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 1281061799 254 NTHVYITGLPEDVTIDEVVEVFSKCGIIKEDPETKKPRVKLYVDKEtGKTKGDALVTYLKEPSVALAMQILDGTPLRPGG 333
Cdd:cd12281     1 NTNVYVSGLPLDITVEEFVELFSKCGIIMEDPETGEPKIKLYRDEN-GNLKGDALCCYLKEESVELALQLLDGTEIGRGY 79

                          90
                  ....*....|....*
gi 1281061799 334 KilMSVTQAKFEQKG 348
Cdd:cd12281    80 K--IHVERAKFELKG 92

GYF domain 2; This domain is found in bacteria, archaea and eukaryotes, and is approximately 50 amino acids in length. It contains an evolutionary conserved signature W-X-Y-X6-11-GPF-X4-M-X2-W-X3-GYF, the site of interaction with proline-rich peptides. Family members include RME-8 (Required for receptor-mediated endocytosis 8), a DNAJC13 protein. RME-8 was first identified as a protein that is required for endocytosis in Caenorhabditis elegans. It coordinates the activity of the WASH complex with the function of the retromer SNX dimer to control endosomal tubulation. Family members found in Arabidopsis include Arabidopsis trithorax-related3 (Atxr3), also known as set domain group 2 (Sdg2). It is the major enzyme responsible for H3K4me3 in Arabidopsis and SDG2-dependent H3K4m3 is critical for regulating gene expression and plant development. Another family member found in Arabidopsis is Tic56. It is an essential subunit of a 1-MDa protein complex at the inner chloroplast envelope membrane. Furthermore, Tic56 is important for rRNA processing and chloroplast ribosome assembly.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1281061799  17 WYILGEDQQhVGPYAFSELRDHFLNGYLMESTLVWCEGQSEWHPLSSILGL 67
Cdd:pfam14237   1 WYYAVNGQQ-QGPFSLEELRQLAASGEITPDTLVWREGMDDWKPASDVPEL 50

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 1281061799 254 NTHVYITGLPEDVTIDEVVEVFSKCGIIKEDPETKKPRVKLYVDKEtGKTKGDALVTYLKEPSVALAMQILDGTPLRPGG 333
Cdd:cd12281     1 NTNVYVSGLPLDITVEEFVELFSKCGIIMEDPETGEPKIKLYRDEN-GNLKGDALCCYLKEESVELALQLLDGTEIGRGY 79

                          90
                  ....*....|....*
gi 1281061799 334 KilMSVTQAKFEQKG 348
Cdd:cd12281    80 K--IHVERAKFELKG 92

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281061799 257 VYITGLPEDVTIDEVVEVFSKCGIIKEdpetkkprVKLYVDKETGKTKGDALVTYlKEPSVA-LAMQILDGTPLrpGGKI 335
Cdd:TIGR01642 298 IYIGNLPLYLGEDQIKELLESFGDLKA--------FNLIKDIATGLSKGYAFCEY-KDPSVTdVAIAALNGKDT--GDNK 366

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281061799 336 LmSVTQAKFEQKGDKFVSKKVDNKKKKKLKKVEDKILGWGGRddakisiPATVV-LRFMFTPAEMRTDENLAsEIEADVK 414
Cdd:TIGR01642 367 L-HVQRACVGANQATIDTSNGMAPVTLLAKALSQSILQIGGK-------PTKVVqLTNLVTGDDLMDDEEYE-EIYEDVK 437

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1281061799 415 EESTRFGPVDSVKVCENHPQGV-------VLIRFKDRKDAQKCIELMNGRWFGGRQI 464
Cdd:TIGR01642 438 TEFSKYGPLINIVIPRPNGDRNstpgvgkVFLEYADVRSAEKAMEGMNGRKFNDRVV 494

RNA recognition motif;

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281061799  257 VYITGLPEDVTIDEVVEVFSKCGIIKedpetkkpRVKLYVDKETGKTKGDALVTYLKEPSVALAMQILDGTPLrpGGKIL 336
Cdd:smart00360   2 LFVGNLPPDTTEEELRELFSKFGKVE--------SVRLVRDKETGKSKGFAFVEFESEEDAEKALEALNGKEL--DGRPL 71

