RNA recognition motif 3 (RRM3) found in plant Mei2-like proteins; This subgroup corresponds to the RRM3 of Mei2-like proteins, representing an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and is highly conserved between plants and fungi. To date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17979281 655 LMIKNIPNKYTSKMLLAAIDEKNQGTYNFLYLPIDFKNKCNVGYAFINMLNPELIIPFYEAFNGKKWEKFNSEKVASLAY 734
Cdd:cd12531   1 LMIKNIPNKYTQKMLLAAIDEKHRGTYDFFYLPIDFKNKCNVGYAFINMISPELIVPFYKAFNGKKWEKFNSEKVCSLAY 80

                ....*.
gi 17979281 735 ARIQGK 740
Cdd:cd12531  81 ARIQGK 86

RNA recognition motif 2 (RRM2) found in plant Mei2-like proteins; This subgroup corresponds to the RRM2 of Mei2-like proteins that represent an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and is highly conserved between plants and fungi. To date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 17979281 252 QGTLVVFNLDPSISNDDLHGIFGAHGEIKEIRETPHKRHHKFVEFYDVRGAEAALKALNRCEIAGKRIKVE 322
Cdd:cd12529   1 QGTLVVFNLDPSISNDDLHQIFGAYGEIKEIRETPNKRHHKFIEFYDVRSAEAALKALNKSEIAGKRIKLE 71

RNA recognition motif 3 (RRM3) found in plant Mei2-like proteins; This subgroup corresponds to the RRM3 of Mei2-like proteins, representing an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and is highly conserved between plants and fungi. To date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17979281 655 LMIKNIPNKYTSKMLLAAIDEKNQGTYNFLYLPIDFKNKCNVGYAFINMLNPELIIPFYEAFNGKKWEKFNSEKVASLAY 734
Cdd:cd12531   1 LMIKNIPNKYTQKMLLAAIDEKHRGTYDFFYLPIDFKNKCNVGYAFINMISPELIVPFYKAFNGKKWEKFNSEKVCSLAY 80

                ....*.
gi 17979281 735 ARIQGK 740
Cdd:cd12531  81 ARIQGK 86

RNA recognition motif 1 (RRM1) found in plant Mei2-like proteins; This subgroup corresponds to the RRM1 of Mei2-like proteins that represent an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and it is highly conserved between plants and fungi. Up to date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 17979281 167 SRTLFVRNINSNVEDSELTALFEQYGDIRTLYTTCKHRGFVMISYYDIRSARMAMRSLQNKPLRRRKLDIHFSIPKD 243
Cdd:cd12524   1 SRTLFVRNINSSVEDEELRALFEQFGEIRTLYTACKHRGFIMVSYYDIRAAQSAKRALQGTELGGRKLDIHFSIPKD 77

RNA recognition motif;

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 17979281    254 TLVVFNLDPSISNDDLHGIFGAHGEIKEIRETPHKRHHK-----FVEFYDVRGAEAALKALNRCEIAGKRIKV 321
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKskgfaFVEFESEEDAEKALEALNGKELDGRPLKV 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        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17979281   255 LVVFNLDPSISNDDLHGIFGAHGEIKEIR----ETPHKRHHKFVEFYDVRGAEAALKALNRCEIAGKRIK 320
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFGPIKSIRlvrdETGRSKGFAFVEFEDEEDAEKAIEALNGKELGGRELK 70

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 17979281   164 EHPSRTLFVRNINSNVEDSELTALFEQYGDIRTLY-----TTCKHRGFVMISYYDIRSARMAMrSLQNKPLRRRKLDIHF 238
Cdd:TIGR01622 111 ERDRRTVFVQQLAARARERDLYEFFSKVGKVRDVQiikdrNSRRSKGVGYVEFYDVDSVQAAL-ALTGQKLLGIPVIVQL 189

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17979281   239 SIPKDNPSEKDMN--QGT---------LVVFNLDPSISNDDLHGIFGAHGEIKEIR-----ETPHKRHHKFVEFYDVRGA 302
Cdd:TIGR01622 190 SEAEKNRAARAATetSGHhpnsipfhrLYVGNLHFNITEQDLRQIFEPFGEIEFVQlqkdpETGRSKGYGFIQFRDAEQA 269

