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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148613864 175 LLRECFRDLSWLALIHSVRGEAGLLVTSIVPKTPFFWAMHVTEALHQNMQALFSTLAQAEEQQPYLEGSTVMRGTRCLAE 254
Cdd:cd20432    1 MLKDCFGDLSWLASIMKVHGEVGLLVTDTFPHTPYFWAILLTEESQQNMQQLFSTLAEVESQQPFLAKEDVHRGRRCLAE 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 148613864 255 YHLGDYGHAWNRCWVLDRVDTWAVVMFIDFGQLATIPVQSLRSLDSDDFWTIPPLTQPF 313
Cdd:cd20432   81 CPLGEEGGAWNRCWVLDVVEDFAVVFFVDFGSTANIPLPSLRSLDEDEFWQIPPLAQPF 139

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148613864 175 LLRECFRDLSWLALIHSVRGEAGLLVTSIVPKTPFFWAMHVTEALHQNMQALFSTLAQAEEQQPYLEGSTVMRGTRCLAE 254
Cdd:cd20432    1 MLKDCFGDLSWLASIMKVHGEVGLLVTDTFPHTPYFWAILLTEESQQNMQQLFSTLAEVESQQPFLAKEDVHRGRRCLAE 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 148613864 255 YHLGDYGHAWNRCWVLDRVDTWAVVMFIDFGQLATIPVQSLRSLDSDDFWTIPPLTQPF 313
Cdd:cd20432   81 CPLGEEGGAWNRCWVLDVVEDFAVVFFVDFGSTANIPLPSLRSLDEDEFWQIPPLAQPF 139

RNA recognition motif;

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 148613864    36 VYVGNLPLDISKEEILYLLKDFNPL-DVH----KIQNGCKCFAFVDLGSMQKVTLAIQELNGKLFHKRKLFV 102
Cdd:smart00360   2 LFVGNLPPDTTEEELRELFSKFGKVeSVRlvrdKETGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV 73

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.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 148613864   36 VYVGNLPLDISKEEILYLLKDFNP---LDVHKIQNG-CKCFAFV---DLGSMQKvtlAIQELNGKLFHKRKL 100
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFGPiksIRLVRDETGrSKGFAFVefeDEEDAEK---AIEALNGKELGGREL 69

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148613864   36 VYVGNLPLDISKEEILYLLKDFNPLDVHKI----QNGCKCFAFVDLGSMQKVTLAIQELNGKLFHKRKLFVNTSKRPPKR 111
Cdd:TIGR01628 288 LYVKNLDDTVTDEKLRELFSECGEITSAKVmldeKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQRKEQR 367

                          90
                  ....*....|....
gi 148613864  112 TP---DMIQQPRAP 122
Cdd:TIGR01628 368 RAhlqDQFMQLQPR 381

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148613864 175 LLRECFRDLSWLALIHSVRGEAGLLVTSIVPKTPFFWAMHVTEALHQNMQALFSTLAQAEEQQPYLEGSTVMRGTRCLAE 254
Cdd:cd20432    1 MLKDCFGDLSWLASIMKVHGEVGLLVTDTFPHTPYFWAILLTEESQQNMQQLFSTLAEVESQQPFLAKEDVHRGRRCLAE 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 148613864 255 YHLGDYGHAWNRCWVLDRVDTWAVVMFIDFGQLATIPVQSLRSLDSDDFWTIPPLTQPF 313
Cdd:cd20432   81 CPLGEEGGAWNRCWVLDVVEDFAVVFFVDFGSTANIPLPSLRSLDEDEFWQIPPLAQPF 139

RNA recognition motif;

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 148613864    36 VYVGNLPLDISKEEILYLLKDFNPL-DVH----KIQNGCKCFAFVDLGSMQKVTLAIQELNGKLFHKRKLFV 102
Cdd:smart00360   2 LFVGNLPPDTTEEELRELFSKFGKVeSVRlvrdKETGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV 73

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148613864  37 YVGNLPLDISKEEILYLLKDFNplDVHKIQ-------NGCKCFAFVDLGSMQKVTLAIQELNGKLFHKRKLFVNTSKRPP 109
Cdd:COG0724    5 YVGNLPYSVTEEDLRELFSEYG--EVTSVKlitdretGRSRGFGFVEMPDDEEAQAAIEALNGAELMGRTLKVNEARPRE 82

