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SIX2 SIX homeobox 2 [ Homo sapiens (human) ]

Gene ID: 10736, updated on 1-Aug-2020

Summary

Official Symbol
SIX2provided by HGNC
Official Full Name
SIX homeobox 2provided by HGNC
Primary source
HGNC:HGNC:10888
See related
Ensembl:ENSG00000170577 MIM:604994
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
Summary
This gene is a member of the vertebrate gene family which encode proteins homologous to the Drosophila 'sine oculis' homeobox protein. The encoded protein is a transcription factor which, like other members of this gene family, may be involved in limb or eye development. [provided by RefSeq, Dec 2008]
Expression
Biased expression in salivary gland (RPKM 4.1), prostate (RPKM 2.7) and 4 other tissues See more
Orthologs

Genomic context

See SIX2 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 (45005182..45009645, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (45232324..45236580, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene SIX3 antisense RNA 1 Neighboring gene SIX homeobox 3 Neighboring gene keratinocyte-associated protein 2-like Neighboring gene KRTCAP2 pseudogene 1 Neighboring gene uncharacterized LOC107985809 Neighboring gene long intergenic non-protein coding RNA 1121 Neighboring gene uncharacterized LOC105374576

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

NHGRI GWAS Catalog

Description
Genome-wide association meta-analysis identifies novel variants associated with fasting plasma glucose in East Asians.
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

Gene Ontology Provided by GOA

Process Evidence Code Pubs
anatomical structure development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
anatomical structure morphogenesis TAS
Traceable Author Statement
more info
PubMed 
anterior/posterior axis specification ISS
Inferred from Sequence or Structural Similarity
more info
 
cell migration IDA
Inferred from Direct Assay
more info
PubMed 
cell proliferation IDA
Inferred from Direct Assay
more info
PubMed 
chondrocyte differentiation IEA
Inferred from Electronic Annotation
more info
 
condensed mesenchymal cell proliferation IEA
Inferred from Electronic Annotation
more info
 
embryonic cranial skeleton morphogenesis IEA
Inferred from Electronic Annotation
more info
 
embryonic digestive tract morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
kidney development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
kidney development IMP
Inferred from Mutant Phenotype
more info
PubMed 
kidney development ISS
Inferred from Sequence or Structural Similarity
more info
 
mesenchymal cell differentiation involved in kidney development ISS
Inferred from Sequence or Structural Similarity
more info
 
mesenchymal stem cell maintenance involved in nephron morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
mesenchymal stem cell proliferation ISS
Inferred from Sequence or Structural Similarity
more info
 
mesenchymal to epithelial transition involved in metanephros morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
mesodermal cell fate specification ISS
Inferred from Sequence or Structural Similarity
more info
 
middle ear morphogenesis IEA
Inferred from Electronic Annotation
more info
 
negative regulation of cell differentiation IEA
Inferred from Electronic Annotation
more info
 
negative regulation of transcription, DNA-templated IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nephron development ISS
Inferred from Sequence or Structural Similarity
more info
 
nephron morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of chondrocyte proliferation 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
 
regulation of branching involved in ureteric bud morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of chondrocyte differentiation IEA
Inferred from Electronic Annotation
more info
 
regulation of ossification IEA
Inferred from Electronic Annotation
more info
 
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 SIX2
Names
sine oculis homeobox homolog 2

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_009360.1 RefSeqGene

    Range
    4952..9222
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_016932.5NP_058628.3  homeobox protein SIX2

    See identical proteins and their annotated locations for NP_058628.3

    Status: REVIEWED

    Source sequence(s)
    AC012354, AF332197, AI299144, AI697804, BC024033
    Consensus CDS
    CCDS1822.1
    UniProtKB/Swiss-Prot
    Q9NPC8
    UniProtKB/TrEMBL
    Q8TBA2
    Related
    ENSP00000304502.6, ENST00000303077.7
    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 109.20200522

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
    45005182..45009645 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005264100.3XP_005264157.1  homeobox protein SIX2 isoform X1

    See identical proteins and their annotated locations for XP_005264157.1

    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
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