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SIX1 SIX homeobox 1 [ Homo sapiens (human) ]

Gene ID: 6495, updated on 16-Sep-2018

Summary

Official Symbol
SIX1provided by HGNC
Official Full Name
SIX homeobox 1provided by HGNC
Primary source
HGNC:HGNC:10887
See related
Ensembl:ENSG00000126778 MIM:601205; Vega:OTTHUMG00000140334
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
BOS3; TIP39; DFNA23
Summary
The protein encoded by this gene is a homeobox protein that is similar to the Drosophila 'sine oculis' gene product. This gene is found in a cluster of related genes on chromosome 14 and is thought to be involved in limb development. Defects in this gene are a cause of autosomal dominant deafness type 23 (DFNA23) and branchiootic syndrome type 3 (BOS3). [provided by RefSeq, Jul 2008]
Expression
Biased expression in salivary gland (RPKM 12.9), prostate (RPKM 9.2) and 6 other tissues See more
Orthologs

Genomic context

See SIX1 in Genome Data Viewer
Location:
14q23.1
Exon count:
2
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 14 NC_000014.9 (60644699..60649489, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (61111417..61116155, complement)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105378189 Neighboring gene ribosomal protein S15a pseudogene 4 Neighboring gene senescence associated long non-coding RNA 1 Neighboring gene VISTA enhancer hs1602 Neighboring gene SIX homeobox 4

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

Copy number response

Description
Copy number response
Haploinsufficency

No evidence available (Last evaluated (2012-03-22)

ClinGen Genome Curation Page
Triplosensitivity

No evidence available (Last evaluated (2012-03-22)

ClinGen Genome Curation Page

NHGRI GWAS Catalog

Description
A genome-wide association study in the Japanese population confirms 9p21 and 14q23 as susceptibility loci for primary open angle glaucoma.
NHGRI GWA Catalog
A genome-wide association study of optic disc parameters.
NHGRI GWA Catalog
A meta-analysis of 87,040 individuals identifies 23 new susceptibility loci for prostate cancer.
NHGRI GWA Catalog
Common variants at 9p21 and 8q22 are associated with increased susceptibility to optic nerve degeneration in glaucoma.
NHGRI GWA Catalog
Genome-wide association identifies ATOH7 as a major gene determining human optic disc size.
NHGRI GWA Catalog
Meta-analysis of genome-wide association studies identifies novel loci that influence cupping and the glaucomatous process.
NHGRI GWA Catalog

Pathways from BioSystems

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
DNA-binding transcription factor activity IDA
Inferred from Direct Assay
more info
PubMed 
DNA-binding transcription factor activity ISS
Inferred from Sequence or Structural Similarity
more info
 
DNA-binding transcription factor activity, RNA polymerase II-specific ISA
Inferred from Sequence Alignment
more info
 
DNA-binding transcription factor activity, RNA polymerase II-specific ISM
Inferred from Sequence Model
more info
PubMed 
DNA-binding transcription factor activity, RNA polymerase II-specific NAS
Non-traceable Author Statement
more info
PubMed 
RNA polymerase II proximal promoter sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
RNA polymerase II proximal promoter sequence-specific DNA binding IMP
Inferred from Mutant Phenotype
more info
PubMed 
chromatin binding IEA
Inferred from Electronic Annotation
more info
 
distal enhancer DNA-binding transcription activator activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
proximal promoter DNA-binding transcription activator activity, RNA polymerase II-specific IDA
Inferred from Direct Assay
more info
PubMed 
proximal promoter DNA-binding transcription activator activity, RNA polymerase II-specific IMP
Inferred from Mutant Phenotype
more info
PubMed 
sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
transcription coactivator binding IEA
Inferred from Electronic Annotation
more info
 
transcription regulatory region DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
transcription regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
anatomical structure development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
aorta morphogenesis IEA
Inferred from Electronic Annotation
more info
 
apoptotic process IEA
Inferred from Electronic Annotation
more info
 
branching involved in ureteric bud morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
cell proliferation IEA
Inferred from Electronic Annotation
more info
 
cellular response to 3,3',5-triiodo-L-thyronine IEA
Inferred from Electronic Annotation
more info
 
cochlea morphogenesis IEA
Inferred from Electronic Annotation
more info
 
embryonic cranial skeleton morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
embryonic skeletal system morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
epithelial cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
facial nerve morphogenesis IEA
Inferred from Electronic Annotation
more info
 
fungiform papilla morphogenesis IEA
Inferred from Electronic Annotation
more info
 
