RNA recognition motif (RRM) found in eukaryotic RNA-binding protein 25 and similar proteins; This subfamily corresponds to the RRM of RBM25, also termed Arg/Glu/Asp-rich protein of 120 kDa (RED120), or protein S164, or RNA-binding region-containing protein 7, an evolutionary-conserved splicing coactivator SRm160 (SR-related nuclear matrix protein of 160 kDa, )-interacting protein. RBM25 belongs to a family of RNA-binding proteins containing a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminus, a RE/RD-rich (ER) central region, and a C-terminal proline-tryptophan-isoleucine (PWI) motif. It localizes to the nuclear speckles and associates with multiple splicing components, including splicing cofactors SRm160/300, U snRNAs, assembled splicing complexes, and spliced mRNAs. It may play an important role in pre-mRNA processing by coupling splicing with mRNA 3'-end formation. Additional research indicates that RBM25 is one of the RNA-binding regulators that direct the alternative splicing of apoptotic factors. It can activate proapoptotic Bcl-xS 5'ss by binding to the exonic splicing enhancer, CGGGCA, and stabilize the pre-mRNA-U1 snRNP through interaction with hLuc7A, a U1 snRNP-associated factor.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 308811773  18 HRAYVGKIPDSVDDASLTRILRVvCGdGFVGFKRVSDPrTNAGKSFGFASFASAESAMTCVWVLDGLEIVGGRLTSSANA 97
Cdd:cd12446    1 TTVFVGNIPDDVSDDFIRQLLEK-CG-KVLSWKRVQDP-SGKLKAFGFCEFEDPEGALRALRLLNGLELGGKKLLVKVDA 77

                 ....
gi 308811773  98 ATRD 101
Cdd:cd12446   78 KTKK 81

splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 308811773  180 GKNDDEGVRGRAS-SDGGSSRERREGRTRARSGERDGSRERDARRDgyhgaRFGDARAPRGHDYEVTERIE-RLCREREK 257
Cdd:TIGR01622   1 RYRDRERERLRDSsSAGDRDRRRDKGRERSRDRSRDRERSRSRRRD-----RHRDRDYYRGRERRSRSRRPnRRYRPREK 75

                          90       100       110
                  ....*....|....*....|....*....|...
gi 308811773  258 VCDEIAATTSR---LRSRREKLARERKVDRREA 287
Cdd:TIGR01622  76 RRRRGDSYRRRrddRRSRREKPRARDGTPEPLT 108

RNA recognition motif (RRM) found in eukaryotic RNA-binding protein 25 and similar proteins; This subfamily corresponds to the RRM of RBM25, also termed Arg/Glu/Asp-rich protein of 120 kDa (RED120), or protein S164, or RNA-binding region-containing protein 7, an evolutionary-conserved splicing coactivator SRm160 (SR-related nuclear matrix protein of 160 kDa, )-interacting protein. RBM25 belongs to a family of RNA-binding proteins containing a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminus, a RE/RD-rich (ER) central region, and a C-terminal proline-tryptophan-isoleucine (PWI) motif. It localizes to the nuclear speckles and associates with multiple splicing components, including splicing cofactors SRm160/300, U snRNAs, assembled splicing complexes, and spliced mRNAs. It may play an important role in pre-mRNA processing by coupling splicing with mRNA 3'-end formation. Additional research indicates that RBM25 is one of the RNA-binding regulators that direct the alternative splicing of apoptotic factors. It can activate proapoptotic Bcl-xS 5'ss by binding to the exonic splicing enhancer, CGGGCA, and stabilize the pre-mRNA-U1 snRNP through interaction with hLuc7A, a U1 snRNP-associated factor.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 308811773  18 HRAYVGKIPDSVDDASLTRILRVvCGdGFVGFKRVSDPrTNAGKSFGFASFASAESAMTCVWVLDGLEIVGGRLTSSANA 97
Cdd:cd12446    1 TTVFVGNIPDDVSDDFIRQLLEK-CG-KVLSWKRVQDP-SGKLKAFGFCEFEDPEGALRALRLLNGLELGGKKLLVKVDA 77

                 ....
gi 308811773  98 ATRD 101
Cdd:cd12446   78 KTKK 81

PWI domain;

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 308811773  487 RWISKKFVDLLGEPEPSIIRFVLDKLSER-PKPLSLVSALAPILDQDiADDFVLALWRVLIF 547
Cdd:pfam01480   5 PWIEKKITEILGFEDDVVVEYVVNLLEEKfPDPKELQIQLTGFLDKD-AAKFVKELWKLLLS 65

splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 308811773  180 GKNDDEGVRGRAS-SDGGSSRERREGRTRARSGERDGSRERDARRDgyhgaRFGDARAPRGHDYEVTERIE-RLCREREK 257
Cdd:TIGR01622   1 RYRDRERERLRDSsSAGDRDRRRDKGRERSRDRSRDRERSRSRRRD-----RHRDRDYYRGRERRSRSRRPnRRYRPREK 75

