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Col9a3
Gene Detail
Symbol

Name
ID
Col9a3
collagen, type IX, alpha 3
MGI:894686
Feature Type
protein coding gene
Genetic Map
Chromosome 2
103.14 cM
Detailed Genetic Map ± 1 cM


Mapping data(4)
Sequence Map
Chr2:180597790-180622189 bp, + strand
From VEGA annotation of GRCm38

  24400 bp   ±  kb flank

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


Mouse Genome Browser
Vertebrate
homology
HomoloGene:20438  Vertebrate Homology Class
1 human; 1 mouse; 1 rat; 1 chimpanzee; 1 cattle; 1 dog; 1 chicken; 1 western clawed frog; 1 zebrafish

HCOP human homology predictions: COL9A3
Gene Tree: Col9a3

Human
homologs
COL9A3, collagen, type IX, alpha 3
Orthology source: HGNC, HomoloGene

IDs:
NCBI Gene ID: 1299
neXtProt AC: NX_Q14050

Human Synonyms: DJ885L7.4.1, EDM3, IDD, MED

Human Chr (Location): 20q13.3; chr20:62817062-62841159 (+)  GRCh38.p2

Disease Associations: (2) Diseases Associated with Human COL9A3

Mutations,
alleles, and
phenotypes
All mutations/alleles(3) : Targeted(3)
Incidental mutations (data from Mutagenetix , APF )
Interactions
Col9a3 interacts with 132 markers (Mir7-2, Mir7b, Mir9-1, ...)
Gene Ontology
(GO)
classifications
All GO classifications: (1 annotations)
Component collagen type IX trimer
External Resources: FuncBase
Expression
Literature Summary: (22 records)
Data Summary: Results (308)    Tissues (74)    Images (39)    Tissue x Stage Matrix (view)
Assay TypeResults
RNA in situ 264
RT-PCR 44
cDNA source data(66)
Other mouse links: Allen Institute   GEO   Expression Atlas
Other vertebrate links: Xenbase col9a3 ; ZFIN col9a3    NEW 
Molecular
reagents
All nucleic(70) cDNA(68) Primer pair(1) Other(1)
Microarray probesets(4)
Other database
links
VEGA Gene Model OTTMUSG00000016344 (Evidence)
Ensembl Gene Model ENSMUSG00000027570 (Evidence)
Entrez Gene 12841 (Evidence)
UniGene 141312
DFCI TC1576771
NIA Mouse Gene Index U056872
Consensus CDS Project CCDS17180.1
International Mouse Phenotyping Consortium Status Col9a3
Sequences
Representative SequencesLengthStrain/SpeciesFlank
genomic OTTMUSG00000016344 VEGA Gene Model | MGI Sequence Detail 24400 C57BL/6J ±  kb
transcript OTTMUST00000039291 VEGA | MGI Sequence Detail 3046 Not Applicable 
polypeptide OTTMUSP00000017558 VEGA | MGI Sequence Detail 680 Not Applicable 

For the selected sequences
All sequences(45) RefSeq(6) UniProt(8)
Polymorphisms
SNPs within 2kb(98 from dbSNP Build 137)
Protein-related
information
ResourceIDDescription
InterPro IPR008160 Collagen triple helix repeat
Protein Ontology PR:000005724 collagen alpha-3(IX) chain
References
(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:205051 Miller JA, et al., Conserved molecular signatures of neurogenesis in the hippocampal subgranular zone of rodents and primates. Development. 2013 Nov;140(22):4633-44
All references(49)
Other
accession IDs
MGI:2139235

Contributing Projects:
Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Tumor Biology (MTB), Gene Ontology (GO), MouseCyc
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last database update
07/21/2015
MGI 5.22
The Jackson Laboratory