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SIX4 SIX homeobox 4 [ Homo sapiens (human) ]

Gene ID: 51804, updated on 9-Feb-2020

Summary

Official Symbol
SIX4provided by HGNC
Official Full Name
SIX homeobox 4provided by HGNC
Primary source
HGNC:HGNC:10890
See related
Ensembl:ENSG00000100625 MIM:606342
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
AREC3
Summary
This gene encodes a member of the homeobox family, subfamily SIX. The drosophila homolog is a nuclear homeoprotein required for eye development. Studies in mouse show that this gene product functions as a transcription factor, and may have a role in the differentiation or maturation of neuronal cells. [provided by RefSeq, May 2010]
Expression
Broad expression in prostate (RPKM 2.0), salivary gland (RPKM 1.8) and 16 other tissues See more
Orthologs

Genomic context

See SIX4 in Genome Data Viewer
Location:
14q23.1
Exon count:
5
Annotation release Status Assembly Chr Location
109.20191205 current GRCh38.p13 (GCF_000001405.39) 14 NC_000014.9 (60709539..60724351, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (61176256..61191039, complement)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene VISTA enhancer hs1602 Neighboring gene microRNA 9718 Neighboring gene SIX homeobox 1 Neighboring gene MNAT1 component of CDK activating kinase Neighboring gene mitotic arrest deficient 2 like 1 pseudogene 1 Neighboring gene SRM pseudogene 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

Phenotypes

Copy number response

Description
Copy number response
Haploinsufficency

No evidence available (Last evaluated (2012-05-08)

ClinGen Genome Curation Page
Triplosensitivity

No evidence available (Last evaluated (2012-05-08)

ClinGen Genome Curation Page

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC119450, MGC119452, MGC119453

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 
embryonic cranial skeleton morphogenesis IEA
Inferred from Electronic Annotation
more info
 
fungiform papilla morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
generation of neurons ISS
Inferred from Sequence or Structural Similarity
more info
 
inner ear morphogenesis IEA
Inferred from Electronic Annotation
more info
 
male gonad development ISS
Inferred from Sequence or Structural Similarity
more info
 
male sex determination ISS
Inferred from Sequence or Structural Similarity
more info
 
male sex differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
metanephric mesenchyme development ISS
Inferred from Sequence or Structural Similarity
more info
 
myoblast migration IEA
Inferred from Electronic Annotation
more info
 
myotome development ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of apoptotic process ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of neuron apoptotic process ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of satellite cell 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 ISS
Inferred from Sequence or Structural Similarity
more info
 
olfactory placode formation ISS
Inferred from Sequence or Structural Similarity
more info
 
pharyngeal system development ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of branching involved in ureteric bud morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
positive regulation of transcription, DNA-templated ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of ureteric bud formation ISS
Inferred from Sequence or Structural Similarity
more info
 
protein localization to nucleus ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of branch elongation involved in ureteric bud branching ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of epithelial cell proliferation ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of protein localization IEA
Inferred from Electronic Annotation
more info
 
regulation of synaptic growth at neuromuscular junction IEA
Inferred from Electronic Annotation
more info
 
sarcomere organization ISS
Inferred from Sequence or Structural Similarity
more info
 
skeletal muscle fiber differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
skeletal muscle tissue development ISS
Inferred from Sequence or Structural Similarity
more info
 
thymus development IEA
Inferred from Electronic Annotation
more info
 
tongue development ISS
Inferred from Sequence or Structural Similarity
more info
 
trigeminal ganglion development ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
cytoplasm ISS
Inferred from Sequence or Structural Similarity
more info
 
nuclear chromatin ISA
Inferred from Sequence Alignment
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus ISS
Inferred from Sequence or Structural Similarity
more info
 
transcription factor complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
homeobox protein SIX4
Names
sine oculis homeobox homolog 4

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_021182.1 RefSeqGene

    Range
    4784..19596
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_017420.5NP_059116.3  homeobox protein SIX4

    See identical proteins and their annotated locations for NP_059116.3

    Status: REVIEWED

    Source sequence(s)
    AA424469, AL132777, BC099722
    Consensus CDS
    CCDS9749.2
    UniProtKB/Swiss-Prot
    Q9UIU6
    Related
    ENSP00000216513.4, ENST00000216513.5
    Conserved Domains (2) summary
    cd00086
    Location:228282
    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:108217
    SIX1_SD; Transcriptional regulator, SIX1, N-terminal SD domain

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20191205

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
    60709539..60724351 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005267759.2XP_005267816.1  homeobox protein SIX4 isoform X1

    Conserved Domains (2) summary
    cd00086
    Location:220274
    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:100209
    SIX1_SD; Transcriptional regulator, SIX1, N-terminal SD domain

RNA

  1. XR_001750375.2 RNA Sequence

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