RNA recognition motif (RRM) found in vertebrate Ewing Sarcoma Protein (EWS); This subgroup corresponds to the RRM of EWS, also termed Ewing sarcoma breakpoint region 1 protein, a member of the FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA- and DNA-binding proteins whose expression is altered in cancer. It is a multifunctional protein and may play roles in transcription and RNA processing. EWS is involved in transcriptional regulation by interacting with the preinitiation complex TFIID and the RNA polymerase II (RNAPII) complexes. It is also associated with splicing factors, such as the U1 snRNP protein U1C, suggesting its implication in pre-mRNA splicing. Additionally, EWS has been shown to regulate DNA damage-induced alternative splicing (AS). Like other members in the FET family, EWS contains an N-terminal Ser, Gly, Gln and Tyr-rich region composed of multiple copies of a degenerate hexapeptide repeat motif. The C-terminal region consists of a conserved nuclear import and retention signal (C-NLS), a C2/C2 zinc-finger motif, a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and at least 1 arginine-glycine-glycine (RGG)-repeat region. EWS specifically binds to poly G and poly U RNA. It also binds to the proximal-element DNA of the macrophage-specific promoter of the CSF-1 receptor gene.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1121914449 366 SSVYVQGLNDNVTLEDLADFFKQCGVVKMNKRTGQPMIHLYIDKETGKPKGDATVSYDDPSTAKTAVEWFDGKDFQGSKL 445
Cdd:cd12533     1 STIYVQGLNENVTLEELADFFKHCGVVKINKRTGQPMINIYTDKETGKPKGDATVSYEDPPAAKAAVEWFDGKDFQGNKL 80

                  ....
gi 1121914449 446 KVSL 449
Cdd:cd12533    81 KVSM 84

Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate chromosome transmission during cell division.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1121914449  29 QPAQGYAQTTQTYGQQSYGTYGQPTDASYTQPQTTAT----YGQTAY-------ATSYGQPPTGYTAPTAPPAySQPVQG 97
Cdd:pfam09770 106 QPAARAAQSSAQPPASSLPQYQYASQQSQQPSKPVRTgyekYKEPEPipdlqvdASLWGVAPKKAAAPAPAPQ-PAAQPA 184

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1121914449  98 YGTAAY---------DTSTATVTTTQASYAAPSYGTQPAYPAYGQQPPAA-VPPRPQDGSKPAETSQPPSSTTGYSQP-- 165
Cdd:pfam09770 185 SLPAPSrkmmsleevEAAMRAQAKKPAQQPAPAPAQPPAAPPAQQAQQQQqFPPQIQQQQQPQQQPQQPQQHPGQGHPvt 264

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1121914449 166 SLGYGQSNYSYPQVPASYPmQPVTAPPSYPPTSYSSTQ----PS--SYDQSTYSQQSTYGQQnTYSQQTSYGQQSSYAQQ 239
Cdd:pfam09770 265 ILQRPQSPQPDPAQPSIQP-QAQQFHQQPPPVPVQPTQilqnPNrlSAARVGYPQNPQPGVQ-PAPAHQAHRQQGSFGRQ 342

                  ....*....
gi 1121914449 240 PPPTSYPPQ 248
Cdd:pfam09770 343 APIITHPQQ 351

RNA recognition motif (RRM) found in vertebrate Ewing Sarcoma Protein (EWS); This subgroup corresponds to the RRM of EWS, also termed Ewing sarcoma breakpoint region 1 protein, a member of the FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA- and DNA-binding proteins whose expression is altered in cancer. It is a multifunctional protein and may play roles in transcription and RNA processing. EWS is involved in transcriptional regulation by interacting with the preinitiation complex TFIID and the RNA polymerase II (RNAPII) complexes. It is also associated with splicing factors, such as the U1 snRNP protein U1C, suggesting its implication in pre-mRNA splicing. Additionally, EWS has been shown to regulate DNA damage-induced alternative splicing (AS). Like other members in the FET family, EWS contains an N-terminal Ser, Gly, Gln and Tyr-rich region composed of multiple copies of a degenerate hexapeptide repeat motif. The C-terminal region consists of a conserved nuclear import and retention signal (C-NLS), a C2/C2 zinc-finger motif, a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and at least 1 arginine-glycine-glycine (RGG)-repeat region. EWS specifically binds to poly G and poly U RNA. It also binds to the proximal-element DNA of the macrophage-specific promoter of the CSF-1 receptor gene.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1121914449 366 SSVYVQGLNDNVTLEDLADFFKQCGVVKMNKRTGQPMIHLYIDKETGKPKGDATVSYDDPSTAKTAVEWFDGKDFQGSKL 445
Cdd:cd12533     1 STIYVQGLNENVTLEELADFFKHCGVVKINKRTGQPMINIYTDKETGKPKGDATVSYEDPPAAKAAVEWFDGKDFQGNKL 80

