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        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190339205   90 KRSRWSSETPD-QKTVIPGMPTVIPPGLTRDQERAYIVQLQIEDLTRKLRTGDLGIPVNPEDRSPSPEPIYNSEGKRLNT 168
Cdd:pfam16275   1 RKSRWGGEPEKtDKPPIPGLPTAIPGGLTPEQLDAYLLQFRIEEITRKLRTGDLGVPPSPEERSPSPPPIYDANGKRTNT 80

                          90       100       110
                  ....*....|....*....|....*....|....
gi 190339205  169 REYRTRKKLEEERHSLITEMVGLNPEFKPPADYK 202
Cdd:pfam16275  81 REVRYRKKLEKERHRLIEEAMKINPNFRPPADYK 114

K homology RNA-binding domain;

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190339205   206 TRVSDKVMIPQdeypeiNFVGLLIGPRGNTLKNIEKECCAKIMIrgkgsvkegkvgrkdgqmlPGEDEPLHALVTANTME 285
Cdd:smart00322   1 DPVTIEVLIPA------DKVGLIIGKGGSTIKKIEEETGVKIDI-------------------PGPGSEERVVEITGPPE 55

                           90
                   ....*....|...
gi 190339205   286 NVKKAVEQIRNIL 298
Cdd:smart00322  56 NVEKAAELILEIL 68

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        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190339205   90 KRSRWSSETPD-QKTVIPGMPTVIPPGLTRDQERAYIVQLQIEDLTRKLRTGDLGIPVNPEDRSPSPEPIYNSEGKRLNT 168
Cdd:pfam16275   1 RKSRWGGEPEKtDKPPIPGLPTAIPGGLTPEQLDAYLLQFRIEEITRKLRTGDLGVPPSPEERSPSPPPIYDANGKRTNT 80

                          90       100       110
                  ....*....|....*....|....*....|....
gi 190339205  169 REYRTRKKLEEERHSLITEMVGLNPEFKPPADYK 202
Cdd:pfam16275  81 REVRYRKKLEKERHRLIEEAMKINPNFRPPADYK 114

type I K homology (KH) RNA-binding domain found in yeast branchpoint-bridging protein (BBP) and similar proteins; Yeast BBP, also called mud synthetic-lethal 5 protein, or splicing factor 1, or zinc finger protein BBP, is a mammalian splicing factor SF1 ortholog. It is involved in protein-protein interactions that bridge the 3' and 5' splice-site ends of the intron during the early steps of yeast pre-mRNA splicing. BBP interacts specifically with the pre-mRNA branchpoint sequence UACUAAC.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190339205 207 RVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECCAKIMIRGKGSVKEGKvGRKDGQMLPGEDEPLHALVTANTMEN 286
Cdd:cd02395    1 KKQRKIYIPVDEYPDYNFIGLIIGPRGNTQKRMEKESGAKIAIRGKGSVKEGK-GRSDPQPDPDEEEDLHVLITADTEEK 79

                         90
                 ....*....|..
gi 190339205 287 VKKAVEQIRNIL 298
Cdd:cd02395   80 VDKAAKLIEKLL 91

type I K homology (KH) RNA-binding domain found in Drosophila protein held out wings (how) and similar proteins; 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 190339205 204 PATRVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECCAKIMIRGKGSVKEGKV-----GRKDGQMLpgeDEPLHAL 278
Cdd:cd22466    2 PSVTLSEKVYVPVKEHPDYNFVGRILGPRGMTAKQLEQETGCKIMVRGKGSMRDKKKedlnrGKPNWEHL---NDELHVL 78

                         90       100
                 ....*....|....*....|....*
gi 190339205 279 VTANTMEN-----VKKAVEQIRNIL 298
Cdd:cd22466   79 ITVEDTENrakvkLQRAVEEVRKLL 103