                         170
                  ....*....|....*....
gi 17979281   303 EAALKALNRCEIAGKRIKV 321
Cdd:TIGR01622 270 KEALEKMNGFELAGRPIKV 288

ELAV/HuD family splicing factor; This model describes the ELAV/HuD subfamily of splicing factors found in metazoa. HuD stands for the human paraneoplastic encephalomyelitis antigen D of which there are 4 variants in human. ELAV stnds for the Drosophila Embryonic lethal abnormal visual protein. ELAV-like splicing factors are also known in human as HuB (ELAV-like protein 2), HuC (ELAV-like protein 3, Paraneoplastic cerebellar degeneration-associated antigen) and HuR (ELAV-like protein 1). These genes are most closely related to the sex-lethal subfamily of splicing factors found in Dipteran insects (TIGR01659). These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17979281   124 DNLSMSGPPRLSLSSLGGNAIPQFNIPNGAGTVAG--EHPYGEHPSRT---LFVRNINSNVEDSELTALFEQYGD----- 193
Cdd:TIGR01661 221 DFTAVLAHQQQQHAVAQQHAAQRASPPATDGQTAGlaAGAQISASDGAgycIFVYNLSPDTDETVLWQLFGPFGAvqnvk 300

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 17979281   194 -IRTLYTT-CKHRGFVMISYYDirSARMAMRSLQNKPLRRRKLDIHFSIPK 242
Cdd:TIGR01661 301 iIRDLTTNqCKGYGFVSMTNYD--EAAMAILSLNGYTLGNRVLQVSFKTNK 349

RNA recognition motif;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 17979281    654 TLMIKNIPNKYTSKMLLAAIdeKNQGTYNFLYLPIDFKNKCNVGYAFINMLNPELIIPFYEAFNGKKW 721
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELF--SKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEALNGKEL 66

RNA recognition motif 3 (RRM3) found in plant Mei2-like proteins; This subgroup corresponds to the RRM3 of Mei2-like proteins, representing an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and is highly conserved between plants and fungi. To date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17979281 655 LMIKNIPNKYTSKMLLAAIDEKNQGTYNFLYLPIDFKNKCNVGYAFINMLNPELIIPFYEAFNGKKWEKFNSEKVASLAY 734
Cdd:cd12531   1 LMIKNIPNKYTQKMLLAAIDEKHRGTYDFFYLPIDFKNKCNVGYAFINMISPELIVPFYKAFNGKKWEKFNSEKVCSLAY 80

                ....*.
gi 17979281 735 ARIQGK 740
Cdd:cd12531  81 ARIQGK 86

RNA recognition motif 1 (RRM1) found in plant Mei2-like proteins; This subgroup corresponds to the RRM1 of Mei2-like proteins that represent an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and it is highly conserved between plants and fungi. Up to date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 17979281 167 SRTLFVRNINSNVEDSELTALFEQYGDIRTLYTTCKHRGFVMISYYDIRSARMAMRSLQNKPLRRRKLDIHFSIPKD 243
Cdd:cd12524   1 SRTLFVRNINSSVEDEELRALFEQFGEIRTLYTACKHRGFIMVSYYDIRAAQSAKRALQGTELGGRKLDIHFSIPKD 77

RNA recognition motif 3 (RRM3) found in fungal Mei2-like proteins; This subgroup corresponds to the RRM3 of fungal Mei2-like proteins. The Mei2 protein is an essential component of the switch from mitotic to meiotic growth in the fission yeast Schizosaccharomyces pombe. It is an RNA-binding protein that contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In the nucleus, S. pombe Mei2 stimulates meiosis upon binding a specific non-coding RNA through its C-terminal RRM motif.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17979281 652 RTTLMIKNIPNKYTSKMLLAAIDEKNQGTYNFLYLPIDFKNKCNVGYAFINMLNPELIIPFYEAFNGKKWEKFNSEKVAS 731
Cdd:cd12532   1 RTTCMIKNIPNKFTQQMLKEYLDETNKGTYDFVYLRIDFKNNCNVGYAFINFTEPESIVTFYKARQGKKWNKFNSEKICD 80