                  ....
gi 1121914449 446 KVSL 449
Cdd:cd12533    81 KVSM 84

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1121914449 367 SVYVQGLNDNVTLEDLADFFKQCGVVKMnkrtgqpmIHLYIDKETGKPKGDATVSYDDPSTAKTAVEWFDGKDFQGSKLK 446
Cdd:COG0724     3 KIYVGNLPYSVTEEDLRELFSEYGEVTS--------VKLITDRETGRSRGFGFVEMPDDEEAQAAIEALNGAELMGRTLK 74

                  ....*....
gi 1121914449 447 VSLTRKKGP 455
Cdd:COG0724    75 VNEARPREE 83

Zn-finger in Ran binding protein and others;

                          10        20        30
                  ....*....|....*....|....*....|
gi 1121914449 528 RAGDWQCPnpGCGNQNFAWRTECNQCKAPK 557
Cdd:pfam00641   1 REGDWDCS--KCLVQNFATSTKCVACQAPK 28

Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate chromosome transmission during cell division.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1121914449  29 QPAQGYAQTTQTYGQQSYGTYGQPTDASYTQPQTTAT----YGQTAY-------ATSYGQPPTGYTAPTAPPAySQPVQG 97
Cdd:pfam09770 106 QPAARAAQSSAQPPASSLPQYQYASQQSQQPSKPVRTgyekYKEPEPipdlqvdASLWGVAPKKAAAPAPAPQ-PAAQPA 184

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1121914449  98 YGTAAY---------DTSTATVTTTQASYAAPSYGTQPAYPAYGQQPPAA-VPPRPQDGSKPAETSQPPSSTTGYSQP-- 165
Cdd:pfam09770 185 SLPAPSrkmmsleevEAAMRAQAKKPAQQPAPAPAQPPAAPPAQQAQQQQqFPPQIQQQQQPQQQPQQPQQHPGQGHPvt 264

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1121914449 166 SLGYGQSNYSYPQVPASYPmQPVTAPPSYPPTSYSSTQ----PS--SYDQSTYSQQSTYGQQnTYSQQTSYGQQSSYAQQ 239
Cdd:pfam09770 265 ILQRPQSPQPDPAQPSIQP-QAQQFHQQPPPVPVQPTQilqnPNrlSAARVGYPQNPQPGVQ-PAPAHQAHRQQGSFGRQ 342

                  ....*....
gi 1121914449 240 PPPTSYPPQ 248
Cdd:pfam09770 343 APIITHPQQ 351

large tegument protein UL36; Provisional

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1121914449   76 GQPPTGYTAPTAPPA--YSQPVQGYGTAAYDTSTATVTTTQASYAAPSYGTQPAYPAYGQ-QPPAAVPPRPQDGSKPAET 152
Cdd:PHA03247  2869 RSPAAKPAAPARPPVrrLARPAVSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQpQPPPPPPPRPQPPLAPTTD 2948

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1121914449  153 SQP-PSSTTGYSQPSLGY---GQSNYSYPQVPASYPMQPVTAPPSYPPTSYSSTQPSSYDQS 210
Cdd:PHA03247  2949 PAGaGEPSGAVPQPWLGAlvpGRVAVPRFRVPQPAPSREAPASSTPPLTGHSLSRVSSWASS 3010

glycine-rich RNA-binding protein 4; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1121914449 365 NSSVYVQGLNDNVTLEDLADFFKQCGVVKMNKrtgqpmihLYIDKETGKPKGDATVSYDDPSTAKTAVEWFDGKDFQGSK 444
Cdd:PLN03134   34 STKLFIGGLSWGTDDASLRDAFAHFGDVVDAK--------VIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRH 105