RNA recognition motif;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1281061799  404 NLASEI-EADVKEESTRFGPVDSVKVC----ENHPQGVVLIRFKDRKDAQKCIELMNGRWFGGRQIH 465
Cdd:smart00360   6 NLPPDTtEEELRELFSKFGKVESVRLVrdkeTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLK 72

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 1281061799 404 NLASEI-EADVKEESTRFGPVDSVKVCEN---HPQGVVLIRFKDRKDAQKCIELMNGRWFGGRQIH 465
Cdd:pfam00076   5 NLPPDTtEEDLKDLFSKFGPIKSIRLVRDetgRSKGFAFVEFEDEEDAEKAIEALNGKELGGRELK 70

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

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1281061799 404 NLASEI-EADVKEESTRFGPVDSVKVCENH----PQGVVLIRFKDRKDAQKCIELMNGRWFGGRQI 464
Cdd:COG0724     8 NLPYSVtEEDLRELFSEYGEVTSVKLITDRetgrSRGFGFVEMPDDEEAQAAIEALNGAELMGRTL 73

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 1281061799 254 NTHVYITGLPEDVTIDEVVEVFSKCGIIKEDPETKKPRVKLYVDKEtGKTKGDALVTYLKEPSVALAMQILDGTPLRPGG 333
Cdd:cd12281     1 NTNVYVSGLPLDITVEEFVELFSKCGIIMEDPETGEPKIKLYRDEN-GNLKGDALCCYLKEESVELALQLLDGTEIGRGY 79

                          90
                  ....*....|....*
gi 1281061799 334 KilMSVTQAKFEQKG 348
Cdd:cd12281    80 K--IHVERAKFELKG 92

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        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281061799 257 VYITGLPEDVTIDEVVEVFSKCGIIKEDPETKKPRVKLYVDKETGKTKGDALVTYLKEPSVALAMQILDGTPLRpGGKIL 336
Cdd:cd12280     1 IFVSGLPPDVTIDELADLFGQIGIIKRYKDTWPPKIKIYTDKETGKPKGEATLTYEDPSAAKAAIEWFNGKEFR-GNKIK 79

                  ..
gi 1281061799 337 MS 338
Cdd:cd12280    80 VS 81

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 1281061799 257 VYITGLPEDVTIDEVVEVFSKCGIIKEDPETKKPRVKLYVDKETGKTKGDALVTYLKEPSVALAMQILDGTPLRpGGKIL 336
Cdd:cd12533     3 IYVQGLNENVTLEELADFFKHCGVVKINKRTGQPMINIYTDKETGKPKGDATVSYEDPPAAKAAVEWFDGKDFQ-GNKLK 81

                  ...
gi 1281061799 337 MSV 339
Cdd:cd12533    82 VSM 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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1281061799 254 NTHVYITGLPEDVTIDEVVEVFSKCGIIKEDPETKKPRVKLYVDKETGKTKGDALVTYLKEPSVALAMQILDG 326
Cdd:cd12535     2 NNTIFVQGLGEDVTIDSVADYFKQIGIIKTNKKTGKPMINLYTDKETGKLKGEATVSFDDPPSAKAAIDWFDG 74

