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Aliases for COL6A1 Gene

Aliases for COL6A1 Gene

  • Collagen, Type VI, Alpha 1 2 3
  • OPLL 3 6
  • Collagen VI, Alpha-1 Polypeptide 3
  • Alpha 1 (VI) Chain (61 AA) 3
  • Collagen Alpha-1(VI) Chain 3

External Ids for COL6A1 Gene

Previous GeneCards Identifiers for COL6A1 Gene

  • GC21P043908
  • GC21P046259
  • GC21P046260
  • GC21P046261
  • GC21P046226
  • GC21P047401
  • GC21P032782

Summaries for COL6A1 Gene

Entrez Gene Summary for COL6A1 Gene

  • The collagens are a superfamily of proteins that play a role in maintaining the integrity of various tissues. Collagens are extracellular matrix proteins and have a triple-helical domain as their common structural element. Collagen VI is a major structural component of microfibrils. The basic structural unit of collagen VI is a heterotrimer of the alpha1(VI), alpha2(VI), and alpha3(VI) chains. The alpha2(VI) and alpha3(VI) chains are encoded by the COL6A2 and COL6A3 genes, respectively. The protein encoded by this gene is the alpha 1 subunit of type VI collagen (alpha1(VI) chain). Mutations in the genes that code for the collagen VI subunits result in the autosomal dominant disorder, Bethlem myopathy. [provided by RefSeq, Jul 2008]

GeneCards Summary for COL6A1 Gene

COL6A1 (Collagen, Type VI, Alpha 1) is a Protein Coding gene. Diseases associated with COL6A1 include collagen type vi-related disorders and bethlem myopathy. Among its related pathways are PI3K-Akt signaling pathway and Signaling by FGFR. GO annotations related to this gene include platelet-derived growth factor binding. An important paralog of this gene is SCARA3.

UniProtKB/Swiss-Prot for COL6A1 Gene

  • Collagen VI acts as a cell-binding protein

Gene Wiki entry for COL6A1 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for COL6A1 Gene

Genomics for COL6A1 Gene

Regulatory Elements for COL6A1 Gene

Epigenetics Products

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat

Genomic Location for COL6A1 Gene

Start:
45,981,737 bp from pter
End:
46,005,050 bp from pter
Size:
23,314 bases
Orientation:
Plus strand

Genomic View for COL6A1 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for COL6A1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for COL6A1 Gene

Proteins for COL6A1 Gene

  • Protein details for COL6A1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P12109-CO6A1_HUMAN
    Recommended name:
    Collagen alpha-1(VI) chain
    Protein Accession:
    P12109
    Secondary Accessions:
    • O00117
    • O00118
    • Q14040
    • Q14041
    • Q16258
    • Q7Z645
    • Q9BSA8

    Protein attributes for COL6A1 Gene

    Size:
    1028 amino acids
    Molecular mass:
    108529 Da
    Quaternary structure:
    • Trimers composed of three different chains: alpha-1(VI), alpha-2(VI), and alpha-3(VI) or alpha-5(VI) or alpha-6(VI)

neXtProt entry for COL6A1 Gene

Proteomics data for COL6A1 Gene at MOPED

Post-translational modifications for COL6A1 Gene

  • Prolines at the third position of the tripeptide repeating unit (G-X-Y) are hydroxylated in some or all of the chains
  • Glycosylation at Asn212, Asn516, Asn537, Asn804, and Asn896
  • Modification sites at PhosphoSitePlus

Other Protein References for COL6A1 Gene

ENSEMBL proteins:
Reactome Protein details:
REFSEQ proteins:

Antibody Products

Protein Products

No data available for DME Specific Peptides for COL6A1 Gene

Domains for COL6A1 Gene

Gene Families for COL6A1 Gene

HGNC:

Graphical View of Domain Structure for InterPro Entry

P12109

UniProtKB/Swiss-Prot:

CO6A1_HUMAN :
  • P12109
Domain:
  • Contains 3 VWFA domains.
Family:
  • Belongs to the type VI collagen family.
genes like me logo Genes that share domains with COL6A1: view

Function for COL6A1 Gene

Molecular function for COL6A1 Gene

GENATLAS Biochemistry:
collagen type VI,alpha 1 (150kDa),microfibrillar
UniProtKB/Swiss-Prot Function:
Collagen VI acts as a cell-binding protein

Gene Ontology (GO) - Molecular Function for COL6A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0048407 platelet-derived growth factor binding IDA 8900172
genes like me logo Genes that share ontologies with COL6A1: view

Phenotypes for COL6A1 Gene

genes like me logo Genes that share phenotypes with COL6A1: view

Animal Models for COL6A1 Gene

MGI Knock Outs for COL6A1:

Animal Model Products

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for COL6A1

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targeting and HOMER Transcription for COL6A1 Gene

Localization for COL6A1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for COL6A1 Gene

