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SIX2 SIX homeobox 2 [ Homo sapiens (human) ]

Gene ID: 10736, updated on 10-Dec-2024

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; AllianceGenome:HGNC:10888
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
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Genomic context

See SIX2 in Genome Data Viewer
Location:
2p21
Exon count:
2
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (45005182..45009452, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (45010408..45014884, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (45232321..45236591, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:45169884-45170608 Neighboring gene NANOG hESC enhancer GRCh37_chr2:45172898-45173404 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11435 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11436 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:45182266-45182972 Neighboring gene SIX3 antisense RNA 1 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:45199471-45200338 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:45202291-45203066 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:45203067-45203842 Neighboring gene SIX homeobox 3 Neighboring gene keratinocyte-associated protein 2-like Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:45227219-45228192 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:45233469-45234012 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:45232925-45233468 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:45235286-45236059 Neighboring gene KRTCAP2 pseudogene 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:45237064-45237663 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:45239927-45240747 Neighboring gene NANOG hESC enhancer GRCh37_chr2:45261729-45262230 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:45266703-45267902 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:45291852-45292470 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:45298897-45299398 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:45299399-45299898 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:45303064-45303728 Neighboring gene uncharacterized LOC107985809 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:45396231-45396731 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:45397597-45398226 Neighboring gene long intergenic non-protein coding RNA 1121 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:45417644-45418148 Neighboring gene uncharacterized LOC105374576

Genomic regions, transcripts, and products

Expression

  • Project title: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

EBI GWAS Catalog

Description
Genome-wide association meta-analysis identifies novel variants associated with fasting plasma glucose in East Asians.
EBI GWAS Catalog
Large-scale genome-wide association studies in East Asians identify new genetic loci influencing metabolic traits.
EBI GWAS Catalog

Pathways from PubChem

Interactions

General gene information

Gene Ontology Provided by GOA

Items 1 - 25 of 27
Process Evidence Code Pubs
involved_in anatomical structure morphogenesis PubMed 
involved_in anterior/posterior axis specification  
involved_in cell migration PubMed 
involved_in cell population proliferation PubMed 
involved_in chondrocyte differentiation  
involved_in condensed mesenchymal cell proliferation  
involved_in embryonic cranial skeleton morphogenesis  
involved_in embryonic digestive tract morphogenesis  
involved_in kidney development  
involved_in kidney development PubMed 
involved_in kidney development  
involved_in mesenchymal cell differentiation involved in kidney development  
involved_in mesenchymal stem cell maintenance involved in nephron morphogenesis  
involved_in mesenchymal stem cell proliferation  
involved_in mesenchymal to epithelial transition involved in metanephros morphogenesis  
involved_in mesodermal cell fate specification  
involved_in middle ear morphogenesis  
involved_in negative regulation of epithelial cell differentiation  
involved_in nephron development  
involved_in nephron morphogenesis  
involved_in positive regulation of chondrocyte proliferation  
involved_in positive regulation of transcription by RNA polymerase II  
involved_in protein import into nucleus  
involved_in regulation of branching involved in ureteric bud morphogenesis  
involved_in regulation of chondrocyte differentiation  
involved_in regulation of ossification  
involved_in regulation of transcription by RNA polymerase II  
Items 1 - 25 of 27
Component Evidence Code Pubs
located_in chromatin  
is_active_in nucleus  
part_of transcription regulator complex  

General protein information

Preferred Names
homeobox protein SIX2
Names
sine oculis homeobox homolog 2

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_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
    Q9BXH7, 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: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    45005182..45009452 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005264100.4XP_005264157.1  homeobox protein SIX2 isoform X1

    See identical proteins and their annotated locations for XP_005264157.1

    UniProtKB/TrEMBL
    Q8TBA2
    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

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    45010408..45014884 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054340217.1XP_054196192.1  homeobox protein SIX2 isoform X1

    UniProtKB/TrEMBL
    Q8TBA2
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