SPOC (Spen paralog and ortholog C-terminal) domain found in vertebrate RNA binding motif protein 15 (RBM15); RBM15, also called one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possesses mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RBM15 belongs to the Spen (split end) protein family, which contain three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. The model corresponds to the SPOC domain that is involved in developmental signaling and has also been proposed to be a phosphorylation binding module.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 944208227 599 AWQGMLLLKNSNFPSNMHLLQGDLGVASSLLVEGATGGKVAQLKITQRLRLDQPKLDEVNRRIKVAGPNGYAILLAVPGA 678
Cdd:cd21549    1 AWQGMLLLKNSNFPSNMHLLEGDLSVASSLLVDGSTGGKVAQLKITQRLRLDQPKLDEVTRRIKVAGPNGYAVLLAVPGS 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 944208227 679 SDNRSaagaSEAATTSTQRPLRNLVSYLKQKQAAGVISLPVGGNKDKENSGVLHAFPPCDFSQQFLDSTAKALAKSEDDY 758
Cdd:cd21549   81 SEVSS----VSDQATSTQRPLRNLVSYLKQKQAAGVISLPVGGSKDKDNTGVLHAFPPCDFSQQFLDSSAKALAKSEEDY 156

                 ....*...
gi 944208227 759 LVMIIVRG 766
Cdd:cd21549  157 LVMIIVRG 164

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
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 944208227 278 EFDRFGTIRTIDYRKGDSWAYIQYESLDAAQAACTHMRGFPLGGPDRRLRVDFAD 332
Cdd:cd12557   19 EFDRFGTIRTIDYRKGDSWAYIQYESLDAAQAACTHMRGFPLGGPDRRLRVDFAD 73

SPOC (Spen paralog and ortholog C-terminal) domain found in vertebrate RNA binding motif protein 15 (RBM15); RBM15, also called one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possesses mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RBM15 belongs to the Spen (split end) protein family, which contain three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. The model corresponds to the SPOC domain that is involved in developmental signaling and has also been proposed to be a phosphorylation binding module.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 944208227 599 AWQGMLLLKNSNFPSNMHLLQGDLGVASSLLVEGATGGKVAQLKITQRLRLDQPKLDEVNRRIKVAGPNGYAILLAVPGA 678
Cdd:cd21549    1 AWQGMLLLKNSNFPSNMHLLEGDLSVASSLLVDGSTGGKVAQLKITQRLRLDQPKLDEVTRRIKVAGPNGYAVLLAVPGS 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 944208227 679 SDNRSaagaSEAATTSTQRPLRNLVSYLKQKQAAGVISLPVGGNKDKENSGVLHAFPPCDFSQQFLDSTAKALAKSEDDY 758
Cdd:cd21549   81 SEVSS----VSDQATSTQRPLRNLVSYLKQKQAAGVISLPVGGSKDKDNTGVLHAFPPCDFSQQFLDSSAKALAKSEEDY 156

                 ....*...
gi 944208227 759 LVMIIVRG 766
Cdd:cd21549  157 LVMIIVRG 164

RNA recognition motif 3 (RRM3) found in vertebrate RNA binding motif protein 15 (RBM15); This subgroup corresponds to the RRM3 of RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, a novel mRNA export factor component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possesses mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RBM15 belongs to the Spen (split end) protein family, which contains three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralogue and ortholog C-terminal) domain. This family also includes a RBM15-MKL1 (OTT-MAL) fusion protein that RBM15 is N-terminally fused to megakaryoblastic leukemia 1 protein (MKL1) at the C-terminus in a translocation involving chromosome 1 and 22, resulting in acute megakaryoblastic leukemia. The fusion protein could interact with the mRNA export machinery. Although it maintains the specific transactivator function of MKL1, the fusion protein cannot activate RTE-mediated mRNA expression and has lost the post-transcriptional activator function of RBM15. However, it has transdominant suppressor function contributing to its oncogenic properties.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 944208227 278 EFDRFGTIRTIDYRKGDSWAYIQYESLDAAQAACTHMRGFPLGGPDRRLRVDFAD 332
Cdd:cd12557   19 EFDRFGTIRTIDYRKGDSWAYIQYESLDAAQAACTHMRGFPLGGPDRRLRVDFAD 73

