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Col9a2 collagen, type IX, alpha 2 [ Mus musculus (house mouse) ]

Gene ID: 12840, updated on 26-Sep-2022

Summary

Official Symbol
Col9a2provided by MGI
Official Full Name
collagen, type IX, alpha 2provided by MGI
Primary source
MGI:MGI:88466
See related
Ensembl:ENSMUSG00000028626 AllianceGenome:MGI:88466
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
Col9a-2
Summary
Predicted to be an extracellular matrix structural constituent. Predicted to be involved in extracellular matrix organization. Located in collagen-containing extracellular matrix. Is expressed in several structures, including cap mesenchyme; central nervous system; limb mesenchyme; sensory organ; and skeleton. Human ortholog(s) of this gene implicated in Stickler syndrome; multiple epiphyseal dysplasia 2; and osteochondrodysplasia. Orthologous to human COL9A2 (collagen type IX alpha 2 chain). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in limb E14.5 (RPKM 84.1), CNS E14 (RPKM 17.5) and 4 other tissues See more
Orthologs
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Genomic context

See Col9a2 in Genome Data Viewer
Location:
4 D2.2; 4 56.78 cM
Exon count:
32
Annotation release Status Assembly Chr Location
109 current GRCm39 (GCF_000001635.27) 4 NC_000070.7 (120896763..120912522)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 4 NC_000070.6 (121039566..121055325)

Chromosome 4 - NC_000070.7Genomic Context describing neighboring genes Neighboring gene zinc finger protein 69 Neighboring gene small ArfGAP 2 Neighboring gene microRNA 7015 Neighboring gene zinc metallopeptidase, STE24 Neighboring gene predicted gene, 23540 Neighboring gene transmembrane and coiled-coil domains 2

Genomic regions, transcripts, and products

Expression

  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Targeted (2) 
  • Endonuclease-mediated (2) 

General gene information

Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables extracellular matrix structural constituent IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables extracellular matrix structural constituent conferring tensile strength RCA
inferred from Reviewed Computational Analysis
more info
PubMed 
Process Evidence Code Pubs
involved_in extracellular matrix organization IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
part_of collagen trimer IEA
Inferred from Electronic Annotation
more info
 
part_of collagen type IX trimer ISO
Inferred from Sequence Orthology
more info
 
located_in collagen-containing extracellular matrix HDA PubMed 
is_active_in extracellular matrix IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in extracellular region IEA
Inferred from Electronic Annotation
more info
 
is_active_in extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
collagen alpha-2(IX) chain
Names
procollagen, type IX, alpha 2

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_007741.2NP_031767.2  collagen alpha-2(IX) chain precursor

    Status: VALIDATED

    Source sequence(s)
    AA171281, BB732275, BQ964231, BU512853, BY088510, BY232299, BY732235, CJ046324, CJ312879, CX243824
    Consensus CDS
    CCDS18599.1
    UniProtKB/TrEMBL
    I7HJR1
    Related
    ENSMUSP00000030372.6, ENSMUST00000030372.6
    Conserved Domains (1) summary
    pfam01391
    Location:258315
    Collagen; Collagen triple helix repeat (20 copies)

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 109 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000070.7 Reference GRCm39 C57BL/6J

    Range
    120896763..120912522
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)