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 281362255 132 GSVVTMNEKVYVPVREHPDFNFVGRILGPRGMTAKQLEQETGCKIMVRGKGSMRDKKKEDANRGKPNWEHLSDDLHVLIT 211
Cdd:cd22466    1 GPSVTLSEKVYVPVKEHPDYNFVGRILGPRGMTAKQLEQETGCKIMVRGKGSMRDKKKEDLNRGKPNWEHLNDELHVLIT 80

                         90       100
                 ....*....|....*....|....*
gi 281362255 212 VEDTENRATVKLAQAVAEVQKLLVP 236
Cdd:cd22466   81 VEDTENRAKVKLQRAVEEVRKLLVP 105

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 281362255 132 GSVVTMNEKVYVPVREHPDFNFVGRILGPRGMTAKQLEQETGCKIMVRGKGSMRDKKKEDANRGKPNWEHLSDDLHVLIT 211
Cdd:cd22466    1 GPSVTLSEKVYVPVKEHPDYNFVGRILGPRGMTAKQLEQETGCKIMVRGKGSMRDKKKEDLNRGKPNWEHLNDELHVLIT 80

                         90       100
                 ....*....|....*....|....*
gi 281362255 212 VEDTENRATVKLAQAVAEVQKLLVP 236
Cdd:cd22466   81 VEDTENRAKVKLQRAVEEVRKLLVP 105

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 281362255   75 IADYLAQLLKDRKQLAAFPNVFTHVERLLDEEIARVRASLFQINGVKK 122
Cdd:pfam16544   5 TPDYLAQLLKDKKQLAAFPNVFPHLERLLDEEISRVRGDLFNKGFGDK 52

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

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 281362255  139 EKVYVPVRehpdfnFVGRILGPRGMTAKQLEQETGCKIMVRGKGS 183
Cdd:pfam00013   2 VEILVPSS------LVGLIIGKGGSNIKEIREETGAKIQIPPSES 40

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 281362255 132 GSVVTMNEKVYVPVREHPDFNFVGRILGPRGMTAKQLEQETGCKIMVRGKGSMRDKKKEDANRGKPNWEHLSDDLHVLIT 211
Cdd:cd22466    1 GPSVTLSEKVYVPVKEHPDYNFVGRILGPRGMTAKQLEQETGCKIMVRGKGSMRDKKKEDLNRGKPNWEHLNDELHVLIT 80

                         90       100
                 ....*....|....*....|....*
gi 281362255 212 VEDTENRATVKLAQAVAEVQKLLVP 236
Cdd:cd22466   81 VEDTENRAKVKLQRAVEEVRKLLVP 105

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 281362255 136 TMNEKVYVPVREHPDFNFVGRILGPRGMTAKQLEQETGCKIMVRGKGSMRDKKKEDANRGKPNWEHLSDDLHVLITVEDT 215
Cdd:cd22465    1 QLQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHLNEDLHVLITVEDA 80

                         90       100
                 ....*....|....*....|...
gi 281362255 216 ENRATVKLAQAVAEVQKLLVPQA 238
Cdd:cd22465   81 QNRAEIKLKRAVEEVKKLLVPAA 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 281362255 138 NEKVYVPVREHPDFNFVGRILGPRGMTAKQLEQETGCKIMVRGKGSMRDKKKEDANRGKPNWEhlsDDLHVLITVEDTEn 217
Cdd:cd02395    3 QRKIYIPVDEYPDYNFIGLIIGPRGNTQKRMEKESGAKIAIRGKGSVKEGKGRSDPQPDPDEE---EDLHVLITADTEE- 78

                         90
                 ....*....|....*...
gi 281362255 218 ratvKLAQAVAEVQKLLV 235
Cdd:cd02395   79 ----KVDKAAKLIEKLLI 92

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 281362255 143 VPVREHPDFNFVGRILGPRGMTAKQLEQETGCKIMVRGKGSMRDKKKEDANRGKPNWEHLSDDLHVLITVEDTENRATVK 222
Cdd:cd22467    8 VPVDKYPNFNFVGRILGPRGNSLKRVEATTGCRVFIRGRGSIKDTAKEEKLRDKPGYEHLNEPLHVLIEAELPANIIDAR 87

