potassium uptake protein, Trk family; The proteins of the Trk family are derived from Gram-negative and Gram-positive bacteria, yeast and wheat. The proteins of E. coli K12 TrkH and TrkG as well as several yeast proteins have been functionally characterized.The E. coli TrkH and TrkG proteins are complexed to two peripheral membrane proteins, TrkA, an NAD-binding protein, and TrkE, an ATP-binding protein. This complex forms the potassium uptake system. This family is specific for the eukaryotic Trk system. [Transport and binding proteins, Cations and iron carrying compounds]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2296754393 148 RRVRIDISNSSNDDRRGNRMGRDNRRDNYDDPERTSGDWRSGPReelldedshrsrydnrdrrddrdrhdydnkpGAWRE 227
Cdd:TIGR00934 131 ERYFDGIRDSSKQRFFLRRTKTLLQRELEDRPETGVAGRVTVPH-------------------------------GSAKR 179

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2296754393 228 RDNNDKGFKDRGGFRDDSKDRDWNRYSDRGRSKDRDGDRSSSFGPrrnygdsdwdRRQDRDAKPELRQRPKLQLQPRTKP 307
Cdd:TIGR00934 180 RDFQDKLFSGEFVKRDEPDQNSPDVKSDTRADESISDLEFEKFAK----------RRGSRDVDPEDLYRSIMMLQGIHER 249

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2296754393 308 VEplaiskdQTEESAVESRSTTGSELTQRAPAPTPISAVNIFGAAKP--VDTTAREREIEERLAKSY--AESRSREE-TD 382
Cdd:TIGR00934 250 IR-------EKSSANSRSDERSSESIQEQVERRPSTSDIERNSQSLTrrYDDKSFDKAVRLRRSKTIdrAEACDLEElDR 322

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2296754393 383 SKERKDGTSGRRNGEGRDDKERGRPTWRLEEDKGTRIEKSAPRSQLARSEEQNESKASSTSRPEPPTFKVFHKSTEKDTR 462
Cdd:TIGR00934 323 AKDFEKMTYDNWKAHHRKKKNFRPRGWNLKFRKASRFPKDSDRNYEDNGNHLSASSSFGSEEPSLSSEENLYPTYNKKRE 402

                         330       340
                  ....*....|....*....|
gi 2296754393 463 ATLERDRKDKEKDEISRMPK 482
Cdd:TIGR00934 403 DSRHTLSKTMSTNYLSWQPT 422

RNA recognition motif;

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2296754393   86 YLTNLPYDIDEADLADFFADM-KISNMRLPKDAN--KIRGYGYVEFEDRQSLIDALSMTNTT-IKTRRVRI 152
Cdd:smart00360   3 FVGNLPPDTTEEELRELFSKFgKVESVRLVRDKEtgKSKGFAFVEFESEEDAEKALEALNGKeLDGRPLKV 73

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

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2296754393  86 YLTNLPYDIDEADLADFFADM-KISNMRLPKD--ANKIRGYGYVEFEDR---QSLIDAL 138
Cdd:COG0724     5 YVGNLPYSVTEEDLRELFSEYgEVTSVKLITDreTGRSRGFGFVEMPDDeeaQAAIEAL 63

potassium uptake protein, Trk family; The proteins of the Trk family are derived from Gram-negative and Gram-positive bacteria, yeast and wheat. The proteins of E. coli K12 TrkH and TrkG as well as several yeast proteins have been functionally characterized.The E. coli TrkH and TrkG proteins are complexed to two peripheral membrane proteins, TrkA, an NAD-binding protein, and TrkE, an ATP-binding protein. This complex forms the potassium uptake system. This family is specific for the eukaryotic Trk system. [Transport and binding proteins, Cations and iron carrying compounds]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2296754393 148 RRVRIDISNSSNDDRRGNRMGRDNRRDNYDDPERTSGDWRSGPReelldedshrsrydnrdrrddrdrhdydnkpGAWRE 227
Cdd:TIGR00934 131 ERYFDGIRDSSKQRFFLRRTKTLLQRELEDRPETGVAGRVTVPH-------------------------------GSAKR 179

