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

Gene ID: 12816, updated on 21-Apr-2024

Summary

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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. Predicted to act upstream of or within cell adhesion. 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 Ullrich congenital muscular dystrophy. Orthologous to human COL12A1 (collagen type XII alpha 1 chain). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in limb E14.5 (RPKM 27.9), bladder adult (RPKM 22.2) and 9 other tissues See more
Orthologs
human all
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Genomic context

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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

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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. The mouse alpha 1(XII) and human alpha 1(XII)-like collagen genes are localized on mouse chromosome 9 and human chromosome 6. Oh SP, et al. Genomics, 1992 Oct. PMID 1427837

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

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Alleles

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

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

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 RCA
inferred from Reviewed Computational Analysis
more info
 PubMed 
Process Evidence Code Pubs
acts_upstream_of_or_within cell adhesion IEA
Inferred from Electronic Annotation
more info
  
involved_in endodermal cell differentiation IBA
Inferred from Biological aspect of Ancestor
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 
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
  
located_in extracellular space HDA PubMed 

General protein information

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

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