                ....*....
gi 17979281 732 LAYARIQGK 740
Cdd:cd12532  81 ISYANIQGK 89

RNA recognition motif 3 (RRM3) found in terminal EAR1-like proteins; This subgroup corresponds to the RRM3 of terminal EAR1-like proteins, including terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) found in land plants. They may play a role in the regulation of leaf initiation. The terminal EAR1-like proteins are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and TEL characteristic motifs that allow sequence and putative functional discrimination between the terminal EAR1-like proteins and Mei2-like proteins.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17979281 652 RTTLMIKNIPNKYTSKMLLAAID----EKNQ---------GTYNFLYLPIDFKNKCNVGYAFINMLNPELIIPFYEAFNG 718
Cdd:cd12530   1 RTTLMIKNIPNKYSQKLLLDMLDthciQCNQhiedssqpvSSYDFVYLPIDFKNKCNLGYAFVNFTSPEATWRFYKAFHN 80

                        90       100
                ....*....|....*....|.
gi 17979281 719 KKWEKFNSEKVASLAYARIQG 739
Cdd:cd12530  81 QQWEEFNSRKICQITYARVQG 101

RNA recognition motif 1 (RRM1) found in Mei2-like proteins and terminal EAR1-like proteins; This subfamily corresponds to the RRM1 of Mei2-like proteins from plant and fungi, terminal EAR1-like proteins from plant, and other eukaryotic homologs. Mei2-like proteins represent an ancient eukaryotic RNA-binding protein family whose corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. In the fission yeast Schizosaccharomyces pombe, the Mei2 protein is an essential component of the switch from mitotic to meiotic growth. S. pombe Mei2 stimulates meiosis in the nucleus upon binding a specific non-coding RNA. The terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are mainly found in land plants. They may play a role in the regulation of leaf initiation. All members in this family are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In addition to the RRMs, the terminal EAR1-like proteins also contain TEL characteristic motifs that allow sequence and putative functional discrimination between them and Mei2-like proteins.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 17979281 167 SRTLFVRNINSNVEDSELTALFEQYGDIRTLYTTCKHRGFVMISYYDIRSARMAMRSLQNKPLRRRKLDIH 237
Cdd:cd12275   1 SRSLFVINVPRDVTESTLRRLFEVYGDVRGVQTERISEGIVTVHFYDIRDAKRAVRELCGRHMQQQALGGS 71

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 17979281 255 LVVFNLDPSISNDDLHGIFGAHGEIKEIR----ETPHKRHHKFVEFYDVRGAEAALKALNRCEIAGKRIKVE 322
Cdd:cd00590   1 LFVGNLPPDTTEEDLRELFSKFGEVVSVRivrdRDGKSKGFAFVEFESPEDAEKALEALNGTELGGRPLKVS 72

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

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 17979281 254 TLVVFNLDPSISNDDLHGIFGAHGEIKEI-----RETPHKRHHKFVEFYDVRGAEAALKALNRCEIAGKRIKVEPSRP 326
Cdd:COG0724   3 KIYVGNLPYSVTEEDLRELFSEYGEVTSVklitdRETGRSRGFGFVEMPDDEEAQAAIEALNGAELMGRTLKVNEARP 80

RNA recognition motif;

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 17979281    169 TLFVRNINSNVEDSELTALFEQYGDIRTLY-----TTCKHRGFVMISYYDIRSARMAMRSLQNKPLRRRKLDI 236
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFGKVESVRlvrdkETGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV 73

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

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 17979281 254 TLVVFNLDPSISNDDLHGIFGAHGEIKEI-----RETPHKRHHKFVEFYDVRGAEAALKALNRCEIAGKRIKV 321
Cdd:cd21608   1 KLYVGNLSWDTTEDDLRDLFSEFGEVESAkvitdRETGRSRGFGFVTFSTAEAAEAAIDALNGKELDGRSIVV 73

