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

Gene ID: 12816, updated on 7-Sep-2021

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
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
Expression
Biased expression in limb E14.5 (RPKM 27.9), bladder adult (RPKM 22.2) and 9 other tissues See more
Orthologs
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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
109 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)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 9 NC_000075.5 (79446798..79566485, complement)

Chromosome 9 - NC_000075.7Genomic Context describing neighboring genes Neighboring gene predicted gene 10635 Neighboring gene predicted gene 8125 Neighboring gene predicted gene, 51685 Neighboring gene cytochrome c oxidase subunit 7A2 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)

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

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
PubMed 
Component Evidence Code Pubs
part_of collagen trimer IEA
Inferred from Electronic Annotation
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
PubMed 
located_in extracellular region IEA
Inferred from Electronic Annotation
more info
 
located_in extracellular space HDA PubMed 
is_active_in extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

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_001290308.1NP_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/Swiss-Prot
    Q60847
    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: Mus musculus Annotation Release 109 details...Open this link in a new tab

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

    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.
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