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UniProtKB/Swiss-Prot entry Q8N196


[Entry info] [Name and origin] [References] [Comments] [Cross-references] [Keywords] [Features] [Sequence] [Tools]

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Entry information
Entry name SIX5_HUMAN
Primary accession number Q8N196
Secondary accession numbers None
Integrated into Swiss-Prot on April 13, 2004
Sequence was last modified on June 26, 2007 (Sequence version 3)
Annotations were last modified on    November 25, 2008 (Entry version 54)
Name and origin of the protein
Protein name Homeobox protein SIX5
Synonym DM locus-associated homeodomain protein
Gene name
Name: SIX5
Synonyms: DMAHP
From
Homo sapiens (Human) [TaxID: 9606] 
Taxonomy Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo.
Protein existence 1: Evidence at protein level;
References
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
DOI=10.1093/hmg/4.10.1919; PubMed=8595416 [NCBI, ExPASy, EBI, Israel, Japan]
Boucher C.A., King S.K., Carey N., Krahe R., Winchester C.L., Rahman S., Creavin T., Meghji P., Bailey M.E., Chartier F.L., Brown S.D., Sicilliano M.J., Johnson K.J.;
"A novel homeodomain-encoding gene is associated with a large CpG island interrupted by the myotonic dystrophy unstable (CTG)n repeat.";
Hum. Mol. Genet. 4:1919-1925(1995).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
DOI=10.1038/nature02399; PubMed=15057824 [NCBI, ExPASy, EBI, Israel, Japan]
Grimwood J., Gordon L.A., Olsen A.S., Terry A., Schmutz J., Lamerdin J.E., Hellsten U., Goodstein D., Couronne O., Tran-Gyamfi M., Aerts A., Altherr M., Ashworth L., Bajorek E., Black S., Branscomb E., Caenepeel S., Carrano A.V., Caoile C., Chan Y.M., Christensen M., Cleland C.A., Copeland A., Dalin E., Dehal P., Denys M., Detter J.C., Escobar J., Flowers D., Fotopulos D., Garcia C., Georgescu A.M., Glavina T., Gomez M., Gonzales E., Groza M., Hammon N., Hawkins T., Haydu L., Ho I., Huang W., Israni S., Jett J., Kadner K., Kimball H., Kobayashi A., Larionov V., Leem S.-H., Lopez F., Lou Y., Lowry S., Malfatti S., Martinez D., McCready P.M., Medina C., Morgan J., Nelson K., Nolan M., Ovcharenko I., Pitluck S., Pollard M., Popkie A.P., Predki P., Quan G., Ramirez L., Rash S., Retterer J., Rodriguez A., Rogers S., Salamov A., Salazar A., She X., Smith D., Slezak T., Solovyev V., Thayer N., Tice H., Tsai M., Ustaszewska A., Vo N., Wagner M., Wheeler J., Wu K., Xie G., Yang J., Dubchak I., Furey T.S., DeJong P., Dickson M., Gordon D., Eichler E.E., Pennacchio L.A., Richardson P., Stubbs L., Rokhsar D.S., Myers R.M., Rubin E.M., Lucas S.M.;
"The DNA sequence and biology of human chromosome 19.";
Nature 428:529-535(2004).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
TISSUE=Eye;
DOI=10.1101/gr.2596504; PubMed=15489334 [NCBI, ExPASy, EBI, Israel, Japan]
The MGC Project Team;
"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).";
Genome Res. 14:2121-2127(2004).
[4]
RECONSTRUCTION FROM GENOMIC SEQUENCE AND ESTS, AND CONCEPTUAL TRANSLATION OF 5-184 (ISOFORM 1).
Roechert B.;
Unpublished observations (JAN-2004).
[5]
NUCLEOTIDE SEQUENCE OF 74-290 (ISOFORM 1).
The MGC Project Team;
Submitted (OCT-2002) to the EMBL/GenBank/DDBJ databases.
[6]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 185-739 (ISOFORM 1).
DOI=10.1038/ng1285; PubMed=14702039 [NCBI, ExPASy, EBI, Israel, Japan]
Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S., Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.;
"Complete sequencing and characterization of 21,243 full-length human cDNAs.";
Nat. Genet. 36:40-45(2004).
[7]
TISSUE SPECIFICITY.
DOI=10.1093/hmg/8.3.481; PubMed=9949207 [NCBI, ExPASy, EBI, Israel, Japan]
Winchester C.L., Ferrier R.K., Sermoni A., Clark B.J., Johnson K.J.;
"Characterization of the expression of DMPK and SIX5 in the human eye and implications for pathogenesis in myotonic dystrophy.";