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2296754393 228 RDNNDKGFKDRGGFRDDSKDRDWNRYSDRGRSKDRDGDRSSSFGPrrnygdsdwdRRQDRDAKPELRQRPKLQLQPRTKP 307
Cdd:TIGR00934 180 RDFQDKLFSGEFVKRDEPDQNSPDVKSDTRADESISDLEFEKFAK----------RRGSRDVDPEDLYRSIMMLQGIHER 249

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2296754393 308 VEplaiskdQTEESAVESRSTTGSELTQRAPAPTPISAVNIFGAAKP--VDTTAREREIEERLAKSY--AESRSREE-TD 382
Cdd:TIGR00934 250 IR-------EKSSANSRSDERSSESIQEQVERRPSTSDIERNSQSLTrrYDDKSFDKAVRLRRSKTIdrAEACDLEElDR 322

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2296754393 383 SKERKDGTSGRRNGEGRDDKERGRPTWRLEEDKGTRIEKSAPRSQLARSEEQNESKASSTSRPEPPTFKVFHKSTEKDTR 462
Cdd:TIGR00934 323 AKDFEKMTYDNWKAHHRKKKNFRPRGWNLKFRKASRFPKDSDRNYEDNGNHLSASSSFGSEEPSLSSEENLYPTYNKKRE 402

                         330       340
                  ....*....|....*....|
gi 2296754393 463 ATLERDRKDKEKDEISRMPK 482
Cdd:TIGR00934 403 DSRHTLSKTMSTNYLSWQPT 422

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 2296754393  78 PTSPPYVAYLTNLPYDIDEADLADFFADMKISNMRLPKD--ANKIRGYGYVEFEDRQSLIDALSMTNTTIKTRRVRIDIS 155
Cdd:cd12401     1 PTEPPFTAYVGNLPFNTVQGDLDAIFKDLKVRSVRLVRDreTDKFKGFCYVEFEDLESLKEALEYDGALFEDRPLRVDIA 80

                  ....
gi 2296754393 156 NSSN 159
Cdd:cd12401    81 EGRK 84

RNA recognition motif;

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2296754393   86 YLTNLPYDIDEADLADFFADM-KISNMRLPKDAN--KIRGYGYVEFEDRQSLIDALSMTNTT-IKTRRVRI 152
Cdd:smart00360   3 FVGNLPPDTTEEELRELFSKFgKVESVRLVRDKEtgKSKGFAFVEFESEEDAEKALEALNGKeLDGRPLKV 73

RNA recognition motif (RRM) found in Saccharomyces cerevisiae nucleolar protein 6 (Nop6) and similar proteins; This subfamily corresponds to the RRM of Nop6, also known as Ydl213c, a component of 90S pre-ribosomal particles in yeast S. cerevisiae. It is enriched in the nucleolus and is required for 40S ribosomal subunit biogenesis. Nop6 is a non-essential putative RNA-binding protein with two N-terminal putative nuclear localisation sequences (NLS-1 and NLS-2) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It binds to the pre-rRNA early during transcription and plays an essential role in pre-rRNA processing.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2296754393  83 YVAYLTNLPYDIDEADLADFFADM-KISNMRLP--KDANKIRGYGYVEFEDRQSLIDALSMTNTTIKTRRVRI 152
Cdd:cd12400     1 YILFVGNLPYDTTAEDLKEHFKKAgEPPSVRLLtdKKTGKSKGCAFVEFDNQKALQKALKLHHTSLGGRKINV 73

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.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2296754393  89 NLPYDIDEADLADFFADM-KISNMRLPKDA--NKIRGYGYVEFEDRQSLIDALSMTNTTIKTRRVRI 152
Cdd:cd12395     6 NLPFDIEEEELRKHFEDCgDVEAVRIVRDRetGIGKGFGYVLFKDKDSVDLALKLNGSKLRGRKLRV 72

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 39 (RBM39) and similar proteins; This subfamily corresponds to the RRM1 of RNA-binding protein 39 (RBM39), RNA-binding protein 23 (RBM23) and similar proteins. RBM39 (also termed HCC1) is a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Although the cellular function of RBM23 remains unclear, it shows high sequence homology to RBM39 and contains two RRMs. It may possibly function as a pre-mRNA splicing factor.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2296754393  89 NLPYDIDEADLADFFADM-KISNMRLPKDAN--KIRGYGYVEFEDRQSLIDALSMTNTTIKTRRVRI 152
Cdd:cd12283     6 QLSLKARERDLYEFFSKAgKVRDVRLIMDRNsrRSKGVAYVEFYDVESVPLALALTGQRLLGQPIMV 72

