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SIX3 SIX homeobox 3 [ Homo sapiens (human) ]

Gene ID: 6496, updated on 1-Jun-2020

Summary

Official Symbol
SIX3provided by HGNC
Official Full Name
SIX homeobox 3provided by HGNC
Primary source
HGNC:HGNC:10889
See related
Ensembl:ENSG00000138083 MIM:603714
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
HPE2
Summary
This gene encodes a member of the sine oculis homeobox transcription factor family. The encoded protein plays a role in eye development. Mutations in this gene have been associated with holoprosencephaly type 2. [provided by RefSeq, Oct 2009]
Expression
Low expression observed in reference dataset See more
Orthologs

Genomic context

See SIX3 in Genome Data Viewer
Location:
2p21
Exon count:
2
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 2 NC_000002.12 (44941702..44946071)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (45169037..45173216)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene VISTA enhancer hs149 Neighboring gene long intergenic non-protein coding RNA 1833 Neighboring gene SIX3 antisense RNA 1 Neighboring gene keratinocyte-associated protein 2-like Neighboring gene KRTCAP2 pseudogene 1 Neighboring gene SIX homeobox 2

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 Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated (2011-11-07)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated (2011-11-07)

ClinGen Genome Curation PagePubMed

NHGRI GWAS Catalog

Description
Genome-wide association meta-analysis identifies novel variants associated with fasting plasma glucose in East Asians.
NHGRI GWA Catalog
Genome-wide search for replicable risk gene regions in alcohol and nicotine co-dependence.
NHGRI GWA Catalog
Large-scale genome-wide association studies in East Asians identify new genetic loci influencing metabolic traits.
NHGRI GWA Catalog

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • AC012354.6

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA-binding transcription activator activity, RNA polymerase II-specific IEA
Inferred from Electronic Annotation
more info
 
DNA-binding transcription factor activity ISS
Inferred from Sequence or Structural Similarity
more info
 
DNA-binding transcription factor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 
RNA polymerase II proximal promoter sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
histone deacetylase binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
signaling receptor binding IEA
Inferred from Electronic Annotation
more info
 
transcription coactivator activity ISS
Inferred from Sequence or Structural Similarity
more info
 
transcription corepressor binding IPI
Inferred from Physical Interaction
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 
apoptotic process involved in development ISS
Inferred from Sequence or Structural Similarity
more info
 
brain development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cell proliferation in forebrain ISS
Inferred from Sequence or Structural Similarity
more info
 
circadian behavior IEA
Inferred from Electronic Annotation
more info
 
epithelial cell maturation ISS
Inferred from Sequence or Structural Similarity
more info
 
eye development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
eye development IDA
Inferred from Direct Assay
more info
PubMed 
forebrain anterior/posterior pattern specification IEA
Inferred from Electronic Annotation
more info
 
forebrain dorsal/ventral pattern formation IDA
Inferred from Direct Assay
more info
PubMed 
lens development in camera-type eye ISS
Inferred from Sequence or Structural Similarity
more info
 
lens fiber cell apoptotic process ISS
Inferred from Sequence or Structural Similarity
more info
 
lens fiber cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
lens induction in camera-type eye IEA
Inferred from Electronic Annotation
more info
 
negative regulation of Wnt signaling pathway IEA
Inferred from Electronic Annotation
more info
 
negative regulation of neuron differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of transcription, DNA-templated IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
neuroblast differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
neuroblast migration ISS
Inferred from Sequence or Structural Similarity
more info
 
optic vesicle morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
pituitary gland development ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
protein import into nucleus IEA
Inferred from Electronic Annotation
more info
 
proximal/distal axis specification ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of cell cycle phase transition ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of cell proliferation ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of neural precursor cell proliferation ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of neural retina development ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of neuroblast proliferation ISS
Inferred from Sequence or Structural Similarity
more info
 
telencephalon development ISS
Inferred from Sequence or Structural Similarity
more info
 
telencephalon regionalization ISS
Inferred from Sequence or Structural Similarity
more info
 
visual perception TAS
Traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
nuclear chromatin ISA
Inferred from Sequence Alignment
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
transcription factor complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
homeobox protein SIX3
Names
sine oculis homeobox homolog 3
sine oculis homeobox-like protein 3
truncated SIX3

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_016222.1 RefSeqGene

    Range
    4805..9174
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_005413.4NP_005404.1  homeobox protein SIX3

    See identical proteins and their annotated locations for NP_005404.1

    Status: REVIEWED

    Source sequence(s)
    AC012354, AJ012611, BF570321, CD673488, EL952320
    Consensus CDS
    CCDS1821.1
    UniProtKB/Swiss-Prot
    O95343
    Related
    ENSP00000260653.3, ENST00000260653.5
    Conserved Domains (2) summary
    cd00086
    Location:208256
    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:87200
    SIX1_SD; Transcriptional regulator, SIX1, N-terminal SD domain

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p13 Primary Assembly

    Range
    44941702..44946071
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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