                          90       100
                  ....*....|....*....|
gi 1121914449 445 LKVSLT--RKKGPMNSMRGG 462
Cdd:PLN03134  106 IRVNPAndRPSAPRAYGGGG 125

RNA recognition motif (RRM) found in vertebrate Ewing Sarcoma Protein (EWS); This subgroup corresponds to the RRM of EWS, also termed Ewing sarcoma breakpoint region 1 protein, a member of the FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA- and DNA-binding proteins whose expression is altered in cancer. It is a multifunctional protein and may play roles in transcription and RNA processing. EWS is involved in transcriptional regulation by interacting with the preinitiation complex TFIID and the RNA polymerase II (RNAPII) complexes. It is also associated with splicing factors, such as the U1 snRNP protein U1C, suggesting its implication in pre-mRNA splicing. Additionally, EWS has been shown to regulate DNA damage-induced alternative splicing (AS). Like other members in the FET family, EWS contains an N-terminal Ser, Gly, Gln and Tyr-rich region composed of multiple copies of a degenerate hexapeptide repeat motif. The C-terminal region consists of a conserved nuclear import and retention signal (C-NLS), a C2/C2 zinc-finger motif, a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and at least 1 arginine-glycine-glycine (RGG)-repeat region. EWS specifically binds to poly G and poly U RNA. It also binds to the proximal-element DNA of the macrophage-specific promoter of the CSF-1 receptor gene.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1121914449 366 SSVYVQGLNDNVTLEDLADFFKQCGVVKMNKRTGQPMIHLYIDKETGKPKGDATVSYDDPSTAKTAVEWFDGKDFQGSKL 445
Cdd:cd12533     1 STIYVQGLNENVTLEELADFFKHCGVVKINKRTGQPMINIYTDKETGKPKGDATVSYEDPPAAKAAVEWFDGKDFQGNKL 80

                  ....
gi 1121914449 446 KVSL 449
Cdd:cd12533    81 KVSM 84

RNA recognition motif (RRM) found in vertebrate fused in Ewing's sarcoma protein (FUS), TATA-binding protein-associated factor 15 (TAF15) and similar proteins; This subgroup corresponds to the RRM of FUS and TAF15. FUS (TLS or Pigpen or hnRNP P2), also termed 75 kDa DNA-pairing protein (POMp75), or oncoprotein TLS (Translocated in liposarcoma), is a member of the FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA- and DNA-binding proteins whose expression is altered in cancer. It is a multi-functional protein and has been implicated in pre-mRNA splicing, chromosome stability, cell spreading, and transcription. FUS was originally identified in human myxoid and round cell liposarcomas as an oncogenic fusion with the stress-induced DNA-binding transcription factor CHOP (CCAAT enhancer-binding homologous protein) and later as hnRNP P2, a component of hnRNP H complex assembled on pre-mRNA. It can form ternary complexes with hnRNP A1 and hnRNP C1/C2. Additional research indicates that FUS binds preferentially to GGUG-containing RNAs. In the presence of Mg2+, it can bind both single- and double-stranded DNA (ssDNA/dsDNA) and promote ATP-independent annealing of complementary ssDNA and D-loop formation in superhelical dsDNA. FUS has been shown to be recruited by single stranded noncoding RNAs to the regulatory regions of target genes such as cyclin D1, where it represses transcription by disrupting complex formation. TAF15 (TAFII68), also termed TATA-binding protein-associated factor 2N (TAF2N), or RNA-binding protein 56 (RBP56), originally identified as a TAF in the general transcription initiation TFIID complex, is a novel RNA/ssDNA-binding protein with homology to the proto-oncoproteins FUS and EWS (also termed EWSR1), belonging to the FET family as well. TAF15 likely functions in RNA polymerase II (RNAP II) transcription by interacting with TFIID and subunits of RNAP II itself. TAF15 is also associated with U1 snRNA, chromatin and RNA, in a complex distinct from the Sm-containing U1 snRNP that functions in splicing. Like other members in the FET family, both FUS and TAF15 contain an N-terminal Ser, Gly, Gln and Tyr-rich region composed of multiple copies of a degenerate hexapeptide repeat motif. The C-terminal region consists of a conserved nuclear import and retention signal (C-NLS), a C2/C2 zinc-finger motif, a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and at least 1 arginine-glycine-glycine (RGG)-repeat region.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1121914449 364 DNSSVYVQGLNDNVTLEDLADFFKQCGVVKMNKRTGQPMIHLYIDKETGKPKGDATVSYDDPSTAKTAVEWFDGKDFQGS 443
Cdd:cd12535     1 DNNTIFVQGLGEDVTIDSVADYFKQIGIIKTNKKTGKPMINLYTDKETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGN 80