RNA recognition motif 1 (RRM1) found in nucleolin-like proteins mainly from plants; This subfamily corresponds to the RRM1 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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2296754393  89 NLPYDIDEADLADFFADM-KISNMRLPKDA--NKIRGYGYVEFEDRQSLIDALSMTNTTIKTRRVRIDISN 156
Cdd:cd12450     6 NLSWSATQDDLENFFSDCgEVVDVRIAMDRddGRSKGFGHVEFASAESAQKALEKSGQDLGGREIRLDLAN 76

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

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2296754393  84 VAYLTNLPYDIDEADLADFFADMKI--SNMRLPKDANKIR-GYGYVEFEDRQSLIDALSMTNTTIKTRRVRI 152
Cdd:cd12254     1 VVRLRGLPFSATEEDIRDFFSGLDIppDGIHIVYDDDGRPtGEAYVEFASEEDAQRALRRHKGKMGGRYIEV 72

RNA recognition motif 2 (RRM2) found in yeast protein gar2 and similar proteins; This subfamily corresponds to the RRM2 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2296754393  86 YLTNLPYDIDEADLADFFADM-KISNMRLPKD--ANKIRGYGYVEFEDRQSLIDALSMTNT-TIKTRRVRID 153
Cdd:cd12448     2 FVGNLPFSATQDALYEAFSQHgSIVSVRLPTDreTGQPKGFGYVDFSTIDSAEAAIDALGGeYIDGRPIRLD 73

RNA recognition motif (RRM) found in Saccharomyces cerevisiae U1 small nuclear ribonucleoprotein SNP1 and similar proteins; SNP1, also called U1 snRNP protein SNP1, or U1 small nuclear ribonucleoprotein 70 kDa homolog, or U1 70K, or U1 snRNP 70 kDa homolog, interacts with mRNA and is involved in nuclear mRNA splicing. It is a component of the spliceosome, where it is associated with snRNP U1 by binding stem loop I of U1 snRNA. Members in this family contain an N-terminal U1snRNP70 domain and an RNA recognition motif (RRM), also called RBD (RNA binding domain) or RNP (ribonucleoprotein domain).

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2296754393  76 NIPTSPPY-VAYLTNLPYDIDEADLADFFADM-KISNMRLPKD--ANKIRGYGYVEFEDRQSLIDAL----SMTNTTIKT 147
Cdd:cd21615    11 HIADGDPYkTLFVGRLDYSLTELELQKKFSKFgEIEKIRIVRDkeTGKSRGYAFIVFKSESDAKNAFkegnGLRGLKIND 90

                  ....*..
gi 2296754393 148 RRVRIDI 154
Cdd:cd21615    91 RTCIVDI 97

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 2296754393  86 YLTNLPYDIDEADLADFFADMK-ISNMRLPKDANKIR--GYGYVEFEDRQSLIDAL-SMTNTTIKTRRVRIDISNSSNDD 161
Cdd:TIGR01628   4 YVGDLDPDVTEAKLYDLFKPFGpVLSVRVCRDSVTRRslGYGYVNFQNPADAERALeTMNFKRLGGKPIRIMWSQRDPSL 83

                  ....*..
gi 2296754393 162 RR---GN 165
Cdd:TIGR01628  84 RRsgvGN 90

RNA recognition motif in nucleolar protein interacting with the FHA domain of pKI-67 (NIFK) and similar proteins; This subgroup corresponds to the RRM of NIFK and Nop15p. NIFK, also termed MKI67 FHA domain-interacting nucleolar phosphoprotein, or nucleolar phosphoprotein Nopp34, is a putative RNA-binding protein interacting with the forkhead associated (FHA) domain of pKi-67 antigen in a mitosis-specific and phosphorylation-dependent manner. It is nucleolar in interphase but associates with condensed mitotic chromosomes. This family also includes Saccharomyces cerevisiae YNL110C gene encoding ribosome biogenesis protein 15 (Nop15p), also termed nucleolar protein 15. Both, NIFK and Nop15p, contain an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2296754393  84 VAYLTNLPYDIDEADLADFFADM-KISNMRLP--KDANKIRGYGYVEFEDRQ-SLIDALSMTN 142
Cdd:cd12307     1 VVYIGHLPHGFYEPELRKYFSQFgTVTRLRLSrsKKTGKSKGYAFVEFEDPEvAKIVAETMNN 63

