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Col9a1 Gene Detail
Summary
  • Symbol
    Col9a1
  • Name
    collagen, type IX, alpha 1
  • Synonyms
    Col9a-1
  • Feature Type
    protein coding gene
  • IDs
    MGI:88465
    NCBI Gene: 12839
  • Alliance
    genome feature page
  • Transcription Start Sites
    6 TSS
Location &
Maps
more
  • Sequence Map
    Chr1:24216691-24291765 bp, + strand
    From Ensembl annotation of GRCm39
  • View this region in JBrowse
  • Genome Browsers
    Ensembl | UCSC | NCBI
  • Genetic Map
    Chromosome 1, 9.95 cM
  • Mapping Data
    7 experiments
Strain
Comparison
more
  • SNPs within 2kb
    2574 from dbSNP Build 142
  • Strain Annotations
    19
  • RFLP
    2
For selected strains:
Strain Gene Model ID Feature Type Coordinates Select Strains
C57BL/6J MGI_C57BL6J_88465
 protein coding gene Chr1:24216670-24291819 (+)
129S1/SvImJ ENSMUSG00200000602
 protein coding gene Chr1:21643240-21718323 (+)
A/J ENSMUSG00195000063
 protein coding gene Chr1:21386746-21461822 (+)
AKR/J ENSMUSG00220000551
 protein coding gene Chr1:21458747-21533790 (+)
BALB/cJ ENSMUSG00180001081
 protein coding gene Chr1:21499100-21574588 (+)
C3H/HeJ ENSMUSG00175000636
 protein coding gene Chr1:21377757-21452833 (+)
C57BL/6NJ ENSMUSG00215001026
 protein coding gene Chr1:21477053-21552136 (+)
CAROLI/EiJ MGP_CAROLIEiJ_G0013999
 protein coding gene Chr1:19648602-19724539 (+)
CAST/EiJ ENSTCUG00005000379
 protein coding gene Chr1:21690565-21765425 (+)
CBA/J ENSMUSG00210010542
 protein coding gene Chr1:21251655-21326730 (+)
DBA/2J ENSMUSG00185016285
 protein coding gene Chr1:22298413-22373480 (+)
FVB/NJ ENSMUSG00205006783
 protein coding gene Chr1:21400269-21475349 (+)
JF1/MsJ ENSUMUG00000000183
 protein coding gene Chr1:21598387-21673691 (+)
LP/J ENSMUSG00230000424
 protein coding gene Chr1:22325487-22400579 (+)
NOD/ShiLtJ ENSMUSG00190000058
 protein coding gene Chr1:21395780-21470852 (+)
NZO/HlLtJ ENSMUSG00225000308
 protein coding gene Chr1:25604641-25679704 (+)
PWK/PhJ ENSLUMG00010000104
 protein coding gene Chr1:21184121-21259814 (+)
SPRET/EiJ ENSMSPG00010000566
 protein coding gene Chr1:22182397-22269663 (+)
WSB/EiJ ENSIUOG00005001798
 protein coding gene Chr1:21384814-21459927 (+)



Homology
more
  • Human Ortholog
    COL9A1, collagen type IX alpha 1 chain
  • Vertebrate Orthologs
    4
Vertebrate Orthology Source
Alliance of Genome Resources
  • Human Ortholog
    COL9A1, collagen type IX alpha 1 chain
  • Synonyms
    DJ149L1.1.2, EDM6, MED, STL4
  • Links
    NCBI Gene ID: 1297
    UniProt: P20849

  • Chr Location
    6q13; chr6:70215061-70303084 (-)  GRCh38
Human Diseases
more
  • Diseases
    1 with Col9a1 mouse models; 3 with human COL9A1 associations

Human Disease Mouse Models
      
IDs
 View 1 model
      
IDs
IDs
IDs
Click on a disease name to see all genes associated with that disease.

  • Mutations/Alleles
    1 with disease annotations
  • References
    1 with disease annotations
Mutations,
Alleles, and
Phenotypes
less
  • Phenotype Summary
    15 phenotypes from 1 allele in 2 genetic backgrounds
    1 phenotype from multigenic genotypes
    2 images
    24 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.
Homozygotes for a targeted mutation show no conspicuous skeletal abnormalities at birth but develop early-onset degenerative joint disease resembling osteoarthritis as well as progressive hearing loss; restoration and remodeling of trabecular bone is perturbed with minimal effects on cortical bone.
Gene Ontology
(GO)
Classifications
less
  • All GO Annotations
    18
  • 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
    1071
  • Tissues
    172
  • cDNA Data
    111
  • Literature Summary
    52
  • Comparison Matrix
    Gene Expression + Phenotype
    • Sequences &
    Gene Models
    less
    Representative SequencesLengthStrain/SpeciesFlank
    genomic ENSMUSG00000026147 Ensembl Gene Model | MGI Sequence Detail 75075 C57BL/6J ±  kb
    transcript ENSMUST00000054588 Ensembl | MGI Sequence Detail 3834 Not Applicable  
    polypeptide ENSMUSP00000051579 Ensembl | MGI Sequence Detail 921 Not Applicable  
    For the selected sequence
    Protein
    Information
    less
    Molecular
    Reagents
    less
    • All nucleic 128
      Genomic 2
      cDNA 113
      Primer pair 10
      Other 3
      Antibodies 2

      Microarray probesets 4
    Other
    Accession IDs
    less
    MGD-MRK-2083, MGD-MRK-2085
    References
    more
    • Summaries
      All 110
      Developmental Gene Expression 52
      Diseases 1
      Gene Ontology 7
      Phenotypes 24
    • Earliest
      J:11264 Metsaranta M, et al., Specific hybridization probes for mouse type I, II, III and IX collagen mRNAs. Biochim Biophys Acta. 1991 Jun 13;1089(2):241-3
    • Latest
      J:372760 Olson S, et al., Genetic knockout suggests Isl1 enhancer redundancy in mouse hindlimb development. Dev Biol. 2025 Sep 17;528:217-227
    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
    09/01/2026
    MGI 6.24     		The Jackson Laboratory