                  ....*.
gi 1121914449 444 KLKVSL 449
Cdd:cd12535    81 PIKVSF 86

RNA recognition motif 1 (RRM1) found in HIV Tat-specific factor 1 (Tat-SF1) and similar proteins; This subfamily corresponds to the RRM1 of Tat-SF1 and CUS2. Tat-SF1 is the cofactor for stimulation of transcriptional elongation by human immunodeficiency virus-type 1 (HIV-1) Tat. It is a substrate of an associated cellular kinase. Tat-SF1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a highly acidic carboxyl-terminal half. The family also includes CUS2, a yeast homolog of human Tat-SF1. CUS2 interacts with U2 RNA in splicing extracts and functions as a splicing factor that aids assembly of the splicing-competent U2 snRNP in vivo. CUS2 also associates with PRP11 that is a subunit of the conserved splicing factor SF3a. Like Tat-SF1, CUS2 contains two RRMs as well.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1121914449 365 NSSVYVQGLNDNVTLEDLADFFKQCGVVKMNKRTGQPMIHLYIDKEtGKPKGDATVSYDDPSTAKTAVEWFDGKD-FQGS 443
Cdd:cd12281     1 NTNVYVSGLPLDITVEEFVELFSKCGIIMEDPETGEPKIKLYRDEN-GNLKGDALCCYLKEESVELALQLLDGTEiGRGY 79

                  ....*
gi 1121914449 444 KLKVS 448
Cdd:cd12281    80 KIHVE 84

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).

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1121914449 368 VYVQGLNDNVTLEDLADFFKQCGVVKMnkrtgqpmIHLYIDKEtGKPKGDATVSYDDPSTAKTAVEWFDGKDFQGSKLKV 447
Cdd:cd00590     1 LFVGNLPPDTTEEDLRELFSKFGEVVS--------VRIVRDRD-GKSKGFAFVEFESPEDAEKALEALNGTELGGRPLKV 71

                  .
gi 1121914449 448 S 448
Cdd:cd00590    72 S 72

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1121914449 367 SVYVQGLNDNVTLEDLADFFKQCGVVkmNKRTgqpmihLYIDKETGKPKGDATVSYDDPSTAKTAVEwFDGKDFQGSKLK 446
Cdd:cd12306     1 SIYVGNVDYGTTPEELQAHFKSCGTI--NRVT------ILCDKFTGQPKGFAYIEFVDKSSVENALL-LNESEFRGRQIK 71

                  ..
gi 1121914449 447 VS 448
Cdd:cd12306    72 VT 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 1121914449 368 VYVQGLNDNVTLEDLADFFKQCGVVKMNKRtgqpmihlyIDKETGKPKGDATVSYDDPSTAKTAVEWFDGKDFQGSKLK 446
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFGPIKSIRL---------VRDETGRSKGFAFVEFEDEEDAEKAIEALNGKELGGRELK 70

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        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1121914449 368 VYVQGLNDNVTLEDLADFFKQCGVVKMnkrtgqpmIHLYIDKETGKPKGDATVSYDDPSTAKTAVEWFDGKDFQGSKLKV 447
Cdd:cd12399     1 LYVGNLPYSASEEQLKSLFGQFGAVFD--------VKLPMDRETKRPRGFGFVELQEEESAEKAIAKLDGTDFMGRTIRV 72

