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

Gene ID: 12841, updated on 5-Mar-2024

Summary

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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 be an extracellular matrix structural constituent. Acts upstream of or within female gonad development and male gonad development. Located in collagen-containing extracellular matrix. Is expressed in several structures, including brain; cranium; eye; hindlimb digit mesenchyme; and reproductive system. Human ortholog(s) of this gene implicated in multiple epiphyseal dysplasia 3 and osteochondrodysplasia. Orthologous to human COL9A3 (collagen type IX alpha 3 chain). [provided by Alliance of Genome Resources, Apr 2022]
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

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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_000068.8Genomic Context describing neighboring genes Neighboring gene predicted gene, 30144 Neighboring gene STARR-positive B cell enhancer ABC_E4530 Neighboring gene MRG/MORF4L binding protein Neighboring gene opioid growth factor receptor Neighboring gene transcription factor-like 5 (basic helix-loop-helix) Neighboring gene predicted gene, 54097 Neighboring gene death inducer-obliterator 1 Neighboring gene predicted gene, 22502

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. Early changes in morphology, bone mineral density and matrix composition of vertebrae lead to disc degeneration in aged collagen IX -/- mice. Kamper M, et al. Matrix Biol, 2016 Jan. PMID 26429145
  2. Comparative proteomic analysis of normal and collagen IX null mouse cartilage reveals altered extracellular matrix composition and novel components of the collagen IX interactome. Brachvogel B, et al. J Biol Chem, 2013 May 10. PMID 23530037, Free PMC Article
  3. Expression patterns of cartilage collagens and Sox9 during mouse heart development. Rahkonen O, et al. Histochem Cell Biol, 2003 Aug. PMID 12883905
  4. Type II and type IX collagen transcript isoforms are expressed during mouse testis development. McClive PJ, et al. Biol Reprod, 2003 May. PMID 12606408
  5. The complete primary structure of the long form of mouse alpha 1(IX) collagen chain and its expression during limb development. Abe N, et al. Biochim Biophys Acta, 1994 Jan 11. PMID 8305476

See all (47) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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.
Submit: New GeneRIF Correction

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

Homology

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
  
involved_in female gonad development IEP
Inferred from Expression Pattern
more info
 PubMed 
involved_in male gonad development IEP
Inferred from Expression Pattern
more info
 PubMed 
Component Evidence Code Pubs
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
  
located_in collagen-containing extracellular matrix HDA PubMed 
is_active_in collagen-containing extracellular matrix IBA
Inferred from Biological aspect of Ancestor
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)

  1. 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)

  2. 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

  1. NC_000068.8 Reference GRCm39 C57BL/6J

    Range
    180239895..180263985
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. 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)
Nucleotide Protein Strain
Heading Accession and Version

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