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 cattle; 1 dog; 1 chicken; 1 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)		6q12-q14; chr6:70925743-71012786 (-)  GRCh37.p10
Disease Associations		(2) Diseases Associated with Human COL9A1

Alleles and phenotypes

All alleles(2) : Targeted(1) Gene trapped(1)
 

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)

Gene Ontology (GO) classifications

All GO classifications: (9 annotations)

Process	cartilage development, growth plate cartilage development, ...
Component	collagen, collagen type IX, ...
Function	metal ion binding

External Resources: FuncBase

Expression

Literature Summary: (34 records)
Data Summary: Results (402)    Tissues (124)    Images (49)
Theiler Stages: 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 28

Assay Type	Results
Immunohistochemistry	2
RNA in situ	370
Northern blot	7
Western blot	4
RT-PCR	19

cDNA source data(107)
External Resources: Allen Institute   GEO   ArrayExpress

Molecular reagents

All nucleic(116) Genomic(2) cDNA(109) 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.97367838
NIA Mouse Gene Index	U000107
Consensus CDS Project	CCDS35527.1
International Mouse Knockout Project Status	Col9a1

Sequences

Length	Strain/Species
genomic	OTTMUSG00000022796	VEGA Gene Model | MGI Sequence Detail	75075	C57BL/6J
transcript	OTTMUST00000054775	VEGA | MGI Sequence Detail	3834	Not Applicable
polypeptide	OTTMUSP00000026168	VEGA | MGI Sequence Detail	921	Not Applicable

All sequences(45) RefSeq(2) UniProt(8)

Polymorphisms

RFLP(2) : SNPs(731 from dbSNP Build 128)

Protein-related information

Resource	ID	Description
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:194035 Kan A, et al., c-Jun is required for the specification of joint cell fates. Genes Dev. 2013 Mar 1;27(5):514-24
All references(84)

Other accession IDs

MGD-MRK-2083, MGD-MRK-2085