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Col9a1 collagen, type IX, alpha 1 [ Mus musculus (house mouse) ]

Gene ID: 12839, updated on 2-Nov-2024

Summary

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Official Symbol
Col9a1provided by MGI
Official Full Name
collagen, type IX, alpha 1provided by MGI
Primary source
MGI:MGI:88465
See related
Ensembl:ENSMUSG00000026147 AllianceGenome:MGI:88465
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-1
Summary
Predicted to enable carbohydrate binding activity and protein homodimerization activity. Predicted to be an extracellular matrix structural constituent conferring tensile strength. Acts upstream of or within chondrocyte proliferation; growth plate cartilage development; and tissue homeostasis. Predicted to be located in extracellular region. Predicted to be part of collagen type IX trimer. Predicted to be active in collagen-containing extracellular matrix and extracellular space. Is expressed in several structures, including genitourinary system; respiratory system; salivary gland primordium; sensory organ; and skeletal system. Used to study osteoarthritis. Human ortholog(s) of this gene implicated in Stickler syndrome; multiple epiphyseal dysplasia 6; and osteochondrodysplasia. Orthologous to human COL9A1 (collagen type IX alpha 1 chain). [provided by Alliance of Genome Resources, Nov 2024]
Expression
Biased expression in limb E14.5 (RPKM 74.4), CNS E14 (RPKM 10.9) and 1 other tissue See more
Orthologs
human all
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Genomic context

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See Col9a1 in Genome Data Viewer
Location:
1 A5; 1 9.95 cM
Exon count:
40
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 1 NC_000067.7 (24216670..24291819)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 1 NC_000067.6 (24177589..24252738)

Chromosome 1 - NC_000067.7Genomic Context describing neighboring genes Neighboring gene predicted gene 53062 Neighboring gene succinate dehydrogenase complex assembly factor 4 Neighboring gene family with sequence similarity 135, member A Neighboring gene STARR-seq mESC enhancer starr_00443 Neighboring gene STARR-seq mESC enhancer starr_00445 Neighboring gene predicted gene, 30756 Neighboring gene STARR-seq mESC enhancer starr_00447 Neighboring gene collagen, type XIX, alpha 1 Neighboring gene STARR-seq mESC enhancer starr_00448 Neighboring gene STARR-seq mESC enhancer starr_00450 Neighboring gene STARR-seq mESC enhancer starr_00451 Neighboring gene predicted gene, 26418 Neighboring gene tubulin, beta 4B class IVB, pseudogene 2

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 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. Trabecular bone deterioration in col9a1+/- mice associated with enlarged osteoclasts adhered to collagen IX-deficient bone. Wang CJ, et al. J Bone Miner Res, 2008 Jun. PMID 18251701, Free PMC Article
  2. A short isoform of Col9a1 supports alveolar bone repair. Ting K, et al. Am J Pathol, 1999 Dec. PMID 10595929, Free PMC Article
  3. Locomotor activity and gait in aged mice deficient for type IX collagen. Costello KE, et al. J Appl Physiol (1985), 2010 Jul. PMID 20360435, Free PMC Article
  4. Depletion of Collagen IX Alpha1 Impairs Myeloid Cell Function. Probst K, et al. Stem Cells, 2018 Nov. PMID 30063808
  5. Osteoarthritis associated with mild chondrodysplasia in transgenic mice expressing alpha 1(IX) collagen chains with a central deletion. Nakata K, et al. Proc Natl Acad Sci U S A, 1993 Apr 1. PMID 8464901, Free PMC Article

