Col9a3 collagen, type IX, alpha 3 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Col9a3provided by MGI
Official Full Name: collagen, type IX, alpha 3provided by MGI
Primary source: MGI:MGI:894686
See related: Ensembl:ENSMUSG00000027570 AllianceGenome:MGI:894686
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
Summary: Predicted to enable protein homodimerization activity. Predicted to be an extracellular matrix structural constituent conferring tensile strength. Predicted to be involved in extracellular matrix organization. Predicted to be part of collagen type IX trimer. Predicted to be active in basement membrane and extracellular space. Is expressed in several structures, including brain; cranium; hindlimb digit mesenchyme; reproductive system; and sensory organ. Human ortholog(s) of this gene implicated in Stickler syndrome; multiple epiphyseal dysplasia 3; and osteochondrodysplasia. Orthologous to human COL9A3 (collagen type IX alpha 3 chain). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in limb E14.5 (RPKM 147.4), CNS E14 (RPKM 29.8) and 2 other tissues See more
Orthologs: human all
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Genomic context

Location:: 2 H4; 2 103.14 cM

Exon count:: 32

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	2	NC_000068.8 (180239895..180263985)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	2	NC_000068.7 (180598102..180622192)

Chromosome 2 - NC_000068.8 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?

SOX9-COL9A3-dependent regulation of choroid plexus epithelial polarity governs blood-cerebrospinal fluid barrier integrity.
Title: SOX9-COL9A3-dependent regulation of choroid plexus epithelial polarity governs blood-cerebrospinal fluid barrier integrity.
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)

Endonuclease-mediated (4)

General gene information

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Markers

Col9a3 (e-PCR), detects polymorphism
- UniSTS:464659

AV260129 (e-PCR)
- UniSTS:178794

AV006866 (e-PCR)
- UniSTS:178795

PMC15572P1 (e-PCR)
- UniSTS:271347

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 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
is_active_in basement membrane	IBA Inferred from Biological aspect of Ancestor more info
part_of collagen type IX trimer	IBA Inferred from Biological aspect of Ancestor more info
part_of collagen type IX trimer	ISO Inferred from Sequence Orthology 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-3(IX) chain

Names: procollagen, type IX, alpha 3

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)

NM_001378777.1 → NP_001365706.1 collagen alpha-3(IX) chain isoform 1 precursor

Status: VALIDATED

Source sequence(s)

AL669926

Conserved Domains (1) summary

pfam01391
Location:324 → 378

Collagen; Collagen triple helix repeat (20 copies)
NM_009936.2 → NP_034066.2 collagen alpha-3(IX) chain isoform 2 precursor

See identical proteins and their annotated locations for NP_034066.2

Status: VALIDATED

Source sequence(s)

AK030350, AK038481, CK623954

Consensus CDS

CCDS17180.1

UniProtKB/TrEMBL

A2ACT7

Related

ENSMUSP00000099348.2, ENSMUST00000103059.2

Conserved Domains (1) summary

pfam01391
Location:315 → 374

Collagen; Collagen triple helix repeat (20 copies)

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000068.8 Reference GRCm39 C57BL/6J

Range

180239895..180263985

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006500553.3 → XP_006500616.1 collagen alpha-3(IX) chain isoform X1

Conserved Domains (1) summary

pfam01391
Location:279 → 338

Collagen; Collagen triple helix repeat (20 copies)