                          90       100       110
                  ....*....|....*....|....*....|...
gi 308811773  258 VCDEIAATTSR---LRSRREKLARERKVDRREA 287
Cdd:TIGR01622  76 RRRRGDSYRRRrddRRSRREKPRARDGTPEPLT 108

RNA recognition motif (RRM) found in eukaryotic RNA-binding protein 25 and similar proteins; This subfamily corresponds to the RRM of RBM25, also termed Arg/Glu/Asp-rich protein of 120 kDa (RED120), or protein S164, or RNA-binding region-containing protein 7, an evolutionary-conserved splicing coactivator SRm160 (SR-related nuclear matrix protein of 160 kDa, )-interacting protein. RBM25 belongs to a family of RNA-binding proteins containing a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminus, a RE/RD-rich (ER) central region, and a C-terminal proline-tryptophan-isoleucine (PWI) motif. It localizes to the nuclear speckles and associates with multiple splicing components, including splicing cofactors SRm160/300, U snRNAs, assembled splicing complexes, and spliced mRNAs. It may play an important role in pre-mRNA processing by coupling splicing with mRNA 3'-end formation. Additional research indicates that RBM25 is one of the RNA-binding regulators that direct the alternative splicing of apoptotic factors. It can activate proapoptotic Bcl-xS 5'ss by binding to the exonic splicing enhancer, CGGGCA, and stabilize the pre-mRNA-U1 snRNP through interaction with hLuc7A, a U1 snRNP-associated factor.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 308811773  18 HRAYVGKIPDSVDDASLTRILRVvCGdGFVGFKRVSDPrTNAGKSFGFASFASAESAMTCVWVLDGLEIVGGRLTSSANA 97
Cdd:cd12446    1 TTVFVGNIPDDVSDDFIRQLLEK-CG-KVLSWKRVQDP-SGKLKAFGFCEFEDPEGALRALRLLNGLELGGKKLLVKVDA 77

                 ....
gi 308811773  98 ATRD 101
Cdd:cd12446   78 KTKK 81

PWI domain;

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 308811773  487 RWISKKFVDLLGEPEPSIIRFVLDKLSER-PKPLSLVSALAPILDQDiADDFVLALWRVLIF 547
Cdd:pfam01480   5 PWIEKKITEILGFEDDVVVEYVVNLLEEKfPDPKELQIQLTGFLDKD-AAKFVKELWKLLLS 65

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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 308811773  21 YVGKIPDSVDDASLTRILRVVCGDGFVgfkRVSDPRTNAGKSFGFASFASAESAMTCVWVLDGLEIVGGRLT 92
Cdd:cd00590    2 FVGNLPPDTTEEDLRELFSKFGEVVSV---RIVRDRDGKSKGFAFVEFESPEDAEKALEALNGTELGGRPLK 70

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 308811773  21 YVGKIPDSVDDASLTRILRVVcGDgFVGFKRVSDPRTNAGKSFGFASFASAESAMTCVWVLDGLEIvGGR 90
Cdd:cd12398    4 FVGNIPYDATEEQLKEIFSEV-GP-VVSFRLVTDRETGKPKGYGFCEFRDAETALSAVRNLNGYEL-NGR 70

transcription termination factor Rho; Provisional

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 308811773  92 TSSANAATRDAHAENGGKRRSESDLETMREMVRGVLTKGGGVGREGEEEGEIADASDVARAGVASGTRETAASENGSGRD 171
Cdd:PRK12678  71 AAPAAAARRAARAAAAARQAEQPAAEAAAAKAEAAPAARAAAAAAAEAASAPEAAQARERRERGEAARRGAARKAGEGGE 150

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 308811773 172 GERSCDQVGKND----DEGVRGRASSDGGSSRERREGRTRARSGE--RDGSRERDARRDGYHGARFGDARAPRGHDYEVT 245
Cdd:PRK12678 151 QPATEARADAAErteeEERDERRRRGDREDRQAEAERGERGRREErgRDGDDRDRRDRREQGDRREERGRRDGGDRRGRR 230

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 308811773 246 ERIERLCREREKVCDEIAATTSRLRSRREKLARERKVDRREAMRRDLEDMEGEDGEI 302
Cdd:PRK12678 231 RRRDRRDARGDDNREDRGDRDGDDGEGRGGRRGRRFRDRDRRGRRGGDGGNEREPEL 287

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

                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 308811773  54 DPRTNAGKSFGFASFASAESAMTCVWVLDGLEIVGGRLT 92
Cdd:cd12362   33 DKNTGRSKGFGFVSYDNPLSAQAAIKAMNGFQVGGKRLK 71