Splicing factor 1 helix-hairpin domain; This domain, approximately 100 residues in length, is mainly found in splicing factor 1 from yeast to human. It is a helix-hairpin domain, which forms a secondary, hydrophobic interface with U2AF65(UHM) to lock the orientation of the two subunits, which is essential for cooperative formation of the ternary SF1-U2AF65-RNA complex. In this domain, it contains a highly conserved SPSP motif in its C terminal and phophorylation of SPSP motif induces a disorder-to-order transition within a novel SF1/U2AF65 interface, indicating a phosphorylation-dependent control of pre-mRNA splicing factors.

                          10
                  ....*....|....*....
gi 3406779      1 LITEMVALNPDFKPPADYK 19
Cdd:pfam16275  96 LIEEAMKINPNFRPPADYK 114

Splicing factor (branch point binding protein) [RNA processing and modification];

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3406779   10 PDFKPPADYKPPaTRVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGED 89
Cdd:COG5176 134 PRFVLPNDYIRP-SKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSGSVKEGKISSDTPESLKNAE 212

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 3406779   90 EPLHALVTANTMENVKKAVEQIRNILKQGIETPEDQNDLRKMQLRELARLNGTLRED 146
Cdd:COG5176 213 AVLHCLIEADSEDKICRLIKSQLNAIREARRNPEGQNDLKRFQLRWLAHLNGTLRAD 269

KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3406779     26 SDKVMIPQDeypeinFVGLLIGPRGNTLKNIEKECNAKImirgkgsvkegkvgrkdgQMLPGEDEPLHALVT-ANTMENV 104
Cdd:pfam00013   1 TVEILVPSS------LVGLIIGKGGSNIKEIREETGAKI------------------QIPPSESEGNERIVTiTGTPEAV 56

                  ....*....
gi 3406779    105 KKAVEQIRN 113
Cdd:pfam00013  57 EAAKALIEE 65

Splicing factor 1 helix-hairpin domain; This domain, approximately 100 residues in length, is mainly found in splicing factor 1 from yeast to human. It is a helix-hairpin domain, which forms a secondary, hydrophobic interface with U2AF65(UHM) to lock the orientation of the two subunits, which is essential for cooperative formation of the ternary SF1-U2AF65-RNA complex. In this domain, it contains a highly conserved SPSP motif in its C terminal and phophorylation of SPSP motif induces a disorder-to-order transition within a novel SF1/U2AF65 interface, indicating a phosphorylation-dependent control of pre-mRNA splicing factors.

                          10
                  ....*....|....*....
gi 3406779      1 LITEMVALNPDFKPPADYK 19
Cdd:pfam16275  96 LIEEAMKINPNFRPPADYK 114

Splicing factor (branch point binding protein) [RNA processing and modification];

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3406779   10 PDFKPPADYKPPaTRVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGED 89
Cdd:COG5176 134 PRFVLPNDYIRP-SKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSGSVKEGKISSDTPESLKNAE 212

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 3406779   90 EPLHALVTANTMENVKKAVEQIRNILKQGIETPEDQNDLRKMQLRELARLNGTLRED 146
Cdd:COG5176 213 AVLHCLIEADSEDKICRLIKSQLNAIREARRNPEGQNDLKRFQLRWLAHLNGTLRAD 269

type I K homology (KH) RNA-binding domain found in protein quaking (Hqk) family; The Hqk family includes Hqk and protein held out wings (how) found in Drosophila. Hqk, also called HqkI, is an RNA-binding protein that plays a central role in myelinization. It binds to the 5'-NACUAAY-N(1,20)-UAAY-3' RNA core sequence and regulates target mRNA stability. It acts by regulating pre-mRNA splicing, mRNA export and protein translation. Hqk is a regulator of oligodendrocyte differentiation and maturation in the brain that may play a role in myelin and oligodendrocyte dysfunction in schizophrenia. How, also called KH domain protein KH93F, or protein muscle-specific, or protein Struthio, or protein wings held out (who), or Quaking-related 93F (qkr93F), is an RNA-binding protein involved in the control of muscular and cardiac activity. It is required for integrin-mediated cell-adhesion in wing blade. It plays essential roles during embryogenesis, in late stages of somatic muscle development, for myotube migration and during metamorphosis for muscle reorganization.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3406779   25 VSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEG-KVGRKDGQmlPGE---DEPLHALVTANT 100
Cdd:cd22383   2 LSEKVYVPVDEYPDYNFVGRILGPRGMTAKQLEQDTGCKIMIRGKGSMRDKkKEEANRGK--PNWehlNDDLHVLITVED 79