Secreted, extracellular space, extracellular matrix.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for COL6A1 Gene COMPARTMENTS Subcellular localization image for COL6A1 gene
Compartment Confidence
extracellular 5
endoplasmic reticulum 4
mitochondrion 2
plasma membrane 2
cytosol 1
nucleus 1

Gene Ontology (GO) - Cellular Components for COL6A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS --
GO:0005578 proteinaceous extracellular matrix --
GO:0005589 collagen type VI trimer NAS 2551668
GO:0005765 lysosomal membrane IDA 17897319
GO:0005788 endoplasmic reticulum lumen TAS --
genes like me logo Genes that share ontologies with COL6A1: view

Pathways for COL6A1 Gene

genes like me logo Genes that share pathways with COL6A1: view

PCR Array Products

  • Pathway & Disease-focused RT² Profiler PCR Arrays
    • Extracellular Matrix & Adhesion Molecules in human,mouse,rat
    • Osteogenesis in human,mouse,rat

Gene Ontology (GO) - Biological Process for COL6A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001649 osteoblast differentiation IDA 16210410
GO:0007155 cell adhesion IEA --
GO:0007411 axon guidance TAS --
GO:0022617 extracellular matrix disassembly TAS --
GO:0030198 extracellular matrix organization TAS --
genes like me logo Genes that share ontologies with COL6A1: view

Compounds for COL6A1 Gene

(1) Novoseek inferred chemical compound relationships for COL6A1 Gene

Compound -log(P) Hits PubMed IDs
cysteine 9.14 1
genes like me logo Genes that share compounds with COL6A1: view

Transcripts for COL6A1 Gene

mRNA/cDNA for COL6A1 Gene

Unigene Clusters for COL6A1 Gene

Collagen, type VI, alpha 1:
Representative Sequences:

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for COL6A1

Primer Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for COL6A1 Gene

No ASD Table

Relevant External Links for COL6A1 Gene

GeneLoc Exon Structure for
COL6A1
ECgene alternative splicing isoforms for
COL6A1

Expression for COL6A1 Gene

mRNA expression in normal human tissues for COL6A1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues for COL6A1 Gene

This gene is overexpressed in Adipocyte (16.2), Urinary Bladder (11.7), Bone marrow mesenchymal stem cell (8.0), and Colon muscle (7.7).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for COL6A1 Gene

SOURCE GeneReport for Unigene cluster for COL6A1 Gene Hs.474053

genes like me logo Genes that share expressions with COL6A1: view

Expression partners for COL6A1 Gene

In Situ Assay Products

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for COL6A1 Gene

Orthologs for COL6A1 Gene

This gene was present in the common ancestor of animals.

Orthologs for COL6A1 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia COL6A1 35
  • 87.44 (n)
  • 91.52 (a)
COL6A1 36
  • 91 (a)
OneToOne
dog
(Canis familiaris)
Mammalia COL6A1 35
  • 88.37 (n)
  • 91.23 (a)
COL6A1 36
  • 91 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Col6a1 35
  • 83.15 (n)
  • 90.31 (a)
Col6a1 16
Col6a1 36
  • 90 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia COL6A1 35
  • 99.12 (n)
  • 99.12 (a)
COL6A1 36
  • 99 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Col6a1 35
  • 83.61 (n)
  • 89.81 (a)
oppossum
(Monodelphis domestica)
Mammalia COL6A1 36
  • 69 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia COL6A1 36
  • 74 (a)
OneToOne
chicken
(Gallus gallus)
Aves COL6A1 35
  • 70.63 (n)
  • 70.3 (a)
COL6A1 36
  • 69 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia COL6A1 36
  • 69 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia col6a1 35
  • 63.12 (n)
  • 64.94 (a)
African clawed frog
(Xenopus laevis)
Amphibia col6a1-prov 35
zebrafish
(Danio rerio)
Actinopterygii col6a1 35
  • 59.8 (n)
  • 56.97 (a)
col6a1 36
  • 55 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea mec-5 36
  • 39 (a)
OneToMany
Species with no ortholog for COL6A1:
  • 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)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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)

Evolution for COL6A1 Gene

ENSEMBL:
Gene Tree for COL6A1 (if available)
TreeFam:
Gene Tree for COL6A1 (if available)

Paralogs for COL6A1 Gene

Paralogs for COL6A1 Gene

Selected SIMAP similar genes for COL6A1 Gene using alignment to 3 proteins:

genes like me logo Genes that share paralogs with COL6A1: view

Variants for COL6A1 Gene

Sequence variations from dbSNP and Humsavar for COL6A1 Gene

SNP ID Clin Chr 21 pos Sequence Context AA Info Type MAF
rs7671 Benign 45,981,846(-) TGTCT(C/G)GGGCC utr-variant-5-prime
rs9254 -- 46,004,432(+) GCTGC(A/G)TCCCA utr-variant-3-prime
rs13879 other 46,003,662(+) AACGA(C/T)GCCAC reference, synonymous-codon, utr-variant-3-prime
rs741956 Benign 45,986,507(-) GGCAG(C/T)GTGAG intron-variant
rs754507 Benign 45,986,698(-) GGGGG(G/T)GCCGG intron-variant

