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COL12A1 collagen type XII alpha 1 chain [ Homo sapiens (human) ]

Gene ID: 1303, updated on 12-Aug-2018

Summary

Official Symbol
COL12A1provided by HGNC
Official Full Name
collagen type XII alpha 1 chainprovided by HGNC
Primary source
HGNC:HGNC:2188
See related
Ensembl:ENSG00000111799 MIM:120320; Vega:OTTHUMG00000015051
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
UCMD2; BTHLM2; EDSMYP; COL12A1L; BA209D8.1; DJ234P15.1
Summary
This gene encodes the alpha chain of type XII collagen, a member of the FACIT (fibril-associated collagens with interrupted triple helices) collagen family. Type XII collagen is a homotrimer found in association with type I collagen, an association that is thought to modify the interactions between collagen I fibrils and the surrounding matrix. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]
Expression
Broad expression in endometrium (RPKM 41.5), ovary (RPKM 33.4) and 18 other tissues See more
Orthologs

Genomic context

See COL12A1 in Genome Data Viewer
Location:
6q13-q14.1
Exon count:
67
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 6 NC_000006.12 (75084326..75206262, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (75794042..75915623, complement)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101928516 Neighboring gene uncharacterized LOC105377858 Neighboring gene nucleoporin 50kDa pseudogene Neighboring gene small nucleolar RNA, C/D box 156 Neighboring gene cytochrome c oxidase subunit 7A2 Neighboring gene transmembrane protein 30A

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Pathways from BioSystems

  • Collagen biosynthesis and modifying enzymes, organism-specific biosystem (from REACTOME)
    Collagen biosynthesis and modifying enzymes, organism-specific biosystemThe biosynthesis of collagen is a multistep process. Collagen propeptides are cotranslationally translocated into the ER lumen. Propeptides undergo a number of post-translational modifications. Proli...
  • Collagen chain trimerization, organism-specific biosystem (from REACTOME)
    Collagen chain trimerization, organism-specific biosystemThe C-propeptides of collagen propeptide chains are essential for the association of three peptide chains into a trimeric but non-helical procollagen. This initial binding event determines the compo...
  • Collagen degradation, organism-specific biosystem (from REACTOME)
    Collagen degradation, organism-specific biosystemCollagen fibril diameter and spatial organisation are dependent on the species, tissue type and stage of development (Parry 1988). The lengths of collagen fibrils in mature tissues are largely unknow...
  • Collagen formation, organism-specific biosystem (from REACTOME)
    Collagen formation, organism-specific biosystemCollagen is a family of at least 29 structural proteins derived from over 40 human genes (Myllyharju & Kivirikko 2004). It is the main component of connective tissue, and the most abundant protein in...
  • Degradation of the extracellular matrix, organism-specific biosystem (from REACTOME)
    Degradation of the extracellular matrix, organism-specific biosystemMatrix metalloproteinases (MMPs), previously referred to as matrixins because of their role in degradation of the extracellular matrix (ECM), are zinc and calcium dependent proteases belonging to the...
  • Extracellular matrix organization, organism-specific biosystem (from REACTOME)
    Extracellular matrix organization, organism-specific biosystemThe extracellular matrix is a component of all mammalian tissues, a network consisting largely of the fibrous proteins collagen, elastin and associated-microfibrils, fibronectin and laminins embedded...
  • Protein digestion and absorption, organism-specific biosystem (from KEGG)
    Protein digestion and absorption, organism-specific biosystemProtein is a dietary component essential for nutritional homeostasis in humans. Normally, ingested protein undergoes a complex series of degradative processes following the action of gastric, pancrea...
  • Protein digestion and absorption, conserved biosystem (from KEGG)
    Protein digestion and absorption, conserved biosystemProtein is a dietary component essential for nutritional homeostasis in humans. Normally, ingested protein undergoes a complex series of degradative processes following the action of gastric, pancrea...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Process Evidence Code Pubs
cell adhesion IEA
Inferred from Electronic Annotation
more info
 
collagen fibril organization NAS
Non-traceable Author Statement
more info
PubMed 
endodermal cell differentiation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
endodermal cell differentiation IEP
Inferred from Expression Pattern
more info
PubMed 
growth plate cartilage chondrocyte morphogenesis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
skeletal system development TAS
Traceable Author Statement
more info
PubMed 

General protein information

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

NCBI Reference Sequences (RefSeq)

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.

