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SIX3 SIX homeobox 3 [ Homo sapiens (human) ]

Gene ID: 6496, updated on 15-Jun-2021

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
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Genomic context

See SIX3 in Genome Data Viewer
Location:
2p21
Exon count:
2
Annotation release Status Assembly Chr Location
109.20210514 current GRCh38.p13 (GCF_000001405.39) 2 NC_000002.12 (44941702..44946071)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (45168841..45173210)

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

Associated conditions

Description Tests
Anophthalmia-microphthalmia syndrome
MedGen: CN120488 GeneReviews: Not available
Compare labs
Genome-wide association meta-analysis identifies novel variants associated with fasting plasma glucose in East Asians.
GeneReviews: Not available
Genome-wide search for replicable risk gene regions in alcohol and nicotine co-dependence.
GeneReviews: Not available
Holoprosencephaly 2
MedGen: C1834877 OMIM: 157170 GeneReviews: Holoprosencephaly Overview
Compare labs
Large-scale genome-wide association studies in East Asians identify new genetic loci influencing metabolic traits.
GeneReviews: Not available
Schizencephaly
MedGen: C0266484 OMIM: 269160 GeneReviews: Not available
Compare labs

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated 2020-09-23)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated 2020-09-23)

ClinGen Genome Curation PagePubMed

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • AC012354.6

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in apoptotic process involved in development ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in brain development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in cell proliferation in forebrain ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in epithelial cell maturation ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in eye development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in eye development IDA
Inferred from Direct Assay
more info
PubMed 
involved_in forebrain dorsal/ventral pattern formation IDA
Inferred from Direct Assay
more info
PubMed 
involved_in lens development in camera-type eye ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in lens fiber cell apoptotic process ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in lens fiber cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in negative regulation of neuron differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in negative regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
involved_in neuroblast differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in neuroblast migration ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in optic vesicle morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in pituitary gland development ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in positive regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
involved_in proximal/distal axis specification ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in regulation of cell cycle phase transition ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in regulation of cell population proliferation ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in regulation of neural precursor cell proliferation ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in regulation of neural retina development ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in regulation of neuroblast proliferation ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in telencephalon development ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in telencephalon regionalization ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in visual perception TAS
Traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
located_in chromatin ISA
Inferred from Sequence Alignment
more info
 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
part_of transcription regulator 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)

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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 109.20210514

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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