Format

Send to:

Choose Destination

SIX6 SIX homeobox 6 [ Homo sapiens (human) ]

Gene ID: 4990, updated on 17-May-2020

Summary

Official Symbol
SIX6provided by HGNC
Official Full Name
SIX homeobox 6provided by HGNC
Primary source
HGNC:HGNC:10892
See related
Ensembl:ENSG00000184302 MIM:606326
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
Six9; ODRMD; OPTX2; MCOPCT2
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 eye development. Defects in this gene are a cause of isolated microphthalmia with cataract type 2 (MCOPCT2). [provided by RefSeq, Jul 2008]
Expression
Low expression observed in reference dataset See more
Orthologs

Genomic context

See SIX6 in Genome Data Viewer
Location:
14q23.1
Exon count:
2
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 14 NC_000014.9 (60509146..60512850)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (60975938..60978525)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene GNRHR2 pseudogene 1 Neighboring gene RNA binding motif protein 8B pseudogene Neighboring gene chromosome 14 open reading frame 39 Neighboring gene spalt like transcription factor 4 pseudogene 7 Neighboring gene vomeronasal 1 receptor 59 pseudogene Neighboring gene ribosomal protein L37 pseudogene 5

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
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
Common variants at 9p21 and 8q22 are associated with increased susceptibility to optic nerve degeneration in glaucoma.
NHGRI GWA Catalog
Common variants near ABCA1, AFAP1 and GMDS confer risk of primary open-angle glaucoma.
NHGRI GWA Catalog
Genome-wide meta-analyses of multiancestry cohorts identify multiple new susceptibility loci for refractive error and myopia.
NHGRI GWA Catalog
Hundreds of variants clustered in genomic loci and biological pathways affect human height.
NHGRI GWA Catalog
Meta-analysis of genome-wide association studies identifies novel loci that influence cupping and the glaucomatous process.
NHGRI GWA Catalog
Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel loci.
NHGRI GWA Catalog
Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche.
NHGRI GWA Catalog

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Process Evidence Code Pubs
anatomical structure development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
animal organ morphogenesis TAS
Traceable Author Statement
more info
PubMed 
eye development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative regulation of transcription, DNA-templated IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
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 SIX6
Names
homeodomain protein OPTX2
optic homeobox 2
sine oculis homeobox homolog 6
sine oculis homeobox protein 6
sine oculis homeobox-like protein 6

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_008203.1 RefSeqGene

    Range
    4927..8631
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_007374.3NP_031400.2  homeobox protein SIX6

    See identical proteins and their annotated locations for NP_031400.2

    Status: REVIEWED

    Source sequence(s)
    AL049874, BC065831
    Consensus CDS
    CCDS9747.1
    UniProtKB/Swiss-Prot
    O95475
    UniProtKB/TrEMBL
    Q6P051
    Related
    ENSP00000328596.5, ENST00000327720.6
    Conserved Domains (2) summary
    cd00086
    Location:130178
    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:9122
    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_000014.9 Reference GRCh38.p13 Primary Assembly

    Range
    60509146..60512850
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Support Center