Free for academic non-profit institutions. Other users need a Commercial license

Aliases for COL6A6 Gene

Aliases for COL6A6 Gene

  • Collagen Type VI Alpha 6 2 3
  • Collagen, Type VI, Alpha 6 2 5

External Ids for COL6A6 Gene

Previous GeneCards Identifiers for COL6A6 Gene

  • GC03P131715
  • GC03P130280
  • GC03P127663

Summaries for COL6A6 Gene

GeneCards Summary for COL6A6 Gene

COL6A6 (Collagen Type VI Alpha 6) is a Protein Coding gene. Among its related pathways are Developmental Biology and PI3K-Akt signaling pathway. An important paralog of this gene is MATN1.

UniProtKB/Swiss-Prot for COL6A6 Gene

  • Collagen VI acts as a cell-binding protein.

No data available for Entrez Gene Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for COL6A6 Gene

Genomics for COL6A6 Gene

Regulatory Elements for COL6A6 Gene

Enhancers for COL6A6 Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around COL6A6 on UCSC Golden Path with GeneCards custom track

Genomic Location for COL6A6 Gene

Chromosome:
3
Start:
130,517,177 bp from pter
End:
130,678,155 bp from pter
Size:
160,979 bases
Orientation:
Plus strand

Genomic View for COL6A6 Gene

Genes around COL6A6 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
COL6A6 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for COL6A6 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for COL6A6 Gene

Proteins for COL6A6 Gene

  • Protein details for COL6A6 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    A6NMZ7-CO6A6_HUMAN
    Recommended name:
    Collagen alpha-6(VI) chain
    Protein Accession:
    A6NMZ7
    Secondary Accessions:
    • A7DZQ0
    • A7DZQ1
    • A7DZQ2
    • Q69YT0

    Protein attributes for COL6A6 Gene

    Size:
    2263 amino acids
    Molecular mass:
    247173 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).

    Alternative splice isoforms for COL6A6 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for COL6A6 Gene

Proteomics data for COL6A6 Gene at MOPED

Post-translational modifications for COL6A6 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 Asn 198, Asn 275, Asn 288, Asn 298, Asn 347, Asn 520, Asn 930, Asn 988, Asn 1290, and Asn 2034
  • Modification sites at PhosphoSitePlus

Other Protein References for COL6A6 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for COL6A6 Gene

Domains & Families for COL6A6 Gene

Gene Families for COL6A6 Gene

Protein Domains for COL6A6 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for COL6A6 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

A6NMZ7

UniProtKB/Swiss-Prot:

CO6A6_HUMAN :
  • Contains 9 VWFA domains.
  • Belongs to the type VI collagen family.
Domain:
  • Contains 9 VWFA domains.
Family:
  • Belongs to the type VI collagen family.
genes like me logo Genes that share domains with COL6A6: view

Function for COL6A6 Gene

Molecular function for COL6A6 Gene

UniProtKB/Swiss-Prot Function:
Collagen VI acts as a cell-binding protein.

Phenotypes for COL6A6 Gene

GenomeRNAi human phenotypes for COL6A6:
genes like me logo Genes that share phenotypes with COL6A6: view

Animal Model Products

miRNA for COL6A6 Gene

miRTarBase miRNAs that target COL6A6

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for COL6A6 Gene

Localization for COL6A6 Gene

Subcellular locations from UniProtKB/Swiss-Prot for COL6A6 Gene

Secreted, extracellular space, extracellular matrix. Note=Deposed in the extracellular matrix of skeletal muscle. {ECO:0000250}.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for COL6A6 Gene COMPARTMENTS Subcellular localization image for COL6A6 gene
Compartment Confidence
extracellular 5
endoplasmic reticulum 3
plasma membrane 1

Gene Ontology (GO) - Cellular Components for COL6A6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS --
genes like me logo Genes that share ontologies with COL6A6: view

