About   Help   FAQ
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
Location & Maps
more
  • Sequence Map
    Chr1:24177610-24252684 bp, + strand
  • From VEGA annotation of GRCm38

    Mouse Genome Browser

  • Download
    Sequence
      75075 bp   ±  kb flank

  • Genome Browsers
  • Genetic Map
    Chromosome 1, 9.95 cM
  • Mapping Data
    6 experiments
Homology
more
  • Human Ortholog
    COL9A1, collagen type IX alpha 1
  • Vertebrate Orthologs
    10
  • Human Ortholog
    COL9A1, collagen type IX alpha 1
    Orthology source: HGNC, HomoloGene
  • Synonyms
    DJ149L1.1.2, EDM6, MED, STL4
  • Links
    NCBI Gene ID: 1297
    neXtProt AC: NX_P20849

  • Chr Location
    6q13; chr6:70215061-70303083 (-)  GRCh38.p2

Human Diseases
more
  • Diseases
    1 with Col9a1 mouse models; 2 with human COL9A1 associations

Human Disease Mouse Models
       Osteoarthritis Susceptibility 1; OS1   OMIM: 165720 View 1 model
       Epiphyseal Dysplasia, Multiple, 6; EDM6   OMIM: 614135
Stickler Syndrome, Type IV; STL4   OMIM: 614134
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
    14 phenotypes from 1 allele in 2 genetic backgrounds
    1 phenotype from multigenic genotypes
    2 images
    18 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.
  • All Mutations and Alleles
    3
  • Chemically induced (other)
    1
  • Gene trapped
    1
  • Targeted
    1
  • Genomic Mutations
    1 involving Col9a1
  • Incidental Mutations
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
  • GO References
Molecular Function

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

nucleic acid-templated transcription
carbohydrate derivative metabolism
cell death
cell differentiation
cell proliferation
cellular component organization
establishment of localization
homeostatic process
immune system process
lipid metabolic process
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
non-membrane-bounded organelle
nucleus
organelle envelope
organelle lumen
plasma membrane
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
  • Tissues
  • cDNA Data
  • Literature Summary
Interactions
less
Sequences &
Gene Models
less
Representative SequencesLengthStrain/SpeciesFlank
genomic OTTMUSG00000022796 VEGA Gene Model | MGI Sequence Detail 75075 C57BL/6J ±  kb
transcript OTTMUST00000054775 VEGA | MGI Sequence Detail 3834 Not Applicable  
polypeptide OTTMUSP00000026168 VEGA | MGI Sequence Detail 921 Not Applicable  
For the selected sequence
Polymorphisms
less
  • SNPs within 2kb
    754 from dbSNP Build 142
  • RFLP
Protein
Information
less
  • UniProt
    8 Sequences
  • Protein Ontology
    PR:000005722 collagen alpha-1(IX) chain
  • InterPro Domains
    IPR008160 Collagen triple helix repeat
    IPR013320 Concanavalin A-like lectin/glucanase domain
    IPR001791 Laminin G domain
Molecular
Reagents
less
  • All nucleic 117
    Genomic 2
    cDNA 109
    Primer pair 5
    Other 1

    Microarray probesets 4
Other
Accession IDs
less
MGD-MRK-2083, MGD-MRK-2085
References
more
  • Summaries
    All 81
    Developmental Gene Expression 37
    Diseases 1
    Gene Ontology 5
    Phenotypes 18
  • 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:213873 Chen Z, et al., FGF signaling activates a Sox9-Sox10 pathway for the formation and branching morphogenesis of mouse ocular glands. Development. 2014 Jul;141(13):2691-701

Contributing Projects:
Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Tumor Biology (MTB), Gene Ontology (GO), MouseCyc
Citing These Resources
Funding Information
Warranty Disclaimer & Copyright Notice
Send questions and comments to User Support.
last database update
07/12/2016
MGI 6.04
The Jackson Laboratory