RNA recognition motif 1 (RRM1) found in Kinetoplastid-Specific Ribosomal Protein (KSRP) and similar proteins; KSRP is an essential protein located at the solvent face of the 40S subunit, where it binds and stabilizes kinetoplastid-specific domains of rRNA, suggesting its role in ribosome integrity. It also interacts with the kinetoplastid-specific C-terminal region of protein eS6. KSRP contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the first RRM motif.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2027070878  76 NGLYVKNWGQGSVDDARALFGTAGKVVGVRVRRRRYAIIFFENAAAVKKAIDLFNGKEFMGNVLSVVPAKT 146
Cdd:cd21613     1 NGVYVKNWGQGSVADATALFSAAGKVVGVQIRRRRYAIIFFENAAAVKKAIDLFNGKEVLGNTVSVVPAKT 71

RNA recognition motif 1 (RRM1) found in Kinetoplastid-Specific Ribosomal Protein (KSRP) and similar proteins; KSRP is an essential protein located at the solvent face of the 40S subunit, where it binds and stabilizes kinetoplastid-specific domains of rRNA, suggesting its role in ribosome integrity. It also interacts with the kinetoplastid-specific C-terminal region of protein eS6. KSRP contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the first RRM motif.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2027070878  76 NGLYVKNWGQGSVDDARALFGTAGKVVGVRVRRRRYAIIFFENAAAVKKAIDLFNGKEFMGNVLSVVPAKT 146
Cdd:cd21613     1 NGVYVKNWGQGSVADATALFSAAGKVVGVQIRRRRYAIIFFENAAAVKKAIDLFNGKEVLGNTVSVVPAKT 71

RNA recognition motif;

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2027070878  158 VVFVSPIfRASTTKKQILELFS--GmKVLRLRTYRN-------NYAYVYLDTPAAAQRAVKEKNGAEFRGKQLRV 223
Cdd:smart00360   1 TLFVGNL-PPDTTEEELRELFSkfG-KVESVRLVRDketgkskGFAFVEFESEEDAEKALEALNGKELDGRPLKV 73

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

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2027070878 168 STTKKQILELFSG------MKVLRLR-TYRN-NYAYVYLDTPAAAQRAVKEKNGAEFRGKQLRValstrSLAKDRAR 236
Cdd:COG0724    12 SVTEEDLRELFSEygevtsVKLITDReTGRSrGFGFVEMPDDEEAQAAIEALNGAELMGRTLKV-----NEARPREE 83

RNA recognition motif;

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2027070878   78 LYVKN-WGQGSVDDARALFGTAGK-------VVGVRVRRRRYAIIFFENAAAVKKAIDLFNGKEFMGNVLSV 141
Cdd:smart00360   2 LFVGNlPPDTTEEELRELFSKFGKvesvrlvRDKETGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV 73

RNA recognition motif 1 (RRM1) found in Kinetoplastid-Specific Ribosomal Protein (KSRP) and similar proteins; KSRP is an essential protein located at the solvent face of the 40S subunit, where it binds and stabilizes kinetoplastid-specific domains of rRNA, suggesting its role in ribosome integrity. It also interacts with the kinetoplastid-specific C-terminal region of protein eS6. KSRP contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the first RRM motif.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2027070878  76 NGLYVKNWGQGSVDDARALFGTAGKVVGVRVRRRRYAIIFFENAAAVKKAIDLFNGKEFMGNVLSVVPAKT 146
Cdd:cd21613     1 NGVYVKNWGQGSVADATALFSAAGKVVGVQIRRRRYAIIFFENAAAVKKAIDLFNGKEVLGNTVSVVPAKT 71

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 2027070878  64 RDAKQrsdAANHNGLYVKNWGQgSVDDA--RALFGTAGK------VVGVRVRRRRYAIIFFENAAAVKKAIDLFNGKEF- 134
Cdd:TIGR01628 170 REAAP---LKKFTNLYVKNLDP-SVNEDklRELFAKFGEitsaavMKDGSGRSRGFAFVNFEKHEDAAKAVEEMNGKKIg 245

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2027070878 135 ---MGNVLSVVPAKttPKPDPHANSSVVF----VSPIFRA------------STTKKQILELFS------GMKVLRLRTY 189
Cdd:TIGR01628 246 lakEGKKLYVGRAQ--KRAEREAELRRKFeelqQERKMKAqgvnlyvknlddTVTDEKLRELFSecgeitSAKVMLDEKG 323

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2027070878 190 RNN-YAYVYLDTPAAAQRAVKEKNGAEFRGKQLRVALSTRslaKDraraerARLLMAAQKFNKRK 253
Cdd:TIGR01628 324 VSRgFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQR---KE------QRRAHLQDQFMQLQ 379

