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 15240750 210 SRILFVRNVDSSIEDCELGVLFKQFGDVRALHTAGKNRGFIMVSYYDIRAAQKAARALHGRLLRGRKLDIRYSIPKE 286
Cdd:cd12524   1 SRTLFVRNINSSVEDEELRALFEQFGEIRTLYTACKHRGFIMVSYYDIRAAQSAKRALQGTELGGRKLDIHFSIPKD 77

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 15240750 744 LMIKNIPNKYTSKMLLAAIDEYCKGTYDFLYLPIDFKNKCNVGYAFINLIEPENIVPFYKAFNGKKWEKFNSEKVASLAY 823
Cdd:cd12531   1 LMIKNIPNKYTQKMLLAAIDEKHRGTYDFFYLPIDFKNKCNVGYAFINMISPELIVPFYKAFNGKKWEKFNSEKVCSLAY 80

                ....*.
gi 15240750 824 GRIQGK 829
Cdd:cd12531  81 ARIQGK 86

RNA recognition motif 2 (RRM2) found in Mei2-like proteins and terminal EAR1-like proteins; This subfamily corresponds to the RRM2 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 proteins 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 15240750 294 EGALWVNNLDSSISNEELHGIFSSYGEIREVRRTMHENSQVYIEFFDVRKAKVALQGLNGLEVAGRQLKLA 364
Cdd:cd12276   1 QGTLLVFNLDAPVSNDELKSLFSKFGEIKEIRPTPDKPSQKFVEFYDVRDAEAALDGLNGRELLGGKLKVA 71

RNA recognition motif;

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15240750    297 LWVNNLDSSISNEELHGIFSSYGEIREVRRTMHENSQ-----VYIEFFDVRKAKVALQGLNGLEVAGRQLKL 363
Cdd:smart00360   2 LFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGkskgfAFVEFESEEDAEKALEALNGKELDGRPLKV 73

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

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15240750 213 LFVRNVDSSIEDCELGVLFKQFGDVRALH------TaGKNRGFIMVSYYDIRAAQKAARALHGRLLRGRKLDIRYSIPKE 286
Cdd:COG0724   4 IYVGNLPYSVTEEDLRELFSEYGEVTSVKlitdreT-GRSRGFGFVEMPDDEEAQAAIEALNGAELMGRTLKVNEARPRE 82

                .
gi 15240750 287 N 287
Cdd:COG0724  83 E 83

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 15240750   213 LFVRNVDSSIEDCELGVLFKQFGDVRAL----HTAGKNRGFIMVSYYDIRAAQKAARALHGRLLRGRKL 277
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFGPIKSIrlvrDETGRSKGFAFVEFEDEEDAEKAIEALNGKELGGREL 69

hnRNP-L/PTB/hephaestus splicing factor family; Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15240750   210 SRILFVRNVDSSIEDCELGVLFKQFGDV-RALHTAGKNRGFI----------MVSYYDIRAAQkaaralhgrlLRGRKLD 278
Cdd:TIGR01649   2 SPVVHVRNLPQDVVEADLVEALIPFGPVsYVMMLPGKRQALVefedeesakaCVNFATSVPIY----------IRGQPAF 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15240750   279 IRYSIPKENPKENSSEGA---------LWVNNLDSSISNEELHGIFSSYGEIREVRrTMHENS--QVYIEFFDVRKAKVA 347
Cdd:TIGR01649  72 FNYSTSQEIKRDGNSDFDsagpnkvlrVIVENPMYPITLDVLYQIFNPYGKVLRIV-TFTKNNvfQALVEFESVNSAQHA 150

                  ....*....
gi 15240750   348 LQGLNGLEV 356
Cdd:TIGR01649 151 KAALNGADI 159

RNA recognition motif;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 15240750    743 TLMIKNIPNKYTSKMLLAAIDEYckGTYDFLYLPIDFKNKCNVGYAFINLIEPENIVPFYKAFNGKKW 810
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKF--GKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEALNGKEL 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 15240750 744 LMIKNIPNKYTSKMLLAAIDEYCKGTYDFLYLPIDFKNKCNVGYAFINLIEPENIVPFYKAFNGKKWEKFNSEKVASLAY 823
Cdd:cd12531   1 LMIKNIPNKYTQKMLLAAIDEKHRGTYDFFYLPIDFKNKCNVGYAFINMISPELIVPFYKAFNGKKWEKFNSEKVCSLAY 80

                ....*.
gi 15240750 824 GRIQGK 829
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 15240750 210 SRILFVRNVDSSIEDCELGVLFKQFGDVRALHTAGKNRGFIMVSYYDIRAAQKAARALHGRLLRGRKLDIRYSIPKE 286
Cdd:cd12524   1 SRTLFVRNINSSVEDEELRALFEQFGEIRTLYTACKHRGFIMVSYYDIRAAQSAKRALQGTELGGRKLDIHFSIPKD 77

