About   Help   FAQ
Six3 Gene Detail
Summary
  • Symbol
    Six3
  • Name
    sine oculis-related homeobox 3
  • Synonyms
    E130112M24Rik
  • Feature Type
    protein coding gene
  • IDs
    MGI:102764
    NCBI Gene: 20473
  • Alliance
    genome feature page
  • Transcription Start Sites
    15 TSS
Location &
Maps
more
  • Sequence Map
    Chr17:85921036-85933619 bp, + strand
    From NCBI annotation of GRCm39
  • View this region in JBrowse
  • Genome Browsers
    Ensembl | UCSC | NCBI
  • Genetic Map
    Chromosome 17, 55.42 cM
  • Mapping Data
    2 experiments
Strain
Comparison
more
  • SNPs within 2kb
    250 from dbSNP Build 142
  • Strain Annotations
    19
  • RFLP
    1
For selected strains:
Strain Gene Model ID Feature Type Coordinates Select Strains
C57BL/6J MGI_C57BL6J_102764
 protein coding gene Chr17:85921036-85936730 (+)
129S1/SvImJ ENSMUSG00200022054
 protein coding gene Chr17:81323070-81338736 (+)
A/J ENSMUSG00195027620
 protein coding gene Chr17:82696741-82712480 (+)
AKR/J ENSMUSG00220016265
 protein coding gene Chr17:81646518-81662190 (+)
BALB/cJ ENSMUSG00180024842
 protein coding gene Chr17:82370169-82385874 (+)
C3H/HeJ ENSMUSG00175006798
 protein coding gene Chr17:81634899-81650637 (+)
C57BL/6NJ ENSMUSG00215014082
 protein coding gene Chr17:81363477-81379185 (+)
CAROLI/EiJ MGP_CAROLIEiJ_G0021932
 protein coding gene Chr17:81215581-81231303 (+)
CAST/EiJ ENSTCUG00005011555
 protein coding gene Chr17:82190289-82205957 (+)
CBA/J ENSMUSG00210022146
 protein coding gene Chr17:81493699-81509429 (+)
DBA/2J ENSMUSG00185019551
 protein coding gene Chr17:84309952-84325655 (+)
FVB/NJ ENSMUSG00205005896
 protein coding gene Chr17:82115106-82130839 (+)
JF1/MsJ ENSUMUG00000008837
 protein coding gene Chr17:84037895-84053758 (+)
LP/J ENSMUSG00230009599
 protein coding gene Chr17:85341543-85357260 (+)
NOD/ShiLtJ ENSMUSG00190009337
 protein coding gene Chr17:81390394-81406134 (+)
NZO/HlLtJ ENSMUSG00225030093
 protein coding gene Chr17:87599370-87615114 (+)
PWK/PhJ ENSLUMG00010031206
 protein coding gene Chr17:81253740-81269551 (+)
SPRET/EiJ ENSMSPG00010019828
 protein coding gene Chr17:81834076-81849847 (+)
WSB/EiJ ENSIUOG00005020859
 protein coding gene Chr17:82308056-82323791 (+)



Homology
more
  • Human Ortholog
    SIX3, SIX homeobox 3
  • Vertebrate Orthologs
    4
Vertebrate Orthology Source
Alliance of Genome Resources
  • Human Ortholog
    SIX3, SIX homeobox 3
  • Synonyms
    HPE2
  • Links
    NCBI Gene ID: 6496
    UniProt: O95343

  • Chr Location
    2p21; chr2:44941702-44946071 (+)  GRCh38
Human Diseases
more
  • Diseases
    1 with Six3 mouse models; 2 with human SIX3 associations

Human Disease Mouse Models
      
IDs
 View 4 models
      
IDs
Click on a disease name to see all genes associated with that disease.

