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Aliases for COL12A1 Gene

Aliases for COL12A1 Gene

  • Collagen Type XII Alpha 1 2 3
  • Collagen, Type XII, Alpha 1 2 3 5
  • Collagen Type XII Proteoglycan 2 3
  • COL12A1L 3 4
  • Collagen, Type XII, Alpha 1-Like 2
  • DJ234P15.1 3
  • BA209D8.1 3
  • BTHLM2 3
  • UCMD2 3

External Ids for COL12A1 Gene

Previous HGNC Symbols for COL12A1 Gene

  • COL12A1L

Previous GeneCards Identifiers for COL12A1 Gene

  • GC06M075743
  • GC06M075789
  • GC06M075850
  • GC06M072993

Summaries for COL12A1 Gene

Entrez Gene Summary for COL12A1 Gene

  • 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]

GeneCards Summary for COL12A1 Gene

COL12A1 (Collagen Type XII Alpha 1) is a Protein Coding gene. Diseases associated with COL12A1 include bethlem myopathy 2 and ullrich congenital muscular dystrophy 2. Among its related pathways are Degradation of the extracellular matrix and ERK Signaling. GO annotations related to this gene include extracellular matrix structural constituent conferring tensile strength. An important paralog of this gene is MATN1.

UniProtKB/Swiss-Prot for COL12A1 Gene

  • Type XII collagen interacts with type I collagen-containing fibrils, the COL1 domain could be associated with the surface of the fibrils, and the COL2 and NC3 domains may be localized in the perifibrillar matrix.

Gene Wiki entry for COL12A1 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for COL12A1 Gene

Genomics for COL12A1 Gene

Regulatory Elements for COL12A1 Gene

Promoters for COL12A1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around COL12A1 on UCSC Golden Path with GeneCards custom track

Genomic Location for COL12A1 Gene

Chromosome:
6
Start:
75,084,326 bp from pter
End:
75,206,202 bp from pter
Size:
121,877 bases
Orientation:
Minus strand

Genomic View for COL12A1 Gene

Genes around COL12A1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
COL12A1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for COL12A1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for COL12A1 Gene

Proteins for COL12A1 Gene

  • Protein details for COL12A1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q99715-COCA1_HUMAN
    Recommended name:
    Collagen alpha-1(XII) chain
    Protein Accession:
    Q99715
    Secondary Accessions:
    • O43853
    • Q15955
    • Q5VYK1
    • Q5VYK2
    • Q71UR3
    • Q99716

    Protein attributes for COL12A1 Gene

    Size:
    3063 amino acids
    Molecular mass:
    333147 Da
    Quaternary structure:
    • Trimer of identical chains each containing 190 kDa of non-triple-helical sequences.

    Alternative splice isoforms for COL12A1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for COL12A1 Gene

Proteomics data for COL12A1 Gene at MOPED

Post-translational modifications for COL12A1 Gene

  • Hydroxylation on proline residues within the sequence motif, GXPG, is most likely to be 4-hydroxy as this fits the requirement for 4-hydroxylation in vertebrates.
  • Isoform 1 O-glycosylation; glycosaminoglycan of chondroitin-sulfate type.
  • The triple-helical tail is stabilized by disulfide bonds at each end.
  • Glycosylation at Asn 700, Ser 798, Ser 889, Ser 981, Thr 1099, Thr 1106, Thr 1120, Thr 1124, Thr 1748, Asn 1763, Asn 2206, Thr 2303, Asn 2528, and Asn 2679
  • Modification sites at PhosphoSitePlus

Antibody Products

No data available for DME Specific Peptides for COL12A1 Gene

Domains & Families for COL12A1 Gene

Graphical View of Domain Structure for InterPro Entry

Q99715

UniProtKB/Swiss-Prot:

COCA1_HUMAN :
  • Contains 4 collagen-like domains.
  • Belongs to the fibril-associated collagens with interrupted helices (FACIT) family.
Domain:
  • Contains 4 collagen-like domains.
  • Contains 18 fibronectin type-III domains.
  • Contains 1 laminin G-like domain.
  • Contains 4 VWFA domains.
Family:
  • Belongs to the fibril-associated collagens with interrupted helices (FACIT) family.
genes like me logo Genes that share domains with COL12A1: view