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 15240750 741 RTTLMIKNIPNKYTSKMLLAAIDEYCK-------------GTYDFLYLPIDFKNKCNVGYAFINLIEPENIVPFYKAFNG 807
Cdd:cd12530   1 RTTLMIKNIPNKYSQKLLLDMLDTHCIqcnqhiedssqpvSSYDFVYLPIDFKNKCNLGYAFVNFTSPEATWRFYKAFHN 80

                        90       100
                ....*....|....*....|.
gi 15240750 808 KKWEKFNSEKVASLAYGRIQG 828
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 15240750 210 SRILFVRNVDSSIEDCELGVLFKQFGDVRALHTAGKNRGFIMVSYYDIRAAQKAARALHGRLLRGRKLDI 279
Cdd:cd12275   1 SRSLFVINVPRDVTESTLRRLFEVYGDVRGVQTERISEGIVTVHFYDIRDAKRAVRELCGRHMQQQALGG 70

RNA recognition motif 2 (RRM2) found in terminal EAR1-like proteins; This subgroup corresponds to the RRM2 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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 15240750 294 EGALWVNNLDSSISNEELHGIFSSYGEIREVRRTMHENSQVYIEFFDVRKAKVALQGLNGLEVAGRQL 361
Cdd:cd12527   1 QGSLVILNLLPAVSSFTLREIFQVYGDVKDVRETPLKPSQRFVEFFDVRDAARALHEMNGKEIFGKRL 68

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 15240750   211 RILFVRNVDSSIEDCELGVLFKQFGDVRALH-----TAGKNRGFIMVSYYDIRAAQKAArALHGRLLRGRKLDIRYSIPK 285
Cdd:TIGR01622 115 RTVFVQQLAARARERDLYEFFSKVGKVRDVQiikdrNSRRSKGVGYVEFYDVDSVQAAL-ALTGQKLLGIPVIVQLSEAE 193

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15240750   286 EN-----PKENSSEGA-------LWVNNLDSSISNEELHGIFSSYGEIREVRRTMHENSQV-----YIEFFDVRKAKVAL 348
Cdd:TIGR01622 194 KNraaraATETSGHHPnsipfhrLYVGNLHFNITEQDLRQIFEPFGEIEFVQLQKDPETGRskgygFIQFRDAEQAKEAL 273

                         170
                  ....*....|....*
gi 15240750   349 QGLNGLEVAGRQLKL 363
Cdd:TIGR01622 274 EKMNGFELAGRPIKV 288

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 15240750   213 LFVRNVDSSIEDCELGVLFKQFGDVRALHT----AGKNRGFIMVSYYDIRAAQKAARALHGRLL------------RGRK 276
Cdd:TIGR01628 181 LYVKNLDPSVNEDKLRELFAKFGEITSAAVmkdgSGRSRGFAFVNFEKHEDAAKAVEEMNGKKIglakegkklyvgRAQK 260

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15240750   277 LDIRYSIPKENPKE------NSSEGA-LWVNNLDSSISNEELHGIFSSYGEIREVRRTMHENSQV----YIEFFDVRKAK 345
Cdd:TIGR01628 261 RAEREAELRRKFEElqqerkMKAQGVnLYVKNLDDTVTDEKLRELFSECGEITSAKVMLDEKGVSrgfgFVCFSNPEEAN 340

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15240750   346 VALQGLNGLEVAGRQL---------------------------KLAPTCPEGTSFW-PQFASDDGEGGLPKMAFNNLSSA 397
Cdd:TIGR01628 341 RAVTEMHGRMLGGKPLyvalaqrkeqrrahlqdqfmqlqprmrQLPMGSPMGGAMGqPPYYGQGPQQQFNGQPLGWPRMS 420

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15240750   398 HMGrhfpgilaSTSIDGGSIRGM----HNSVGSPMNSFIERHQSLDV-PIGLPPSARVISASKPVGLQE----FGNPFDN 468
Cdd:TIGR01628 421 MMP--------TPMGPGGPLRPNglapMNAVRAPSRNAQNAAQKPPMqPVMYPPNYQSLPLSQDLPQPQstasQGGQNKK 492

                         330       340
                  ....*....|....*....|....
gi 15240750   469 SKTGIQSMP----------NLHPH 482
Cdd:TIGR01628 493 LAQVLASATpqmqkqvlgeRLFPL 516