RNA recognition motif (RRM) found in U2 small nuclear ribonucleoprotein auxiliary factor U2AF 35 kDa subunit (U2AF35) and similar proteins; This subfamily corresponds to the RRM in U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF) which has been implicated in the recruitment of U2 snRNP to pre-mRNAs. It is a highly conserved heterodimer composed of large and small subunits; this family includes the small subunit of U2AF (U2AF35 or U2AF1) and U2AF 35 kDa subunit B (U2AF35B or C3H60). U2AF35 directly binds to the 3' splice site of the conserved AG dinucleotide and performs multiple functions in the splicing process in a substrate-specific manner. It promotes U2 snRNP binding to the branch-point sequences of introns through association with the large subunit of U2AF (U2AF65 or U2AF2). Although the biological role of U2AF35B remains unclear, it shows high sequence homolgy to U2AF35, which contains two N-terminal zinc fingers, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal arginine/serine (SR) -rich segment interrupted by glycines. In contrast to U2AF35, U2AF35B has a plant-specific conserved C-terminal region containing SERE motif(s), which may have an important function specific to higher plants.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281061799 387 TVVLRFMF-----------TPAEMRTDENLASEIEA---DVKEESTRFGPVDSVKVCEN---HPQGVVLIRFKDRKDAQK 449
Cdd:cd12287     1 TLLLKNMYpnpdnfissldDGSLTLSEEEIQEHFDEfyeDVFLELSRFGEIEDLVVCSNlndHLLGNVYVKFESEEDAEA 80

                          90
                  ....*....|....*...
gi 1281061799 450 CIELMNGRWFGGRQIHAS 467
Cdd:cd12287    81 ALQALNGRYYAGRPLYPE 98

RNA recognition motif;

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281061799  257 VYITGLPEDVTIDEVVEVFSKCGIIKedpetkkpRVKLYVDKETGKTKGDALVTYLKEPSVALAMQILDGTPLrpGGKIL 336
Cdd:smart00360   2 LFVGNLPPDTTEEELRELFSKFGKVE--------SVRLVRDKETGKSKGFAFVEFESEEDAEKALEALNGKEL--DGRPL 71

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281061799 389 VLRF--MFTPAEMRTDENLAsEIEADVKEESTRFGPVDSVKV-----CENHPQGV--VLIRFKDRKDAQKCIELMNGRWF 459
Cdd:cd12232     3 VLCLlnMVTPEELEDDEEYE-EILEDVKEECSKYGKVLSVVIprpeaEGVDVPGVgkVFVEFEDVEDAQKAQKALAGRKF 81

                  ....*...
gi 1281061799 460 GGRQIHAS 467
Cdd:cd12232    82 DGRTVVAS 89

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 1281061799 257 VYITGLPEDVTIDEVVEVFSKCGIIKEdpetkkprVKLYVDKEtGKTKGDALVTYLKEPSVALAMQILDGTPLrpGGKIL 336
Cdd:cd00590     1 LFVGNLPPDTTEEDLRELFSKFGEVVS--------VRIVRDRD-GKSKGFAFVEFESPEDAEKALEALNGTEL--GGRPL 69

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 1281061799 257 VYITGLPEDVTIDEVVEVFSKCGIIKEdpetkkprVKLyVDKETGKTKGDALVTYLKEPSVALAMQILDGTPLR 330
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFGPIKS--------IRL-VRDETGRSKGFAFVEFEDEEDAEKAIEALNGKELG 65

RNA recognition motif (RRM) found in U2 small nuclear ribonucleoprotein auxiliary factor 35 kDa subunit-related protein 1 (U2AFBPL) and similar proteins; This subgroup corresponds to the RRM of U2AFBPL, a human homolog of the imprinted mouse gene U2afbp-rs, which encodes a U2 small nuclear ribonucleoprotein auxiliary factor 35 kDa subunit-related protein 1 (U2AFBPL), also termed CCCH type zinc finger, RNA-binding motif and serine/arginine rich protein 1 (U2AF1RS1), or U2 small nuclear RNA auxiliary factor 1-like 1 (U2AF1L1). Although the biological role of U2AFBPL remains unclear, it shows high sequence homology to splicing factor U2AF 35 kDa subunit (U2AF35 or U2AF1) that directly binds to the 3' splice site of the conserved AG dinucleotide and performs multiple functions in the splicing process in a substrate-specific manner. Like U2AF35, U2AFBPL contains two N-terminal zinc fingers, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal arginine/serine (SR)-rich domain.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281061799 387 TVVLRFMFTP--------AEMRTDENLA-SEIEA---------DVKEESTRFGPVDSVKVCEN---HPQGVVLIRFKDRK 445
Cdd:cd12540     1 TLLIPNMFNTfgleqckrDDYDTDAGLEySEEDLysdflefyeDVLPEFKKFGKVVQFKVCCNsepHLRGNVYVQYQSEE 80