                  .
gi 1121914449 448 S 448
Cdd:cd12399    73 N 73

RNA recognition motif 1 (RRM1) found in the c-myc gene single-strand binding proteins (MSSP) family; This subfamily corresponds to the RRM1 of c-myc gene single-strand binding proteins (MSSP) family, including single-stranded DNA-binding protein MSSP-1 (also termed RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3). All MSSP family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity. Both, MSSP-1 and -2, have been identified as protein factors binding to a putative DNA replication origin/transcriptional enhancer sequence present upstream from the human c-myc gene in both single- and double-stranded forms. Thus, they have been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with c-MYC, the product of protooncogene c-myc. Moreover, the family includes a new member termed RNA-binding motif, single-stranded-interacting protein 3 (RBMS3), which is not a transcriptional regulator. RBMS3 binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. In addition, a putative meiosis-specific RNA-binding protein termed sporulation-specific protein 5 (SPO5, or meiotic RNA-binding protein 1, or meiotically up-regulated gene 12 protein), encoded by Schizosaccharomyces pombe Spo5/Mug12 gene, is also included in this family. SPO5 is a novel meiosis I regulator that may function in the vicinity of the Mei2 dot.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1121914449 368 VYVQGLNDNVTLEDLADFFKQCGVVKMNKrtgqpmihLYIDKETGKPKGDATVSYDDPSTAKTAVEWFDGKDFQGS 443
Cdd:cd12243     3 VYIRGLPPNTTDEDLLLLCQSFGKIISTK--------AIIDKQTNKCKGYGFVDFDSPEAALKAIEGLNGRGVQAS 70

RNA recognition motif 2 (RRM2) found in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins; This subfamily corresponds to the RRM2 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), is an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1121914449 368 VYVQGLNDNVTLEDLADFFKQCGVVKMnkrtgqpmIHLYIDKeTGKPKGDATVSYDDPSTAKTAVEWFDGKDFQGSKLKV 447
Cdd:cd12392     5 LFVKGLPFSCTKEELEELFKQHGTVKD--------VRLVTYR-NGKPKGLAYVEYENEADASQAVLKTDGTEIKDHTISV 75

                  ....
gi 1121914449 448 SLTR 451
Cdd:cd12392    76 AISN 79

RNA recognition motif (RRM) found in the Aly/REF family; This subfamily corresponds to the RRM of Aly/REF family which includes THO complex subunit 4 (THOC4, also termed Aly/REF), S6K1 Aly/REF-like target (SKAR, also termed PDIP3 or PDIP46) and similar proteins. THOC4 is an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus, and was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid, and might be a novel transcription cofactor for erythroid-specific genes. SKAR shows high sequence homology with THOC4 and possesses one RRM as well. SKAR is widely expressed and localizes to the nucleus. It may be a critical player in the function of S6K1 in cell and organism growth control by binding the activated, hyperphosphorylated form of S6K1 but not S6K2. Furthermore, SKAR functions as a protein partner of the p50 subunit of DNA polymerase delta. In addition, SKAR may have particular importance in pancreatic beta cell size determination and insulin secretion.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1121914449 368 VYVQGLNDNVTLEDLADFFKQCGVVKmnkrtgqpmiHLYID-KETGKPKGDATVSYDDPSTAKTAVEWFDGKDFQGSKLK 446
Cdd:cd12418     3 VRVSNLHPDVTEEDLRELFGRVGPVK----------SVKINyDRSGRSTGTAYVVFERPEDAEKAIKQFDGVLLDGQPMK 72

                  ...
gi 1121914449 447 VSL 449
Cdd:cd12418    73 VEL 75

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1121914449 368 VYVQGLNDNVTLEDLADFFKQCGvvkmnkrtgqPMIHLYIDK-ETGKPKGDATVSYDDPSTAKTAVEWFDGKDFQGSKLK 446
Cdd:cd12380     4 VYVKNFGEDVDDDELKELFEKYG----------KITSAKVMKdDSGKSKGFGFVNFENHEAAQKAVEELNGKELNGKKLY 73