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 15240750 297 LWVNNLDSSISNEELHGIFSSYGEIREVR----RTMHENSQVYIEFFDVRKAKVALQGLNGLEVAGRQLKL 363
Cdd:cd00590   1 LFVGNLPPDTTEEDLRELFSKFGEVVSVRivrdRDGKSKGFAFVEFESPEDAEKALEALNGTELGGRPLKV 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 15240750 213 LFVRNVDSSIEDCELGVLFKQFGDVRAL----HTAGKNRGFIMVSYYDIRAAQKAARALHGRLLRGRKLDIR 280
Cdd:cd00590   1 LFVGNLPPDTTEEDLRELFSKFGEVVSVrivrDRDGKSKGFAFVEFESPEDAEKALEALNGTELGGRPLKVS 72

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteriztic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15240750   297 LWVNNLDSSISNEELHGIFSSYGEIREVR--RTMHENSQVY--IEFFDVRKAKVALQGLNGLEVAGRQLK 362
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFGPIKSIRlvRDETGRSKGFafVEFEDEEDAEKAIEALNGKELGGRELK 70

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15240750 297 LWVNNLDSSISNEELHGIFSSYGEIREVRRTMHENSQVYIEFFDVRKAKVALQGLNGLEVAGRQLK 362
Cdd:cd12524   4 LFVRNINSSVEDEELRALFEQFGEIRTLYTACKHRGFIMVSYYDIRAAQSAKRALQGTELGGRKLD 69

RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein RBM23, RBM39 and similar proteins; This subfamily corresponds to the RRM2 of RBM39 (also termed HCC1), a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Although the cellular function of RBM23 remains unclear, it shows high sequence homology to RBM39 and contains two RRMs. It may possibly function as a pre-mRNA splicing factor.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15240750 297 LWVNNLDSSISNEELHGIFSSYGEIREV---RRTMHENSQVY--IEFFDVRKAKVALQGLNGLEVAGRQLKLAP 365
Cdd:cd12284   1 LYVGSLHFNITEDMLRGIFEPFGKIEFVqlqKDPETGRSKGYgfIQFRDAEDAKKALEQLNGFELAGRPMKVGH 74

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 15240750 297 LWVNNLDSSISNEELHGIFSSYGEIREVR----RTMHENSQVYIEFFDVRKAKVALQGLNGLEVAGRQLKLAPTCP 368
Cdd:cd12392   5 LFVKGLPFSCTKEELEELFKQHGTVKDVRlvtyRNGKPKGLAYVEYENEADASQAVLKTDGTEIKDHTISVAISNP 80

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.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15240750   213 LFVRNVDSSIEDCELGVLFKQFGDVRAL----HTAGKNRGFIMVSYYDIRAAQKAARALHGRLLRGRKL 277
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFGPIKSIrlvrDETGRSKGFAFVEFEDEEDAEKAIEALNGKELGGREL 69

RNA recognition motif 3 (RRM3) found in RNA-binding protein 19 (RBM19) and RNA recognition motif 2 found in multiple RNA-binding domain-containing protein 1 (MRD1); This subfamily corresponds to the RRM3 of RBM19 and RRM2 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events.

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                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15240750 213 LFVRNVD-SSIEDcELGVLFKQFGDVRALH-----TAGKNRGFIMVSYYDIRAAQKAARALHGRLLRGRKLDI 279
Cdd:cd12316   2 LFVRNLPfTATED-ELRELFEAFGKISEVHipldkQTKRSKGFAFVLFVIPEDAVKAYQELDGSIFQGRLLHV 73

RNA recognition motif 1 (RRM1) found in the U1A/U2B"/SNF protein family; This subfamily corresponds to the RRM1 of U1A/U2B"/SNF protein family which contains Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which consist of two RNA recognition motifs (RRMs), connected by a variable, flexible linker. SNF is an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila where it is essential in sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). U1A is an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. Moreover, U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins. U2B", initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a unique protein that comprises of the U2 snRNP. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. Moreover, U2B" does not require an auxiliary protein for binding to RNA, and its nuclear transport is independent of U2 snRNA binding.

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                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15240750 297 LWVNNLDSSISNEE----LHGIFSSYGEIREV--RRTMHENSQVYIEFFDVRKAKVALQGLNGLEVAGRQLKL 363
Cdd:cd12246   2 LYINNLNEKIKKDElkrsLYALFSQFGPVLDIvaSKSLKMRGQAFVVFKDVESATNALRALQGFPFYGKPMRI 74

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.