                          90       100
                  ....*....|....*....|
gi 1281061799 446 DAQKCIELMNGRWFGGRQIH 465
Cdd:cd12540    81 EALKAFTSFNGRWYAGKQLQ 100

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 1281061799 404 NLASEI-EADVKEESTRFGPVDSVKVCEN---HPQGVVLIRFKDRKDAQKCIELMNGRWFGGRQIH 465
Cdd:pfam00076   5 NLPPDTtEEDLKDLFSKFGPIKSIRLVRDetgRSKGFAFVEFEDEEDAEKAIEALNGKELGGRELK 70

RNA recognition motif (RRM) found in U2 small nuclear ribonucleoprotein auxiliary factor U2AF 35 kDa subunit (U2AF35); This subgroup corresponds to the RRM of U2AF35, also termed U2AF1, which is one of the small subunits of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF). It has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF35 directly binds to the 3' splice site of the conserved AG dinucleotide and performs multiple functions in the splicing process in a substrate-specific manner. It promotes U2 snRNP binding to the branch-point sequences of introns through association with the large subunit of U2AF, U2AF65 (also termed U2AF2). U2AF35 contains two N-terminal zinc fingers, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal arginine/serine (SR)-rich segment interrupted by glycines. U2AF35 binds both U2AF65 and the pre-mRNA through its RRM domain.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1281061799 415 EESTRFGPVDSVKVCEN---HPQGVVLIRFKDRKDAQKCIELMNGRWFGGRQIHA 466
Cdd:cd12538    46 ELEEKYGEIEEMNVCDNlgdHLVGNVYVKFRREEDAEKAVNDLNNRWFNGQPIYA 100

RNA recognition motif (RRM) found in splicing factor U2AF 35 kDa subunit B (U2AF35B); This subgroup corresponds to the RRM of U2AF35B, also termed zinc finger CCCH domain-containing protein 60 (C3H60), which is one of the small subunits of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF). It has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. Members in this family are mainly found in plant. They show high sequence homology to vertebrates U2AF35 that directly binds to the 3' splice site of the conserved AG dinucleotide and performs multiple functions in the splicing process in a substrate-specific manner. U2AF35B contains two N-terminal zinc fingers, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal arginine/serine (SR)-rich domain. In contrast to U2AF35, U2AF35B has a plant-specific conserved C-terminal region containing SERE motif(s), which may have an important function specific to higher plants.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1281061799 412 DVKEESTRFGPVDSVKVCEN---HPQGVVLIRFKDRKDAQKCIELMNGRWFGGRQI 464
Cdd:cd12539    41 DVFEELSKFGEVEALNVCDNlgdHMVGNVYVKFRDEEHAAAALKALQGRFYAGRPI 96

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281061799 258 YITGLPEDVTIDEVVEVFSKCGIIKedpetkkpRVKLYVDKETGKTKGDALVTYLKEPSVALAMQILDGTPLrpGGKILm 337
Cdd:COG0724     5 YVGNLPYSVTEEDLRELFSEYGEVT--------SVKLITDRETGRSRGFGFVEMPDDEEAQAAIEALNGAEL--MGRTL- 73

                  ....*.
gi 1281061799 338 SVTQAK 343
Cdd:COG0724    74 KVNEAR 79

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins; This subfamily corresponds to the RRM1 in hnRNP R, hnRNP Q, APOBEC-1 complementation factor (ACF), and dead end protein homolog 1 (DND1). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically binds mRNAs with a preference for poly(U) stretches. It has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone, and play a key role in cell growth and differentiation. DND1 is essential for maintaining viable germ cells in vertebrates. It interacts with the 3'-untranslated region (3'-UTR) of multiple messenger RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated repression of mRNA. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members in this family, except for DND1, contain three conserved RNA recognition motifs (RRMs); DND1 harbors only two RRMs.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1281061799 255 THVYITGLPEDVTIDEVVEVFSKCGIIKEdpetkkprVKLYVDKeTGKTKGDALVTYLKEPSVALAMQILDGTPLRPG 332
Cdd:cd12249     2 CEVFVGKIPRDVFEDELVPLFEKCGKIYE--------LRLMMDF-SGLNRGYAFVTYTNKEAAQRAVKTLNNYEIRPG 70

