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

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: human all
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Genomic context

Location:: 4 D2.2; 4 56.78 cM

Exon count:: 32

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	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_000070.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Results show that absence of Col IX induces early developmental, structural and biomechanical alterations in both vertebral body and intervertebral disc which eventually cause severe degenerative changes in the aging spine.
Title: Early changes in morphology, bone mineral density and matrix composition of vertebrae lead to disc degeneration in aged collagen IX -/- mice.

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Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Targeted (2)
Endonuclease-mediated (2)

General gene information

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Markers

AI427499 (e-PCR)
- UniSTS:159280

Col9a2 (e-PCR), detects polymorphism
- UniSTS:141372

UniSTS:478965 (e-PCR)
- UniSTS:478965

Col9a2 (e-PCR), detects polymorphism
- UniSTS:478965

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables extracellular matrix structural constituent conferring tensile strength	IBA Inferred from Biological aspect of Ancestor more info
enables extracellular matrix structural constituent conferring tensile strength	RCA inferred from Reviewed Computational Analysis more info	PubMed
enables protein homodimerization activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in extracellular matrix organization	IBA Inferred from Biological aspect of Ancestor more info

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 more info	PubMed
is_active_in collagen-containing extracellular matrix	IBA Inferred from Biological aspect of Ancestor more info
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

General protein information

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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.