RNA recognition motif 2 (RRM2) found in vertebrate RNA binding motif protein 15 (RBM15); This subgroup corresponds to the RRM2 of RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possesses mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RBM15 belongs to the Spen (split end) protein family, which contain three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. This family also includes a RBM15-MKL1 (OTT-MAL) fusion protein that RBM15 is N-terminally fused to megakaryoblastic leukemia 1 protein (MKL1) at the C-terminus in a translocation involving chromosome 1 and 22, resulting in acute megakaryoblastic leukemia. The fusion protein could interact with the mRNA export machinery. Although it maintains the specific transactivator function of MKL1, the fusion protein cannot activate RTE-mediated mRNA expression and has lost the post-transcriptional activator function of RBM15. However, it has transdominant suppressor function contributing to its oncogenic properties.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 944208227 233 EDDQRANRTLFLGNLDIT------------------------------------FENLDMAHRAKLAMSGKVLLRNPIKI 276
Cdd:cd12555    1 EDDQRANRTLFLGNLDITvtendlrrafdrfgvitevdikrpgrgqtstygflkFENLDMAHRAKLAMSGKVIGRNPIKI 80

                 .
gi 944208227 277 G 277
Cdd:cd12555   81 G 81

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 944208227   32 EDGLFHEFKRFGDV-SVKISRlpPGTGAADeRVAFVNFRRPEDARAAKHARGRLVLYDRPLK 92
Cdd:pfam00076  12 EEDLKDLFSKFGPIkSIRLVR--DETGRSK-GFAFVEFEDEEDAEKAIEALNGKELGGRELK 70

SPOC (Spen paralog and ortholog C-terminal) domain found in vertebrate RNA binding motif protein 15 (RBM15); RBM15, also called one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possesses mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RBM15 belongs to the Spen (split end) protein family, which contain three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. The model corresponds to the SPOC domain that is involved in developmental signaling and has also been proposed to be a phosphorylation binding module.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 944208227 599 AWQGMLLLKNSNFPSNMHLLQGDLGVASSLLVEGATGGKVAQLKITQRLRLDQPKLDEVNRRIKVAGPNGYAILLAVPGA 678
Cdd:cd21549    1 AWQGMLLLKNSNFPSNMHLLEGDLSVASSLLVDGSTGGKVAQLKITQRLRLDQPKLDEVTRRIKVAGPNGYAVLLAVPGS 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 944208227 679 SDNRSaagaSEAATTSTQRPLRNLVSYLKQKQAAGVISLPVGGNKDKENSGVLHAFPPCDFSQQFLDSTAKALAKSEDDY 758
Cdd:cd21549   81 SEVSS----VSDQATSTQRPLRNLVSYLKQKQAAGVISLPVGGSKDKDNTGVLHAFPPCDFSQQFLDSSAKALAKSEEDY 156

                 ....*...
gi 944208227 759 LVMIIVRG 766
Cdd:cd21549  157 LVMIIVRG 164

SPOC (Spen paralog and ortholog C-terminal) domain found in putative RNA binding motif protein 15B (RBM15B); RBM15B, also called one-twenty two 3 (OTT3), is a paralog of RNA binding motif protein 15 (RBM15), which is also known as one-twenty two protein 1 (OTT1). Like RBM15, RBM15B has post-transcriptional regulatory activity. It is a nuclear protein that shares with RBM15, the association with the splicing factor compartment and the nuclear envelope, as well as the binding to mRNA export factors NXF1 and Aly/REF. RBM15B belongs to the Spen (split end) protein family, which contains a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC domain. This model corresponds to the SPOC domain that is involved in developmental signaling and has also been proposed to be a phosphorylation binding module.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 944208227 599 AWQGMLLLKNSNFPSNMHLLQGDLGVASSLLVEGATGGKVAQLKITQRLRLDQPKLDEVNRRIKVAGPNGYAILLAVPgA 678
Cdd:cd21550    1 AWNGVLVLKNSCFPTNMHILEGDLGVVNILLKDYTSGGKLTQLKIAQRLRLDQPKLDEVTRRIKQGSPDGYAVLLATQ-A 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 944208227 679 SDNRSAAGASEAATTSTQRPLRNLVSYLKQKQAAGVISLPVGGNKDKENSGVLHAFPPCDFSQQFLDSTAKALAKSEDDY 758
Cdd:cd21550   80 PQGGEGGGAPPVEPGLQRRLLRNLVSYLKQKQAAGVISLPVGGSKDRDNTGMLYAFPPCDFSQQYLQSALRTLGKLEEEH 159

