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 17507875 204 SITEKIYVPKNEYPDYNFVGRILGPRGMTAKQLEQDTGCKIMVRGKGSMRDKSKESAHRGKANWEHLEDDLHVLVQCEDT 283
Cdd:cd22383   1 KLSEKVYVPVDEYPDYNFVGRILGPRGMTAKQLEQDTGCKIMIRGKGSMRDKKKEEANRGKPNWEHLNDDLHVLITVEDT 80

                        90       100
                ....*....|....*....|.
gi 17507875 284 ENRVHIKLQAALEQVKKLLIP 304
Cdd:cd22383  81 ENRAHIKLAKAVEEVKKLLIP 101

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 17507875 204 SITEKIYVPKNEYPDYNFVGRILGPRGMTAKQLEQDTGCKIMVRGKGSMRDKSKESAHRGKANWEHLEDDLHVLVQCEDT 283
Cdd:cd22383   1 KLSEKVYVPVDEYPDYNFVGRILGPRGMTAKQLEQDTGCKIMIRGKGSMRDKKKEEANRGKPNWEHLNDDLHVLITVEDT 80

                        90       100
                ....*....|....*....|.
gi 17507875 284 ENRVHIKLQAALEQVKKLLIP 304
Cdd:cd22383  81 ENRAHIKLAKAVEEVKKLLIP 101

Homodimerization region of STAR domain protein; This family is the homodimerization domain of quaking proteins. Quaking-dimer is a helix-turn-helix dimer with an additional helix in the turn region. dimerization is required for adequate RNA-binding. Quaking is a prototypical member of the STAR (signal transducer and activator of RNA) protein family, which plays key roles in post-transcriptional gene regulation by controlling mRNA translation, stability and splicing. STAR_dimer is the homodimerization domain, Qua1 of the STAR domain of a series of proteins referred to as STAR/GSG, or Signal Transduction and Activation of RNA/GRP33, Sam68, GLD-1 family. These are conserved in higher eukaryotes and are RNA-binding transcriptional regulators. The STAR domain is a KH domain flanked by two homologous regions, Qua1 and Qua2. Qua1, this family, is the homodimerization domain, and the KH plus Qua2 is the RNA-binding region.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 17507875   146 TVEYLADLVKEKKHLTLFPHMFSNVERLLDDEIGRVRVALFQTEF 190
Cdd:pfam16544   5 TPDYLAQLLKDKKQLAAFPNVFPHLERLLDEEISRVRGDLFNKGF 49

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

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 17507875   206 TEKIYVPKNeypdynFVGRILGPRGMTAKQLEQDTGCKIMVRGKGS 251
Cdd:pfam00013   1 TVEILVPSS------LVGLIIGKGGSNIKEIREETGAKIQIPPSES 40

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 17507875 204 SITEKIYVPKNEYPDYNFVGRILGPRGMTAKQLEQDTGCKIMVRGKGSMRDKSKESAHRGKANWEHLEDDLHVLVQCEDT 283
Cdd:cd22383   1 KLSEKVYVPVDEYPDYNFVGRILGPRGMTAKQLEQDTGCKIMIRGKGSMRDKKKEEANRGKPNWEHLNDDLHVLITVEDT 80

                        90       100
                ....*....|....*....|.
gi 17507875 284 ENRVHIKLQAALEQVKKLLIP 304
Cdd:cd22383  81 ENRAHIKLAKAVEEVKKLLIP 101

type I K homology (KH) RNA-binding domain found in protein quaking (Hqk) and similar proteins; 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.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17507875 205 ITEKIYVPKNEYPDYNFVGRILGPRGMTAKQLEQDTGCKIMVRGKGSMRDKSKESAHRGKANWEHLEDDLHVLVQCEDTE 284
Cdd:cd22465   2 LQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHLNEDLHVLITVEDAQ 81

                        90       100
                ....*....|....*....|..
gi 17507875 285 NRVHIKLQAALEQVKKLLIPAP 306
Cdd:cd22465  82 NRAEIKLKRAVEEVKKLLVPAA 103

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 17507875 206 TEKIYVPKNEYPDYNFVGRILGPRGMTAKQLEQDTGCKIMVRGKGSmrdkSKESAHRGKANWE-HLEDDLHVLVqCEDTE 284
Cdd:cd02395   3 QRKIYIPVDEYPDYNFIGLIIGPRGNTQKRMEKESGAKIAIRGKGS----VKEGKGRSDPQPDpDEEEDLHVLI-TADTE 77

                        90
                ....*....|....*....
gi 17507875 285 NrvhiKLQAALEQVKKLLI 303
Cdd:cd02395  78 E----KVDKAAKLIEKLLI 92

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        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17507875 203 ISITEKIYVPKNEYPDYNFVGRILGPRGMTAKQLEQDTGCKIMVRGKGSMRDKSKESAHR--GKANWEHLEDDLHVLVQC 280
Cdd:cd22468   3 MKLKERILIPVKQYPKFNFVGKILGPQGNTIKRLQEETGAKISVLGKGSMRDKAKEEELRkgGDPKYAHLNMDLHVFIEV 82

                        90       100
                ....*....|....*....|....
gi 17507875 281 EDTENRVHIKLQAALEQVKKLLIP 304
Cdd:cd22468  83 FGPPCEAYARMAHAMEEVKKFLVP 106