Hum. Mol. Genet. 8:481-492(1999).
[8]
DNA-BINDING.
DOI=10.1093/nar/28.9.1871; PubMed=10756185 [NCBI, ExPASy, EBI, Israel, Japan]
Harris S.E., Winchester C.L., Johnson K.J.;
"Functional analysis of the homeodomain protein SIX5.";
Nucleic Acids Res. 28:1871-1878(2000).
[9]
SUBCELLULAR LOCATION, AND DEVELOPMENTAL STAGE.
DOI=10.1023/A:1020990825644; PubMed=12500905 [NCBI, ExPASy, EBI, Israel, Japan]
Fougerousse F., Durand M., Lopez S., Suel L., Demignon J., Thornton C., Ozaki H., Kawakami K., Barbet P., Beckmann J.S., Maire P.;
"Six and Eya expression during human somitogenesis and MyoD gene family activation.";
J. Muscle Res. Cell Motil. 23:255-264(2002).
[10]
VARIANTS BOR2 THR-158; THR-296; ARG-365 AND MET-552, AND CHARACTERIZATION OF VARIANTS BOR2 THR-158 AND MET-552.
DOI=10.1086/513322; PubMed=17357085 [NCBI, ExPASy, EBI, Israel, Japan]
Hoskins B.E., Cramer C.H., Silvius D., Zou D., Raymond R.M., Orten D.J., Kimberling W.J., Smith R.J.H., Weil D., Petit C., Otto E.A., Xu P.-X., Hildebrandt F.;
"Transcription factor SIX5 is mutated in patients with branchio-oto-renal syndrome.";
Am. J. Hum. Genet. 80:800-804(2007).
Comments
  • FUNCTION: Transcription factor that is thought to be involved in regulation of organogenesis. May be involved in determination and maintenance of retina formation. Binds a 5'-GGTGTCAG-3' motif present in the ARE regulatory element of ATP1A1. Binds a 5'-TCA[AG][AG]TTNC-3' motif present in the MEF3 element in the myogenin promoter, and in the IGFBP5 promoter (By similarity). Thought to be regulated by association with Dach and Eya proteins, and seems to be coactivated by EYA1, EYA2 and EYA3 (By similarity).
  • SUBUNIT: Probably binds DNA dimer. Interacts with EYA3, and probably EYA1 and EYA2 (By similarity).
  • INTERACTION:
    P54253:ATXN1; NbExp=1; IntAct=EBI-946167, EBI-930964;
  • SUBCELLULAR LOCATION: Cytoplasm. Nucleus.
  • ALTERNATIVE PRODUCTS: 2 named isoforms [FASTA] produced by alternative splicing.
    Name1
    Isoform IDQ8N196-1
    This is the isoform sequence displayed in this entry.
    Name2
    Isoform IDQ8N196-2
    Features which should be applied to build the isoform sequence: VSP_010072.
  • TISSUE SPECIFICITY: Expressed in adult but not in fetal eyes. Found in corneal epithelium and endothelium, lens epithelium, ciliary body epithelia, cellular layers of the retina and the sclera.
  • DEVELOPMENTAL STAGE: At the begin of fourth week of development detected in cytoplasm of somite cells, and at the end of fourth week is accumulated in the nucleus. Between the sixth and eighth week of development detected in the nucleus of limb bud cells.
  • DISEASE: Defects in SIX5 are the cause of branchiootorenal syndrome type 2 (BOR2) [MIM:610896]. BOR is an autosomal dominant disorder manifested by various combinations of preauricular pits, branchial fistulae or cysts, lacrimal duct stenosis, hearing loss, structural defects of the outer, middle, or inner ear, and renal dysplasia. Associated defects include asthenic habitus, long narrow facies, constricted palate, deep overbite, and myopia. Hearing loss may be due to mondini type cochlear defect and stapes fixation. Penetrance of BOR syndrome is high, although expressivity can be extremely variable.
  • SIMILARITY: Belongs to the SIX/Sine oculis homeobox family.
  • SIMILARITY: Contains 1 homeobox DNA-binding domain.
  • CAUTION: The region from 1 to 184 was deduced from the genomic sequence and ESTs.
Copyright
Copyrighted by the UniProt Consortium, see http://www.uniprot.org/terms. Distributed under the Creative Commons Attribution-NoDerivs License.
Cross-references
Sequence databases
EMBL
X84813; -; NOT_ANNOTATED_CDS; Genomic_DNA.[EMBL / GenBank / DDBJ]
AC074212; -; NOT_ANNOTATED_CDS; Genomic_DNA.[EMBL / GenBank / DDBJ]
BC033204; AAH33204.1; -; mRNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