                 ....*..
gi 944208227 759 LVMIIVR 765
Cdd:cd21550  160 MVIVIVK 166

RNA recognition motif 1 (RRM1) found in vertebrate RNA binding motif protein 15 (RBM15); This subgroup corresponds to the RRM1 of RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possesses mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RBM15 belongs to the Spen (split end) protein family, which contains three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. This family also includes a RBM15-MKL1 (OTT-MAL) fusion protein that RBM15 is N-terminally fused to megakaryoblastic leukemia 1 protein (MKL1) at the C-terminus in a translocation involving chromosome 1 and 22, resulting in acute megakaryoblastic leukemia. The fusion protein could interact with the mRNA export machinery. Although it maintains the specific transactivator function of MKL1, the fusion protein cannot activate RTE-mediated mRNA expression and has lost the post-transcriptional activator function of RBM15. However, it has transdominant suppressor function contributing to its oncogenic properties.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 944208227  14 YKTLKISELGSALSDEAVEDGLFHEFKRFGDVSVKISRLppgtgaADERVAFVNFRRPEDARAAKHARGRLVLYDRPLKI 93
Cdd:cd12553    1 YKTLKISELGSQLSDEAVEDGLFHEFKKFGDVSVKISRL------GDERVAFVNFRRPEDARAAKHARGRLVLYDRPLKI 74

                 ....
gi 944208227  94 EAVY 97
Cdd:cd12553   75 EAVY 78

RNA recognition motif 3 (RRM3) found in vertebrate RNA binding motif protein 15 (RBM15); This subgroup corresponds to the RRM3 of RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, a novel mRNA export factor component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possesses mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RBM15 belongs to the Spen (split end) protein family, which contains three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralogue and ortholog C-terminal) domain. This family also includes a RBM15-MKL1 (OTT-MAL) fusion protein that RBM15 is N-terminally fused to megakaryoblastic leukemia 1 protein (MKL1) at the C-terminus in a translocation involving chromosome 1 and 22, resulting in acute megakaryoblastic leukemia. The fusion protein could interact with the mRNA export machinery. Although it maintains the specific transactivator function of MKL1, the fusion protein cannot activate RTE-mediated mRNA expression and has lost the post-transcriptional activator function of RBM15. However, it has transdominant suppressor function contributing to its oncogenic properties.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 944208227 278 EFDRFGTIRTIDYRKGDSWAYIQYESLDAAQAACTHMRGFPLGGPDRRLRVDFAD 332
Cdd:cd12557   19 EFDRFGTIRTIDYRKGDSWAYIQYESLDAAQAACTHMRGFPLGGPDRRLRVDFAD 73

SPOC (Spen paralog and ortholog C-terminal) domain found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins; SHARP, also called Msx2-interacting protein (MINT), or Spen homolog, is an estrogen-inducible transcriptional repressor that interacts directly with transcriptional corepressors silencing mediator for retinoid and thyroid receptor (SMRT)/nuclear receptor corepressor (NCoR), histone deacetylases (HDACs), and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also called RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain that binds to SMRT/NcoR. This model corresponds to the SPOC domain that is involved in developmental signaling and has also been proposed to be a phosphorylation binding module.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 944208227 600 WQGMLLLKNSNFPSNMHLLQGDLGVASSLLVEGATGGKVAQLKITQRLRLDQPKLDEVNRRIKVagPNGYAILLAVPgas 679
Cdd:cd21543    6 WQGLLALKNDEAAVQMHYVSGNQDLAKRSLPRHLTNGNLPPLRIAQRMRLEPSQLEGVARKMQD--ESEYCLLLALP--- 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 944208227 680 dnrsaAGASEAATTSTQRPLRN-LVSYLKQKQAAGVISLPVGGNKDkeNSGVLHAFPPCDFSQQFLDSTAKALAKS--ED 756
Cdd:cd21543   81 -----CGRDQEDVLKQTNNLKNgFITYLQQKQAAGIVNVPNPGSQQ--PAYVVHIFPPCEFSNSHLSRLAPDLLNSiaDI 153

