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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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    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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