potassium uptake protein, Trk family; The proteins of the Trk family are derived from Gram-negative and Gram-positive bacteria, yeast and wheat. The proteins of E. coli K12 TrkH and TrkG as well as several yeast proteins have been functionally characterized.The E. coli TrkH and TrkG proteins are complexed to two peripheral membrane proteins, TrkA, an NAD-binding protein, and TrkE, an ATP-binding protein. This complex forms the potassium uptake system. This family is specific for the eukaryotic Trk system. [Transport and binding proteins, Cations and iron carrying compounds]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2296754393 148 RRVRIDISNSSNDDRRGNRMGRDNRRDNYDDPERTSGDWRSGPReelldedshrsrydnrdrrddrdrhdydnkpGAWRE 227
Cdd:TIGR00934 131 ERYFDGIRDSSKQRFFLRRTKTLLQRELEDRPETGVAGRVTVPH-------------------------------GSAKR 179

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2296754393 228 RDNNDKGFKDRGGFRDDSKDRDWNRYSDRGRSKDRDGDRSSSFGPrrnygdsdwdRRQDRDAKPELRQRPKLQLQPRTKP 307
Cdd:TIGR00934 180 RDFQDKLFSGEFVKRDEPDQNSPDVKSDTRADESISDLEFEKFAK----------RRGSRDVDPEDLYRSIMMLQGIHER 249

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2296754393 308 VEplaiskdQTEESAVESRSTTGSELTQRAPAPTPISAVNIFGAAKP--VDTTAREREIEERLAKSY--AESRSREE-TD 382
Cdd:TIGR00934 250 IR-------EKSSANSRSDERSSESIQEQVERRPSTSDIERNSQSLTrrYDDKSFDKAVRLRRSKTIdrAEACDLEElDR 322

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2296754393 383 SKERKDGTSGRRNGEGRDDKERGRPTWRLEEDKGTRIEKSAPRSQLARSEEQNESKASSTSRPEPPTFKVFHKSTEKDTR 462
Cdd:TIGR00934 323 AKDFEKMTYDNWKAHHRKKKNFRPRGWNLKFRKASRFPKDSDRNYEDNGNHLSASSSFGSEEPSLSSEENLYPTYNKKRE 402

                         330       340
                  ....*....|....*....|
gi 2296754393 463 ATLERDRKDKEKDEISRMPK 482
Cdd:TIGR00934 403 DSRHTLSKTMSTNYLSWQPT 422

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

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2296754393  88 TNLPYDIDEADLADFFADM-KISNMRLPKD--ANKIRGYGYVEFEDRQSLIDALSMTN 142
Cdd:cd12408     5 TNLSEDATEEDLRELFRPFgPISRVYLAKDkeTGQSKGFAFVTFETREDAERAIEKLN 62

RNA recognition motif 2 (RRM2) found in (U)-binding-splicing factor PUF60 and similar proteins; This subfamily corresponds to the RRM2 of PUF60, also termed FUSE-binding protein-interacting repressor (FBP-interacting repressor or FIR), or Ro-binding protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1). PUF60 is an essential splicing factor that functions as a poly-U RNA-binding protein required to reconstitute splicing in depleted nuclear extracts. Its function is enhanced through interaction with U2 auxiliary factor U2AF65. PUF60 also controls human c-myc gene expression by binding and inhibiting the transcription factor far upstream sequence element (FUSE)-binding-protein (FBP), an activator of c-myc promoters. PUF60 contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors another RRM and binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) in several nuclear proteins. Research indicates that PUF60 binds FUSE as a dimer, and only the first two RRM domains participate in the single-stranded DNA recognition.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2296754393  86 YLTNLPYDIDEADLADFF-ADMKISNMRLPKDA--NKIRGYGYVEFEDRQSLIDALSMTN 142
Cdd:cd12371     4 YVASVHPDLSEDDIKSVFeAFGKIKSCSLAPDPetGKHKGYGFIEYENPQSAQDAIASMN 63