                 ....*...
gi 944208227 757 DYLVMIIV 764
Cdd:cd21543  154 PHLMIVIA 161

RNA recognition motif 3 (RRM3) found in putative RNA-binding protein 15B (RBM15B) from vertebrate; This subgroup corresponds to the RRM3 of RBM15B, also termed one twenty-two 3 (OTT3), a paralog of RNA binding motif protein 15 (RBM15), also known as One-twenty two protein 1 (OTT1). Like RBM15, RBM15B has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. RBM15B belongs to the Spen (split end) protein family, which shares a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 944208227 278 EFDRFGTIRTIDYRKGDSWAYIQYESLDAAQAACTHMRGFPLGGPDRRLRVDFA 331
Cdd:cd12558   22 EFDRFGSIRTIDYVKGDSFAYIQYESLDAAQAACAQMRGFPLGGPDRRLRVDFA 75

RNA recognition motif 2 (RRM2) found in vertebrate RNA binding motif protein 15 (RBM15); This subgroup corresponds to the RRM2 of RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possesses mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RBM15 belongs to the Spen (split end) protein family, which contain three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. This family also includes a RBM15-MKL1 (OTT-MAL) fusion protein that RBM15 is N-terminally fused to megakaryoblastic leukemia 1 protein (MKL1) at the C-terminus in a translocation involving chromosome 1 and 22, resulting in acute megakaryoblastic leukemia. The fusion protein could interact with the mRNA export machinery. Although it maintains the specific transactivator function of MKL1, the fusion protein cannot activate RTE-mediated mRNA expression and has lost the post-transcriptional activator function of RBM15. However, it has transdominant suppressor function contributing to its oncogenic properties.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 944208227 233 EDDQRANRTLFLGNLDIT------------------------------------FENLDMAHRAKLAMSGKVLLRNPIKI 276
Cdd:cd12555    1 EDDQRANRTLFLGNLDITvtendlrrafdrfgvitevdikrpgrgqtstygflkFENLDMAHRAKLAMSGKVIGRNPIKI 80

                 .
gi 944208227 277 G 277
Cdd:cd12555   81 G 81

RNA recognition motif 2 (RRM2) found in putative RNA binding motif protein 15B (RBM15B) from vertebrate; This subgroup corresponds to the RRM2 of RBM15B, also termed one twenty-two 3 (OTT3), a paralog of RNA binding motif protein 15 (RBM15), also known as One-twenty two protein 1 (OTT1). Like RBM15, RBM15B has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. RBM15B belongs to the Spen (split end) protein family, which shares a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 944208227 232 PEDDQRANRTLFLGNLD------------------------------------ITFENLDMAHRAKLAMSGKVLLRNPIK 275
Cdd:cd12556    1 PEDDQRATRNLFIGNLDhnvsevelrrafekygiieevvikrpargqggayafLKFQNLDMAHRAKVAMSGRVIGRNPIK 80

                 ..
gi 944208227 276 IG 277
Cdd:cd12556   81 IG 82

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 944208227  26 LSDEAVEDGLFHEFKRFGDV-SVKISRLPPGtgaADERVAFVNFRRPEDARAAKHARGRLVLYDRPLKIE 94
Cdd:cd00590    6 LPPDTTEEDLRELFSKFGEVvSVRIVRDRDG---KSKGFAFVEFESPEDAEKALEALNGTELGGRPLKVS 72

