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 15224909    29 SSQYLTELLAEHQKLTPFMQVLPICSRLLNQEMFRVSGMMSNQGFGD 75
Cdd:pfam16544   5 TPDYLAQLLKDKKQLAAFPNVFPHLERLLDEEISRVRGDLFNKGFGD 51

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

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15224909  82 RSPSPMASSNLMSNVSNTGLGGWNG-LSQER--LSGTPGMTMDWQGAPG---SPSSYTVKrilrLEIPVDNYPNFNFVGR 155
Cdd:COG5176  92 RSPSPPPRYDEIGRRLNTREARYNKkLEDERlwLKERAQKILPRFVLPNdyiRPSKYQNK----IYIPVQEYPESNFVGL 167

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15224909 156 LLGPRGNSLKRVEATTGCRVFIRGKGSIKdpEKEDKLRGRPGYEHLNEQLHILIEADLPASIVEIRLRQAQEIIEELLKP 235
Cdd:COG5176 168 LIGPRGSTLKQLERISRAKIAIRGSGSVK--EGKISSDTPESLKNAEAVLHCLIEADSEDKICRLIKSQLNAIREARRNP 245

                       170       180
                ....*....|....*....|....*..
gi 15224909 236 vdESQDFIKRQQLRELALLNSnNLREE 262
Cdd:COG5176 246 --EGQNDLKRFQLRWLAHLNG-TLRAD 269

K homology RNA-binding domain;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15224909    135 KRILRLEIPVdnypnfNFVGRLLGPRGNSLKRVEATTGCRVFIRGKGSikdPEKEDKLRGRP 196
Cdd:smart00322   2 PVTIEVLIPA------DKVGLIIGKGGSTIKKIEEETGVKIDIPGPGS---EERVVEITGPP 54

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 15224909 135 KRILRLEIPVDNYPNFNFVGRLLGPRGNSLKRVEATTGCRVFIRGKGSIKDPEKEDKLRGRPGYEHLNEQLHILIEADLP 214
Cdd:cd22383   1 KLSEKVYVPVDEYPDYNFVGRILGPRGMTAKQLEQDTGCKIMIRGKGSMRDKKKEEANRGKPNWEHLNDDLHVLITVEDT 80

                        90       100
                ....*....|....*....|.
gi 15224909 215 ASIVEIRLRQAQEIIEELLKP 235
Cdd:cd22383  81 ENRAHIKLAKAVEEVKKLLIP 101

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        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15224909 133 TVKRILRLEIPVDNYPNFNFVGRLLGPRGNSLKRVEATTGCRVFIRGKGSIKDPEKEDKLR--GRPGYEHLNEQLHILIE 210
Cdd:cd22384   2 PIKLSEKVLIPVKEFPKFNFVGKLLGPRGNTLKRLQEETGTKMSILGKGSMRDKAKEEELRksGDPKYAHLNEDLHVLIE 81

                .
gi 15224909 211 A 211
Cdd:cd22384  82 A 82

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 15224909 135 KRILRLEIPVDNYPNFNFVGRLLGPRGNSLKRVEATTGCRVFIRGKGSIKDPEKEDKLRGRPGyehLNEQLHILIEADLP 214
Cdd:cd02395   1 KKQRKIYIPVDEYPDYNFIGLIIGPRGNTQKRMEKESGAKIAIRGKGSVKEGKGRSDPQPDPD---EEEDLHVLITADTE 77

                        90
                ....*....|....*....
gi 15224909 215 ASIveirlRQAQEIIEELL 233
Cdd:cd02395  78 EKV-----DKAAKLIEKLL 91

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 15224909 130 SSYTVKRILRLEIPVDNYPNFNFVGRLLGPRGNSLKRVEATTGCRVFIRGKGSIKDPEKEDKLR--GRPGYEHLNEQLHI 207
Cdd:cd22469   1 SNKNIKLSERVLIPVKQYPKFNFVGKLLGPRGNSLKRLQEETGAKMSILGKGSMRDKAKEEELRksGEAKYAHLSDELHV 80

