also termed psi inducibility protein 4 or modifier of damage tolerance Mdt1, a novel phosphothreonine (pThr)-containing protein that specifically interacts with the pThr-binding site of the Rad53 FHA1 domain. It is encoded by gene MDT1 (YBL051C) from yeast Saccharomyces cerevisiae. PIN4 is involved in normal G2/M cell cycle progression in the absence of DNA damage and functions as a novel target of checkpoint-dependent cell cycle arrest pathways. It contains an N-terminal RRM, a nuclear localization signal, a coiled coil, and a total of 15 SQ/TQ motifs. cip1 (Csx1-interacting protein 1) and cip2 (Csx1-interacting protein 2) are novel cytoplasmic RRM-containing proteins that counteract Csx1 function during oxidative stress. They are not essential for viability in fission yeast Schizosaccharomyces pombe. Both cip1 and cip2 contain one RRM. Like PIN4, Cip2 also possesses an R3H motif that may function in sequence-specific binding to single-stranded nucleic acids.


Pssm-ID: 240699 [Multi-domain]  Cd Length: 79  Bit Score: 35.89  E-value: 4.27e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1331831441  34 TEVYVGNLPLDISKEEILYLLKDFNP-----LDVHkIQNGC-KCFAFVDLGSMQKVTLAIQELNGKLFHKRKLFV 102
Cdd:cd12253     2 TAIVIKNIPFSLRKEQLLDIIEDLGIplpyaFNYH-FDNGVfRGLAFANFRSPEEAQTVVEALNGYEISGRRLRV 75
RRM_eIF4B cd12402
RNA recognition motif (RRM) found in eukaryotic translation initiation factor 4B (eIF-4B) and ...
37-103 4.70e-03

RNA recognition motif (RRM) found in eukaryotic translation initiation factor 4B (eIF-4B) and similar proteins; This subfamily corresponds to the RRM of eIF-4B, a multi-domain RNA-binding protein that has been primarily implicated in promoting the binding of 40S ribosomal subunits to mRNA during translation initiation. It contains two RNA-binding domains; the N-terminal well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), binds the 18S rRNA of the 40S ribosomal subunit and the C-terminal basic domain (BD), including two arginine-rich motifs (ARMs), binds mRNA during initiation, and is primarily responsible for the stimulation of the helicase activity of eIF-4A. eIF-4B also contains a DRYG domain (a region rich in Asp, Arg, Tyr, and Gly amino acids) in the middle, which is responsible for both, self-association of eIF-4B and binding to the p170 subunit of eIF3. Additional research indicates that eIF-4B can interact with the poly(A) binding protein (PABP) in mammalian cells, which can stimulate both, the eIF-4B-mediated activation of the helicase activity of eIF-4A and binding of poly(A) by PABP. eIF-4B has also been shown to interact specifically with the internal ribosome entry sites (IRES) of several picornaviruses which facilitate cap-independent translation initiation.


Pssm-ID: 409836 [Multi-domain]  Cd Length: 81  Bit Score: 35.66  E-value: 4.70e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1331831441  37 YVGNLPLDISKEEILYLLKDFNPLDVHKIQNGC----KCFAFVDLGSMQKVTLAIQeLNGKLFHKRKLFVN 103
Cdd:cd12402     6 YLGNLPYDVTEDDIEDFFRGLNISSVRLPRENGpgrlRGFGYVEFEDRESLIQALS-LNEESLKNRRIRVD 75
RRM_SR140 cd12223
RNA recognition motif (RRM) found in U2-associated protein SR140 and similar proteins; This ...
34-106 5.31e-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: 35.73  E-value: 5.31e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1331831441  34 TEVYVGNLPLDISKEEILYLLKDFNPLDVHKI-----------QNGCkcfAFVDLGSMQKVTLAIQELNGKLFHKRKLFV 102
Cdd:cd12223     2 TNLYVGNLPPSVTEEVLLREFGRFGPLASVKImwprteeerrrNRNC---GFVAFMSRADAERAMRELNGKDVMGYELKL 78

                  ....
gi 1331831441 103 NTSK 106
Cdd:cd12223    79 GWGK 82
RRM4_I_PABPs cd12381
RNA recognition motif 4 (RRM4) found in type I polyadenylate-binding proteins; This subfamily ...
37-107 5.94e-03

RNA recognition motif 4 (RRM4) found in type I polyadenylate-binding proteins; This subfamily corresponds to the RRM4 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in theThe CD corresponds to the RRM. regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions.


