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Hoxc9 Gene Detail
Summary
  • Symbol
    Hoxc9
  • Name
    homeobox C9
  • Synonyms
    Hox-3.2
  • Feature Type
    protein coding gene
  • IDs
    MGI:96199
    NCBI Gene: 15427
  • Member of
    Hoxc cluster
  • Alliance
    gene page
  • Transcription Start Sites
    3 TSS
Location &
Maps
more
  • Sequence Map
    Chr15:102885467-102893324 bp, + strand
    From NCBI annotation of GRCm39
  • View this region in JBrowse
  • Genome Browsers
    Ensembl | UCSC | NCBI
  • Genetic Map
    Chromosome 15, 58.04 cM
  • Mapping Data
    4 experiments
Strain
Comparison
more
  • SNPs within 2kb
    83 from dbSNP Build 142
  • Strain Annotations
    18
  • RFLP
    1
For selected strains:
Strain Gene Model ID Feature Type Coordinates Select Strains
C57BL/6J MGI_C57BL6J_96199
 protein coding gene Chr15:102884874-102893531 (+)
129S1/SvImJ MGP_129S1SvImJ_G0022429
 protein coding gene Chr15:105211969-105220526 (+)
A/J MGP_AJ_G0022391
 protein coding gene Chr15:101055666-101064289 (+)
AKR/J MGP_AKRJ_G0022366
 protein coding gene Chr15:104124362-104132961 (+)
BALB/cJ MGP_BALBcJ_G0022395
 protein coding gene Chr15:101103096-101111665 (+)
C3H/HeJ MGP_C3HHeJ_G0022162
 protein coding gene Chr15:104200994-104209563 (+)
C57BL/6NJ MGP_C57BL6NJ_G0022844
 protein coding gene Chr15:109107633-109116356 (+)
CAROLI/EiJ MGP_CAROLIEiJ_G0020367
 protein coding gene Chr15:96824739-96833347 (+)
CAST/EiJ MGP_CASTEiJ_G0021688
 protein coding gene Chr15:105074292-105084593 (+)
CBA/J MGP_CBAJ_G0022131
 protein coding gene Chr15:112940475-112949022 (+)
DBA/2J MGP_DBA2J_G0022262
 protein coding gene Chr15:100325431-100334018 (+)
FVB/NJ MGP_FVBNJ_G0022238
 protein coding gene Chr15:99395021-99403624 (+)
LP/J MGP_LPJ_G0022331
 protein coding gene Chr15:105347097-105355642 (+)
NOD/ShiLtJ MGP_NODShiLtJ_G0022260
 protein coding gene Chr15:116455807-116464394 (+)
NZO/HlLtJ MGP_NZOHlLtJ_G0022856
 protein coding gene Chr15:104163187-104171789 (+)
PWK/PhJ MGP_PWKPhJ_G0021428
 protein coding gene Chr15:100505549-100513769 (+)
SPRET/EiJ MGP_SPRETEiJ_G0021260
 protein coding gene Chr15:103994702-104003236 (+)
WSB/EiJ MGP_WSBEiJ_G0021738
 protein coding gene Chr15:104777864-104786757 (+)



Homology
more
  • Human Ortholog
    HOXC9, homeobox C9
  • Vertebrate Orthologs
    3
Vertebrate Orthology Source
Alliance of Genome Resources
  • Human Ortholog
    HOXC9, homeobox C9
  • Synonyms
    HOX3, HOX3B
  • Links
    NCBI Gene ID: 3225
    neXtProt AC: NX_P31274
    UniProt: P31274

  • Chr Location
    12q13.13; chr12:53994895-54003337 (+)  GRCh38
Human Diseases
less
  • References
    1 with disease annotations
Mutations,
Alleles, and
Phenotypes
less
  • Phenotype Summary
    11 phenotypes from 1 allele in 1 genetic background
    12 phenotypes from multigenic genotypes
    37 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 in this gene grow more slowly than normal and develop hunched backs. Forward transformations seen in vertebrae from L1 and forward to around T10. Abnormalities in the sternum and ribs attachments to the sternum are also seen.
Gene Ontology
(GO)
Classifications
less
  • All GO Annotations
    26
  • GO References
    7
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
    1074
  • Tissues
    262
  • cDNA Data
    26
  • Literature Summary
    66
  • Comparison Matrix
    Gene Expression + Phenotype
    • Sequences &
    Gene Models
    less
    Representative SequencesLengthStrain/SpeciesFlank
    genomic 15427 NCBI Gene Model | MGI Sequence Detail 7858 C57BL/6J ±  kb
    transcript NM_008272 RefSeq | MGI Sequence Detail 1719 ZRU/MplStud  
    polypeptide P09633 UniProt | EBI | MGI Sequence Detail 260 Not Applicable  
    For the selected sequence
    Protein
    Information
    less
    Molecular
    Reagents
    less
    • All nucleic 58
      Genomic 10
      cDNA 31
      Primer pair 10
      Other 7

      Microarray probesets 3
    Other
    Accession IDs
    less
    MGD-MRK-10840, MGD-MRK-10900
    References
    more
    • Summaries
      All 129
      Developmental Gene Expression 66
      Diseases 1
      Gene Ontology 7
      Phenotypes 37
    • Earliest
      J:7688 Lane PW, et al., Association of megacolon with a new dominant spotting gene (Dom) in the mouse. J Hered. 1984 Nov-Dec;75(6):435-9
    • Latest
      J:351383 Song L, et al., Single-cell multiomics reveals ENL mutation perturbs kidney developmental trajectory by rewiring gene regulatory landscape. Nat Commun. 2024 Jul 15;15(1):5937
    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
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    Send questions and comments to User Support.     		last database update
    11/05/2024
    MGI 6.24     		The Jackson Laboratory