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    Col12a1 collagen, type XII, alpha 1 [ Mus musculus (house mouse) ]

    Gene ID: 12816, updated on 9-Dec-2024

    Summary

    Official Symbol
    Col12a1provided by MGI
    Official Full Name
    collagen, type XII, alpha 1provided by MGI
    Primary source
    MGI:MGI:88448
    See related
    Ensembl:ENSMUSG00000032332 AllianceGenome:MGI:88448
    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 conferring tensile strength. Predicted to be involved in endodermal cell differentiation. Located in collagen-containing extracellular matrix and extracellular space. Is expressed in several structures, including connective tissue; mitral valve; sensory organ; skeleton; and skin. Human ortholog(s) of this gene implicated in Bethlem myopathy and Ullrich congenital muscular dystrophy 2. Orthologous to human COL12A1 (collagen type XII alpha 1 chain). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in limb E14.5 (RPKM 27.9), bladder adult (RPKM 22.2) and 9 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See Col12a1 in Genome Data Viewer
    Location:
    9 E1; 9 43.82 cM
    Exon count:
    66
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 9 NC_000075.7 (79506269..79628423, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 9 NC_000075.6 (79598987..79721141, complement)

    Chromosome 9 - NC_000075.7Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_24744 Neighboring gene predicted gene 10635 Neighboring gene STARR-seq mESC enhancer starr_24745 Neighboring gene predicted gene 8125 Neighboring gene STARR-seq mESC enhancer starr_24746 Neighboring gene STARR-seq mESC enhancer starr_24747 Neighboring gene STARR-positive B cell enhancer ABC_E2297 Neighboring gene predicted gene, 51685 Neighboring gene cytochrome c oxidase subunit 7A2 Neighboring gene STARR-positive B cell enhancer ABC_E5090 Neighboring gene transmembrane protein 30A

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Variation

    Alleles

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

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General protein information

    Preferred Names
    collagen alpha-1(XII) chain
    Names
    procollagen, type XII, alpha 1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001290308.1NP_001277237.1  collagen alpha-1(XII) chain precursor

      Status: VALIDATED

      Source sequence(s)
      AC157477, AC166055, AK028536, AK076278, CA315556, CB722900, CF532120, CF535620, CK624229, CN669497
      Consensus CDS
      CCDS72284.1
      UniProtKB/TrEMBL
      E9PX70
      Related
      ENSMUSP00000071662.7, ENSMUST00000071750.13
      Conserved Domains (6) summary
      pfam01391
      Location:27662893
      Collagen; Collagen triple helix repeat (20 copies)
      smart00060
      Location:14741548
      FN3; Fibronectin type 3 domain
      smart00210
      Location:25222714
      TSPN; Thrombospondin N-terminal -like domains
      cd00063
      Location:724805
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      cd01482
      Location:11981361
      vWA_collagen_alphaI-XII-like; Collagen: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different ...
      pfam00041
      Location:17561836
      fn3; Fibronectin type III domain

    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_000075.7 Reference GRCm39 C57BL/6J

      Range
      79506269..79628423 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006510797.4XP_006510860.1  collagen alpha-1(XII) chain isoform X1

      UniProtKB/Swiss-Prot
      P70322, Q60847
      Conserved Domains (6) summary
      pfam01391
      Location:27662893
      Collagen; Collagen triple helix repeat (20 copies)
      smart00060
      Location:14741548
      FN3; Fibronectin type 3 domain
      smart00210
      Location:25222714
      TSPN; Thrombospondin N-terminal -like domains
      cd00063
      Location:724805
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      cd01482
      Location:11981361
      vWA_collagen_alphaI-XII-like; Collagen: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different ...
      pfam00041
      Location:17581836
      fn3; Fibronectin type III domain
    2. XM_006510800.5XP_006510863.1  collagen alpha-1(XII) chain isoform X2

      Conserved Domains (6) summary
      pfam01391
      Location:17071735
      Collagen; Collagen triple helix repeat (20 copies)
      smart00060
      Location:310384
      FN3; Fibronectin type 3 domain
      smart00210
      Location:13581550
      TSPN; Thrombospondin N-terminal -like domains
      cd00063
      Location:9561035
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      cd01482
      Location:34197
      vWA_collagen_alphaI-XII-like; Collagen: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different ...
      pfam00041
      Location:594672
      fn3; Fibronectin type III domain

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_007730.2: Suppressed sequence

      Description
      NM_007730.2: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.