Genomic

  1. NG_042181.1 RefSeqGene

    Range
    5001..126582
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_004370.5NP_004361.3  collagen alpha-1(XII) chain long isoform precursor

    See identical proteins and their annotated locations for NP_004361.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (long) represents the longer transcript and encodes the longer isoform (long).
    Source sequence(s)
    AI752603, AL080250, AL096771, AL354664, BP286308, DA661773, U73778
    Consensus CDS
    CCDS43482.1
    UniProtKB/Swiss-Prot
    Q99715
    Related
    ENSP00000325146.8, OTTHUMP00000016752, ENST00000322507.12, OTTHUMT00000041249
    Conserved Domains (6) summary
    pfam01391
    Location:27652891
    Collagen; Collagen triple helix repeat (20 copies)
    smart00060
    Location:14741548
    FN3; Fibronectin type 3 domain
    smart00210
    Location:25202712
    TSPN; Thrombospondin N-terminal -like domains
    cd00063
    Location:21182197
    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:17541834
    fn3; Fibronectin type III domain
  2. NM_080645.2NP_542376.2  collagen alpha-1(XII) chain short isoform precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (short) lacks multiple exons in the 5' coding region compared to the long variant. The encoded isoform (short) is shorter but has identical N-and C-termini compared to the long isoform.
    Source sequence(s)
    AI752603, AL096771, DA661773, U73778
    Consensus CDS
    CCDS43481.1
    UniProtKB/Swiss-Prot
    Q99715
    Related
    ENSP00000305147.9, OTTHUMP00000016753, ENST00000345356.10, OTTHUMT00000041250
    Conserved Domains (6) summary
    pfam01391
    Location:17051733
    Collagen; Collagen triple helix repeat (20 copies)
    smart00060
    Location:310384
    FN3; Fibronectin type 3 domain
    smart00210
    Location:13561548
    TSPN; Thrombospondin N-terminal -like domains
    cd00063
    Location:9541033
    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:590670
    fn3; Fibronectin type III domain

RefSeqs of Annotated Genomes: Homo sapiens 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 GRCh38.p12 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p12 Primary Assembly

    Range
    75084326..75206262 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011535436.2XP_011533738.1  collagen alpha-1(XII) chain isoform X4

    Conserved Domains (6) summary
    pfam01391
    Location:17051733
    Collagen; Collagen triple helix repeat (20 copies)
    smart00060
    Location:310384
    FN3; Fibronectin type 3 domain
    smart00210
    Location:13561548
    TSPN; Thrombospondin N-terminal -like domains
    cd00063
    Location:9541033
    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:590670
    fn3; Fibronectin type III domain
  2. XM_011535435.1XP_011533737.1  collagen alpha-1(XII) chain isoform X3

    Conserved Domains (6) summary
    pfam01391
    Location:26742800
    Collagen; Collagen triple helix repeat (20 copies)
    smart00060
    Location:13831457
    FN3; Fibronectin type 3 domain
    smart00210
    Location:24292621
    TSPN; Thrombospondin N-terminal -like domains
    cd00063
    Location:20272106
    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:11071270
    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:16631743
    fn3; Fibronectin type III domain
  3. XM_011535434.1XP_011533736.1  collagen alpha-1(XII) chain isoform X1

    Related
    ENSP00000421216.1, OTTHUMP00000219428, ENST00000483888.6, OTTHUMT00000041251
    Conserved Domains (6) summary
    pfam01391
    Location:27652891
    Collagen; Collagen triple helix repeat (20 copies)
    smart00060
    Location:14741548
    FN3; Fibronectin type 3 domain
    smart00210
    Location:25202712
    TSPN; Thrombospondin N-terminal -like domains
    cd00063
    Location:21182197
    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:17541834
    fn3; Fibronectin type III domain
  4. XM_017010252.2XP_016865741.1  collagen alpha-1(XII) chain isoform X2

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