generation of neurons ISS
Inferred from Sequence or Structural Similarity
more info
 
inner ear development ISS
Inferred from Sequence or Structural Similarity
more info
 
inner ear morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
kidney development ISS
Inferred from Sequence or Structural Similarity
more info
 
mesonephric tubule formation ISS
Inferred from Sequence or Structural Similarity
more info
 
metanephric mesenchyme development ISS
Inferred from Sequence or Structural Similarity
more info
 
middle ear morphogenesis IEA
Inferred from Electronic Annotation
more info
 
myoblast migration ISS
Inferred from Sequence or Structural Similarity
more info
 
myotome development IEA
Inferred from Electronic Annotation
more info
 
negative regulation of branching involved in ureteric bud morphogenesis IEA
Inferred from Electronic Annotation
more info
 
negative regulation of neuron apoptotic process ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
negative regulation of transcription, DNA-templated IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
neuron fate specification IEA
Inferred from Electronic Annotation
more info
 
olfactory placode formation IEA
Inferred from Electronic Annotation
more info
 
organ induction ISS
Inferred from Sequence or Structural Similarity
more info
 
otic vesicle development IEA
Inferred from Electronic Annotation
more info
 
outflow tract morphogenesis IEA
Inferred from Electronic Annotation
more info
 
pattern specification process ISS
Inferred from Sequence or Structural Similarity
more info
 
pharyngeal system development IEA
Inferred from Electronic Annotation
more info
 
positive regulation of branching involved in ureteric bud morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of mesenchymal cell proliferation involved in ureter development IEA
Inferred from Electronic Annotation
more info
 
positive regulation of secondary heart field cardioblast proliferation IEA
Inferred from Electronic Annotation
more info
 
positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of transcription, DNA-templated ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of ureteric bud formation ISS
Inferred from Sequence or Structural Similarity
more info
 
protein localization to nucleus IDA
Inferred from Direct Assay
more info
PubMed 
regulation of branch elongation involved in ureteric bud branching ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of epithelial cell proliferation IEA
Inferred from Electronic Annotation
more info
 
regulation of neuron differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of protein localization IEA
Inferred from Electronic Annotation
more info
 
regulation of skeletal muscle cell differentiation IEA
Inferred from Electronic Annotation
more info
 
regulation of skeletal muscle satellite cell proliferation IEA
Inferred from Electronic Annotation
more info
 
regulation of synaptic growth at neuromuscular junction IEA
Inferred from Electronic Annotation
more info
 
regulation of transcription, DNA-templated ISS
Inferred from Sequence or Structural Similarity
more info
 
sensory perception of sound IEA
Inferred from Electronic Annotation
more info
 
skeletal muscle tissue development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
skeletal muscle tissue development ISS
Inferred from Sequence or Structural Similarity
more info
 
thymus development ISS
Inferred from Sequence or Structural Similarity
more info
 
thyroid gland development ISS
Inferred from Sequence or Structural Similarity
more info
 
transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
trigeminal ganglion development IEA
Inferred from Electronic Annotation
more info
 
ureter smooth muscle cell differentiation IEA
Inferred from Electronic Annotation
more info
 
ureteric bud development ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
cytoplasm IEA
Inferred from Electronic Annotation
more info
 
nucleolus IDA
Inferred from Direct Assay
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
transcription factor complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
transcription factor complex ISS
Inferred from Sequence or Structural Similarity
more info
 

General protein information

Preferred Names
homeobox protein SIX1
Names
sine oculis homeobox homolog 1

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_008231.1 RefSeqGene

    Range
    5001..9739
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_005982.3NP_005973.1  homeobox protein SIX1

    See identical proteins and their annotated locations for NP_005973.1

    Status: REVIEWED

    Source sequence(s)
    AL049874, BC008874, X91868
    Consensus CDS
    CCDS9748.1
    UniProtKB/Swiss-Prot
    Q15475
    Related
    ENSP00000494686.1, OTTHUMP00000179042, ENST00000645694.1, OTTHUMT00000276951
    Conserved Domains (2) summary
    cd00086
    Location:129180
    homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
    pfam16878
    Location:9118
    SIX1_SD; Transcriptional regulator, SIX1, N-terminal SD domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000014.9 Reference GRCh38.p12 Primary Assembly

    Range
    60644699..60649489 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017021602.2XP_016877091.1  homeobox protein SIX1 isoform X1

    Conserved Domains (2) summary
    pfam16878
    Location:9118
    SIX1_SD; Transcriptional regulator, SIX1, N-terminal SD domain
    cl00084
    Location:142167
    homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
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