                        90       100
                ....*....|....*....|.
gi 3406779  101 MEN-----VKKAVEQIRNILK 116
Cdd:cd22383  80 TENrahikLAKAVEEVKKLLI 100

type I K homology (KH) RNA-binding domain found in the KH domain-containing, RNA-binding, signal transduction-associated protein (KHDRBS) family; The KHDRBS family includes three members, KHDRBS1-3. KHDRBS1, also called GAP-associated tyrosine phosphoprotein p62, or Src-associated in mitosis 68 kDa protein, or Sam68, or p21 Ras GTPase-activating protein-associated p62, or p68, is an RNA-binding protein that plays a role in the regulation of alternative splicing and influences mRNA splice site selection and exon inclusion. It binds to RNA containing 5'-[AU]UAA-3' as a bipartite motif spaced by more than 15 nucleotides. It also binds poly(A). KHDRBS1 acts as a putative regulator of mRNA stability and/or translation rates and mediates mRNA nuclear export. It is recruited and tyrosine phosphorylated by several receptor systems, for example the T-cell, leptin and insulin receptors. KHDRBS2, also called Sam68-like mammalian protein 1, or SLM-1, is an RNA-binding protein that plays a role in the regulation of alternative splicing and influences mRNA splice site selection and exon inclusion. It binds both poly(A) and poly(U) homopolymers. KHDRBS2 may function as an adapter protein for Src kinases during mitosis. KHDRBS3, also called RNA-binding protein T-Star, or Sam68-like mammalian protein 2, or SLM-2, or Sam68-like phosphotyrosine protein, is an RNA-binding protein that plays a role in the regulation of alternative splicing and influences mRNA splice site selection and exon inclusion. It binds optimally to RNA containing 5'-[AU]UAA-3' as a bipartite motif spaced by more than 15 nucleotides. It also binds poly(A). KHDRBS3 may play a role as a negative regulator of cell growth.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 3406779   24 RVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSV----KEGKVGRKDGQMLPGEDEPLHALVTA 98
Cdd:cd22384   4 KLSEKVLIPVKEFPKFNFVGKLLGPRGNTLKRLQEETGTKMSILGKGSMrdkaKEEELRKSGDPKYAHLNEDLHVLIEA 82

type I K homology (KH) RNA-binding domain found in Oryza sativa SPL11-interacting protein 1 (SPIN1) and similar proteins; SPIN1 is a K homology domain protein negatively regulated and ubiquitinated by the E3 ubiquitin ligase SPL11. It is involved in flowering time control in rice. SPIN1 binds DNA and RNA in vitro.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3406779   31 IPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKE-GKVGRKDGQmlPGED---EPLHALVTANTMENV-- 104
Cdd:cd22467   8 VPVDKYPNFNFVGRILGPRGNSLKRVEATTGCRVFIRGRGSIKDtAKEEKLRDK--PGYEhlnEPLHVLIEAELPANIid 85

                        90
                ....*....|....*
gi 3406779  105 ---KKAVEQIRNILK 116
Cdd:cd22467  86 arlQHAQEIIEDLLK 100

type I K homology (KH) RNA-binding domain found in KH domain-containing, RNA-binding, signal transduction-associated protein 2 (KHDRBS2) and similar proteins; KHDRBS2, also called Sam68-like mammalian protein 1, or SLM-1, is an RNA-binding protein that plays a role in the regulation of alternative splicing and influences mRNA splice site selection and exon inclusion. It binds both poly(A) and poly(U) homopolymers. KHDRBS2 may function as an adapter protein for Src kinases during mitosis.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3406779   24 RVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGS----VKEGKVGRKDGQMLPGEDEPLHALVT-- 97
Cdd:cd22469   6 KLSERVLIPVKQYPKFNFVGKLLGPRGNSLKRLQEETGAKMSILGKGSmrdkAKEEELRKSGEAKYAHLSDELHVLIEvf 85

                        90       100       110
                ....*....|....*....|....*....|....*...
gi 3406779   98 ---ANTMENVKKAVEQIRNILkqgieTPEDQNDLRKMQ 132
Cdd:cd22469  86 appGEAYSRMSHALEEIKKFL-----VPDYNDEIRQEQ 118

type I K homology (KH) RNA-binding domain found in KH domain-containing, RNA-binding, signal transduction-associated protein 3 (KHDRBS3) and similar proteins; KHDRBS3, also called RNA-binding protein T-Star, or Sam68-like mammalian protein 2, or SLM-2, or Sam68-like phosphotyrosine protein, is an RNA-binding protein that plays a role in the regulation of alternative splicing and influences mRNA splice site selection and exon inclusion. It binds optimally to RNA containing 5'-[AU]UAA-3' as a bipartite motif spaced by more than 15 nucleotides. It also binds poly(A). KHDRBS3 may play a role as a negative regulator of cell growth.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 3406779   24 RVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKE 74
Cdd:cd22470   8 KLGQKVLIPVKQFPKFNFVGKLLGPRGNSLKRLQEETLTKMSILGKGSMRD 58