RNA recognition motif;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 944208227    26 LSDEAVEDGLFHEFKRFGDV-SVKISRlPPGTGAADeRVAFVNFRRPEDARAAKHARGRLVLYDRPLKI 93
Cdd:smart00360   7 LPPDTTEEELRELFSKFGKVeSVRLVR-DKETGKSK-GFAFVEFESEEDAEKALEALNGKELDGRPLKV 73

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
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 944208227 279 FDRFGTIRTIDYRKGDS-----WAYIQYESLDAAQAACTHMRGFPLGGpdRRLRVD 329
Cdd:cd00590   19 FSKFGEVVSVRIVRDRDgkskgFAFVEFESPEDAEKALEALNGTELGG--RPLKVS 72

RNA recognition motif 3 (RRM3) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins; This subfamily corresponds to the RRM3 of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 944208227 238 ANRTLFLGNLDITFENLDmahraklamsgkvlLRNpikigEFDRFGTIRTIDYRK---GDSWAYIQYESLDAAQAACTHM 314
Cdd:cd12350    1 ATRTLFIGNLEKTTTYGD--------------LRN-----IFERFGEIIDIDIKKqngNPQYAFLQYCDIASVVKAIKKM 61

                 ....*..
gi 944208227 315 RGFPLGG 321
Cdd:cd12350   62 DGEYLGN 68

RNA recognition motif 1 (RRM1) found in (U)-binding-splicing factor PUF60 and similar proteins; This subfamily corresponds to the RRM1 of PUF60, also termed FUSE-binding protein-interacting repressor (FBP-interacting repressor or FIR), or Ro-binding protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1). PUF60 is an essential splicing factor that functions as a poly-U RNA-binding protein required to reconstitute splicing in depleted nuclear extracts. Its function is enhanced through interaction with U2 auxiliary factor U2AF65. PUF60 also controls human c-myc gene expression by binding and inhibiting the transcription factor far upstream sequence element (FUSE)-binding-protein (FBP), an activator of c-myc promoters. PUF60 contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors another RRM and binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) in several nuclear proteins. Research indicates that PUF60 binds FUSE as a dimer, and only the first two RRM domains participate in the single-stranded DNA recognition.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 944208227 279 FDRFGTIRTIDY------RKGDSWAYIQYESLDAAQAACTHMRGFPLGGpdRRLRV 328
Cdd:cd12370   21 FAPFGPIKSIDMswdpvtMKHKGFAFVEYEVPEAAQLALEQMNGVMLGG--RNIKV 74

RNA recognition motif (RRM) found in peptidyl-prolyl cis-trans isomerase-like 4 (PPIase) and similar proteins; This subfamily corresponds to the RRM of PPIase, also termed cyclophilin-like protein PPIL4, or rotamase PPIL4, a novel nuclear RNA-binding protein encoded by cyclophilin-like PPIL4 gene. The precise role of PPIase remains unclear. PPIase contains a conserved N-terminal peptidyl-prolyl cistrans isomerase (PPIase) motif, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a lysine rich domain, and a pair of bipartite nuclear targeting sequences (NLS) at the C-terminus.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 944208227 272 NPIKIGE-----FDRFGTIRTI----DYRKGDS--WAYIQYESLDAAQAACTHMRGFPLGgpDRRLRVDF 330
Cdd:cd12235   12 NPVTTDEdleiiFSRFGKIKSCevirDKKTGDSlqYAFIEFETKESCEEAYFKMDNVLID--DRRIHVDF 79

RNA recognition motif (RRM) found in apoptotic chromatin condensation inducer in the nucleus (acinus) and similar proteins; This subfamily corresponds to the RRM of Acinus, a caspase-3-activated nuclear factor that induces apoptotic chromatin condensation after cleavage by caspase-3 without inducing DNA fragmentation. It is essential for apoptotic chromatin condensation and may also participate in nuclear structural changes occurring in normal cells. Acinus contains a P-loop motif and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which indicates Acinus might have ATPase and DNA/RNA-binding activity.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 944208227 295 SWAYIQYESLDAAQAACTHMRG--FPLGGPdRRLRVDFADTE 334
Cdd:cd12432   40 SHCYVTYSSEEEAVATREALHGvvWPSSNG-KRLKVEFVTEE 80