Tyrosine-rich domain of Sam68; Sam68-YY is a short tyrosine-rich domain on Src-associated in mitosis, 68 kDa protein (Sam68), a protein that regulates TCF-1 alternative splicing. It is a crucial binding-partner of the APC-Arm domain that forms a superhelix with a positively charged groove, the surface-residues of which groove form numerous interactions with Sam68-YY to fix it in a bent conformation. APC-Arm is the armadillo repeat domain of the tumour-suppressor protein adenomatous polyposis coli or APC. APC plays plays important roles in Wnt signalling and other cellular processes.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 18875400   267 YEEYGYDDGYGGEYDDQTYEAYDNSYVTPTQSVPEYYDYGHGVNEDAYDSYAPEE 321
Cdd:pfam16568   1 YEEYGYDDGYGGEYDEQSYESYDNSYYSQAQSDPEYYDYGHGESQESYDSYGQEE 55

Tyrosine-rich domain of Sam68; Sam68-YY is a short tyrosine-rich domain on Src-associated in mitosis, 68 kDa protein (Sam68), a protein that regulates TCF-1 alternative splicing. It is a crucial binding-partner of the APC-Arm domain that forms a superhelix with a positively charged groove, the surface-residues of which groove form numerous interactions with Sam68-YY to fix it in a bent conformation. APC-Arm is the armadillo repeat domain of the tumour-suppressor protein adenomatous polyposis coli or APC. APC plays plays important roles in Wnt signalling and other cellular processes.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 18875400   267 YEEYGYDDGYGGEYDDQTYEAYDNSYVTPTQSVPEYYDYGHGVNEDAYDSYAPEE 321
Cdd:pfam16568   1 YEEYGYDDGYGGEYDEQSYESYDNSYYSQAQSDPEYYDYGHGESQESYDSYGQEE 55

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

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18875400  59 KLSERVLIPVKQYPKFNFVGKLLGPRGNSLKRLQEETGAKMSILGKGSMrdktKEEELRKSGEAKYAHLSDELHVLIEVF 138
Cdd:COG5176 147 KYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSGSV----KEGKISSDTPESLKNAEAVLHCLIEAD 222

                        90       100       110       120
                ....*....|....*....|....*....|....*....|...
gi 18875400 139 APPGEAYSRMSHALEEIKKFLVPDYNDEIRQEQLRELSYLNGS 181
Cdd:COG5176 223 SEDKICRLIKSQLNAIREARRNPEGQNDLKRFQLRWLAHLNGT 265

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

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 18875400    61 SERVLIPVKQypkfnfVGKLLGPRGNSLKRLQEETGAKMSILGKGS 106
Cdd:pfam00013   1 TVEILVPSSL------VGLIIGKGGSNIKEIREETGAKIQIPPSES 40

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 18875400  56 KNIKLSERVLIPVKQYPKFNFVGKLLGPRGNSLKRLQEETGAKMSILGKGSMRDKTKEEELRKSGEAKYAHLSDELHVLI 135
Cdd:cd22384   1 KPIKLSEKVLIPVKEFPKFNFVGKLLGPRGNTLKRLQEETGTKMSILGKGSMRDKAKEEELRKSGDPKYAHLNEDLHVLI 80

                        90       100
                ....*....|....*....|..
gi 18875400 136 EVFAPPGEAYSRMSHALEEIKK 157
Cdd:cd22384  81 EAFAPPAEAYARLAHALAELRK 102

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 18875400  52 VISNKNIKLSERVLIPVKQYPKFNFVGKLLGPRGNSLKRLQEETGAKMSILGKGSMRDKTKEEELRKSGEAKYAHLSDEL 131
Cdd:cd22470   1 VVINKNMKLGQKVLIPVKQFPKFNFVGKLLGPRGNSLKRLQEETLTKMSILGKGSMRDKAKEEELRKSGEAKYFHLNDDL 80

                        90       100       110
                ....*....|....*....|....*....|...
gi 18875400 132 HVLIEVFAPPGEAYSRMSHALEEIKKFLVPDYN 164
Cdd:cd22470  81 HVLIEVFAPPAEAYARMGHALEEIKKFLIPDYN 113

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 18875400  58 IKLSERVLIPVKQYPKFNFVGKLLGPRGNSLKRLQEETGAKMSILGKGSMRDKTKEEELRksGEAKYAHLSDELHVLIEV 137
Cdd:cd22466   4 VTLSEKVYVPVKEHPDYNFVGRILGPRGMTAKQLEQETGCKIMVRGKGSMRDKKKEDLNR--GKPNWEHLNDELHVLITV 81

                        90       100
                ....*....|....*....|....
gi 18875400 138 FAPPGEAYSRMSHALEEIKKFLVP 161
Cdd:cd22466  82 EDTENRAKVKLQRAVEEVRKLLVP 105

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 18875400  59 KLSERVLIPVKQYPKFNFVGKLLGPRGNSLKRLQEETGAKMSILGKGSMRDKTKEEELRksGEAKYAHLSDELHVLIEVF 138
Cdd:cd22467   1 KKVLRLDVPVDKYPNFNFVGRILGPRGNSLKRVEATTGCRVFIRGRGSIKDTAKEEKLR--DKPGYEHLNEPLHVLIEAE 78