RNA recognition motif 1 (RRM1) found in fungal Mei2-like proteins; This subgroup corresponds to the RRM1 of fungal Mei2-like proteins. The Mei2 protein is an essential component of the switch from mitotic to meiotic growth in the fission yeast Schizosaccharomyces pombe. It is an RNA-binding protein that contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In the nucleus, S. pombe Mei2 stimulates meiosis upon binding a specific non-coding RNA through its C-terminal RRM motif.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17979281 163 GEHPSRTLFVRNINSNVEDSELTALFEQYGDIRTLYTT-CKHRGFVMISYYDIRSARMAMRSLQNKPL--RRRKLDIHFS 239
Cdd:cd12525   3 GSVPTRYLKVTGVPKDVSTSNLKEIFEKMGDVKGIFVKkLLSKGIVIVSFHDLRQAIKAYKDLQSKWRfiNDRYLTAQFC 82

                ..
gi 17979281 240 IP 241
Cdd:cd12525  83 VN 84

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 17979281   170 LFVRNINSNVEDSELTALFEQYGDIRTLyTTCKH-----RGFVMISYYDIRSARMAMRSL-------------------Q 225
Cdd:TIGR01628 181 LYVKNLDPSVNEDKLRELFAKFGEITSA-AVMKDgsgrsRGFAFVNFEKHEDAAKAVEEMngkkiglakegkklyvgraQ 259

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17979281   226 NKPLRRRKLDIHFSipKDNPSEKDMNQGT-LVVFNLDPSISNDDLHGIFGAHGEIKEIR----ETPHKRHHKFVEFYDVR 300
Cdd:TIGR01628 260 KRAEREAELRRKFE--ELQQERKMKAQGVnLYVKNLDDTVTDEKLRELFSECGEITSAKvmldEKGVSRGFGFVCFSNPE 337

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17979281   301 GAEAALKALNRCEIAGKRIKVEPSRPGGARRSlMLQlNQDLENDDLHYLPMIGSPMansPPMQGNWPLNSPVEGSPLQSV 380
Cdd:TIGR01628 338 EANRAVTEMHGRMLGGKPLYVALAQRKEQRRA-HLQ-DQFMQLQPRMRQLPMGSPM---GGAMGQPPYYGQGPQQQFNGQ 412

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 17979281   381 lsrspvfglsPTRNGHLSGLASALNSQGPSS--KLAPIGRGQIGSNGFQQSSHlfQEPKMDNKYTGN 445
Cdd:TIGR01628 413 ----------PLGWPRMSMMPTPMGPGGPLRpnGLAPMNAVRAPSRNAQNAAQ--KPPMQPVMYPPN 467

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 17979281   170 LFVRNINSNVEDSELTALFEQYGDIRTLY----TTCKHRGFVMISYYDIRSARMAMRSLQNKPLRRRKL 234
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFGPIKSIRlvrdETGRSKGFAFVEFEDEEDAEKAIEALNGKELGGREL 69

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor SRSF10, SRSF12 and similar proteins; This subfamily corresponds to the RRM of SRSF10 and SRSF12. SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). It is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19), is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. Both, SRSF10 and SRSF12, contain 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.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 17979281 169 TLFVRNINSNVEDSELTALFEQYGDIRTLYT-----TCKHRGFVMISYYDIRSARMAMRSLQNKPLRRRKLDIHFS 239
Cdd:cd12312   2 SLFVRNVADDTRPDDLRREFGRYGPIVDVYIpldfyTRRPRGFAYIQFEDVRDAEDALYYLDRTRFLGREIEIQFA 77

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

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 17979281 254 TLVVFNLDPSISNDDLHGIFGAHGEIKEIR----ETPHKRhHKFVEFYDVRGAEAALKaLNRCEIAGKRIKVEPSR 325
Cdd:cd12260   6 TVYVGNLDPSTTADQLLEFFSQAGEVKYVRmagdETQPTR-YAFVEFAEQTSVINALK-LNGKMFGGRPLKVNHSN 79