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 3 (SRSF3) and similar proteins; This subfamily corresponds to the RRM of two serine/arginine (SR) proteins, serine/arginine-rich splicing factor 3 (SRSF3) and serine/arginine-rich splicing factor 7 (SRSF7). SRSF3, also termed pre-mRNA-splicing factor SRp20, modulates alternative splicing by interacting with RNA cis-elements in a concentration- and cell differentiation-dependent manner. It is also involved in termination of transcription, alternative RNA polyadenylation, RNA export, and protein translation. SRSF3 is critical for cell proliferation, and tumor induction and maintenance. It can shuttle between the nucleus and cytoplasm. SRSF7, also termed splicing factor 9G8, plays a crucial role in both constitutive splicing and alternative splicing of many pre-mRNAs. Its localization and functions are tightly regulated by phosphorylation. SRSF7 is predominantly present in the nuclear and can shuttle between nucleus and cytoplasm. It cooperates with the export protein, Tap/NXF1, helps mRNA export to the cytoplasm, and enhances the expression of unspliced mRNA. Moreover, SRSF7 inhibits tau E10 inclusion through directly interacting with the proximal downstream intron of E10, a clustering region for frontotemporal dementia with Parkinsonism (FTDP) mutations. Both SRSF3 and SRSF7 contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1281061799 404 NLASEI-EADVKEESTRFGPVDSVKVCENhPQGVVLIRFKDRKDAQKCIELMNGRWFGGRQI 464
Cdd:cd12373     6 NLGPRVtKRELEDAFEKYGPLRNVWVARN-PPGFAFVEFEDPRDAEDAVRALDGRRICGSRV 66

RNA recognition motif 2 (RRM2) found in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins; The CD corresponds to the RRM2 of PHIP1. A. thaliana PHIP1 and its homologs represent a novel class of plant-specific RNA-binding proteins that may play a unique role in the polarized mRNA transport to the vicinity of the cell plate. The family members consist of multiple functional domains, including a lysine-rich domain (KRD domain) that contains three nuclear localization motifs (KKKR/NK), two RNA recognition motifs (RRMs), and three CCHC-type zinc fingers. PHIP1 is a peripheral membrane protein and is localized at the cell plate during cytokinesis in plants. In addition to phragmoplastin, PHIP1 interacts with two Arabidopsis small GTP-binding proteins, Rop1 and Ran2. However, PHIP1 interacted only with the GTP-bound form of Rop1 but not the GDP-bound form. It also binds specifically to Ran2 mRNA.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1281061799 257 VYITGLPEDVTIDEVVEVFSKCGIIKEdpetkkprVKLYVDKETGKTKGDALVTYLKEPSVALAMQiLDGTPLR 330
Cdd:cd12272     2 VYIGNLAWDIDEDDLRELFAECCEITN--------VRLHTDKETGEFKGYGHVEFADEESLDAALK-LAGTKLC 66

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        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281061799 255 THVYITGLPEDVTIDEVVEVFSKCGIIKEdpetkkprVKLYVDKETGKTKGDALVTYLKEPSVALAMQILDGTpLRPGGK 334
Cdd:cd12651     3 TNLYVTNLPRTITEDELDTIFGAYGNIVQ--------KNLLRDKLTGRPRGVAFVRYDKREEAQAAISALNGT-IPEGGT 73