                         90
                 ....*....|....
gi 281362255 223 LAQAVAEVQKLLVP 236
Cdd:cd22467   88 LQHAQEIIEDLLKP 101

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362255 139 EKVYVPVREHPDFNFVGRILGPRGMTAKQLEQETGCKIMVRGKGSmrDKKKEDANRGKPNWEHLSDDLHVLIT--VEDTE 216
Cdd:COG5176  150 NKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSGS--VKEGKISSDTPESLKNAEAVLHCLIEadSEDKI 227

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 281362255 217 NRATVKLAQAVAEVQKllVPqaEGEDELKKRQLMELAIINGTYRD 261
Cdd:COG5176  228 CRLIKSQLNAIREARR--NP--EGQNDLKRFQLRWLAHLNGTLRA 268

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 281362255   75 IADYLAQLLKDRKQLAAFPNVFTHVERLLDEEIARVRASLFQINGVKK 122
Cdd:pfam16544   5 TPDYLAQLLKDKKQLAAFPNVFPHLERLLDEEISRVRGDLFNKGFGDK 52

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 281362255 139 EKVYVPV-REHPDFNFVGRILGPRGMTAKQLEQETGCKIMVRGKGSmrdKKKEDANRGKPNwehlsDDLHVLITVEDTEn 217
Cdd:cd22386    5 EKVFVGLeHAPPGFNVRGKLIGPGGSNVKHIQQETGAKVQLRGKGS---GFIEPASGREAD-----EPLHLLISHPDPE- 75

                         90
                 ....*....|....*..
gi 281362255 218 ratvKLAQAVAEVQKLL 234
Cdd:cd22386   76 ----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 281362255 139 EKVYVPVrehpdfNFVGRILGPRGMTAKQLEQETGCKIMVRGKGS 183
Cdd:cd00105    1 EEIEVPS------ELVGLIIGKGGSTIKEIEEETGARIQIPKEGE 39

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

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 281362255  139 EKVYVPVRehpdfnFVGRILGPRGMTAKQLEQETGCKIMVRGKGS 183
Cdd:pfam00013   2 VEILVPSS------LVGLIIGKGGSNIKEIREETGAKIQIPPSES 40

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 281362255 137 MNEKVYVPVRehpdfnFVGRILGPRGMTAKQLEQETGCKIMV 178
Cdd:cd22396    1 VTEEYKVPDK------MVGLIIGRGGEQINRLQAESGAKIQI 36

first type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH domain-containing protein PEPPER and similar proteins; The family includes a group of plant RNA-binding KH domain-containing proteins, such as PEPPER, flowering locus K homology domain protein (FLK), RNA-binding KH domain-containing protein RCF3 and KH domain-containing protein HEN4. PEPPER regulates vegetative and gynoecium development. It acts as a positive regulator of the central floral repressor FLOWERING LOCUS C. In concert with HUA2, PEPPER antagonizes FLK by positively regulating FLC probably at transcriptional and post-transcriptional levels, and thus acts as a negative regulator of flowering. FLK, also called flowering locus KH domain protein, regulates positively flowering by repressing FLC expression and post-transcriptional modification. PEPPER and FLK contain three K-homology (KH) RNA-binding domains. RCF3, also called protein ENHANCED STRESS RESPONSE 1 (ESR1), or protein HIGH OSMOTIC STRESS GENE EXPRESSION 5 (HOS5), or protein REGULATOR OF CBF GENE EXPRESSION 3, or protein SHINY 1 (SHI1), acts as negative regulator of osmotic stress-induced gene expression. It is involved in the regulation of thermotolerance responses under heat stress. It functions as an upstream regulator of heat stress transcription factor (HSF) genes. HEN4, also called protein HUA ENHANCER 4, plays a role in floral reproductive organ identity in the third whorl and floral determinacy specification by specifically promoting the processing of AGAMOUS (AG) pre-mRNA. It functions in association with HUA1 and HUA2. RCF3 and HEN4 contain five KH RNA-binding domains. The model corresponds to the KH1 domain of PEPPER and FLK, as well as KH1 and KH3 domains of RCF3 and HEN4.

                         10        20
                 ....*....|....*....|....*
gi 281362255 154 VGRILGPRGMTAKQLEQETGCKIMV 178
Cdd:cd22459   13 AGSVIGKGGEIIKQLRQETGARIKV 37

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
                 ....*....|....*....|....*...
gi 281362255 152 NFVGRILGPRGMTAKQLEQETGCKIMVR 179
Cdd:cd22395    9 ELVGRLIGKQGRNVKQLKQKSGAKIYIK 36