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 190339205 207 RVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECCAKIMIRGKGSV----KEGKVGRKDGQMLPGEDEPLHALVTA 281
Cdd:cd22384    4 KLSEKVLIPVKEFPKFNFVGKLLGPRGNTLKRLQEETGTKMSILGKGSMrdkaKEEELRKSGDPKYAHLNEDLHVLIEA 82

first type I K homology (KH) RNA-binding domain found in KH homology domain-containing protein 4 (KHDC4) and similar proteins; KHDC4, also called Brings lots of money 7 (Blom7), or pre-mRNA splicing factor protein KHDC4, is an RNA-binding protein involved in pre-mRNA splicing. It interacts with the PRP19C/Prp19 complex/NTC/Nineteen complex which is part of the spliceosome. KHDC4 binds preferentially RNA with A/C rich sequences and poly-C stretches. KHDC4 contains two type I K homology (KH) RNA-binding domains. The model corresponds to the second one.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190339205 208 VSDKVMIPQDEYPE-INFVGLLIGPRGNTLKNIEKECCAKIMIRGKGS-VKEGKVGRKDgqmlpgeDEPLHALVTANTME 285
Cdd:cd22386    3 YQEKVFVGLEHAPPgFNVRGKLIGPGGSNVKHIQQETGAKVQLRGKGSgFIEPASGREA-------DEPLHLLISHPDPE 75

                         90
                 ....*....|....
gi 190339205 286 NVKKAVEQIRNILK 299
Cdd:cd22386   76 GLQQAKKLCEDLLQ 89

type I K homology (KH) RNA-binding domain found in KH domain-containing, RNA-binding, signal transduction-associated protein 1 (KHDRBS1) and similar proteins; 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.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 190339205 207 RVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECCAKIMIRGKGSVKE 257
Cdd:cd22468    4 KLKERILIPVKQYPKFNFVGKILGPQGNTIKRLQEETGAKISVLGKGSMRD 54

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 190339205 210 DKVMIPQDeypeinFVGLLIGPRGNTLKNIEKECCAKIMIRGKGSvkegkvgrkdgqmlpgEDEPLHALVTAnTMENVKK 289
Cdd:cd00105    1 EEIEVPSE------LVGLIIGKGGSTIKEIEEETGARIQIPKEGE----------------GSGERVVTITG-TPEAVEK 57

                 ....*.
gi 190339205 290 AVEQIR 295
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 190339205  209 SDKVMIPQDeypeinFVGLLIGPRGNTLKNIEKECCAKImirgkgsvkegkvgrkdgQMLPGEDEPLHALVT-ANTMENV 287
Cdd:pfam00013   1 TVEILVPSS------LVGLIIGKGGSNIKEIREETGAKI------------------QIPPSESEGNERIVTiTGTPEAV 56

                  ....*....
gi 190339205  288 KKAVEQIRN 296
Cdd:pfam00013  57 EAAKALIEE 65

type I K homology (KH) RNA-binding domain found in polyribonucleotide nucleotidyltransferase (PNPase) and similar proteins; PNPase, also called polynucleotide phosphorylase, is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. It catalyzes the phosphorolysis of single-stranded polyribonucleotides processively in the 3'- to 5'-direction. It is also involved, along with RNase II, in tRNA processing. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. The model corresponds to the KH domain.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190339205 211 KVMIPQDeypeinFVGLLIGPRGNTLKNIEKECCAKIMIRGKGSVKegkvgrkdgqmlpgedeplhalVTANTMENVKKA 290
Cdd:cd02393    7 TIKIPPD------KIGDVIGPGGKTIRAIIEETGAKIDIEDDGTVT----------------------IFATDKESAEAA 58

                 ....*....
gi 190339205 291 VEQIRNILK 299
Cdd:cd02393   59 KAMIEDIVA 67

sixth type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the sixth one.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190339205 208 VSDKVMIPQDEYpeinfvGLLIGPRGNTLKNIEKECCAKIMIrgkgsvkegkvgrkdgqmlPGEDEPLHALVTANTMENV 287
Cdd:cd22451    1 ASIDIDIPKEYH------RAIIGKGGAVLRELEAETGCRIQV-------------------PKKDDPSGKIRITGARDGV 55

                         90
                 ....*....|...
gi 190339205 288 KKAVEQIRNILKQ 300
Cdd:cd22451   56 EAATAKILNISDE 68