RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 26 (RBM26); This subgroup corresponds to the RRM1 of RBM26, also known as cutaneous T-cell lymphoma (CTCL) tumor antigen se70-2, which represents a cutaneous lymphoma (CL)-associated antigen. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The RRMs may play some functional roles in RNA-binding or protein-protein interactions.

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1958680306  541 NTKLELRKVPPELNNISKLNEHFSRFGTLVNLQVAYNGDPEGALIQFATYDEAKKAISSTEAVLNNRFIKVYWHRE 616
Cdd:cd12516      1 NTKLELRKVPPELNNISKLNEHFSKFGTIVNLQVAYQGDPEGALIQFATHEEAKRAISSTEAVLNNRFIKVYWHRE 76

PWI domain;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958680306   11 EALKSWLSKTLEPICDADPSALAKYVLALVKKD-KSEKELKalciDQLDVFLQKETQIFVEKLFDAV 76
Cdd:pfam01480    1 EVLKPWIEKKITEILGFEDDVVVEYVVNLLEEKfPDPKELQ----IQLTGFLDKDAAKFVKELWKLL 63

Chromosome segregation protein NDC80, interacts with SMC proteins [Cell cycle control, cell division, chromosome partitioning];

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958680306  718 QKTLLVSTPAVDNNEAQKKKQEAL-KLQQDVRKRKQEILEKhIETQKMLISKLEKNKTMKS------------------- 777
Cdd:COG5185    261 QNTDLRLEKLGENAESSKRLNENAnNLIKQFENTKEKIAEY-TKSIDIKKATESLEEQLAAaeaeqeleeskretetgiq 339

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958680306  778 EDKAEIMKTLEILTKNITKLKDEVKSTSPGRCLPKSIKTKTQMQKELLDTELDLYKKMQAGEEVT 842
Cdd:COG5185    340 NLTAEIEQGQESLTENLEAIKEEIENIVGEVELSKSSEELDSFKDTIESTKESLDEIPQNQRGYA 404

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 26 (RBM26); This subgroup corresponds to the RRM1 of RBM26, also known as cutaneous T-cell lymphoma (CTCL) tumor antigen se70-2, which represents a cutaneous lymphoma (CL)-associated antigen. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The RRMs may play some functional roles in RNA-binding or protein-protein interactions.

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1958680306  541 NTKLELRKVPPELNNISKLNEHFSRFGTLVNLQVAYNGDPEGALIQFATYDEAKKAISSTEAVLNNRFIKVYWHRE 616
Cdd:cd12516      1 NTKLELRKVPPELNNISKLNEHFSKFGTIVNLQVAYQGDPEGALIQFATHEEAKRAISSTEAVLNNRFIKVYWHRE 76

PWI domain;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958680306   11 EALKSWLSKTLEPICDADPSALAKYVLALVKKD-KSEKELKalciDQLDVFLQKETQIFVEKLFDAV 76
Cdd:pfam01480    1 EVLKPWIEKKITEILGFEDDVVVEYVVNLLEEKfPDPKELQ----IQLTGFLDKDAAKFVKELWKLL 63

RNA recognition motif;

                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1958680306   549 VPPELNNiSKLNEHFSRFGTLVNLQVAYNGDPEG----ALIQFATYDEAKKAISS-TEAVLNNRFIKV 611
Cdd:smart00360    7 LPPDTTE-EELRELFSKFGKVESVRLVRDKETGKskgfAFVEFESEEDAEKALEAlNGKELDGRPLKV 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 1958680306  549 VPPELNNiSKLNEHFSRFGTLVNLQVAY--NGDPEG-ALIQFATYDEAKKAISST-EAVLNNRFIK 610
Cdd:pfam00076    6 LPPDTTE-EDLKDLFSKFGPIKSIRLVRdeTGRSKGfAFVEFEDEEDAEKAIEALnGKELGGRELK 70

Chromosome segregation protein NDC80, interacts with SMC proteins [Cell cycle control, cell division, chromosome partitioning];

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958680306  718 QKTLLVSTPAVDNNEAQKKKQEAL-KLQQDVRKRKQEILEKhIETQKMLISKLEKNKTMKS------------------- 777
Cdd:COG5185    261 QNTDLRLEKLGENAESSKRLNENAnNLIKQFENTKEKIAEY-TKSIDIKKATESLEEQLAAaeaeqeleeskretetgiq 339

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958680306  778 EDKAEIMKTLEILTKNITKLKDEVKSTSPGRCLPKSIKTKTQMQKELLDTELDLYKKMQAGEEVT 842
Cdd:COG5185    340 NLTAEIEQGQESLTENLEAIKEEIENIVGEVELSKSSEELDSFKDTIESTKESLDEIPQNQRGYA 404

