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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

HCOP human homology predictions: COL9A1
Gene Tree: Col9a1

Human
homologs
COL9A1, collagen, type IX, alpha 1
Orthology source: HGNC, HomoloGene

IDs:
NCBI Gene ID: 1297
neXtProt AC: NX_P20849

Human Synonyms: DJ149L1.1.2, EDM6, MED, STL4

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

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 in Mice Using Col9a1 (1)    Mutations 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: (37 records)
Data Summary: Results (402)    Tissues (125)    Images (49)    Tissue x Stage Matrix (view)
Assay TypeResults
Immunohistochemistry 2
RNA in situ 370
Northern blot 7
Western blot 4
RT-PCR 19
cDNA source data(106)
Other mouse links: Allen Institute   GEO   Expression Atlas
Other vertebrate links: GEISHA COL9A1 ZFIN col9a1b    NEW 
Molecular
reagents
All nucleic(115) Genomic(2) cDNA(108) Primer pair(4) Other(1)
Microarray probesets(4)
Other database
links
VEGA Gene Model OTTMUSG00000022796 (Evidence)
Ensembl Gene Model ENSMUSG00000026147 (Evidence)
Entrez Gene 12839 (Evidence)
UniGene 154662
DFCI TC1575100, TC1584852, TC1595111
DoTS DT.101364657, DT.110917650, DT.110917689, DT.97367838
NIA Mouse Gene Index U000107
Consensus CDS Project CCDS35527.1, CCDS69871.1
International Mouse Phenotyping Consortium Status Col9a1
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 IPR013320 Concanavalin A-like lectin/glucanase domain
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: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
All references(84)
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
08/25/2015
MGI 6.0
The Jackson Laboratory