RNA recognition motif (RRM) found in cyclophilin-33 (Cyp33) and similar proteins; This subfamily corresponds to the RRM of Cyp33, also termed peptidyl-prolyl cis-trans isomerase E (PPIase E), or cyclophilin E, or rotamase E. Cyp33 is a nuclear RNA-binding cyclophilin with an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal PPIase domain. Cyp33 possesses RNA-binding activity and preferentially binds to polyribonucleotide polyA and polyU, but hardly to polyG and polyC. It binds specifically to mRNA, which can stimulate its PPIase activity. Moreover, Cyp33 interacts with the third plant homeodomain (PHD3) zinc finger cassette of the mixed lineage leukemia (MLL) proto-oncoprotein and a poly-A RNA sequence through its RRM domain. It further mediates downregulation of the expression of MLL target genes HOXC8, HOXA9, CDKN1B, and C-MYC, in a proline isomerase-dependent manner. Cyp33 also possesses a PPIase activity that catalyzes cis-trans isomerization of the peptide bond preceding a proline, which has been implicated in the stimulation of folding and conformational changes in folded and unfolded proteins. The PPIase activity can be inhibited by the immunosuppressive drug cyclosporin A.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2296754393  86 YLTNLPYDIDEADLADFFADM-KISNMRLPKD--ANKIRGYGYVEFEDRQSLIDAL-SMTNTTIKTRRVRIDIS 155
Cdd:cd12347     2 YVGGLAEEVDEKVLHAAFIPFgDIVDIQIPLDyeTEKHRGFAFVEFEEAEDAAAAIdNMNESELFGRTIRVNLA 75

RNA recognition motif 2 (RRM2) found in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins; This subfamily corresponds to the RRM2 of DAZAP1 or DAZ-associated protein 1, also termed proline-rich RNA binding protein (Prrp), a multi-functional ubiquitous RNA-binding protein expressed most abundantly in the testis and essential for normal cell growth, development, and spermatogenesis. DAZAP1 is a shuttling protein whose acetylated is predominantly nuclear and the nonacetylated form is in cytoplasm. DAZAP1 also functions as a translational regulator that activates translation in an mRNA-specific manner. DAZAP1 was initially identified as a binding partner of Deleted in Azoospermia (DAZ). It also interacts with numerous hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1, hnRNPA/B, and hnRNP D, suggesting DAZAP1 might associate and cooperate with hnRNP particles to regulate adenylate-uridylate-rich elements (AU-rich element or ARE)-containing mRNAs. DAZAP1 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal proline-rich domain.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2296754393  83 YVAYLTNLPYDIDEADLADFFADM-KISNMRLPKDANK--IRGYGYVEFEDRQSLIDALSMTNTTIKTRRVRI 152
Cdd:cd12327     3 KKVFVGGIPHNCGETELRDYFKRYgVVTEVVMMYDAEKqrSRGFGFITFEDEQSVDQAVNMHFHDIMGKKVEV 75

RNA recognition motif 1 and 2 (RRM1, RRM2) found in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins; This subgroup corresponds to the RRM domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2296754393  86 YLTNLPYDIDEADLADFF-ADMKISNMRLPKDANKIRgYGYVEFEDRQSLIDALSMTNTTIKTRRVRIDIS 155
Cdd:cd12225     4 HVGGIDGSLSEDELADYFsNCGEVTQVRLCGDRVHTR-FAWVEFATDASALSALNLDGTTLGGHPLRVSPS 73

RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), cleavage stimulation factor subunit 2 tau variant (CSTF2T) and similar proteins; This subgroup corresponds to the RRM domain of CSTF2, its tau variant and eukaryotic homologs. CSTF2, also termed cleavage stimulation factor 64 kDa subunit (CstF64), is the vertebrate conterpart of yeast mRNA 3'-end-processing protein RNA15. It is expressed in all somatic tissues and is one of three cleavage stimulatory factor (CstF) subunits required for polyadenylation. CstF64 contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a CstF77-binding domain, a repeated MEARA helical region and a conserved C-terminal domain reported to bind the transcription factor PC-4. During polyadenylation, CstF interacts with the pre-mRNA through the RRM of CstF64 at U- or GU-rich sequences within 10 to 30 nucleotides downstream of the cleavage site. CSTF2T, also termed tauCstF64, is a paralog of the X-linked cleavage stimulation factor CstF64 protein that supports polyadenylation in most somatic cells. It is expressed during meiosis and subsequent haploid differentiation in a more limited set of tissues and cell types, largely in meiotic and postmeiotic male germ cells, and to a lesser extent in brain. The loss of CSTF2T will cause male infertility, as it is necessary for spermatogenesis and fertilization. Moreover, CSTF2T is required for expression of genes involved in morphological differentiation of spermatids, as well as for genes having products that function during interaction of motile spermatozoa with eggs. It promotes germ cell-specific patterns of polyadenylation by using its RRM to bind to different sequence elements downstream of polyadenylation sites than does CstF64.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2296754393  86 YLTNLPYDIDEADLADFFADM-KISNMRL--PKDANKIRGYGYVEFEDRQSLIDALSMTNT-TIKTRRVRID 153
Cdd:cd12671    10 FVGNIPYEATEEQLKDIFSEVgPVVSFRLvyDRETGKPKGYGFCEYQDQETALSAMRNLNGyELNGRALRVD 81

RNA recognition motif 3 (RRM3) found in vertebrate nucleolin; This subfamily corresponds to the RRM3 of ubiquitously expressed protein nucleolin, also termed protein C23, is a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2296754393  87 LTNLPYDIDEADLADFFAdmKISNMRLPKDANKIRGYGYVEFEDRQSLIDAL-SMTNTTIKTRRVRID 153
Cdd:cd12405     6 VNNLSYSATEESLQSVFE--KATSIRIPQNNGRPKGYAFVEFESVEDAKEALeSCNNTEIEGRSIRLE 71

RNA recognition motif 1 (RRM1) found in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins; This subgroup corresponds to the RRM1 domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2296754393  86 YLTNLPYDIDEADLADFFADM-KISNMRLPKDANKIRGYGYVEFEDRQSLIDALSMTNTTIKTRRVRI 152
Cdd:cd12459     6 YVSDIDQQVTEEQLAALFSNCgQVVDCRICGDPNSVLRFAFIEFTDEEGARAALSLSGTMLGFYPVRV 73

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

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2296754393  86 YLTNLPYDIDEADLADFFA------DMKISNMRlpkDANKIRGYGYVEFEDRQSLIDALSMTN-TTIKTRRVRIDI 154
Cdd:cd21608     3 YVGNLSWDTTEDDLRDLFSefgeveSAKVITDR---ETGRSRGFGFVTFSTAEAAEAAIDALNgKELDGRSIVVNE 75

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

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2296754393  86 YLTNLPYDIDEADLADFF-ADMKISNMRLPKD--ANKIRGYGYVEFEDRQSLIDALSMTNTTI 145
Cdd:cd12651     6 YVTNLPRTITEDELDTIFgAYGNIVQKNLLRDklTGRPRGVAFVRYDKREEAQAAISALNGTI 68

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2296754393  86 YLTNLPYDIDEADLADFFAD---MKISNMRLPKDANKIRGYGYVEFEDRQSLIDALS-MTNTTIKTRRVRIDIS 155
Cdd:cd12674     4 FVRNLPFDVTLESLTDFFSDigpVKHAVVVTDPETKKSRGYGFVSFSTHDDAEEALAkLKNRKLSGHILKLDFA 77

RNA recognition motif (RRM) found in nucleolar protein 8 (NOL8) and similar proteins; This model corresponds to the RRM of NOL8 (also termed Nop132) encoded by a novel NOL8 gene that is up-regulated in the majority of diffuse-type, but not intestinal-type, gastric cancers. Thus, NOL8 may be a good molecular target for treatment of diffuse-type gastric cancer. Also, NOL8 is a phosphorylated protein that contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), suggesting NOL8 is likely to function as a novel RNA-binding protein. It may be involved in regulation of gene expression at the post-transcriptional level or in ribosome biogenesis in cancer cells.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2296754393  86 YLTNLPYDIDEADLADFFADM-KISNMRLP-KDANKIRGYGYVEFEDR-QSLIDALS-MTNTTIKTRRVRID 153
Cdd:cd12226     3 FVGGLSPSITEDDLERRFSRFgTVSDVEIIrKKDAPDRGFAYIDLRTSeAALQKCLStLNGVKWKGSRLKIQ 74