RNA recognition motif 1 (RRM1) found in granule-associated RNA binding proteins p40-TIA-1 and TIAR; This subfamily corresponds to the RRM1 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        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17979281 255 LVVFNLDPSISNDDLHGIFGAHGEIKE---IRETPHKRHHKFVEFYDVRGAEAALKALNRCEIAGKRIKV 321
Cdd:cd12352   1 LYVGNLDRQVTEDLILQLFSQIGPCKSckmITEHGGNDPYCFVEFYEHNHAAAALQAMNGRKILGKEVKV 70

RNA recognition motif 2 (RRM2) found in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins; This subfamily corresponds to the RRM2 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), is an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 17979281 254 TLVVFNLDPSISNDDLHGIFGAHGEIKEIR----ETPHKRHHKFVEFYDVRGAEAALKALNRCEIAGKRIKVEPSRP 326
Cdd:cd12392   4 KLFVKGLPFSCTKEELEELFKQHGTVKDVRlvtyRNGKPKGLAYVEYENEADASQAVLKTDGTEIKDHTISVAISNP 80

RNA recognition motif 1 (RRM1) found in Schizosaccharomyces pombe mRNA export factor Crp79 and similar proteins; Crp79, also called meiotic expression up-regulated protein 5 (Mug5), or polyadenylate-binding protein crp79, or PABP, or poly(A)-binding protein, is an auxiliary mRNA export factor that binds the poly(A) tail of mRNA and is involved in the export of mRNA from the nucleus to the cytoplasm. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the first RRM motif.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 17979281 167 SRTLFVRNINSNVEDSELTALFEQYGDIRTLY-------TTCKHRGFVMISYYDIRSARMAMRSLQNKPLRRRKLDI 236
Cdd:cd21619   1 SNTIYVGNIDMTINEDALEKIFSRYGQVESVRrppihtdKADRTTGFGFIKYTDAESAERAMQQADGILLGRRRLVV 77

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor SRSF10, SRSF12 and similar proteins; This subfamily corresponds to the RRM of SRSF10 and SRSF12. SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). It is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19), is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. Both, SRSF10 and SRSF12, contain 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.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17979281 254 TLVVFNLDPSISNDDLHGIFGAHGEIKEIR-----ETPHKRHHKFVEFYDVRGAEAALKALNRCEIAGKRIKVEPSRpgG 328
Cdd:cd12312   2 SLFVRNVADDTRPDDLRREFGRYGPIVDVYipldfYTRRPRGFAYIQFEDVRDAEDALYYLDRTRFLGREIEIQFAQ--G 79

                ....
gi 17979281 329 ARRS 332
Cdd:cd12312  80 DRKT 83

RNA recognition motif 2 (RRM2) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM2 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 17979281 255 LVVFNLDPSISNDDLHGIFGAHGEIKEIReTPHKRHHK-----FVEFYDVRGAEAALKALNRCEIAGKRIKV 321
Cdd:cd12414   2 LIVRNLPFKCTEDDLKKLFSKFGKVLEVT-IPKKPDGKlrgfaFVQFTNVADAAKAIKGMNGKKIKGRPVAV 72

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 10 (SRSF10) and similar proteins; This subgroup corresponds to the RRM of SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). SRSF10 is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. 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.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 17979281 166 PSRTLFVRNINSNVEDSELTALFEQYGDIRTLYTTCKH-----RGFVMISYYDIRSARMAMRSLQNKPLRRRKLDIHFS 239
Cdd:cd12559   4 PNTSLFVRNVADDTRSEDLRREFGRYGPIVDVYVPLDFytrrpRGFAYVQFEDVRDAEDALHNLDRKWICGRQIEIQFA 82

