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        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 11527388    10 KPKPTPDYLMQLMNDKKLMSSLPNfcgIFNHLERLLDEEISRVRKDMYNDTLNGS 64
Cdd:pfam16544   1 KPRSTPDYLAQLLKDKKQLAAFPN---VFPHLERLLDEEISRVRGDLFNKGFGDK 52

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

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527388  83 QEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRD-KKKEEQNRGKPNWEhlnEDLHVLIT--VED 159
Cdd:COG5176 149 QNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSGSVKEgKISSDTPESLKNAE---AVLHCLIEadSED 225

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*..
gi 11527388 160 AQNRAEIKLKRAVEEVKKllVPaaEGEDSLKKMQLMELAILNGTYRD 206
Cdd:COG5176 226 KICRLIKSQLNAIREARR--NP--EGQNDLKRFQLRWLAHLNGTLRA 268

K homology RNA-binding domain;

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 11527388     81 QLQEKLYVPVkeypdfNFVGRILGPRGLTAKQLEAETGCKIMVRGKGS 128
Cdd:smart00322   2 PVTIEVLIPA------DKVGLIIGKGGSTIKKIEEETGVKIDIPGPGS 43

DNA polymerase III subunits gamma and tau; Provisional

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 11527388  210 KSPALAFSLAATAQAAPRIITGPAPVLPPAALRTPTPAGPT-IMPLIRQIQTAVMPNGTPHPTAAIVPPGPEA 281
Cdd:PRK14951 379 KTPARPEAAAPAAAPVAQAAAAPAPAAAPAAAASAPAAPPAaAPPAPVAAPAAAAPAAAPAAAPAAVALAPAP 451

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 11527388  81 QLQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHLNEDLHVLITVEDA 160
Cdd:cd22383   1 KLSEKVYVPVDEYPDYNFVGRILGPRGMTAKQLEQDTGCKIMIRGKGSMRDKKKEEANRGKPNWEHLNDDLHVLITVEDT 80

                        90       100
                ....*....|....*....|.
gi 11527388 161 QNRAEIKLKRAVEEVKKLLVP 181
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 11527388  80 VQLQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQ--NRGKPNWEHLNEDLHVLITV 157
Cdd:cd22384   3 IKLSEKVLIPVKEFPKFNFVGKLLGPRGNTLKRLQEETGTKMSILGKGSMRDKAKEEElrKSGDPKYAHLNEDLHVLIEA 82

                        90       100
                ....*....|....*....|
gi 11527388 158 EDAQNRAEIKLKRAVEEVKK 177
Cdd:cd22384  83 FAPPAEAYARLAHALAELRK 102

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 11527388  80 VQLQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNR--GKPNWEHLNEDLHVLITV 157
Cdd:cd22468   3 MKLKERILIPVKQYPKFNFVGKILGPQGNTIKRLQEETGAKISVLGKGSMRDKAKEEELRkgGDPKYAHLNMDLHVFIEV 82

                        90       100
                ....*....|....*....|....
gi 11527388 158 EDAQNRAEIKLKRAVEEVKKLLVP 181
Cdd:cd22468  83 FGPPCEAYARMAHAMEEVKKFLVP 106

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 11527388  80 VQLQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNR--GKPNWEHLNEDLHVLITV 157
Cdd:cd22469   5 IKLSERVLIPVKQYPKFNFVGKLLGPRGNSLKRLQEETGAKMSILGKGSMRDKAKEEELRksGEAKYAHLSDELHVLIEV 84

                        90       100
                ....*....|....*....|....
gi 11527388 158 EDAQNRAEIKLKRAVEEVKKLLVP 181
Cdd:cd22469  85 FAPPGEAYSRMSHALEEIKKFLVP 108

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 11527388  81 QLQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNR--GKPNWEHLNEDLHVLITVE 158
Cdd:cd22470   8 KLGQKVLIPVKQFPKFNFVGKLLGPRGNSLKRLQEETLTKMSILGKGSMRDKAKEEELRksGEAKYFHLNDDLHVLIEVF 87

                        90       100
                ....*....|....*....|...
gi 11527388 159 DAQNRAEIKLKRAVEEVKKLLVP 181
Cdd:cd22470  88 APPAEAYARMGHALEEIKKFLIP 110

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 11527388  82 LQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKeeQNRGKPNWEHLNEDLHVLITVEDAQ 161
Cdd:cd22382   2 VSDKVMIPQEEYPDINFVGLLIGPRGNTLKKIEKETGAKIMIRGKGSVKEGKV--GRKDGQPLPGEDEPLHALVTANTAE 79

                        90
                ....*....|....*...
gi 11527388 162 NraeikLKRAVEEVKKLL 179
Cdd:cd22382  80 S-----VKKAVDKIKEII 92

K homology RNA-binding domain;

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 11527388     81 QLQEKLYVPVkeypdfNFVGRILGPRGLTAKQLEAETGCKIMVRGKGS 128
Cdd:smart00322   2 PVTIEVLIPA------DKVGLIIGKGGSTIKKIEEETGVKIDIPGPGS 43

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        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527388  86 LYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMrdKKKEEQnrgkpnwehlnEDLHVLITVEDAqnrae 165
Cdd:cd22472   7 LYVGIEAPPSFNLAGRIRGPNNSYLQHIASATGATVALRGRGSG--GAPEGP-----------EPLHLFLSASDP----- 68

                        90
                ....*....|...
gi 11527388 166 iklkRAVEEVKKL 178
Cdd:cd22472  69 ----KALEEARGL 77

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
                ....*....|....*....|....*....|
gi 11527388  94 PDfNFVGRILGPRGLTAKQLEAETGCKIMV 123
Cdd:cd22396   8 PD-KMVGLIIGRGGEQINRLQAESGAKIQI 36

second type I K homology (KH) RNA-binding domain found in KRR1 small subunit processome component and similar proteins; KRR1, also called HIV-1 Rev-binding protein 2, or KRR-R motif-containing protein 1, or Rev-interacting protein 1, or Rip-1, or ribosomal RNA assembly protein KRR1, is a nucleolar protein required for 40S ribosome biogenesis. It is involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly. KRR1 contains two K-homology (KH) RNA-binding domains. The model corresponds to the second one.

                        10        20
                ....*....|....*....|....*.
gi 11527388 101 RILGPRGLTAKQLEAETGCKIMVRGK 126
Cdd:cd22394  24 RLIGPNGSTLKAIELLTKCYILVQGN 49