                  ....*..
gi 1121914449 447 VSLTRKK 453
Cdd:cd12380    74 VGRAQKK 80

RNA recognition motif (RRM) found in pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6), pre-mRNA cleavage factor Im 59 kDa subunit (CFIm59 or CPSF7), and similar proteins; This subfamily corresponds to the RRM of cleavage factor Im (CFIm) subunits. Cleavage factor Im (CFIm) is a highly conserved component of the eukaryotic mRNA 3' processing machinery that functions in UGUA-mediated poly(A) site recognition, the regulation of alternative poly(A) site selection, mRNA export, and mRNA splicing. It is a complex composed of a small 25 kDa (CFIm25) subunit and a larger 59/68/72 kDa subunit. Two separate genes, CPSF6 and CPSF7, code for two isoforms of the large subunit, CFIm68 and CFIm59. Structurally related CFIm68 and CFIm59, also termed cleavage and polyadenylation specificity factor subunit 6 (CPSF7), or cleavage and polyadenylation specificity factor 59 kDa subunit (CPSF59), are functionally redundant. Both contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a central proline-rich region, and a C-terminal RS-like domain. Their N-terminal RRM mediates the interaction with CFIm25, and also serves to enhance RNA binding and facilitate RNA looping.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1121914449 368 VYVQGLNDNVTLEDLADFFKQCGVVKMNKrtgqpmIHLYIDKETGKPKGDATVSYDDPSTAKTAVEWFDGKDFQGSKLKV 447
Cdd:cd12372     1 LYVGNLQWWTTDEDLEGACASFGVVDVKE------IKFFEHKANGKSKGYAYVEFASPAAAAAVKEKLEKREFNGRPCVV 74

                  ..
gi 1121914449 448 SL 449
Cdd:cd12372    75 TP 76

RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein A subfamily; This subfamily corresponds to the RRM2 of hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1121914449 368 VYVQGLNDNVTLEDLADFFKQCGVVKMnkrtgqpmIHLYIDKETGKPKGDATVSYDDPSTAKTAV 432
Cdd:cd12328     2 LFVGGLKEDVEEEDLREYFSQFGKVES--------VEIVTDKETGKKRGFAFVTFDDHDSVDKIV 58

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1121914449 368 VYVQGLNDNVTLEDLADFFKQCGVVKMNKrtgqpmihLYIDKETGKPKGDATVSYDDPSTAKTAVEWFDGKDFQGSKLKV 447
Cdd:cd12362     1 LFVYHLPNEFTDQDLYQLFAPFGNVVSAK--------VFVDKNTGRSKGFGFVSYDNPLSAQAAIKAMNGFQVGGKRLKV 72

                  .
gi 1121914449 448 S 448
Cdd:cd12362    73 Q 73

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1121914449 366 SSVYVQGLNDNVTLEDLADFFKQCGVVKmnkrtgQPMIHLyiDKETGKPKGDATVSYDDPSTAKTAVEWFDGKDFQGSKL 445
Cdd:cd12674     1 TTLFVRNLPFDVTLESLTDFFSDIGPVK------HAVVVT--DPETKKSRGYGFVSFSTHDDAEEALAKLKNRKLSGHIL 72

                  ..
gi 1121914449 446 KV 447
Cdd:cd12674    73 KL 74

RNA recognition motif (RRM) found in ist3 family; This subfamily corresponds to the RRM of the ist3 family that includes fungal U2 small nuclear ribonucleoprotein (snRNP) component increased sodium tolerance protein 3 (ist3), X-linked 2 RNA-binding motif proteins (RBMX2) found in Metazoa and plants, and similar proteins. Gene IST3 encoding ist3, also termed U2 snRNP protein SNU17 (Snu17p), is a novel yeast Saccharomyces cerevisiae protein required for the first catalytic step of splicing and for progression of spliceosome assembly. It binds specifically to the U2 snRNP and is an intrinsic component of prespliceosomes and spliceosomes. Yeast ist3 contains an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). In the yeast pre-mRNA retention and splicing complex, the atypical RRM of ist3 functions as a scaffold that organizes the other two constituents, Bud13p (bud site selection 13) and Pml1p (pre-mRNA leakage 1). Fission yeast Schizosaccharomyces pombe gene cwf29 encoding ist3, also termed cell cycle control protein cwf29, is an RNA-binding protein complexed with cdc5 protein 29. It also contains one RRM. The biological function of RBMX2 remains unclear. It shows high sequence similarity to yeast ist3 protein and harbors one RRM as well.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1121914449 360 DEDSDNSSVYVQGLNDNVTLEDLADFFKQCGVVkMNkrtgqpmIHLYIDKETGKPKGDATVSYDDPSTAKTAVEWFDGKD 439
Cdd:cd12411     4 DEYKDSAYIYIGGLPYELTEGDILCVFSQYGEI-VD-------INLVRDKKTGKSKGFAFLAYEDQRSTILAVDNLNGIK 75