Pssm-ID: 409815 [Multi-domain]  Cd Length: 79  Bit Score: 35.32  E-value: 5.94e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1331831441  37 YVGNLPLDISKEEilyLLKDFNP------LDVHKIQNG-CKCFAFVDLGSMQKVTLAIQELNGKLFHKRKLFVNTSKR 107
Cdd:cd12381     5 YVKNLDDTIDDEK---LREEFSPfgtitsAKVMTDEGGrSKGFGFVCFSSPEEATKAVTEMNGRIIGGKPLYVALAQR 79
RRM2_RBM40_like cd12239
RNA recognition motif 2 (RRM2) found in RNA-binding protein 40 (RBM40) and similar proteins; ...
37-102 7.07e-03

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


Pssm-ID: 409685 [Multi-domain]  Cd Length: 82  Bit Score: 35.28  E-value: 7.07e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1331831441  37 YVGNLPLDISKEEILYLLKDF--------NPLDVHKIQNG-CKCFAFVDLGSMQKVTLAIQELNGKLFHKRKLFV 102
Cdd:cd12239     5 YVKNLSKRVSEKDLKYIFGRFvdssseekNMFDIRLMTEGrMKGQAFITFPSEELAEKALNLTNGYVLHGKPMVV 79
RRM_RBM7_like cd12336
RNA recognition motif (RRM) found in RNA-binding protein 7 (RBM7) and similar proteins; This ...
36-100 7.49e-03

RNA recognition motif (RRM) found in RNA-binding protein 7 (RBM7) and similar proteins; This subfamily corresponds to the RRM of RBM7, RBM11 and their eukaryotic homologous. RBM7 is an ubiquitously expressed pre-mRNA splicing factor that enhances messenger RNA (mRNA) splicing in a cell-specific manner or in a certain developmental process, such as spermatogenesis. It interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20, and may play a more specific role in meiosis entry and progression. Together with additional testis-specific RNA-binding proteins, RBM7 may regulate the splicing of specific pre-mRNA species that are important in the meiotic cell cycle. RBM11 is a novel tissue-specific splicing regulator that is selectively expressed in brain, cerebellum and testis, and to a lower extent in kidney. It is localized in the nucleoplasm and enriched in SRSF2-containing splicing speckles. It may play a role in the modulation of alternative splicing during neuron and germ cell differentiation. Both, RBM7 and RBM11, contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. The RRM is responsible for RNA binding, whereas the C-terminal region permits nuclear localization and homodimerization.


Pssm-ID: 409773 [Multi-domain]  Cd Length: 75  Bit Score: 34.97  E-value: 7.49e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1331831441  36 VYVGNLPLDISkEEILY-LLKDFNPLDVHKI----QNGCKCFAFVDLGSMQKVTLAIQELNGKLFHKRKL 100
Cdd:cd12336     4 LFVGNLDPRVT-EEILYeLFLQAGPLEGVKIpkdpNGKPKNFAFVTFKHEVSVPYAIQLLNGIRLFGREI 72
RRM_II_PABPs cd12306
RNA recognition motif in type II polyadenylate-binding proteins; This subfamily corresponds to ...
36-102 9.79e-03

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


Pssm-ID: 409747 [Multi-domain]  Cd Length: 73  Bit Score: 34.59  E-value: 9.79e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1331831441  36 VYVGNLPLDISKEEILYLLKDFNPldVHKIQNGC-------KCFAFVDLGSMQKVTLAIQeLNGKLFHKRKLFV 102
Cdd:cd12306     2 IYVGNVDYGTTPEELQAHFKSCGT--INRVTILCdkftgqpKGFAYIEFVDKSSVENALL-LNESEFRGRQIKV 72
 
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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