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Col9a1
Gene Detail
 Symbol
Name
ID
Col9a1
collagen, type IX, alpha 1
MGI:88465
Synonyms Col9a-1
Feature Type protein coding gene
Genetic Map
Chromosome 1
9.95 cM
Detailed Genetic Map ± 1 cM


Mapping data(6)
Sequence Map
Chr1:24177610-24252684 bp, + strand
From VEGA annotation of GRCm38

  75075 bp   ±  kb flank

VEGA Genome Browser | Ensembl Genome Browser | UCSC Browser | NCBI Map Viewer


Mouse Genome Browser
Vertebrate
homology
HomoloGene:1393  Vertebrate Homology Class
1 human; 1 mouse; 1 rat; 1 chimpanzee; 1 rhesus macaque; 1 dog; 1 chicken; 1 western clawed frog; 2 zebrafish

Gene Tree: Col9a1

Human
homologs
Human Homolog COL9A1, collagen, type IX, alpha 1
NCBI Gene ID 1297
neXtProt AC  NX_P20849
Human Synonyms  DJ149L1.1.2, EDM6, MED, STL4
Human Chr (Location)  6q13; chr6:70216040-70303083 (-)  GRCh38
Disease Associations  (2) Diseases Associated with Human COL9A1
Mutations,
alleles, and
phenotypes
All mutations/alleles(2) : Gene trapped(1) Targeted(1)
Incidental mutations (data from Mutagenetix , APF )
 
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.
 
Human Diseases Modeled Using Mouse Col9a1 (1)    Alleles Annotated to Human Diseases(1)    Phenotype Images(2)
Interactions
Col9a1 interacts with 148 markers (Mir9-1, Mir9-2, Mir9-3, ...)
Gene Ontology
(GO)
classifications
All GO classifications: (9 annotations)
Process cartilage development, growth plate cartilage development, ...
Component collagen trimer, collagen type IX trimer, ...
Function metal ion binding
External Resources: FuncBase
Expression
Literature Summary: (35 records)
Data Summary: Results (402)    Tissues (125)    Images (49)
Theiler Stages: 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28
Assay TypeResults
Immunohistochemistry 2
RNA in situ 370
Northern blot 7
Western blot 4
RT-PCR 19
cDNA source data(106)
External Resources: Allen Institute   GEO   Expression Atlas
Molecular
reagents
All nucleic(115) Genomic(2) cDNA(108) Primer pair(4) Other(1)
Microarray probesets(4)
Other database
links
VEGA Gene ModelOTTMUSG00000022796 (Evidence)
Ensembl Gene ModelENSMUSG00000026147 (Evidence)
Entrez Gene12839 (Evidence)
UniGene154662
DFCITC1575100, TC1584852, TC1595111
DoTSDT.101364657, DT.110917650, DT.110917689, DT.97367838
NIA Mouse Gene IndexU000107
Consensus CDS ProjectCCDS35527.1, CCDS69871.1
International Mouse Knockout Project StatusCol9a1
Sequences
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 sequences
All sequences(51) RefSeq(6) UniProt(8)
Polymorphisms RFLP(2) : SNPs within 2kb(754 from dbSNP Build 137)
Protein-related
information
ResourceIDDescription
InterPro IPR008160 Collagen triple helix repeat
InterPro IPR008985 Concanavalin A-like lectin/glucanases superfamily
InterPro IPR001791 Laminin G domain
Protein Ontology PR:000005722 collagen alpha-1(IX) chain
References (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:198371 Brachvogel B, et al., Comparative proteomic analysis of normal and collagen IX null mouse cartilage reveals altered extracellular matrix composition and novel components of the collagen IX interactome. J Biol Chem. 2013 May 10;288(19):13481-92
All references(86)
Disease annotation references (1)
Other
accession IDs
MGD-MRK-2083, MGD-MRK-2085

Contributing Projects:
Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Tumor Biology (MTB), Gene Ontology (GO), MouseCyc
Citing These Resources
Funding Information
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last database update
09/09/2014
MGI 5.19
The Jackson Laboratory