RNA recognition motif 3 (RRM3) found in yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8 and similar proteins; This subfamily corresponds to the RRM3 of NGR1 and NAM8. NGR1, also termed RNA-binding protein RBP1, is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA) in yeast. It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the carboxyl terminus which also harbors a methionine-rich region. The family also includes protein NAM8, which is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. Like NGR1, NAM8 contains two RRMs.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 17979281 254 TLVVFNLDPSISNDDLHGIFGAHGEIKEIRETPHKrHHKFVEFYDVRGAEAALKALNRCEIAGKRIK 320
Cdd:cd12346   3 TVFVGGLDPNVTEEDLRVLFGPFGEIVYVKIPPGK-GCGFVQFVNRASAEAAIQKLQGTPIGGSRIR 68

RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; This subgroup corresponds to the RRM1 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17979281 168 RTLFVRNINSNVEDSELTALFEQYGDIR-----TLYTTCKHRGFVMISYYDIRSARMAMRSLQNKPLRRRKLDIHFSIPK 242
Cdd:cd12674   1 TTLFVRNLPFDVTLESLTDFFSDIGPVKhavvvTDPETKKSRGYGFVSFSTHDDAEEALAKLKNRKLSGHILKLDFAKPR 80

RNA recognition motif 1 (RRM1) found in serine/arginine-rich splicing factor 1 (SRSF1) and similar proteins; This subgroup corresponds to the RRM1 in three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 1 (SRSF1 or ASF-1), serine/arginine-rich splicing factor 9 (SRSF9 or SRp30C), and plant pre-mRNA-splicing factor SF2 (SR1). SRSF1 is a shuttling SR protein involved in constitutive and alternative splicing, nonsense-mediated mRNA decay (NMD), mRNA export and translation. It also functions as a splicing-factor oncoprotein that regulates apoptosis and proliferation to promote mammary epithelial cell transformation. SRSF9 has been implicated in the activity of many elements that control splice site selection, the alternative splicing of the glucocorticoid receptor beta in neutrophils and in the gonadotropin-releasing hormone pre-mRNA. It can also interact with other proteins implicated in alternative splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. Both, SRSF1 and SRSF9, contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RS domains rich in serine-arginine dipeptides. In contrast, SF2 contains two N-terminal RRMs and a C-terminal PSK domain rich in proline, serine and lysine residues.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17979281 257 VFNLDPSISNDDLHGIFGAHGEIKEIreTPHKRHH----KFVEFYDVRGAEAALKALNRCEIAGKRIKVE 322
Cdd:cd12338   4 VGNLPGDIRERDIEDLFYKYGPILAI--DLKNRRRgppfAFVEFEDPRDAEDAIRGRDGYDFDGYRLRVE 71

RNA recognition motif 1 (RRM1) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM1 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 17979281 254 TLVVFNLDPSISNDDLHGIFGAHGEIKE---IRETPHKRHHKF--VEFYDVRGAEAALKALNRCEIAGKRIKVEPSRP 326
Cdd:cd12413   1 TLFVRNLPYDTTDEQLEELFSDVGPVKRcfvVKDKGKDKCRGFgyVTFALAEDAQRALEEVKGKKFGGRKIKVELAKK 78

RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins; This subfamily corresponds to the RRM3 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 17979281 168 RTLFVRNINSNVEDSELTALFEQYGDIRTLYTTCK--------HRGFVMISYYDIRSARMAMrSLQNKPLRRRKLDI 236
Cdd:cd12298   1 REIRVRNLDFELDEEALRGIFEKFGEIESINIPKKqknrkgrhNNGFAFVTFEDADSAESAL-QLNGTLLDNRKISV 76

RNA recognition motif 1 (RRM1) found in Drosophila sex-lethal (SXL) and similar proteins; This subfamily corresponds to the RRM1 of 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 17979281 254 TLVVFNLDPSISNDDLHGIFGAHGEIKEIRETPHKRH-----HKFVEFYDVRGAEAALKALNRCEIAGKRIKVEPSRPGG 328
Cdd:cd12649   2 NLIVNYLPQDLTDREFRALFRAIGPVNTCKIVRDKKTgysygFGFVDFTSEEDAQRAIKTLNGLQLQNKRLKVAYARPGG 81