                        90       100       110       120
                ....*....|....*....|....*....|....*....|
gi 15224909 208 LIEADLPASIVEIRLRQAQEIIEELLKPvdESQDFIKRQQ 247
Cdd:cd22469  81 LIEVFAPPGEAYSRMSHALEEIKKFLVP--DYNDEIRQEQ 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        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15224909 142 IPVDNYPNFNFVGRLLGPRGNSLKRVEATTGCRVFIRGKGSIKDPEKEDKLR--GRPGYEHLNEQLHILIEADLPASIVE 219
Cdd:cd22470  15 IPVKQFPKFNFVGKLLGPRGNSLKRLQEETLTKMSILGKGSMRDKAKEEELRksGEAKYFHLNDDLHVLIEVFAPPAEAY 94

                        90
                ....*....|....*.
gi 15224909 220 IRLRQAQEIIEELLKP 235
Cdd:cd22470  95 ARMGHALEEIKKFLIP 110

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 15224909 139 RLEIPVDNY-PNFNFVGRLLGPRGNSLKRVEATTGCRVFIRGKGSikdpekeDKLRGRPGYEHlNEQLHILIEADLPASi 217
Cdd:cd22386   6 KVFVGLEHApPGFNVRGKLIGPGGSNVKHIQQETGAKVQLRGKGS-------GFIEPASGREA-DEPLHLLISHPDPEG- 76

                        90       100       110
                ....*....|....*....|....*....|
gi 15224909 218 veirLRQAQEIIEELLKPVdeSQDFIKRQQ 247
Cdd:cd22386  77 ----LQQAKKLCEDLLQTV--HQEYGEFQQ 100

second type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana protein RIK and similar proteins; RIK, also called rough sheath 2-interacting KH domain protein, or RS2-interacting KH domain protein, is a RNA binding protein that acts together with RS2/AS1 in the recruitment of HIRA. RIK contains two type I K homology (KH) RNA-binding domains. The model corresponds to the second one.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 15224909 144 VDNYPNFNFVGRLLGPRGNSLKRVEATTGCRVFIRGKGSIKDPEKEDklrgrpgyehlneQLHILIEADLPASIVEIR 221
Cdd:cd22472  11 IEAPPSFNLAGRIRGPNNSYLQHIASATGATVALRGRGSGGAPEGPE-------------PLHLFLSASDPKALEEAR 75

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
                ....*....|....*....|....*....|....*....|....*....|.
gi 15224909 138 LRLEIPVDnypnfnFVGRLLGPRGNSLKRVEATTGCRVFIRGKGSIKDPEK 188
Cdd:cd00105   1 EEIEVPSE------LVGLIIGKGGSTIKEIEEETGARIQIPKEGEGSGERV 45

second type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1) and similar proteins; IGF2BP1, also called IGF2 mRNA-binding protein 1 (IMP-1), or coding region determinant-binding protein (CRD-BP), or IGF-II mRNA-binding protein 1, or VICKZ family member 1 (VICKZ1), or zipcode-binding protein 1 (ZBP-1), is an RNA-binding factor that recruits target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It functions by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. It regulates localized beta-actin/ACTB mRNA translation, a crucial process for cell polarity, cell migration and neurite outgrowth. IGF2BP1 can form homodimers and heterodimers with IGF2BP1 and IGF2BP3. It contains four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the second one.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15224909 141 EIPVDNYPNFNFVGRLLGPRGNSLKRVEATTGCRVFIRG---------------KGSIKD---PEKEDKLRGRPGYEH-- 200
Cdd:cd22493   4 EVPLKILAHNNFVGRLIGKEGRNLKKVEQDTETKITISPlqdltlynpertitvKGSIEAccrAEQEIMKKVREAYENdv 83

                        90
                ....*....|
gi 15224909 201 --LNEQLHIL 208
Cdd:cd22493  84 aaMNLQSHLI 93