BU859227; -; NOT_ANNOTATED_CDS; mRNA.[EMBL / GenBank / DDBJ]
AK074826; -; NOT_ANNOTATED_CDS; mRNA.[EMBL / GenBank / DDBJ]
UniGene Hs.43314
3D structure databases
ModBase Q8N196.
Protein-protein interaction databases
IntAct Q8N196; -.
PTM databases
PhosphoSite Q8N196; -.
Organism-specific databases
H-InvDB HIX0015240; -.
HGNC HGNC:10891; SIX5.
GenAtlas SIX5.
MIM 600963; gene. [NCBI / EBI]
610896; phenotype. [NCBI / EBI]
Orphanet 107; BOR syndrome.
PharmGKB PA35791; -.
GeneCards Q8N196.
Gene expression databases
ArrayExpress Q8N196; -.
CleanEx HS_SIX5; -.
GermOnline ENSG00000177045; Homo sapiens.
Ontologies
GO
GO:0005737; Cellular component: cytoplasm (inferred from electronic annotation from UniProtKB-KW).
GO:0005634; Cellular component: nucleus (inferred from electronic annotation from InterPro).
GO:0005515; Molecular function: protein binding (inferred from physical interaction from IntAct).
GO:0043565; Molecular function: sequence-specific DNA binding (inferred from electronic annotation from InterPro).
GO:0003700; Molecular function: transcription factor activity (inferred from electronic annotation from InterPro).
GO:0007275; Biological process: multicellular organismal development (inferred from electronic annotation from UniProtKB-KW).
GO:0006355; Biological process: regulation of transcription, DNA-dependent (inferred from electronic annotation from InterPro).
GO:0007605; Biological process: sensory perception of sound (inferred from electronic annotation from UniProtKB-KW).
QuickGo view.
Family and domain databases
InterPro IPR001356; Homeobox.
IPR012287; Homeodomain-rel.
Graphical view of domain structure.
Gene3D G3DSA:1.10.10.60; Homeodomain-rel; 1.
Pfam PF00046; Homeobox; 1.
Pfam graphical view of domain structure.
ProDom PD000010; Homeobox; 1.
[Domain structure / List of seq. sharing at least 1 domain]
SMART SM00389; HOX; 1.
SMART graphical view of domain structure.
PROSITE PS00027; HOMEOBOX_1; 1.
PS50071; HOMEOBOX_2; 1.
PROSITE graphical view of domain structure (profiles).
ProtoNet Q8N196.
Genome annotation databases
Ensembl ENSG00000177045; Homo sapiens. [Contig view]
NMPDR fig|9606.3.peg.16708; -.
Phylogenomic databases
HOGENOM Q8N196; -.
HOVERGEN Q8N196; -.
Other
SOURCE SIX5; Homo sapiens.
UniRef View cluster of proteins with at least 50% / 90% / 100% identity.
Keywords
Activator; Alternative splicing; Cytoplasm; Deafness; Developmental protein; Disease mutation; DNA-binding; Homeobox; Nucleus; Polymorphism; Transcription; Transcription regulation.
Features
SEVIEWER logo Feature table viewer FT aligner logo Feature aligner
KeyFrom   To Length Description FTId
CHAIN   1   739  739     Homeobox protein SIX5. PRO_0000049305
DNA_BIND   201   260  60     Homeobox. 
VAR_SEQ   4   584        Missing (in isoform 2). VSP_010072
VARIANT   158   158  1     A -> T (in BOR2; affects Eya1 binding and the ability to activate gene transcription). VAR_032941 
VARIANT   296   296  1     A -> T (in BOR2). VAR_032942 
VARIANT   365   365  1     G -> R (in BOR2). VAR_032943 
VARIANT   552   552  1     T -> M (in BOR2; affects Eya1 binding and the ability to activate gene transcription). VAR_032944 
VARIANT   556   556  1     L -> V (in dbSNP:rs2014377 [NCBI]). VAR_032945 
VARIANT   635   635  1     P -> S (in dbSNP:rs2014576 [NCBI]). VAR_032946 
VARIANT   693   693  1     V -> M (in dbSNP:rs2341097 [NCBI]). VAR_032947 
CONFLICT   691   691        H -> HT (in Ref. 1). 
CONFLICT   721   721        Missing (in Ref. 6). 
Sequence information
Length: 739 AA [This is the length of the unprocessed precursor] Molecular weight: 74562 Da [This is the MW of the unprocessed precursor] CRC64: D8A2E8DBBBA263A2 [This is a checksum on the sequence]
        10         20         30         40         50         60 
MATLPAEPSA GPAAGGEAVA AAAATEEEEE EARQLLQTLQ AAEGEAAAAA GAGAGAAAAG 