  • Mutations/Alleles
    4 with disease annotations
  • References
    2 with disease annotations
Mutations,
Alleles, and
Phenotypes
less
  • Phenotype Summary
    23 phenotypes from 5 alleles in 4 genetic backgrounds
    12 phenotypes from multigenic genotypes
    32 phenotype references
Phenotype Overview

adipose tissue
behavior/neurological
cardiovascular system
cellular
craniofacial
digestive/alimentary system
embryo
endocrine/exocrine glands
growth/size/body
hearing/vestibular/ear
hematopoietic system
homeostasis/metabolism
integument
immune system
limbs/digits/tail
liver/biliary system
mortality/aging
muscle
nervous system
pigmentation
renal/urinary system
reproductive system
respiratory system
skeleton
taste/olfaction
neoplasm
vision/eye

Click cells to view annotations.
Mice homozygous for disruptions of this gene die at birth with anterior structures of the head and brain undeveloped.
Gene Ontology
(GO)
Classifications
less
  • All GO Annotations
    78
  • GO References
    27
Molecular Function

carbohydrate derivative binding
cytoskeletal protein binding
DNA binding
enzyme regulator
hydrolase
ligase
lipid binding
oxidoreductase
RNA binding
signaling receptor activity
signaling receptor binding
transcription
transferase
transporter
Biological Process

carbohydrate derivative metabolism
cell differentiation
cell population proliferation
cellular component organization
DNA-templated transcription
establishment of localization
homeostatic process
immune system process
lipid metabolic process
programmed cell death
protein metabolic process
response to stimulus
signaling
system development
Cellular Component

cell projection
cytoplasmic vesicle
cytoskeleton
cytosol
endoplasmic reticulum
endosome
extracellular region
Golgi apparatus
mitochondrion
membraneless organelle
nucleus
organelle envelope
organelle lumen
plasma membrane
protein-containing complex
synapse
vacuole
Click cells to view annotations.
Expression
less
Expression Overview

early conceptus
embryo ectoderm
embryo endoderm
embryo mesoderm
embryo mesenchyme
extraembryonic component
alimentary system
auditory system
branchial arches
cardiovascular system
connective tissue
endocrine system
exocrine system
hemolymphoid system
integumental system
limbs
liver and biliary system
musculoskeletal system
nervous system
olfactory system
reproductive system
respiratory system
urinary system
visual system
Click cells to view annotations.


  • Assay Results
    1746
  • Tissues
    444
  • cDNA Data
    19
  • Literature Summary
    281
  • Comparison Matrix
    Gene Expression + Phenotype
    • Sequences &
    Gene Models
    less
    Representative SequencesLengthStrain/SpeciesFlank
    genomic 20473 NCBI Gene Model | MGI Sequence Detail 12584 C57BL/6J ±  kb
    transcript NM_011381 RefSeq | MGI Sequence Detail 3680 C57BL/6  
    polypeptide Q62233 UniProt | EBI | MGI Sequence Detail 333 Not Applicable  
    For the selected sequence
    Protein
    Information
    less
    Molecular
    Reagents
    less
    • All nucleic 87
      cDNA 25
      Primer pair 16
      Other 46
      Antibodies 7

      Microarray probesets 6
    Other
    Accession IDs
    less
    MGD-MRK-19669, MGI:1925249
    References
    more
    • Summaries
      All 338
      Developmental Gene Expression 281
      Diseases 2
      Gene Ontology 27
      Phenotypes 32
    • Earliest
      J:23775 Oliver G, et al., Homeobox genes and connective tissue patterning. Development. 1995 Mar;121(3):693-705
    • Latest
      J:385444 Van Loh BM, et al., The Transcription Factors Six3 and Six6 in Neuromedin-S Neurons Differentially Affect Circadian Rhythms. J Neurosci Res. 2026 Apr;104(4):e70123
    Contributing Projects:
    Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
    Citing These Resources
    Funding Information
    Warranty Disclaimer, Privacy Notice, Licensing, & Copyright
    Send questions and comments to User Support.     		last database update
    09/08/2026
    MGI 6.24     		The Jackson Laboratory