                 ..
gi 148613864 110 KR 111
Cdd:COG0724   83 ER 84

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.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 148613864   36 VYVGNLPLDISKEEILYLLKDFNP---LDVHKIQNG-CKCFAFV---DLGSMQKvtlAIQELNGKLFHKRKL 100
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFGPiksIRLVRDETGrSKGFAFVefeDEEDAEK---AIEALNGKELGGREL 69

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.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 148613864  36 VYVGNLPLDISKEEILYLLKDFNPL-DVHKIQN----GCKCFAFVDLGSMQKVTLAIQELNGKLFHKRKLFVNTS 105
Cdd:cd12399    1 LYVGNLPYSASEEQLKSLFGQFGAVfDVKLPMDretkRPRGFGFVELQEEESAEKAIAKLDGTDFMGRTIRVNEA 75

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.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 148613864  34 TEVYVGNLPLDISKEEILYLLKDFNPLDVHKIQNGcKCFAFVDLGSMQKVTLAIQELNGKLFHKRKLFVNTSKRP 108
Cdd:cd12622    1 TTVYVGNLPPEVTQADLIPLFQNFGVIEEVRVQRD-KGFGFVKYDTHEEAALAIQQLNGQPFLGRPIKCSWGKKR 74

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.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 148613864 248 GTRCLAEYHLGDyghAWNRCWVLDRV-DTWAVVMFIDFGQLATIPVQSLRSL 298
Cdd:cd20379    2 GDLCAAKYEEDG---KWYRARVLEVLsNDKVEVFFVDYGNTETVPLSDLRPL 50

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148613864   36 VYVGNLPLDISKEEILYLLKDFNPLDVHKI----QNGCKCFAFVDLGSMQKVTLAIQELNGKLFHKRKLFVNTSKRPPKR 111
Cdd:TIGR01628 288 LYVKNLDDTVTDEKLRELFSECGEITSAKVmldeKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQRKEQR 367

                          90
                  ....*....|....
gi 148613864  112 TP---DMIQQPRAP 122
Cdd:TIGR01628 368 RAhlqDQFMQLQPR 381

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.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 148613864  37 YVGNLPLDISKEEILYLLKDFNPLDVHKIQNGcKCFAFVDLGSMQKVTLAIQELNGKLFHKRKLFV 102
Cdd:cd12340    3 FVRPFPPDTSESAIREIFSPYGPVKEVKMLSD-SNFAFVEFEELEDAIRAKDSVHGRVLNNEPLYV 67

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148613864  34 TEVYVGNLPLDISKEEILYLLKDFNPLDVHKI---QNGC-KCFAFVDLGSMQKVTLAIQELNGKLFhkrklfvntskrpp 109
Cdd:cd12475    2 TNLYISNLPISMDEQELENMLKPFGHVISTRIlrdANGVsRGVGFARMESTEKCEVVIQHFNGKYL-------------- 67

                         90       100
                 ....*....|....*....|.
gi 148613864 110 kRTPDMIQQPRAPLVLEKASG 130
Cdd:cd12475   68 -KTPPGVPAPTEPLLCKFADG 87

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148613864  33 ETEVYVGNLPLDISKEEILYLLK------DFNPLDVHKIQN----GCKCFAFVDLGSMQKVTLAIQELNGKLFHKRKLFV 102
Cdd:cd21620    1 ERSLYVGNLPQTCQSEDLIILFEpygnvcGAHIASRKKVKVswvkPSKLFAFVEFETKEAATTAIVLLNGITYMGCQLKV 80

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148613864   13 KLFGKNGVLEEqkspgfkkrETEVYVGNLPLDISKEEILYLLKDFNPLD----VHKIQNG-CKCFAFVDLGSMQKVTLAI 87
Cdd:TIGR01642 284 KLVNSTTVLDS---------KDRIYIGNLPLYLGEDQIKELLESFGDLKafnlIKDIATGlSKGYAFCEYKDPSVTDVAI 354

                          90
                  ....*....|....*
gi 148613864   88 QELNGKLFHKRKLFV 102
Cdd:TIGR01642 355 AALNGKDTGDNKLHV 369

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.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148613864  36 VYVGNLPLDISKEEILYLLKDFNPL---DVHKIQNGCKcFAFVDLGSMQKVTLAIQELNGKLFHKRKLFV 102
Cdd:cd12338    2 IYVGNLPGDIRERDIEDLFYKYGPIlaiDLKNRRRGPP-FAFVEFEDPRDAEDAIRGRDGYDFDGYRLRV 70