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                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15240750 213 LFVRNVDSSIEDCELGVLFKQFGDVRALHTAGKNRGFIMVSYYDIRAAQKAARALHGRLLRGRKLDI 279
Cdd:cd12529   4 LVVFNLDPSISNDDLHQIFGAYGEIKEIRETPNKRHHKFIEFYDVRSAEAALKALNKSEIAGKRIKL 70

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

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15240750   182 VFSSVSQRDGKRGSNVSTVAEHPQGeilsriLFVRNVDSSIEDCELGVLFKQFGDVRALH-----TAGKNRGFIMVSYYD 256
Cdd:TIGR01642 273 KNPDDNAKNVEKLVNSTTVLDSKDR------IYIGNLPLYLGEDQIKELLESFGDLKAFNlikdiATGLSKGYAFCEYKD 346

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15240750   257 IRAAQKAARALHGRLLRGRKLDIRYSI-PKENPKENSSEGALWVNNLDSSISNE------------ELHGIF-------- 315
Cdd:TIGR01642 347 PSVTDVAIAALNGKDTGDNKLHVQRACvGANQATIDTSNGMAPVTLLAKALSQSilqiggkptkvvQLTNLVtgddlmdd 426

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15240750   316 SSYGEIREVRRTMHEN----------------------SQVYIEFFDVRKAKVALQGLNGLEVAGRQLkLAPTCPE 369
Cdd:TIGR01642 427 EEYEEIYEDVKTEFSKygpliniviprpngdrnstpgvGKVFLEYADVRSAEKAMEGMNGRKFNDRVV-VAAFYGE 501

RNA recognition motif 2 (RRM2) found in Saccharomyces cerevisiae protein HRB1, G-strand-binding protein 2 (GBP2) and similar proteins; The family includes Saccharomyces cerevisiae protein HRB1 (also called protein TOM34) and GBP2, both of which are SR-like mRNA-binding proteins which shuttle from the nucleus to the cytoplasm when bound to the mature mRNA molecules. They act as quality control factors for spliced mRNAs. GBP2, also called RAP1 localization factor 6, is a single-strand telomeric DNA-binding protein that binds single-stranded telomeric sequences of the type (TG[1-3])n in vitro. It also binds to RNA. GBP2 influences the localization of RAP1 in the nuclei and plays a role in modulating telomere length. 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 second RRM motif.

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                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15240750 213 LFVRNVDSSIEDCELGVLFKQFGDV-RA---LHTAGKNRGFIMVSYYDIRAAQKAARALHGRLLRGRKLDIR 280
Cdd:cd21606   4 VFIANLPYSINWQALKDMFKECGDVlRAdveLDYNGRSRGFGTVIYATEEEMHRAIDTFNGYELEGRVLEVK 75

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

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                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15240750 297 LWVNNLDSSISNEELHGIFSSYGEIREV-----RRTMHENSQVYIEFFDVRKAKVALQGLNGLEVAGRQLK 362
Cdd:cd12393   4 VYVSNLPFSLTNNDLHQIFSKYGKVVKVtilkdKETRKSKGVAFVLFLDRESAHNAVRAMNNKELFGRTLK 74

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.

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                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15240750 213 LFVRNVDSSIEDCELGVLFKQFGDV------RALHTaGKNRGFIMVSYYDIRAAQKAARALHGRLLRGRKL 277
Cdd:cd12362   1 LFVYHLPNEFTDQDLYQLFAPFGNVvsakvfVDKNT-GRSKGFGFVSYDNPLSAQAAIKAMNGFQVGGKRL 70

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.

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                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15240750 299 VNNLDSSISNEELHGIFSSYGEIREVR---RTMHENSQVYIEFFDVRKAKVALQgLNGLEVAGRQLK 362
Cdd:cd12260   9 VGNLDPSTTADQLLEFFSQAGEVKYVRmagDETQPTRYAFVEFAEQTSVINALK-LNGKMFGGRPLK 74

RNA recognition motif 2 (RRM2) found in yeast protein gar2 and similar proteins; This subfamily corresponds to the RRM2 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues.

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                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15240750 297 LWVNNLDSSISNEELHGIFSSYGEIREVR-RTMHENSQV----YIEFFDVRKAKVALQGLNGLEVAGRQLKL 363
Cdd:cd12448   1 LFVGNLPFSATQDALYEAFSQHGSIVSVRlPTDRETGQPkgfgYVDFSTIDSAEAAIDALGGEYIDGRPIRL 72

RNA recognition motif 1 (RRM1) found in the U1A/U2B"/SNF protein family; This subfamily corresponds to the RRM1 of U1A/U2B"/SNF protein family which contains Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which consist of two RNA recognition motifs (RRMs), connected by a variable, flexible linker. SNF is an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila where it is essential in sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). U1A is an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. Moreover, U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins. U2B", initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a unique protein that comprises of the U2 snRNP. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. Moreover, U2B" does not require an auxiliary protein for binding to RNA, and its nuclear transport is independent of U2 snRNA binding.

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                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15240750 213 LFVRNVDSSIEDCELGV----LFKQFG---DVRALHTAgKNRGFIMVSYYDIRAAQKAARALHGRLLRGRKLDIRYS 282
Cdd:cd12246   2 LYINNLNEKIKKDELKRslyaLFSQFGpvlDIVASKSL-KMRGQAFVVFKDVESATNALRALQGFPFYGKPMRIQYA 77