Structural Variations from Database of Genomic Variants (DGV) for COL6A1 Gene

Variant ID Type Subtype PubMed ID
nsv914079 CNV Loss 21882294
nsv914083 CNV Loss 21882294
nsv509804 CNV Insertion 20534489
dgv4805n71 CNV Loss 21882294
nsv470910 CNV Gain 18288195
nsv914088 CNV Loss 21882294
dgv4806n71 CNV Loss 21882294
esv2723849 CNV Deletion 23290073
esv2723851 CNV Deletion 23290073
esv1409667 CNV Insertion 17803354
esv1025241 CNV Insertion 17803354
esv2723852 CNV Deletion 23290073
esv2723853 CNV Deletion 23290073
esv1561412 CNV Insertion 17803354
dgv4807n71 CNV Loss 21882294
dgv4808n71 CNV Loss 21882294
nsv914095 CNV Loss 21882294
dgv254n21 CNV Loss 19592680
nsv513579 CNV Insertion 21212237
esv1396032 CNV Insertion 17803354

Relevant External Links for COL6A1 Gene

HapMap Linkage Disequilibrium report
COL6A1
Human Gene Mutation Database (HGMD)
COL6A1
Locus Specific Mutation Databases (LSDB)
COL6A1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for COL6A1 Gene

Disorders for COL6A1 Gene

(3) OMIM Diseases for COL6A1 Gene (120220)

UniProtKB/Swiss-Prot

CO6A1_HUMAN
  • Bethlem myopathy (BM) [MIM:158810]: A benign autosomal dominant proximal myopathy characterized by early childhood onset and joint contractures most frequently affecting the elbows and ankles. {ECO:0000269 PubMed:11865138, ECO:0000269 PubMed:15689448, ECO:0000269 PubMed:15955946, ECO:0000269 PubMed:8782832}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Ullrich congenital muscular dystrophy (UCMD) [MIM:254090]: UCMD is 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:15689448, ECO:0000269 PubMed:16130093}. Note=The disease is caused by mutations affecting the gene represented in this entry.

(6) Novoseek inferred disease relationships for COL6A1 Gene

Disease -log(P) Hits PubMed IDs
bethlem myopathy 97.8 19
ullrich congenital muscular dystrophy 97.6 12
contracture 71.8 2
myopathy 63.7 2
down syndrome 61.3 16

Relevant External Links for COL6A1

GeneTests
COL6A1
GeneReviews
COL6A1
Genetic Association Database (GAD)
COL6A1
Human Genome Epidemiology (HuGE) Navigator
COL6A1
genes like me logo Genes that share disorders with COL6A1: view

No data available for Genatlas for COL6A1 Gene

Publications for COL6A1 Gene

  1. Human COL6A1: genomic characterization of the globular domains, structural and evolutionary comparison with COL6A2. (PMID: 9107679) Trikka D. … Kessling A.M. (Mamm. Genome 1997) 3 4 23
  2. New molecular mechanism for Ullrich congenital muscular dystrophy: a heterozygous in-frame deletion in the COL6A1 gene causes a severe phenotype. (PMID: 12840783) Pan T.C. … Chu M.L. (Am. J. Hum. Genet. 2003) 3 23 48
  3. Genomewide linkage and linkage disequilibrium analyses identify COL6A1, on chromosome 21, as the locus for ossification of the posterior longitudinal ligament of the spine. (PMID: 12958705) Tanaka T. … Inoue I. (Am. J. Hum. Genet. 2003) 3 23 48
  4. Novel mutations in collagen VI genes: expansion of the Bethlem myopathy phenotype. (PMID: 11865138) Scacheri P.C. … Hoffman E.P. (Neurology 2002) 3 4 23
  5. COL6A1, the candidate gene for ossification of the posterior longitudinal ligament, is associated with diffuse idiopathic skeletal hyperostosis in Japanese. (PMID: 16227896) Tsukahara S. … Inoue I. (Spine 2005) 3 23 48

Products for COL6A1 Gene

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat
  • Pathway & Disease-focused RT² Profiler PCR Arrays
    • Extracellular Matrix & Adhesion Molecules in human,mouse,rat
    • Osteogenesis in human,mouse,rat
  • QIAGEN qRT-PCR Assays for microRNAs that regulate COL6A1
    • QuantiTect SYBR Green Assays in human,mouse,rat
    • Pre-validated RT² qPCR Primer Assay in human,mouse,rat
    • QuantiFast Probe-based Assays in human,mouse,rat
    • Predesigned siRNA for gene silencing in human,mouse,rat for COL6A1
    • Block miRNA regulation of COL6A1 using miScript Target Protectors

    Sources for COL6A1 Gene

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