K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include an N-terminal extension and type I KH domains (e.g. hnRNP K) contain a C-terminal extension. Some KH-I superfamily members contain a divergent KH domain that lacks the RNA-binding GXXG motif. Some others have a mutated GXXG motif which may or may not have nucleic acid binding ability.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3406779   27 DKVMIPQDeypeinFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSvkegkvgrkdgqmlpgEDEPLHALVTAnTMENVKK 106
Cdd:cd00105   1 EEIEVPSE------LVGLIIGKGGSTIKEIEEETGARIQIPKEGE----------------GSGERVVTITG-TPEAVEK 57

                ....*.
gi 3406779  107 AVEQIR 112
Cdd:cd00105  58 AKELIE 63

KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3406779     26 SDKVMIPQDeypeinFVGLLIGPRGNTLKNIEKECNAKImirgkgsvkegkvgrkdgQMLPGEDEPLHALVT-ANTMENV 104
Cdd:pfam00013   1 TVEILVPSS------LVGLIIGKGGSNIKEIREETGAKI------------------QIPPSESEGNERIVTiTGTPEAV 56

                  ....*....
gi 3406779    105 KKAVEQIRN 113
Cdd:pfam00013  57 EAAKALIEE 65

first type I K homology (KH) RNA-binding domain found in Pyrococcus horikoshii Dim2p and similar proteins; The family includes a group of conserved KH domain-containing protein mainly from archaea, such as Dim2p homologues from Pyrococcus horikoshii and Aeropyrum pernix. Dim2p acts as a preribosomal RNA processing factor that has been identified as an essential protein for the maturation of 40S ribosomal subunit in Saccharomyces cerevisiae. It is required for the cleavage at processing site A2 to generate the pre-20S rRNA and for the dimethylation of the 18S rRNA by 18S rRNA dimethyltransferase, Dim1p. Dim2p contains two K-homology (KH) RNA-binding domains. The model corresponds to the first one.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|.
gi 3406779   29 VMIPQDEypeinfVGLLIGPRGNTLKNIEKECNAKIMIRGK 69
Cdd:cd22389   3 VKIPKER------IGVLIGKKGETKREIEERTGVKITVDSE 37

polynucleotide phosphorylase/polyadenylase; Provisional

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3406779    13 KPPADYKPPATRVsDKVMIPQDeypeinFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKegkvgrkdgqmlpgedepl 92
Cdd:PRK11824 543 EPRAELSPYAPRI-ETIKIPPD------KIRDVIGPGGKTIREITEETGAKIDIEDDGTVK------------------- 596

                         90       100
                 ....*....|....*....|..
gi 3406779    93 halVTANTMENVKKAVEQIRNI 114
Cdd:PRK11824 597 ---IAATDGEAAEAAKERIEGI 615

type I K homology (KH) RNA-binding domain found in the family of DEAD box protein 46 (DDX46); The DDX46 family includes DEAD box protein 46 (DDX46), fungal pre-mRNA-processing ATP-dependent RNA helicase PRP5, Arabidopsis thaliana DEAD-box ATP-dependent RNA helicase RH42 and similar proteins. DDX46, also called PRP5 homolog, is an ATP-dependent RNA helicase that plays an essential role in splicing, either prior to, or during splicing A complex formation. It inhibits antiviral innate responses by entrapping selected antiviral transcripts in the nucleus. It is also involved in the development of several tumors. PRP5 is an ATP-dependent RNA helicase involved spliceosome assembly and in nuclear splicing. It catalyzes an ATP-dependent conformational change of U2 snRNP. PRP5 interacts with the U2 snRNP and HSH155. RH42, also called DEAD-box RNA helicase RCF1, or REGULATOR OF CBF GENE EXPRESSION 1, is a helicase required for pre-mRNA splicing, cold-responsive gene regulation and cold tolerance. Members in this family contain a divergent KH domain that lacks the RNA-binding GXXG motif.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 3406779   52 TLKNIEKECNAKIMIRGKGSVKEGKVgrkdgqmLPGEdEPLHALVTANTMENVKKAVEQIRNIL 115
Cdd:cd22387  27 VLNSIMEETGATITIKGQYYPPGKKP-------KPGE-RKLYLLIEGATEESVQSARNEIKRVL 82

putative RNA-processing protein; Provisional

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 3406779    29 VMIPQDEypeinfVGLLIGPRGNTLKNIEKECNAKIMIRGK-GSVK 73
Cdd:PRK13763   7 VKIPKDR------IGVLIGKKGETKKEIEERTGVKLEIDSEtGEVI 46