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

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1958680306  912 DREDLLPHFAQYGEIEDCQI--DDSSL----HAIITFKTRAEAEAA--AVHGARFKGQDLK 964
Cdd:COG0724     14 TEEDLRELFSEYGEVTSVKLitDRETGrsrgFGFVEMPDDEEAQAAieALNGAELMGRTLK 74

Zinc finger C-x8-C-x5-C-x3-H type (and similar);

                           10        20
                   ....*....|....*....|..
gi 1958680306  293 RCRDYDEKGFCMRGDMCPFDHG 314
Cdd:pfam00642    5 LCRFFLRTGYCKYGDRCKFAHG 26

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 26 (RBM26); This subgroup corresponds to the RRM1 of RBM26, also known as cutaneous T-cell lymphoma (CTCL) tumor antigen se70-2, which represents a cutaneous lymphoma (CL)-associated antigen. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The RRMs may play some functional roles in RNA-binding or protein-protein interactions.

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1958680306  541 NTKLELRKVPPELNNISKLNEHFSRFGTLVNLQVAYNGDPEGALIQFATYDEAKKAISSTEAVLNNRFIKVYWHRE 616
Cdd:cd12516      1 NTKLELRKVPPELNNISKLNEHFSKFGTIVNLQVAYQGDPEGALIQFATHEEAKRAISSTEAVLNNRFIKVYWHRE 76

RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein 26 (RBM26) and similar proteins; This subfamily corresponds to the RRM2 of RBM26, also known as cutaneous T-cell lymphoma (CTCL) tumor antigen se70-2, which represents a cutaneous lymphoma (CL)-associated antigen. RBM26 contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The RRMs may play some functional roles in RNA-binding or protein-protein interactions.

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1958680306  896 VDHRPRALEISAFTESDREDLLPHFAQYGEIEDCQIDDSSLHAIITFKTRAEAEAAAVHGARFKGQDLKLAW 967
Cdd:cd12258      1 VDRRPRQLEVTGFTESDKDDLLPHFAQFGEVEDVQVDEEGLHLIITFKTRKEAEIAAVHGARFKGQSLQLAW 72

PWI domain;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958680306   11 EALKSWLSKTLEPICDADPSALAKYVLALVKKD-KSEKELKalciDQLDVFLQKETQIFVEKLFDAV 76
Cdd:pfam01480    1 EVLKPWIEKKITEILGFEDDVVVEYVVNLLEEKfPDPKELQ----IQLTGFLDKDAAKFVKELWKLL 63

RNA recognition motif (RRM) found in Pre-mRNA-splicing factor RBM22 and similar proteins; This subgroup corresponds to the RRM of RBM22 (also known as RNA-binding motif protein 22, or Zinc finger CCCH domain-containing protein 16), a newly discovered RNA-binding motif protein which belongs to the SLT11 gene family. SLT11 gene encoding protein (Slt11p) is a splicing factor in yeast, which is required for spliceosome assembly. Slt11p has two distinct biochemical properties: RNA-annealing and RNA-binding activities. RBM22 is the homolog of SLT11 in vertebrate. It has been reported to be involved in pre-splicesome assembly and to interact with the Ca2+-signaling protein ALG-2. It also plays an important role in embryogenesis. RBM22 contains a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a zinc finger of the unusual type C-x8-C-x5-C-x3-H, and a C-terminus that is unusually rich in the amino acids Gly and Pro, including sequences of tetraprolines.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1958680306  914 EDLLPHFAQYGEIEDCQIDDSSLHAIITFKTRAEAEAAAVHGAR---FKGQDLKLAWNK 969
Cdd:cd12224     16 KDLRDHFYQFGEIRSITVVARQQCAFVQFTTRQAAERAAERTFNkliIKGRRLKVKWGR 74

RNA recognition motif;

                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1958680306   912 DREDLLPHFAQYGEIEDCQI------DDSSLHAIITFKTRAEAEAA--AVHGARFKGQDLKL 965
Cdd:smart00360   12 TEEELRELFSKFGKVESVRLvrdketGKSKGFAFVEFESEEDAEKAleALNGKELDGRPLKV 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 1958680306  912 DREDLLPHFAQYGEIEDCQI-----DDSSLHAIITFKTRAEAEAA--AVHGARFKGQDLK 964
Cdd:pfam00076   11 TEEDLKDLFSKFGPIKSIRLvrdetGRSKGFAFVEFEDEEDAEKAieALNGKELGGRELK 70