Function for COL12A1 Gene

Molecular function for COL12A1 Gene

GENATLAS Biochemistry:
collagen,type XII,alpha 1,extracellular matrix protein,fibril associated collagen with interrupted triple helices (FACIT),with two splice variants 330.8,203.2kDa,respectively,expressed in collagen I-containing tissues
UniProtKB/Swiss-Prot Function:
Type XII collagen interacts with type I collagen-containing fibrils, the COL1 domain could be associated with the surface of the fibrils, and the COL2 and NC3 domains may be localized in the perifibrillar matrix.
genes like me logo Genes that share phenotypes with COL12A1: view

Human Phenotype Ontology for COL12A1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for COL12A1 Gene

MGI Knock Outs for COL12A1:

Animal Model Products

CRISPR Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Transcription Factor Targets and HOMER Transcription for COL12A1 Gene

Localization for COL12A1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for COL12A1 Gene

Secreted, extracellular space, extracellular matrix.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for COL12A1 Gene COMPARTMENTS Subcellular localization image for COL12A1 gene
Compartment Confidence
endoplasmic reticulum 5
extracellular 5
golgi apparatus 1
lysosome 1
plasma membrane 1
vacuole 1

Gene Ontology (GO) - Cellular Components for COL12A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0031012 colocalizes_with extracellular matrix IDA 20551380
GO:1903561 extracellular vesicle IDA 24769233
genes like me logo Genes that share ontologies with COL12A1: view

Pathways & Interactions for COL12A1 Gene

genes like me logo Genes that share pathways with COL12A1: view

Interacting Proteins for COL12A1 Gene

Gene Ontology (GO) - Biological Process for COL12A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007155 cell adhesion IEA --
GO:0022617 extracellular matrix disassembly TAS --
genes like me logo Genes that share ontologies with COL12A1: view

No data available for SIGNOR curated interactions for COL12A1 Gene

Drugs & Compounds for COL12A1 Gene

No Compound Related Data Available

Transcripts for COL12A1 Gene

Unigene Clusters for COL12A1 Gene

Collagen, type XII, alpha 1:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for COL12A1 Gene

No ASD Table

Relevant External Links for COL12A1 Gene

GeneLoc Exon Structure for
COL12A1
ECgene alternative splicing isoforms for
COL12A1

Expression for COL12A1 Gene

mRNA expression in normal human tissues for COL12A1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for COL12A1 Gene

This gene is overexpressed in Bone marrow mesenchymal stem cell (39.3) and Breast (10.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for COL12A1 Gene



SOURCE GeneReport for Unigene cluster for COL12A1 Gene Hs.101302

mRNA Expression by UniProt/SwissProt for COL12A1 Gene

Q99715-COCA1_HUMAN
Tissue specificity: Found in collagen I-containing tissues: both isoform 1 and isoform 2 appear in amnion, chorion, skeletal muscle, small intestine, and in cell culture of dermal fibroblasts, keratinocytes and endothelial cells. Only isoform 2 is found in lung, placenta, kidney and a squamous cell carcinoma cell line. Isoform 1 is also present in the corneal epithelial Bowmans membrane (BM) and the interfibrillar matrix of the corneal stroma, but it is not detected in the limbal BM.
genes like me logo Genes that share expression patterns with COL12A1: view

Protein tissue co-expression partners for COL12A1 Gene

- Elite partner

Primer Products

In Situ Assay Products

No data available for mRNA differential expression in normal tissues for COL12A1 Gene

Orthologs for COL12A1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for COL12A1 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia COL12A1 35
  • 89.53 (n)
  • 94.25 (a)
COL12A1 36
  • 92 (a)
OneToOne
dog
(Canis familiaris)
Mammalia COL12A1 35
  • 91.86 (n)
  • 95.2 (a)
COL12A1 36
  • 95 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Col12a1 35
  • 87.75 (n)
  • 92.32 (a)
Col12a1 16
Col12a1 36
  • 92 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia COL12A1 35
  • 99.58 (n)
  • 99.77 (a)
COL12A1 36
  • 100 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Col12a1 35
  • 87.46 (n)
  • 92.51 (a)
oppossum
(Monodelphis domestica)
Mammalia COL12A1 36
  • 90 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 36
  • 73 (a)
ManyToMany
chicken
(Gallus gallus)
Aves COL12A1 35
  • 75.96 (n)
  • 78.8 (a)
COL12A1 36
  • 77 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia COL12A1 36
  • 77 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia col12a1 35
  • 70.9 (n)
  • 73.29 (a)
Str.12198 35
African clawed frog
(Xenopus laevis)
Amphibia Xl.23790 35
zebrafish
(Danio rerio)
Actinopterygii col12a1a 35
  • 62.69 (n)
  • 61.92 (a)
col12a1a 36
  • 62 (a)
OneToOne
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.3872 35
sea squirt
(Ciona savignyi)
Ascidiacea CSA.10963 36
  • 19 (a)
OneToMany
Species with no ortholog for COL12A1:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for COL12A1 Gene