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

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17507875 172 RLLDDEIGRVRVAlfQTEFPRVELPEPAGDMISITEKIYVPKNEYPDYNFVGRILGPRGMTAKQLEQDTGCKIMVRGKGS 251
Cdd:COG5176 117 KLEDERLWLKERA--QKILPRFVLPNDYIRPSKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSGS 194

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 17507875 252 mrDKSKESAHRGKANWEHLEDDLHVLVQ--CEDTENRVhIKLQaalEQVKKLLIPAPEGTDELKRKQLMELAIINGTYR 328
Cdd:COG5176 195 --VKEGKISSDTPESLKNAEAVLHCLIEadSEDKICRL-IKSQ---LNAIREARRNPEGQNDLKRFQLRWLAHLNGTLR 267

type I K homology (KH) RNA-binding domain found in splicing factor 1 (SF1) and similar proteins; SF1, also called branch point-binding protein, or BBP, or transcription factor ZFM1, or zinc finger gene in MEN1 locus, or zinc finger protein 162, is necessary for the ATP-dependent first step of spliceosome assembly. Binds to the intron branch point sequence (BPS) 5'-UACUAAC-3' of the pre-mRNA. It may act as transcription repressor.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17507875 205 ITEKIYVPKNEYPDYNFVGRILGPRGMTAKQLEQDTGCKIMVRGKGSMRDKskeSAHRGKANWEHLEDD-LHVLVQCEDT 283
Cdd:cd22382   2 VSDKVMIPQEEYPDINFVGLLIGPRGNTLKKIEKETGAKIMIRGKGSVKEG---KVGRKDGQPLPGEDEpLHALVTANTA 78

                        90
                ....*....|....*....
gi 17507875 284 ENrvhikLQAALEQVKKLL 302
Cdd:cd22382  79 ES-----VKKAVDKIKEII 92

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 17507875 205 ITEKIYVP-KNEYPDYNFVGRILGPRGMTAKQLEQDTGCKIMVRGKGSmrdKSKESAHRGKAnwehlEDDLHVLVQCEDT 283
Cdd:cd22386   3 YQEKVFVGlEHAPPGFNVRGKLIGPGGSNVKHIQQETGAKVQLRGKGS---GFIEPASGREA-----DEPLHLLISHPDP 74

                        90
                ....*....|....*....
gi 17507875 284 EnrvhiKLQAALEQVKKLL 302
Cdd:cd22386  75 E-----GLQQAKKLCEDLL 88

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
                ....*....|....*....|....*....|....*....|....*
gi 17507875 207 EKIYVPKNeypdynFVGRILGPRGMTAKQLEQDTGCKIMVRGKGS 251
Cdd:cd00105   1 EEIEVPSE------LVGLIIGKGGSTIKEIEEETGARIQIPKEGE 39

first type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding proteins; The far upstream element-binding protein (FUBP) family includes FUBP1-3. FUBP1, also called FBP, or FUSE-binding protein 1, or DNA helicase V, or DH V, binds RNA and single-stranded DNA (ssDNA) and may act both as activator and repressor of transcription. It regulates MYC expression by binding to a single-stranded far-upstream element (FUSE) upstream of the MYC promoter. FUBP2, also called FUSE-binding protein 2, or KH type-splicing regulatory protein (KSRP), or p75, is a single-strand nucleic acid binding protein implicated in a variety of cellular processes, including splicing in the nucleus, mRNA decay, maturation of miRNA, and transcriptional control of proto-oncogenes such as c-myc. It regulates the stability and/or translatability of many mRNA species, encoding immune-relevant proteins, either by binding to AU-rich elements (AREs) of mRNA 3'UTR or by facilitating miRNA biogenesis to target mRNA. FUBP3, also called FUSE-binding protein 3, or MARTA2, was previously shown to mediate dendritic targeting of MAP2 mRNA in neurons. It may interact with single-stranded DNA from the far-upstream element (FUSE) and activate gene expression. It is required for beta-actin mRNA localization. It also interacts with fibroblast growth factor 9 (FGF9) 3'-UTR UG repeats and positively controls FGF9 expression through increasing translation of FGF9 mRNA. FUBP proteins contain four K-homology (KH) RNA-binding domains. The model corresponds to the first one.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|..
gi 17507875 205 ITEKIYVPKNeypdynFVGRILGPRGMTAKQLEQDTGCKIMV 246
Cdd:cd22396   1 VTEEYKVPDK------MVGLIIGRGGEQINRLQAESGAKIQI 36

type I K homology (KH) RNA-binding domain found in mitochondrial A-kinase anchor protein 1 (AKAP1) and similar proteins; AKAP1, also called A-kinase anchor protein 149 kDa, or AKAP 149, or dual specificity A-kinase-anchoring protein 1, or D-AKAP-1, or protein kinase A-anchoring protein 1 (PRKA1), or spermatid A-kinase anchor protein 84, or S-AKAP84, is a novel developmentally regulated A kinase anchor protein of male germ cells. It binds to type I and II regulatory subunits of protein kinase A and anchors them to the cytoplasmic face of the mitochondrial outer membrane.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|..
gi 17507875 206 TEKIYVPKNEypdynfVGRILGPRGMTAKQLEQDTGCKIMVR 247
Cdd:cd22395   1 VYEFEVPSEL------VGRLIGKQGRNVKQLKQKSGAKIYIK 36