                        90       100
                ....*....|....*....|...
gi 18875400 139 APPGEAYSRMSHALEEIKKFLVP 161
Cdd:cd22467  79 LPANIIDARLQHAQEIIEDLLKP 101

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 18875400  59 KLSERVLIPVKQYPKFNFVGKLLGPRGNSLKRLQEETGAKMSILGKGSMRDKTKEEELRKSGEAkyahlSDELHVLIEvf 138
Cdd:cd02395   1 KKQRKIYIPVDEYPDYNFIGLIIGPRGNTQKRMEKESGAKIAIRGKGSVKEGKGRSDPQPDPDE-----EEDLHVLIT-- 73

                        90       100
                ....*....|....*....|..
gi 18875400 139 appGEAYSRMSHALEEIKKFLV 160
Cdd:cd02395  74 ---ADTEEKVDKAAKLIEKLLI 92

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 18875400  59 KLSERVLIPVKQYPKFNFVGKLLGPRGNSLKRLQEETGAKMSILGKGSmrdkTKEEELRKSGEAKYAHLSDELHVLI 135
Cdd:cd22382   1 RVSDKVMIPQEEYPDINFVGLLIGPRGNTLKKIEKETGAKIMIRGKGS----VKEGKVGRKDGQPLPGEDEPLHALV 73

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 18875400  59 KLSERVLIPVKQYPK-FNFVGKLLGPRGNSLKRLQEETGAKMSILGKGSmrdKTKEEElrkSGEAkyahlSDE-LHVLIE 136
Cdd:cd22386   2 YYQEKVFVGLEHAPPgFNVRGKLIGPGGSNVKHIQQETGAKVQLRGKGS---GFIEPA---SGRE-----ADEpLHLLIS 70

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 18875400  62 ERVLIPVKqypkfnFVGKLLGPRGNSLKRLQEETGAKMSILGKGS 106
Cdd:cd00105   1 EEIEVPSE------LVGLIIGKGGSTIKEIEEETGARIQIPKEGE 39

second type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2) and similar proteins; IGF2BP2, also called IGF2 mRNA-binding protein 2 (IMP-2), or hepatocellular carcinoma autoantigen p62, or IGF-II mRNA-binding protein 2, or VICKZ family member 2 (VICKZ2), 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 also binds to beta-actin/ACTB and MYC transcripts. IGF2BP2 can form homooligomers and heterooligomers with IGF2BP1 and IGF2BP3 in an RNA-dependent manner. 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
                ....*....|....*....|....*....|....*....|....*
gi 18875400  67 PVKQYPKFNFVGKLLGPRGNSLKRLQEETGAKMSIlgkGSMRDKT 111
Cdd:cd22494   1 PLKILAHNSLVGRLIGKEGRNLKKIEQDTGTKITI---SSLQDLT 42

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
                ....*....|....*....|....*....|....*.
gi 18875400  66 IPVKQYPKFNFVGKLLGPRGNSLKRLQEETGAKMSI 101
Cdd:cd22493   5 VPLKILAHNNFVGRLIGKEGRNLKKVEQDTETKITI 40

third type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the third one.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|
gi 18875400  62 ERVLIPVkqypkfNFVGKLLGPRGNSLKRLQEETGAKMSI 101
Cdd:cd22407   2 ERLDIPK------VYHPFIAGPNNENVKELQEETGVRINI 35

third type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ventral antigen (Nova); The family includes two related neuronal RNA-binding proteins, Nova-1 and Nova-2. Nova-1, also called onconeural ventral antigen 1, or paraneoplastic Ri antigen, or ventral neuron-specific protein 1, may regulate RNA splicing or metabolism in a specific subset of developing neurons. It interacts with RNA containing repeats of the YCAY sequence. It is a brain-enriched splicing factor regulating neuronal alternative splicing. Nova-1 is involved in neurological disorders and carcinogenesis. Nova-2, also called astrocytic NOVA1-like RNA-binding protein, is a neuronal RNA-binding protein expressed in a broader central nervous system (CNS) distribution than Nova-1. It functions in neuronal RNA metabolism. NOVA family proteins contain three K-homology (KH) RNA-binding domains. The model corresponds to the third one.

                        10        20        30
                ....*....|....*....|....*....|.
gi 18875400  75 NFVGKLLGPRGNSLKRLQEETGAKMSILGKG 105
Cdd:cd09031  10 NLVGAILGKGGKTLVEIQELTGARIQISKKG 40

second type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 3 (FUBP3) and similar proteins; 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. FUBP3 contains four K-homology (KH) RNA-binding domains. The model corresponds to the second one.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 18875400  62 ERVLIPVKQypkfnfVGKLLGPRGNSLKRLQEETGAKMSILGKGSMrDKTKEEELRKSGEAKYAHLSDELHVLI 135
Cdd:cd22483   7 QEILIPASK------VGLVIGKGGETIKQLQERTGVKMIMIQDGPL-PTGADKPLRITGDPFKVQQAREMVLEI 73