                  ....*...
gi 1281061799 335 ILMSVTQA 342
Cdd:cd12651    74 QPLSVRLA 81

RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins p40-TIA-1 and TIAR; This subfamily corresponds to the RRM2 of nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR), both of which are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. TIA-1 and TIAR share high sequence similarity. They are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis. TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both, TIA-1 and TIAR, bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1281061799 404 NLASEIEA-DVKEESTRFGPVDSVKVCE----NHPQGVVLIRFKDRKDAQKCIELMNGRWFGGRQI 464
Cdd:cd12353     6 DLSPEIETeDLKEAFAPFGEISDARVVKdtqtGKSKGYGFVSFVKKEDAENAIQGMNGQWLGGRNI 71

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 1281061799 250 ELKINTHVYITGLPEDVTIDEVVEVFSKCGIIKEdpetkkprVKLYVDKETGKTKGDALVTYLKEPSVALAMQILDGTPL 329
Cdd:cd12411     5 EYKDSAYIYIGGLPYELTEGDILCVFSQYGEIVD--------INLVRDKKTGKSKGFAFLAYEDQRSTILAVDNLNGIKL 76

                  ....*..
gi 1281061799 330 rpGGKIL 336
Cdd:cd12411    77 --LGRTI 81

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        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1281061799 257 VYITGLPEDVTIDEVVEVFSKCGIIKEdpetkkprVKLYVDKETGKTKGDALVTYLKEPSVALAM----QILDGTPL 329
Cdd:cd12283     2 VFVMQLSLKARERDLYEFFSKAGKVRD--------VRLIMDRNSRRSKGVAYVEFYDVESVPLALaltgQRLLGQPI 70

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 1281061799 257 VYITGLPEDVTIDEVVEVFSKCGIIKEdpetkkprVKLYVDKETGKTKGDALVTYLKEPSVALAMQILDGTPLR 330
Cdd:cd21608     2 LYVGNLSWDTTEDDLRDLFSEFGEVES--------AKVITDRETGRSRGFGFVTFSTAEAAEAAIDALNGKELD 67

RNA recognition motif (RRM) found in Zinc finger CCHC-type and RNA-binding motif-containing protein 1 (ZCRB1) and similar proteins; This subfamily corresponds to the RRM of ZCRB1, also termed MADP-1, or U11/U12 small nuclear ribonucleoprotein 31 kDa protein (U11/U12 snRNP 31 or U11/U12-31K), a novel multi-functional nuclear factor, which may be involved in morphine dependence, cold/heat stress, and hepatocarcinoma. It is located in the nucleoplasm, but outside the nucleolus. ZCRB1 is one of the components of U11/U12 snRNPs that bind to U12-type pre-mRNAs and form a di-snRNP complex, simultaneously recognizing the 5' splice site and branchpoint sequence. ZCRB1 is characterized by an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a CCHC-type Zinc finger motif. In addition, it contains core nucleocapsid motifs, and Lys- and Glu-rich domains.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1281061799 257 VYITGLPEDVTIDEVVEVFSKCGiikedpetKKPRVKLYVDKETGKTKGDALVTYLKEPSVALAMQILDGTPL 329
Cdd:cd12393     4 VYVSNLPFSLTNNDLHQIFSKYG--------KVVKVTILKDKETRKSKGVAFVLFLDRESAHNAVRAMNNKEL 68

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 1281061799 255 THVYITGLPEDVTIDEVVEVFSKCGIIkedpetkkprVKLYVDK-ETGKTKGDALVTYLKEPSVALAMQILDGT--PLRP 331
Cdd:TIGR01628 179 TNLYVKNLDPSVNEDKLRELFAKFGEI----------TSAAVMKdGSGRSRGFAFVNFEKHEDAAKAVEEMNGKkiGLAK 248

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281061799 332 GGKIL-----------MSVTQAKFEQKGDKFVSkkvdnkkkkklkkvedkilgwggrddakISIPATVVLRfmftpaemr 400
Cdd:TIGR01628 249 EGKKLyvgraqkraerEAELRRKFEELQQERKM----------------------------KAQGVNLYVK--------- 291