                  ....*...
gi 1121914449 440 FQGSKLKV 447
Cdd:cd12411    76 LLGRTIRV 83

RNA recognition motif 2 (RRM2) found in serine/arginine-rich splicing factor SRSF1, SRSF4 and similar proteins; This subfamily corresponds to the RRM2 of several serine/arginine (SR) proteins that have been classified into two subgroups. The first subgroup consists of serine/arginine-rich splicing factor 4 (SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5 or SRp40 or SFRS5 or HRS) and serine/arginine-rich splicing factor 6 (SRSF6 or SRp55). The second subgroup is composed of 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). These SR proteins are mainly involved in regulating constitutive and alternative pre-mRNA splicing. They also have been implicated in transcription, genomic stability, mRNA export and translation. All SR proteins in this family, except SRSF5, undergo nucleocytoplasmic shuttling, suggesting their widespread roles in gene expression. These SR proteins share a common domain architecture comprising two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. Both domains can directly contact with RNA. The RRMs appear to determine the binding specificity and the SR domain also mediates protein-protein interactions. In addition, this subfamily includes the yeast nucleolar protein 3 (Npl3p), also termed mitochondrial targeting suppressor 1 protein, or nuclear polyadenylated RNA-binding protein 1. It 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 with two RRMs, separated by a short linker and a C-terminal domain rich in glycine, arginine and serine residues.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1121914449 368 VYVQGLNDNVTLEDLADFFKQCGVVkmnkrtgqpmihLYIDkETGKPKGDATVSYDDPSTAKTAVEWFDGKDFQGSKLKV 447
Cdd:cd12339     3 VVVSNLPERASWQDLKDFMRKAGEV------------TYAD-VHRDREGEGVVEFTSEEDMKRAIEKLDGTEFNGRRIRV 69

RNA recognition motif 3 (RRM3) found in RNA-binding protein 19 (RBM19) and similar proteins; This subgroup corresponds to the RRM3 of RBM19, also termed RNA-binding domain-1 (RBD-1), which is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1121914449 368 VYVQGLNDNVTLEDLADFFKQCGvvkmnkrtgqPM--IHLYIDKETGKPKGDATVSYDDPSTAKTAVEWFDGKDFQGSKL 445
Cdd:cd12567     5 LFVRNLPYTCTEEDLEKLFSKYG----------PLseVHFPIDSLTKKPKGFAFVTYMIPEHAVKAYAELDGTVFQGRLL 74

                  ..
gi 1121914449 446 KV 447
Cdd:cd12567    75 HL 76

RNA recognition motif 3 (RRM3) found in vertebrate myelin expression factor 2 (MEF-2); This subgroup corresponds to the RRM3 of MEF-2, also termed MyEF-2 or MST156, a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may be responsible for its ssDNA binding activity.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1121914449 368 VYVQGLNDNVTLEDLADFFKQCGVVKMNKrtgqpmihlyIDKETGKPKGDATVSYDDPSTAKTAVEWFDGKDFQGSKLKV 447
Cdd:cd12662     2 IFVRNLPFDLTWQKLKEKFSQCGHVMFAE----------IKMENGKSKGCGTVRFDSPESAEKACRLMNGIKISGREIDV 71