RNA recognition motif 1 (RRM1) and 2 (RRM2) found in CELF/Bruno-like family of RNA binding proteins and plant flowering time control protein FCA; This subfamily corresponds to the RRM1 and RRM2 domains of the CUGBP1 and ETR-3-like factors (CELF) as well as plant flowering time control protein FCA. CELF, also termed BRUNOL (Bruno-like) proteins, is a family of structurally related RNA-binding proteins involved in regulation of pre-mRNA splicing in the nucleus, and control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also known as BRUNOL-2, CUG-BP1, NAPOR, EDEN-BP), CELF-2 (also known as BRUNOL-3, ETR-3, CUG-BP2, NAPOR-2), CELF-3 (also known as BRUNOL-1, TNRC4, ETR-1, CAGH4, ER DA4), CELF-4 (BRUNOL-4), CELF-5 (BRUNOL-5) and CELF-6 (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. This subfamily also includes plant flowering time control protein FCA that functions in the posttranscriptional regulation of transcripts involved in the flowering process. FCA contains two RRMs, and a WW protein interaction domain.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1958680306  908 FTEsdrEDLLPHFAQYGEIEDCQI---DDSSLH---AIITFKTRAEAEAA--AVHG 955
Cdd:cd12361     11 ASE---EDVRPLFEQFGNIEEVQIlrdKQTGQSkgcAFVTFSTREEALRAieALHN 63

RNA recognition motif (RRM) found in 80 kDa MCM3-associated protein (Map80) and similar proteins; This subfamily corresponds to the RRM of Map80, also termed germinal center-associated nuclear protein (GANP), involved in the nuclear localization pathway of MCM3, a protein necessary for the initiation of DNA replication and also involves in controls that ensure DNA replication is initiated once per cell cycle. Map80 contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1958680306  542 TKLELRKVPPELNNISKLNEHFSRFGTLVNLQVayNGDPEGALIQFATYDEAKKA 596
Cdd:cd12443      1 TAIVCKNIPEELNDKEILRRHFSKFGKVARVFC--NPRKNLAIVHFKDHESAALA 53

Nup53/35/40-type RNA recognition motif;

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1958680306  900 PRALEISAFTESDREDLLPHFAQYGEIEDCQIDDSSLHAIITFKTRAEAEAA 951
Cdd:pfam14605    1 STWIVVSGYPAELAYLVRRHFADFGEIVKHYFPPETNSMYLKYASRKDAEQA 52

Chromosome segregation protein NDC80, interacts with SMC proteins [Cell cycle control, cell division, chromosome partitioning];

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958680306  718 QKTLLVSTPAVDNNEAQKKKQEAL-KLQQDVRKRKQEILEKhIETQKMLISKLEKNKTMKS------------------- 777
Cdd:COG5185    261 QNTDLRLEKLGENAESSKRLNENAnNLIKQFENTKEKIAEY-TKSIDIKKATESLEEQLAAaeaeqeleeskretetgiq 339

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958680306  778 EDKAEIMKTLEILTKNITKLKDEVKSTSPGRCLPKSIKTKTQMQKELLDTELDLYKKMQAGEEVT 842
Cdd:COG5185    340 NLTAEIEQGQESLTENLEAIKEEIENIVGEVELSKSSEELDSFKDTIESTKESLDEIPQNQRGYA 404

RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins (p40-TIA-1 and TIAR), and yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1; This subfamily corresponds to the RRM3 of TIA-1, TIAR, and PUB1. Nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR) are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. They share high sequence similarity and 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. This subfamily also includes a yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1, termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein, which has been identified as both a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP). It may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. PUB1 is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RRMs, and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1958680306  914 EDLLPHFAQYGEIEDCQIDDSSLHAIITFKTRAEAEAA--AVHGARFKGQDLKLAW 967
Cdd:cd12354     15 ALLQQTFSPFGQILEVRVFPDKGYAFIRFDSHEAATHAivSVNGTIINGQAVKCSW 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
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1958680306  914 EDLLPHFAQYGEIEDCQI--DD----SSLHAIITFKTRAEAEAA--AVHGARFKG 960
Cdd:cd21608     14 DDLRDLFSEFGEVESAKVitDRetgrSRGFGFVTFSTAEAAEAAidALNGKELDG 68

RNA recognition motif 3 (RRM3) found in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins; This subfamily corresponds to the RRM3 of raver-1 and raver-2. Raver-1 is a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-2 is a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It shows high sequence homology to raver-1. Raver-2 exerts a spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Both, raver-1 and raver-2, contain three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. They binds to RNA through the RRMs. In addition, the two [SG][IL]LGxxP motifs serve as the PTB-binding motifs in raver1. However, raver-2 interacts with PTB through the SLLGEPP motif only.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1958680306  548 KVPPELNNISKLNEHFSRFGTLVNLQVAY-NGDPEG-ALIQFATYDEAKKA 596
Cdd:cd12390      9 RLPKDFRDGSELRKLFSQVGKPTFCQLAMgNGVPRGfAFVEFASAEDAEEA 59

RNA recognition motif 1 (RRM1) found in fission yeast pre-mRNA-splicing factor Srp1p and similar proteins; This subgroup corresponds to the RRM domain in Srp1p encoded by gene srp1 from fission yeast Schizosaccharomyces pombe. It plays a role in the pre-mRNA splicing process, but not essential for growth. Srp1p is closely related to the SR protein family found in metazoa. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine hinge and a RS domain in the middle, and a C-terminal domain. Some family members also contain another RRM domain.