        70         80         90        100        110        120 
AEGPGSPGVP GSPPEAASEP PTGLRFSPEQ VACVCEALLQ AGHAGRLSRF LGALPPAERL 

       130        140        150        160        170        180 
RGSDPVLRAR ALVAFQRGEY AELYRLLESR PFPAAHHAFL QDLYLRARYH EAERARGRAL 

       190        200        210        220        230        240 
GAVDKYRLRK KFPLPKTIWD GEETVYCFKE RSRAALKACY RGNRYPTPDE KRRLATLTGL 

       250        260        270        280        290        300 
SLTQVSNWFK NRRQRDRTGA GGGAPCKSES DGNPTTEDES SRSPEDLERG AAPVSAEAAA 

       310        320        330        340        350        360 
QGSIFLAGTG PPAPCPASSS ILVNGSFLAA SGSPAVLLNG GPVIINGLAL GEASSLGPLL 

       370        380        390        400        410        420 
LTGGGGAPPP QPSPQGASET KTSLVLDPQT GEVRLEEAQS EAPETKGAQV AAPGPALGEE 

       430        440        450        460        470        480 
VLGPLAQVVP GPPTAATFPL PPGPVPAVAA PQVVPLSPPP GYPTGLSPTS PLLNLPQVVP 

       490        500        510        520        530        540 
TSQVVTLPQA VGPLQLLAAG PGSPVKVAAA AGPANVHLIN SGVGVTALQL PSATAPGNFL 

       550        560        570        580        590        600 
LANPVSGSPI VTGVALQQGK IILTATFPTS MLVSQVLPPA PGLALPLKPE TAISVPEGGL 

       610        620        630        640        650        660 
PVAPSPALPE AHALGTLSAQ QPPPAAATTS STSLPFSPDS PGLLPNFPAP PPEGLMLSPA 

       670        680        690        700        710        720 
AVPVWSAGLE LSAGTEGLLE AEKGLGTQAP HTVLRLPDPD PEGLLLGATA GGEVDEGLEA 

       730 
EAKVLTQLQS VPVEEPLEL 

Q8N196 in FASTA format

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