                  ....
gi 1121914449 448 SLTR 451
Cdd:cd12662    72 RLDR 75

RNA recognition motif (RRM) found in cold inducible RNA binding protein (CIRBP), RNA binding motif protein 3 (RBM3) and similar proteins; This subfamily corresponds to the RRM domain of two structurally related heterogenous nuclear ribonucleoproteins, CIRBP (also termed CIRP or A18 hnRNP) and RBM3 (also termed RNPL), both of which belong to a highly conserved cold shock proteins family. The cold shock proteins can be induced after exposure to a moderate cold-shock and other cellular stresses such as UV radiation and hypoxia. CIRBP and RBM3 may function in posttranscriptional regulation of gene expression by binding to different transcripts, thus allowing the cell to response rapidly to environmental signals. However, the kinetics and degree of cold induction are different between CIRBP and RBM3. Tissue distribution of their expression is different. CIRBP and RBM3 may be differentially regulated under physiological and stress conditions and may play distinct roles in cold responses of cells. CIRBP, also termed glycine-rich RNA-binding protein CIRP, is localized in the nucleus and mediates the cold-induced suppression of cell cycle progression. CIRBP also binds DNA and possibly serves as a chaperone that assists in the folding/unfolding, assembly/disassembly and transport of various proteins. RBM3 may enhance global protein synthesis and the formation of active polysomes while reducing the levels of ribonucleoprotein complexes containing microRNAs. RBM3 may also serve to prevent the loss of muscle mass by its ability to decrease cell death. Furthermore, RBM3 may be essential for cell proliferation and mitosis. Both, CIRBP and RBM3, contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), that is involved in RNA binding, and C-terminal glycine-rich domain (RGG motif) that probably enhances RNA-binding via protein-protein and/or protein-RNA interactions. Like CIRBP, RBM3 can also bind to both RNA and DNA via its RRM domain.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1121914449 366 SSVYVQGLNDNVTLEDLADFFKQCGVVKMnkrtgqpmIHLYIDKETGKPKGDATVSYDDPSTAKTAVEWFDGKDFQGSKL 445
Cdd:cd12449     1 GKLFVGGLSFDTNEQSLEEVFSKYGQISE--------VVVVKDRETQRSRGFGFVTFENPDDAKDAMMAMNGKSLDGRQI 72

                  ....*...
gi 1121914449 446 KVSLTRKK 453
Cdd:cd12449    73 RVDQAGKS 80

RNA recognition motif (RRM) found in eukaryotic translation initiation factor 4H (eIF-4H) and similar proteins; This subfamily corresponds to the RRM of eIF-4H, also termed Williams-Beuren syndrome chromosomal region 1 protein, which, together with elf-4B/eIF-4G, serves as the accessory protein of RNA helicase eIF-4A. eIF-4H contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It stimulates protein synthesis by enhancing the helicase activity of eIF-4A in the initiation step of mRNA translation.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1121914449 368 VYVQGLNDNVTLEDLADFFKQCGVVKmnkrtgqpmIHLYIDKETGKPKGDATVSYDDPSTAKTAVEwFDGKDFQGSKLKV 447
Cdd:cd12401     8 AYVGNLPFNTVQGDLDAIFKDLKVRS---------VRLVRDRETDKFKGFCYVEFEDLESLKEALE-YDGALFEDRPLRV 77

                  ....*..
gi 1121914449 448 SLTRKKG 454
Cdd:cd12401    78 DIAEGRK 84

RNA recognition motif 3 (RRM3) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM3 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1121914449 367 SVYVQGLNDNVTLEDLADFFKQCGVVKMNKrtgqpmihLYIDKETGKPKGDATVSYDDPSTAKTAVE------WFDGKDF 440
Cdd:cd12415     2 TVFIRNLSFDTTEEDLKEFFSKFGEVKYAR--------IVLDKDTGHSKGTAFVQFKTKESADKCIEaandesEDGGLVL 73

                          90
                  ....*....|
gi 1121914449 441 QGSKLKVSLT 450
Cdd:cd12415    74 DGRKLIVSLA 83

RNA recognition motif 2 (RRM2) found in nucleolin-like proteins mainly from plants; This subfamily corresponds to the RRM2 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1121914449 367 SVYVQGLN----DNVTLEDLADFFKQCGVVKMnkrtgqpmIHLYIDKETGKPKGDATVSYDDPSTAKTAVEwFDGKDFQG 442
Cdd:cd12451     1 TIFVKGFDaslgEDTIRDELREHFGECGEVTN--------VRIPTDRETGELKGFAYIEFSTKEAKEKALE-LNGSDIAG 71

                  ....*..
gi 1121914449 443 SKLKVSL 449
Cdd:cd12451    72 GNLVVDE 78

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1121914449 368 VYVQGLN---DNVTLEdlADFFKQCGVVKmnkrtgqpmIHLYIDKETGKPKGDATVSYDDPSTAKTAVEWFDGKDFQGSK 444
Cdd:cd12382     4 LFIGGLNtetNEKALE--AVFGKYGRIVE---------VLLMKDRETNKSRGFAFVTFESPADAKDAARDMNGKELDGKA 72