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958680306  903 LEISAF-TESDREDLLPHFAQYGEIEDCQI-----DDSSLHAIITFKTRAEAEAA--AVHGARFKGQD--LKLAWNK 969
Cdd:cd12467      2 LYVTGFgAETRARDLAYEFERYGRLVRCDIppprtFQSRPFAFVEYESHRDAEDAyeEMHGRRFPDTGdtLHVQWAK 78

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor SRSF2, SRSF8 and similar proteins; This subfamily corresponds to the RRM of SRSF2 and SRSF8. SRSF2, also termed protein PR264, or splicing component, 35 kDa (splicing factor SC35 or SC-35), is a prototypical SR protein that plays important roles in the alternative splicing of pre-mRNA. It is also involved in transcription elongation by directly or indirectly mediating the recruitment of elongation factors to the C-terminal domain of polymerase II. SRSF2 is exclusively localized in the nucleus and is restricted to nuclear processes. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. The RRM is responsible for the specific recognition of 5'-SSNG-3' (S=C/G) RNA. In the regulation of alternative splicing events, it specifically binds to cis-regulatory elements on the pre-mRNA. The RS domain modulates SRSF2 activity through phosphorylation, directly contacts RNA, and promotes protein-protein interactions with the spliceosome. SRSF8, also termed SRP46 or SFRS2B, is a novel mammalian SR splicing factor encoded by a PR264/SC35 functional retropseudogene. SRSF8 is localized in the nucleus and does not display the same activity as PR264/SC35. It functions as an essential splicing factor in complementing a HeLa cell S100 extract deficient in SR proteins. Like SRSF2, SRSF8 contains a single N-terminal RRM and a C-terminal RS domain.

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1958680306  914 EDLLPHFAQYGEIEDCQI------DDSSLHAIITFKTRAEAEAA--AVHGARFKGQDLKLA 966
Cdd:cd12311     13 DDLRRVFEKYGEVGDVYIprdrytRESRGFAFVRFYDKRDAEDAidAMDGAELDGRELRVQ 73

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein hnRNP A and hnRNP D subfamilies and similar proteins; This subfamily corresponds to the RRM1 in the hnRNP A subfamily which includes hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The hnRNP D subfamily includes hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0 is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus, plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All members in this subfamily contain two putative RRMs and a glycine- and tyrosine-rich C-terminus. The family also contains DAZAP1 (Deleted in azoospermia-associated protein 1), RNA-binding protein Musashi homolog Musashi-1, Musashi-2 and similar proteins. They all harbor two RRMs.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1958680306  910 ESDREDLLPHFAQYGEIEDCQI-DDSSLH-----AIITFKTRAEAEAA 951
Cdd:cd12325      9 ETTEESLREYFSKYGEVVDCVVmKDPATGrsrgfGFVTFKDPSSVDAV 56

RNA recognition motif 2 (RRM2) found in the VICKZ family proteins; This subfamily corresponds to the RRM2 of IGF-II mRNA-binding proteins (IGF2BPs or IMPs) in the VICKZ family that have been implicated in the post-transcriptional regulation of several different RNAs and in subcytoplasmic localization of mRNAs during embryogenesis. IGF2BPs are composed of two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and four hnRNP K homology (KH) domains.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1958680306  913 REDLLPHFAQYGEIEDCQI---DDSSLHAIITFKTRAEAEAAAVH--GARFKGQDLK 964
Cdd:cd12359     14 WEDLDSLLSTYGTVENCEQvntKSETATVNVTYESPEQAQQAVNKlnGYQYEGSALK 70

Predicted nucleic acid-binding protein DR0291, contains C4-type Zn-ribbon domain [General function prediction only];

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958680306  712 AALKAAQKTLLVSTPAVDNNEAQKKKQEA-LKLQQDVRKRKQE------------ILEKHIETQKMLISKLEknktmksE 778
Cdd:COG1579     38 DELAALEARLEAAKTELEDLEKEIKRLELeIEEVEARIKKYEEqlgnvrnnkeyeALQKEIESLKRRISDLE-------D 110

                           90       100
                   ....*....|....*....|....
gi 1958680306  779 DKAEIMKTLEILTKNITKLKDEVK 802
Cdd:COG1579    111 EILELMERIEELEEELAELEAELA 134