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2296754393  86 YLTNLPYDIDEADLADFFADM-KISNMRLPKDAN-KIRGYGYVEFEDRQSLIDA-LSMTNTTIKTRRVRIDISN 156
Cdd:cd12392     6 FVKGLPFSCTKEELEELFKQHgTVKDVRLVTYRNgKPKGLAYVEYENEADASQAvLKTDGTEIKDHTISVAISN 79

transcription termination factor Rho; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2296754393 157 SSNDDRRGNRMGRDNRRDNyddPERTSGDWRSGPREELLDEDSHRSRYDNRDRRDDRDRHDYDNKPGAWRERDNNDKGFK 236
Cdd:PRK12678  169 RDERRRRGDREDRQAEAER---GERGRREERGRDGDDRDRRDRREQGDRREERGRRDGGDRRGRRRRRDRRDARGDDNRE 245

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 2296754393 237 DRGGFRDDSKDRDWNRYSDRGRSKDRDGDRSssfgpRRNYGDSDWDRRQD 286
Cdd:PRK12678  246 DRGDRDGDDGEGRGGRRGRRFRDRDRRGRRG-----GDGGNEREPELRED 290

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
                  ....*....|....*....|....*....|....*....|....*....|
gi 2296754393  86 YLTNLPYDIDEADLADFFADM-KISNMRLPKDAN-KIRGYGYVEFEDRQS 133
Cdd:cd12380     5 YVKNFGEDVDDDELKELFEKYgKITSAKVMKDDSgKSKGFGFVNFENHEA 54

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).

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2296754393  86 YLTNLPYDIDEADLADFFADMKISNMRLPK------DANKIR--GYGYVEF---EDRQSLIDALSmtNTTIKTRRVRI 152
Cdd:cd12409     3 YISNLSYSTTEEELEELLKDYKPVSVLIPSytvrgfRSRKHRplGIAYAEFssvEEAEKVVKDLN--GKVFKGRKLFV 78

RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins; This subgroup corresponds to the RRM2 of hnRNP A0, 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 A0 contains 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 2296754393  93 DIDEADLADFFAD---MKISNMRLPKDANKIRGYGYVEFEDRQSLIDALSMTNTTIKTRRVRI 152
Cdd:cd12579    10 DVGEGDLVEHFSQfgtVEKVEVIADKDTGKKRGFGFVYFEDHDSADKAAVVKFHSINGHRVEV 72

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

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2296754393  86 YLTNLPYDIDEADLADFFAD--MKISNmRLPKDANKI-RGYGYVEFEDRQSLIDALSMTNT-TIKT 147
Cdd:cd12244     4 YISNLPLDMDEQDLENMLKPfgQVIST-RILRDSKGQsRGVGFARMESREKCEDVISKFNGkVLKT 68

RNA recognition motif 1 (RRM1) found in TAR DNA-binding protein 43 (TDP-43) and similar proteins; This subfamily corresponds to the RRM1 of TDP-43 (also termed TARDBP), a ubiquitously expressed pathogenic protein whose normal function and abnormal aggregation are directly linked to the genetic disease cystic fibrosis, and two neurodegenerative disorders: frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). TDP-43 binds both DNA and RNA, and has been implicated in transcriptional repression, pre-mRNA splicing and translational regulation. TDP-43 is a dimeric protein with two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal glycine-rich domain. The RRMs are responsible for DNA and RNA binding; they bind to TAR DNA and RNA sequences with UG-repeats. The glycine-rich domain can interact with the hnRNP family proteins to form the hnRNP-rich complex involved in splicing inhibition. It is also essential for the cystic fibrosis transmembrane conductance regulator (CFTR) exon 9-skipping activity.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2296754393  89 NLPYDIDEADLADFFADM-KISNMRLPKDAN--KIRGYGYVEFEDRQSLIDALS 139
Cdd:cd12321     6 GLPWKTTEQDLKEYFSTFgEVLMVQVKKDPKtgRSKGFGFVRFASYETQVKVLS 59

RNA recognition motif 1 (RRM1) found in type I polyadenylate-binding proteins; This subfamily corresponds to the RRM1 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 a 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 mammals, 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 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.