See all (95) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Collagen IX deficiency leads to premature vascularization and ossification of murine femoral heads through an imbalance of pro- and antiangiogenic factors.
    Title: Collagen IX deficiency leads to premature vascularization and ossification of murine femoral heads through an imbalance of pro- and antiangiogenic factors.
  2. An accelerated hypertrophic differentiation caused by a disturbed Ihh-PTHrP signaling pathway may lead to a higher bone mineral density in the vertebral bodies of newborn Col IX -/- mice and, as a result, to the early onset of disc degeneration.
    Title: Absence of collagen IX accelerates hypertrophic differentiation in the embryonic mouse spine through a disturbance of the Ihh-PTHrP feedback loop.
  3. 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.
  4. Proteomic analysis of interaction partners of collagen alpha1 IX in the articular cartilage of mice.
    Title: Comparative proteomic analysis of normal and collagen IX null mouse cartilage reveals altered extracellular matrix composition and novel components of the collagen IX interactome.
  5. They test the hypothesis that aged Col9a1(-/-) mice would reduce joint pain by adopting locomotor behaviors that reduce both the magnitude and daily frequency of joint loading.
    Title: Locomotor activity and gait in aged mice deficient for type IX collagen.
  6. Loss of type IX collagen and COMP leads to matrix aberrations that may make cartilage more susceptible to degeneration.
    Title: Combined role of type IX collagen and cartilage oligomeric matrix protein in cartilage matrix assembly: cartilage oligomeric matrix protein counteracts type IX collagen-induced limitation of cartilage collagen fibril growth in mouse chondrocyte cultures.
  7. Col9a1(-/-) mice present behavioral changes consistent with anatomic signs of osteoarthritis and intervertebral disc degeneration.
    Title: Decreased physical function and increased pain sensitivity in mice deficient for type IX collagen.
  8. all long bones are shorter and broader in newborn Col9a1-/- mice
    Title: Collagen IX-deficiency seriously compromises growth cartilage development in mice.
  9. mineralized bone matrix deficient of short collagen IX may become susceptible to osteoclastic bone resorption, possibly through a novel non-cell-autonomous mechanism
    Title: Trabecular bone deterioration in col9a1+/- mice associated with enlarged osteoclasts adhered to collagen IX-deficient bone.
  10. A deletion mutation for type IX collagen is associated with connective tissue changes characteristic of musculoskeletal degeneration in bony and cartilaginous tissue regions
    Title: Early-onset degeneration of the intervertebral disc and vertebral end plate in mice deficient in type IX collagen.
Submit: New GeneRIF Correction See all GeneRIFs (14)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Endonuclease-mediated (2) 
  • Targeted (1)  1 citation

Pathways from PubChem

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General gene information

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Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables carbohydrate binding ISO
Inferred from Sequence Orthology
more info
  
enables extracellular matrix structural constituent conferring tensile strength IBA
Inferred from Biological aspect of Ancestor
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein homodimerization activity ISO
Inferred from Sequence Orthology
more info
  
Process Evidence Code Pubs
acts_upstream_of_or_within bone morphogenesis IGI
Inferred from Genetic Interaction
more info
 PubMed 
acts_upstream_of_or_within cartilage development IGI
Inferred from Genetic Interaction
more info
 PubMed 
acts_upstream_of_or_within cartilage development IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within chondrocyte proliferation IGI
Inferred from Genetic Interaction
more info
 PubMed 
involved_in extracellular matrix organization IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within growth plate cartilage development IGI
Inferred from Genetic Interaction
more info
 PubMed 
acts_upstream_of_or_within growth plate cartilage development IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within skeletal system development IGI
Inferred from Genetic Interaction
more info
 PubMed 
acts_upstream_of_or_within tissue homeostasis IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
part_of collagen trimer IEA
Inferred from Electronic Annotation
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 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-1(IX) chain
Names
alpha 1 type IX collagen
procollagen, type IX, alpha 1

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_001290691.1 → NP_001277620.1  collagen alpha-1(IX) chain isoform 2 precursor

    See identical proteins and their annotated locations for NP_001277620.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded protein (isoform 2) has a shorter and distinct N-terminus, compared to isoform 1.
    Source sequence(s)
    AK011547, AK017395, AK160749, BY144829
    Consensus CDS
    CCDS69871.1
    UniProtKB/TrEMBL
    Q9D0D2
    Related
    ENSMUSP00000085687.3, ENSMUST00000088349.3
    Conserved Domains (1) summary
    pfam01391
    Location:267 → 324
    Collagen; Collagen triple helix repeat (20 copies)

  2. NM_007740.3 → NP_031766.3  collagen alpha-1(IX) chain isoform 1 precursor

    See identical proteins and their annotated locations for NP_031766.3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AK004383, AK017395, AK031071, CX207941, L12215
    Consensus CDS
    CCDS35527.1
    UniProtKB/TrEMBL
    G3X995
    Related
    ENSMUSP00000051579.9, ENSMUST00000054588.15
    Conserved Domains (2) summary
    pfam01391
    Location:508 → 565
    Collagen; Collagen triple helix repeat (20 copies)
    smart00210
    Location:50 → 244
    TSPN; Thrombospondin N-terminal -like domains

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_000067.7 Reference GRCm39 C57BL/6J

    Range
    24216670..24291819
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006495649.3 → XP_006495712.1  collagen alpha-1(IX) chain isoform X1

    Conserved Domains (2) summary
    pfam01391
    Location:319 → 350
    Collagen; Collagen triple helix repeat (20 copies)
    smart00210
    Location:50 → 244
    TSPN; Thrombospondin N-terminal -like domains

  2. XM_036157312.1 → XP_036013205.1  collagen alpha-1(IX) chain isoform X2

    Conserved Domains (2) summary
    smart00210
    Location:50 → 244
    TSPN; Thrombospondin N-terminal -like domains
    pfam01391
    Location:496 → 552
    Collagen; Collagen triple helix repeat (20 copies)
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q05722.2 GenPept UniProtKB/Swiss-Prot:Q05722

Gene LinkOut

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