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 2027070878 159 VFVSPIFRaSTTKKQILELFS---GMKVLRLRTYRNN----YAYVYLDTPAAAQRAVKEKNGAEFRGKQLRVALS 226
Cdd:cd12392     5 LFVKGLPF-SCTKEELEELFKqhgTVKDVRLVTYRNGkpkgLAYVEYENEADASQAVLKTDGTEIKDHTISVAIS 78

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 2027070878 111 YAIIFFENAAAVKKAIDLFNGKEFMGNVLSVVP--AKTTPKPDPHANSSVVFVSPiFRASTTKKQILELFS------GMK 182
Cdd:TIGR01628 131 YGFVHFEKEESAKAAIQKVNGMLLNDKEVYVGRfiKKHEREAAPLKKFTNLYVKN-LDPSVNEDKLRELFAkfgeitSAA 209

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2027070878 183 VLRLRTYR-NNYAYVYLDTPAAAQRAVKEKNGAEFRGKQLRVALstrSLAKDRARAERARLLMAaqKFNKRKNHTK 257
Cdd:TIGR01628 210 VMKDGSGRsRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGKKL---YVGRAQKRAEREAELRR--KFEELQQERK 280

RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins; This subfamily 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. The family also includes yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins. RNA15 is a core subunit of cleavage factor IA (CFIA), an essential transcriptional 3'-end processing factor from Saccharomyces cerevisiae. RNA recognition by CFIA is mediated by an N-terminal RRM, which is contained in the RNA15 subunit of the complex. The RRM of RNA15 has a strong preference for GU-rich RNAs, mediated by a binding pocket that is entirely conserved in both yeast and vertebrate RNA15 orthologs.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2027070878 158 VVFVSPIfRASTTKKQILELFSG---MKVLRLRTYRNN-----YAYVYLDTPAAAQRAVKEKNGAEFRGKQLRV 223
Cdd:cd12398     2 SVFVGNI-PYDATEEQLKEIFSEvgpVVSFRLVTDRETgkpkgYGFCEFRDAETALSAVRNLNGYELNGRPLRV 74

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

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2027070878 168 STTKKQILELFSG------MKVLRLR-TYRN-NYAYVYLDTPAAAQRAVKEKNGAEFRGKQLRValstrSLAKDRAR 236
Cdd:COG0724    12 SVTEEDLRELFSEygevtsVKLITDReTGRSrGFGFVEMPDDEEAQAAIEALNGAELMGRTLKV-----NEARPREE 83

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

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2027070878 169 TTKKQILELFSGMKVLRLRTYRNNYAYVYLDTPAAAQRAVKEKNGAEFRGKQLRVALS 226
Cdd:cd12608    12 TSQEELSALFEPYGAVLSCAVMKQFAFVHMRGEAAADRAIRELNGRELHGRALVVEES 69

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

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 2027070878 111 YAIIFFENAAAVKKAIDLFNGKEFMGNVLSVVPAKttPKPD 151
Cdd:COG0724    45 FGFVEMPDDEEAQAAIEALNGAELMGRTLKVNEAR--PREE 83

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

                          10        20        30
                  ....*....|....*....|....*....|...
gi 2027070878 191 NNYAYVYLDTPAAAQRAVKEKNGAEFRGKQLRV 223
Cdd:cd12343    33 KNYAFVHMEKEEDAEDAIKALNGYEFMGSRINV 65

RNA recognition motif (RRM) found in the FET family of RNA-binding proteins; This subfamily corresponds to the RRM of FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA-binding proteins. This ubiquitously expressed family of similarly structured proteins predominantly localizing to the nuclear, includes FUS (also known as TLS or Pigpen or hnRNP P2), EWS (also known as EWSR1), TAF15 (also known as hTAFII68 or TAF2N or RPB56), and Drosophila Cabeza (also known as SARFH). The corresponding coding genes of these proteins are involved in deleterious genomic rearrangements with transcription factor genes in a variety of human sarcomas and acute leukemias. All FET proteins interact with each other and are therefore likely to be part of the very same protein complexes, which suggests a general bridging role for FET proteins coupling RNA transcription, processing, transport, and DNA repair. The FET proteins contain multiple copies of a degenerate hexapeptide repeat motif at the N-terminus. The C-terminal region consists of a conserved nuclear import and retention signal (C-NLS), a putative zinc-finger domain, and a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is flanked by 3 arginine-glycine-glycine (RGG) boxes. FUS and EWS might have similar sequence specificity; both bind preferentially to GGUG-containing RNAs. FUS has also been shown to bind strongly to human telomeric RNA and to small low-copy-number RNAs tethered to the promoter of cyclin D1. To date, nothing is known about the RNA binding specificity of TAF15.