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1281061799 401 tdeNLASEI-EADVKEESTRFGPVDSVKVCENhPQGVV----LIRFKDRKDAQKCIELMNGRWFGGR 462
Cdd:TIGR01628 292 ---NLDDTVtDEKLRELFSECGEITSAKVMLD-EKGVSrgfgFVCFSNPEEANRAVTEMHGRMLGGK 354

RNA recognition motif (RRM) found in inner nuclear membrane protein Man1 (Man1) and similar proteins; This subfamily corresponds to the RRM of Man1, also termed LEM domain-containing protein 3 (LEMD3), an integral protein of the inner nuclear membrane that binds to nuclear lamins and emerin, thus playing a role in nuclear organization. It is part of a protein complex essential for chromatin organization and cell division. It also functions as an important negative regulator for the transforming growth factor (TGF) beta/activin/Nodal signaling pathway by directly interacting with chromatin-associated proteins and transcriptional regulators, including the R-Smads, Smad1, Smad2, and Smad3. Moreover, Man1 is a unique type of left-right (LR) signaling regulator that acts on the inner nuclear membrane. Man1 plays a crucial role in angiogenesis. The vascular remodeling can be regulated at the inner nuclear membrane through the interaction between Man1 and Smads. Man1 contains an N-terminal LEM domain, two putative transmembrane domains, a MAN1-Src1p C-terminal (MSC) domain, and a C-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The LEM domain interacts with the DNA and chromatin-binding protein Barrier-to-Autointegration Factor, and is also necessary for efficient localization of MAN1 in the inner nuclear membrane. Research has indicated that C-terminal nucleoplasmic region of Man1 exhibits a DNA binding winged helix domain and is responsible for both DNA- and Smad-binding.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1281061799 390 LRFMFTPaEMRTDENLASEI-EADVKEESTRFGPVDsVKVCENHPQGVVLIRFKDRKDAQKCIELMNGRWFGGRQI 464
Cdd:cd12286     4 IRNMFDP-EMEIGEDWHVRIqEAILEKCSDNGGIVH-IAVDKNSREGCVYIKCASPEDAGKAFKALHGCWFDGRLV 77

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 1281061799 410 EADVKEESTRFGPVDSVKVCEN----HPQGVVLIRFKDRKDAQKCIELMNGR 457
Cdd:cd12408    13 EEDLRELFRPFGPISRVYLAKDketgQSKGFAFVTFETREDAERAIEKLNGF 64

RNA recognition motif 1 (RRM1) found in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q); This subgroup corresponds to the RRM1 of hnRNP Q, also termed glycine- and tyrosine-rich RNA-binding protein (GRY-RBP), or NS1-associated protein 1 (NASP1), or synaptotagmin-binding, cytoplasmic RNA-interacting protein (SYNCRIP). It is a ubiquitously expressed nuclear RNA-binding protein identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome. As an alternatively spliced version of NSAP, it acts as an interaction partner of a multifunctional protein required for viral replication, and is implicated in the regulation of specific mRNA transport. hnRNP Q has also been identified as SYNCRIP, a dual functional protein participating in both viral RNA replication and translation. As a synaptotagmin-binding protein, hnRNP Q plays a putative role in organelle-based mRNA transport along the cytoskeleton. Moreover, hnRNP Q has been found in protein complexes involved in translationally coupled mRNA turnover and mRNA splicing. It functions as a wild-type survival motor neuron (SMN)-binding protein that may participate in pre-mRNA splicing and modulate mRNA transport along microtubuli. hnRNP Q contains an acidic auxiliary N-terminal region, followed by two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP Q binds RNA through its RRM domains.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281061799 253 INTHVYITGLPEDVTIDEVVEVFSKCGIIKEdpetkkprVKLYVDKETGKTKGDALVTYLKEPSVALAMQILDGTPLRPG 332
Cdd:cd12483     4 VGTEIFVGKIPRDLFEDELVPLFEKAGPIWD--------LRLMMDPLTGLNRGYAFVTFCTKEAAQEAVKLCNNHEIRPG 75

                  ...
gi 1281061799 333 GKI 335
Cdd:cd12483    76 KHI 78