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Col9a3 Gene Detail
Summary
  • Symbol
    Col9a3
  • Name
    collagen, type IX, alpha 3
  • Feature Type
    protein coding gene
  • IDs
    MGI:894686
    NCBI Gene: 12841
  • Alliance
    gene page
  • Transcription Start Sites
    5 TSS
Location &
Maps
more
  • Sequence Map
    Chr2:180239895-180263985 bp, + strand
    From NCBI annotation of GRCm39
  • View this region in JBrowse
  • Genome Browsers
    Ensembl | UCSC | NCBI
  • Genetic Map
    Chromosome 2, 103.14 cM
  • Mapping Data
    4 experiments
Strain
Comparison
more
  • SNPs within 2kb
    467 from dbSNP Build 142
  • Strain Annotations
    18
For selected strains:
Strain Gene Model ID Feature Type Coordinates Select Strains
C57BL/6J MGI_C57BL6J_894686
 protein coding gene Chr2:180239583-180263985 (+)
129S1/SvImJ MGP_129S1SvImJ_G0026998
 protein coding gene Chr2:187129205-187154860 (+)
A/J MGP_AJ_G0026964
 protein coding gene Chr2:179440598-179464903 (+)
AKR/J MGP_AKRJ_G0026934
 protein coding gene Chr2:184819935-184846631 (+)
BALB/cJ MGP_BALBcJ_G0026973
 protein coding gene Chr2:179903726-179928939 (+)
C3H/HeJ MGP_C3HHeJ_G0026714
 protein coding gene Chr2:185170883-185196878 (+)
C57BL/6NJ MGP_C57BL6NJ_G0027419
 protein coding gene Chr2:192529440-192556874 (+)
CAROLI/EiJ MGP_CAROLIEiJ_G0024784
 protein coding gene Chr2:170132488-170155847 (+)
CAST/EiJ MGP_CASTEiJ_G0026173
 protein coding gene Chr2:183412331-183437687 (+)
CBA/J MGP_CBAJ_G0026691
 protein coding gene Chr2:199534137-199558463 (+)
DBA/2J MGP_DBA2J_G0026829
 protein coding gene Chr2:178537959-178562474 (+)
FVB/NJ MGP_FVBNJ_G0026795
 protein coding gene Chr2:177152792-177177886 (+)
LP/J MGP_LPJ_G0026930
 protein coding gene Chr2:187136476-187164596 (+)
NOD/ShiLtJ MGP_NODShiLtJ_G0026814
 protein coding gene Chr2:202130030-202156697 (+)
NZO/HlLtJ MGP_NZOHlLtJ_G0027478
 protein coding gene Chr2:184775901-184801135 (+)
PWK/PhJ MGP_PWKPhJ_G0025909
 protein coding gene Chr2:176049198-176074414 (+)
SPRET/EiJ MGP_SPRETEiJ_G0025709
 protein coding gene Chr2:181267770-181298039 (+)
WSB/EiJ MGP_WSBEiJ_G0026245
 protein coding gene Chr2:185758661-185785942 (+)



Homology
more
  • Human Ortholog
    COL9A3, collagen type IX alpha 3 chain
  • Vertebrate Orthologs
    3
Vertebrate Orthology Source
Alliance of Genome Resources
  • Human Ortholog
    COL9A3, collagen type IX alpha 3 chain
  • Synonyms
    DJ885L7.4.1, EDM3, IDD, MED, STL6
  • Links
    NCBI Gene ID: 1299
    neXtProt AC: NX_Q14050
    UniProt: Q14050

  • Chr Location
    20q13.33; chr20:62816213-62841159 (+)  GRCh38
Human Diseases
more
  • Diseases
    3 with human COL9A3 associations

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

Mutations,
Alleles, and
Phenotypes
less
  • Phenotype Summary
    6 phenotypes from 1 allele in 1 genetic background
    8 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.
Gene Ontology
(GO)
Classifications
less
  • All GO Annotations
    7
  • GO References
    2
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
    1053
  • Tissues
    100
  • cDNA Data
    69
  • Literature Summary
    30
  • Comparison Matrix
    Gene Expression + Phenotype
    • Sequences &
    Gene Models
    less
    Representative SequencesLengthStrain/SpeciesFlank
    genomic 12841 NCBI Gene Model | MGI Sequence Detail 24091 C57BL/6J ±  kb
    transcript NM_001378777 RefSeq | MGI Sequence Detail 2948 ZRU/MplStud  
    polypeptide NP_001365706 RefSeq | MGI Sequence Detail 719 ZRU/MplStud  
    For the selected sequence
    Protein
    Information
    less
    • UniProt
      8 Sequences
    • InterPro Domains
      IPR050938 Collagen and Collagen-like Structural Proteins
      IPR050149 Collagen superfamily
      IPR008160 Collagen triple helix repeat
    Molecular
    Reagents
    less
    • All nucleic 76
      cDNA 71
      Primer pair 4
      Other 1

      Microarray probesets 4
    Other
    Accession IDs
    less
    MGI:2139235
    References
    more
    • Summaries
      All 61
      Developmental Gene Expression 30
      Gene Ontology 2
      Phenotypes 8
    • Earliest
      J:17466 Abe N, et al., The complete primary structure of the long form of mouse alpha 1(IX) collagen chain and its expression during limb development. Biochim Biophys Acta. 1994 Jan 11;1204(1):61-7
    • Latest
      J:345621 Adams DJ, et al., Genetic determinants of micronucleus formation in vivo. Nature. 2024 Mar;627(8002):130-136
    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)
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    Funding Information
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    12/10/2024
    MGI 6.24     		The Jackson Laboratory