                          10        20        30
                  ....*....|....*....|....*....|
gi 2027070878 112 AIIFFENAAAVKKAIDLFNGKEFMGNVLSV 141
Cdd:cd12280    51 ATLTYEDPSAAKAAIEWFNGKEFRGNKIKV 80

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.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2027070878 167 ASTTKKQILELFSGM-KVLRLRTYRN-------NYAYVYLDTPAAAQRAVKEKNGAEFRGKQLRVALSTR 228
Cdd:cd12378     9 PDVTEAMLYEKFSPAgPVLSIRVCRDavtrrslGYAYVNFQQPADAERALDTLNFDVIKGKPIRIMWSQR 78

RNA recognition motif (RRM) found in La-related protein 4 (LARP4), La-related protein 5 (LARP5 or LARP4B) and similar proteins; This subfamily corresponds to the RRM of LARP4 and LARP5. LARP4 is a cytoplasmic factor that can bind poly(A) RNA and interact with poly(A) binding protein (PABP). It may play a role in promoting translation by stabilizing mRNA. LARP5 is a cytosolic protein that co-sediments with polysomes and accumulates upon stress induction in cellular stress granules. It can interact with the cytosolic poly(A) binding protein 1 (PABPC1) and the receptor for activated C Kinase (RACK1), a component of the 40S ribosomal subunit. LARP5 may function as a stimulatory factor of translation through bridging mRNA factors of the 3' end with initiating ribosomes. Both, LARP4 and LARP5, are structurally related to the La autoantigen. Like other La-related proteins (LARPs) family members, LARP4 and LARP5 contain a La motif (LAM) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2027070878 167 ASTTKKQILELFSGM---KVLRLRTYRNNYAYVYLDTPAAAQRAVK--EKNGAEFRGKQLR 222
Cdd:cd12430    10 ESTPEEEVEALFSGQncpKFTSCEFAINDSWYVTFESEEDAQEAYKylREEVKTFNGKPIM 70

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

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2027070878 170 TKKQILELFSGMKVLRLRTYRNN---YAYVYLDTPAAAQRAVKEKNGAEFRGKQLRVA 224
Cdd:cd21617    12 SEEEILQLFKAFNPVLVKKIRSGfkcFAFVDLGSDENVKLAIQQLNGTLFGGRRLVVN 69

RNA recognition motif 2 (RRM2) found in splicing regulatory glutamine/lysine-rich protein 1 (SREK1) and similar proteins; This subfamily corresponds to the RRM2 of SREK1, also termed serine/arginine-rich-splicing regulatory protein 86-kDa (SRrp86), or splicing factor arginine/serine-rich 12 (SFRS12), or splicing regulatory protein 508 amino acid (SRrp508). SREK1 belongs to a family of proteins containing regions rich in serine-arginine dipeptides (SR proteins family), which is involved in bridge-complex formation and splicing by mediating protein-protein interactions across either introns or exons. It is a unique SR family member and it may play a crucial role in determining tissue specific patterns of alternative splicing. SREK1 can alter splice site selection by both positively and negatively modulating the activity of other SR proteins. For instance, SREK1 can activate SRp20 and repress SC35 in a dose-dependent manner both in vitro and in vivo. In addition, SREK1 contains two (some contain only one) RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and two serine-arginine (SR)-rich domains (SR domains) separated by an unusual glutamic acid-lysine (EK) rich region. The RRM and SR domains are highly conserved among other members of the SR superfamily. However, the EK domain is unique to SREK1. It plays a modulatory role controlling SR domain function by involvement in the inhibition of both constitutive and alternative splicing and in the selection of splice-site.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2027070878 168 STTKKQILELFSG---MKVLRL---RTYRNNYAYV-YLDTPAAAqRAVKeKNGAEFRGKQLRVALSTRSLAK 232
Cdd:cd12260    15 STTADQLLEFFSQageVKYVRMagdETQPTRYAFVeFAEQTSVI-NALK-LNGKMFGGRPLKVNHSNNAIVK 84

RNA recognition motif 2 (RRM2) found in vertebrate nucleolin; This subfamily corresponds to the RRM2 of ubiquitously expressed protein nucleolin, also termed protein C23, 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.RRM2, together with RRM1, binds specifically to RNA stem-loops containing the sequence (U/G)CCCG(A/G) in the loop.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2027070878 168 STTKKQILELFSGMKVLRLRTYRNN----YAYVYLDTPAAAQRAVKEKNGAEFRGKQLRV 223
Cdd:cd12404    14 STTQDELKEVFEDAVDIRIPMGRDGrskgIAYIEFKSEAEAEKALEEKQGTEVDGRSIVV 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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2027070878  78 LYVKNWGQG-SVDDARALFGTAGK------VVGVRVRRRRYAIIFFENAAAVKKAIDLFNGKEFMGNVL 139
Cdd:pfam00076   1 LFVGNLPPDtTEEDLKDLFSKFGPiksirlVRDETGRSKGFAFVEFEDEEDAEKAIEALNGKELGGREL 69