ENSEMBL:
Gene Tree for COL12A1 (if available)
TreeFam:
Gene Tree for COL12A1 (if available)

Paralogs for COL12A1 Gene

(4) SIMAP similar genes for COL12A1 Gene using alignment to 6 proteins:

Pseudogenes.org Pseudogenes for COL12A1 Gene

genes like me logo Genes that share paralogs with COL12A1: view

Variants for COL12A1 Gene

Sequence variations from dbSNP and Humsavar for COL12A1 Gene

SNP ID Clin Chr 06 pos Sequence Context AA Info Type
rs34730529 - 75,183,560(-) TTAGA(C/G)CCTTT intron-variant, reference, missense
rs240736 - 75,138,465(-) CCTGA(C/T)TGGCA reference, missense
rs35523808 - 75,125,255(-) CATGG(A/T)AGCCT reference, missense
rs35710072 - 75,113,656(-) TTGCA(A/G)TTTGG reference, missense
rs34438461 - 75,130,857(-) GGGCC(A/G)AACGC reference, missense

Structural Variations from Database of Genomic Variants (DGV) for COL12A1 Gene

Variant ID Type Subtype PubMed ID
nsv830697 CNV Gain+Loss 17160897
nsv886181 CNV Loss 21882294

Variation tolerance for COL12A1 Gene

Residual Variation Intolerance Score: 9.57% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.18; 80.87% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for COL12A1 Gene

HapMap Linkage Disequilibrium report
COL12A1
Human Gene Mutation Database (HGMD)
COL12A1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for COL12A1 Gene

Disorders for COL12A1 Gene

MalaCards: The human disease database

(8) MalaCards diseases for COL12A1 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
bethlem myopathy 2
  • bthlm2
ullrich congenital muscular dystrophy 2
  • ucmd2
col12a1-related muscle diseases
bethlem myopathy 1
  • bethlem myopathy
ullrich congenital muscular dystrophy 1
  • ullrich congenital muscular dystrophy
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

COCA1_HUMAN
  • Bethlem myopathy 2 (BTHLM2) [MIM:616471]: A form of Bethlem myopathy, a benign proximal myopathy characterized by early childhood onset and joint contractures most frequently affecting the elbows and ankles. {ECO:0000269 PubMed:24334604, ECO:0000269 PubMed:24334769}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Ullrich congenital muscular dystrophy 2 (UCMD2) [MIM:616470]: A form of Ullrich muscular dystrophy, a congenital myopathy characterized by muscle weakness and multiple joint contractures, generally noted at birth or early infancy. The clinical course is more severe than in Bethlem myopathy. {ECO:0000269 PubMed:24334604}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for COL12A1

Genetic Association Database (GAD)
COL12A1
Human Genome Epidemiology (HuGE) Navigator
COL12A1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
COL12A1
genes like me logo Genes that share disorders with COL12A1: view

No data available for Genatlas for COL12A1 Gene

Publications for COL12A1 Gene

  1. Complete primary structure of two splice variants of collagen XII, and assignment of alpha 1(XII) collagen (COL12A1), alpha 1(IX) collagen (COL9A1), and alpha 1(XIX) collagen (COL19A1) to human chromosome 6q12-q13. (PMID: 9143499) Gerecke D.R. … Burgeson R.E. (Genomics 1997) 2 3 4 23 67
  2. The COL12A1 and COL14A1 genes and Achilles tendon injuries. (PMID: 17960519) September A.V. … Collins M. (Int J Sports Med 2008) 3 23
  3. The mouse alpha 1(XII) and human alpha 1(XII)-like collagen genes are localized on mouse chromosome 9 and human chromosome 6. (PMID: 1427837) Oh S.P. … Olsen B.R. (Genomics 1992) 3 23
  4. Using a cell line breast cancer progression system to identify biomarker candidates. (PMID: 24262153) Yen T.Y. … Macher B.A. (J Proteomics 2014) 3
  5. Mutations in the collagen XII gene define a new form of extracellular matrix-related myopathy. (PMID: 24334769) Hicks D. … Straub V. (Hum. Mol. Genet. 2014) 3

Products for COL12A1 Gene

Sources for COL12A1 Gene

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