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.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 148613864  37 YVGNLPLDISKEEILYLLKD---FNPLDVHKIQNGCKCfaFVDLGSMQKVTLAIQELNGKLFH 96
Cdd:cd12245    6 FVANLGPNVSEQELRQLFSRqpgFRRLRMHNKGGGPVC--FVEFEDVPFATQALNHLQGAILS 66

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.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148613864   31 KRETEVYVGNLPLDISKEEilyLLKDFNP------LDVHKIQNG-CKCFAFVDLGSMQKVTLAIQELNGK 93
Cdd:TIGR01628 176 KKFTNLYVKNLDPSVNEDK---LRELFAKfgeitsAAVMKDGSGrSRGFAFVNFEKHEDAAKAVEEMNGK 242

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.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 148613864 230 LAQAEEQQPYLEGS-TVMRGTRCLAEYHLGDyghAWNRCWVLD-RVDTWAVVMFIDFGQLATIPVQSLRSLDS 300
Cdd:cd20433   12 LRFEIASNPPLPGSyTPRKGDLCAAKFVEDG---EWYRAKVEKvEGDKKVHVLYIDYGNREVLPSTRLAALPP 81

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.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 148613864  36 VYVGNLPLDISkEEILYLLkdFNP----------LDVHKiqNGCKCFAFVDLGSMQKVTLAIQELNGKLFHKRKLFV 102
Cdd:cd12377    2 IFVYNLAPDAD-ESLLWQL--FGPfgavqnvkiiRDFTT--NKCKGYGFVTMTNYDEAAVAIASLNGYRLGGRVLQV 73

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.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 148613864  35 EVYVGNLPLDISKEEILYLLKDFN--------PLDVHKIQNGcKCFAFVDLGSMQKVTLAIQELNGKLFHKRKLFV 102
Cdd:cd21619    3 TIYVGNIDMTINEDALEKIFSRYGqvesvrrpPIHTDKADRT-TGFGFIKYTDAESAERAMQQADGILLGRRRLVV 77

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).

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gi 148613864  36 VYVGNLPLDISKEEILYLLKDFNP-LDVHKIQN--GCKCFAFVDLGSMQKVTLAIQELNGKLFHKRKLFVN 103
Cdd:cd12407    3 LHVSNIPFRFRDPDLRQMFGQFGTiLDVEIIFNerGSKGFGFVTFANSADADRAREKLNGTVVEGRKIEVN 73

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.

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gi 148613864  35 EVYVGNLPLDISKEEILyllkDF---------------NPldVHKIQ-NGCKCFAFVDLGSMQKVTLAIQeLNGKLFHKR 98
Cdd:cd12230    3 RLYVGNIPPGITEEELM----DFfnqamraagltqapgNP--VLAVQiNPDKNFAFVEFRSVEETTAALA-LDGIIFKGQ 75

                         90
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gi 148613864  99 KLFVntsKRP 108
Cdd:cd12230   76 PLKI---RRP 82

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.

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gi 148613864  36 VYVGNLPLDISKEEILYLLKDFNPLDVHKI---QNGCKC-----FAFVDLGSMQKVTLAIQELNGKLFHKRKLFV 102
Cdd:cd12355    2 LWIGNLDPRLTEYHLLKLLSKYGKIKKFDFlfhKTGPLKgqprgYCFVTFETKEEAEKAIECLNGKLALGKKLVV 76

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.

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gi 148613864  36 VYVGNLPLDISKEEILYLLKDFNPLDV---HKIQNgCKCFA--------FVDLGSMQKVTLAIQELNGKLF 95
Cdd:cd12724    3 VFVGGLPPDIDEDEITASFRRFGPLVVdwpHKAES-KSYFPpkgyafllFQDERSVQALIDACIEEDDKLY 72

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.

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gi 148613864  37 YVGNLPLDISKEEilyLLKDFNP------LDVHKIQNG-CKCFAFVDLGSMQKVTLAIQELNGKLFHKRKLFVNTSKR 107
Cdd:cd12381    5 YVKNLDDTIDDEK---LREEFSPfgtitsAKVMTDEGGrSKGFGFVCFSSPEEATKAVTEMNGRIIGGKPLYVALAQR 79

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.

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gi 148613864  36 VYVGNLPLDISkEEILY-LLKDFNPLDVHKI----QNGCKCFAFVDLGSMQKVTLAIQELNGKLFHKRKL 100
Cdd:cd12336    4 LFVGNLDPRVT-EEILYeLFLQAGPLEGVKIpkdpNGKPKNFAFVTFKHEVSVPYAIQLLNGIRLFGREI 72