U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

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

    Gene ID: 12816, updated on 14-Nov-2024

    Summary

    Go to the top of the page Help
    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, Nov 2024]
    Expression
    Biased expression in limb E14.5 (RPKM 27.9), bladder adult (RPKM 22.2) and 9 other tissues See more
    Orthologs
    human all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    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

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • 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

    Go to the top of the pageHelp

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Collagen XII Regulates Corneal Stromal Structure by Modulating Transforming Growth Factor-beta Activity.
      Title: Collagen XII Regulates Corneal Stromal Structure by Modulating Transforming Growth Factor-β Activity.
    2. Collagen XII mediated cellular and extracellular mechanisms regulate establishment of tendon structure and function.
      Title: Collagen XII mediated cellular and extracellular mechanisms regulate establishment of tendon structure and function.
    3. Role of collagen XII in skin homeostasis and repair.
      Title: Role of collagen XII in skin homeostasis and repair.
    4. These data demonstrate, for the first time, a functional relationship between collagens VI and XII during osteogenesis.
      Title: Collagens VI and XII form complexes mediating osteoblast interactions during osteogenesis.
    5. Type XII collagen is overexpressed in permanent human and mouse corneal scars and could represent a new target to treat corneal scarring.
      Title: NC1 long and NC3 short splice variants of type XII collagen are overexpressed during corneal scarring.
    6. data demonstrate important regulatory roles for type XII collagen in osteoblast differentiation and bone matrix formation
      Title: Type XII collagen regulates osteoblast polarity and communication during bone formation.
    7. new information on the mechanical strain-mediated transcriptional control of alpha 1(XII)-mediated fibrillogenesis in the bone.
      Title: Mechanical strain increases expression of type XII collagen in murine osteoblastic MC3T3-E1 cells.
    Submit: New GeneRIF Correction

    Variation

    Go to the top of the page Help

    Alleles

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

    Pathways from PubChem

    Go to the top of the page

    Interactions

    Go to the top of the page Help
    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Go to the top of the page Help

    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables extracellular matrix structural constituent conferring tensile strength RCA
    inferred from Reviewed Computational Analysis
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cell adhesion IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in endodermal cell differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in endodermal cell differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    part_of collagen trimer IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of collagen type XII trimer ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in collagen-containing extracellular matrix HDA PubMed 
    located_in extracellular space HDA PubMed 

    General protein information

    Go to the top of the page Help
    Preferred Names
    collagen alpha-1(XII) chain
    Names
    procollagen, type XII, alpha 1

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    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_001290308.1 → NP_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:2766 → 2893
      Collagen; Collagen triple helix repeat (20 copies)
      smart00060
      Location:1474 → 1548
      FN3; Fibronectin type 3 domain
      smart00210
      Location:2522 → 2714
      TSPN; Thrombospondin N-terminal -like domains
      cd00063
      Location:724 → 805
      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:1198 → 1361
      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:1756 → 1836
      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_006510797.4 → XP_006510860.1  collagen alpha-1(XII) chain isoform X1

      UniProtKB/Swiss-Prot
      P70322, Q60847
      Conserved Domains (6) summary
      pfam01391
      Location:2766 → 2893
      Collagen; Collagen triple helix repeat (20 copies)
      smart00060
      Location:1474 → 1548
      FN3; Fibronectin type 3 domain
      smart00210
      Location:2522 → 2714
      TSPN; Thrombospondin N-terminal -like domains
      cd00063
      Location:724 → 805
      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:1198 → 1361
      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:1758 → 1836
      fn3; Fibronectin type III domain

    2. XM_006510800.5 → XP_006510863.1  collagen alpha-1(XII) chain isoform X2

      Conserved Domains (6) summary
      pfam01391
      Location:1707 → 1735
      Collagen; Collagen triple helix repeat (20 copies)
      smart00060
      Location:310 → 384
      FN3; Fibronectin type 3 domain
      smart00210
      Location:1358 → 1550
      TSPN; Thrombospondin N-terminal -like domains
      cd00063
      Location:956 → 1035
      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:34 → 197
      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:594 → 672
      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.
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q60847.3 GenPept UniProtKB/Swiss-Prot:Q60847

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools
    Miscellaneous