Pathways & Interactions for COL6A6 Gene

genes like me logo Genes that share pathways with COL6A6: view

Interacting Proteins for COL6A6 Gene

Gene Ontology (GO) - Biological Process for COL6A6 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 COL6A6: view

No data available for SIGNOR curated interactions for COL6A6 Gene

Drugs & Compounds for COL6A6 Gene

No Compound Related Data Available

Transcripts for COL6A6 Gene

Unigene Clusters for COL6A6 Gene

Collagen, type VI, alpha 6:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for COL6A6 Gene

No ASD Table

Relevant External Links for COL6A6 Gene

GeneLoc Exon Structure for
COL6A6
ECgene alternative splicing isoforms for
COL6A6

Expression for COL6A6 Gene

mRNA expression in normal human tissues for COL6A6 Gene

mRNA differential expression in normal tissues according to GTEx for COL6A6 Gene

This gene is overexpressed in Pituitary (x18.0), Lung (x11.1), and Heart - Atrial Appendage (x7.5).

Protein differential expression in normal tissues from HIPED for COL6A6 Gene

This gene is overexpressed in Fetal ovary (10.2), Fetal heart (8.5), Lung (8.2), and Urine (7.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for COL6A6 Gene



SOURCE GeneReport for Unigene cluster for COL6A6 Gene Hs.591282

genes like me logo Genes that share expression patterns with COL6A6: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA Expression by UniProt/SwissProt and Protein tissue co-expression partners for COL6A6 Gene

Orthologs for COL6A6 Gene

This gene was present in the common ancestor of chordates.

Orthologs for COL6A6 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia COL6A6 35
  • 83.87 (n)
  • 83.32 (a)
COL6A6 36
  • 83 (a)
OneToOne
dog
(Canis familiaris)
Mammalia COL6A6 35
  • 87.37 (n)
  • 87.52 (a)
COL6A6 36
  • 87 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Col6a6 35
  • 83.03 (n)
  • 83.47 (a)
Col6a6 16
Col6a6 36
  • 83 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia COL6A6 35
  • 99.4 (n)
  • 99.34 (a)
COL6A6 36
  • 99 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Col6a6 35
  • 83.02 (n)
  • 83.64 (a)
oppossum
(Monodelphis domestica)
Mammalia -- 36
  • 51 (a)
ManyToMany
platypus
(Ornithorhynchus anatinus)
Mammalia -- 36
  • 67 (a)
ManyToMany
chicken
(Gallus gallus)
Aves COL6A6 35
  • 51.86 (n)
  • 40.88 (a)
-- 36
  • 21 (a)
ManyToMany
lizard
(Anolis carolinensis)
Reptilia -- 36
  • 50 (a)
ManyToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100486063 35
  • 52.3 (n)
  • 42.96 (a)
zebrafish
(Danio rerio)
Actinopterygii col6a6 35
  • 49.18 (n)
  • 37.13 (a)
zmp:0000000759 36
  • 24 (a)
ManyToMany
Species with no ortholog for COL6A6:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • worm (Caenorhabditis elegans)

Evolution for COL6A6 Gene

ENSEMBL:
Gene Tree for COL6A6 (if available)
TreeFam:
Gene Tree for COL6A6 (if available)

Paralogs for COL6A6 Gene

(14) SIMAP similar genes for COL6A6 Gene using alignment to 4 proteins:

Pseudogenes.org Pseudogenes for COL6A6 Gene

genes like me logo Genes that share paralogs with COL6A6: view

Variants for COL6A6 Gene

Sequence variations from dbSNP and Humsavar for COL6A6 Gene

SNP ID Clin Chr 03 pos Sequence Context AA Info Type
rs4613427 - 130,565,365(-) GTCTT(C/T)TGAAT nc-transcript-variant, reference, missense
rs9830253 - 130,565,440(+) AGGGC(A/G)CCAGC nc-transcript-variant, reference, missense
rs11921769 - 130,566,801(+) GTCAG(A/C)GGTGG nc-transcript-variant, reference, missense
rs16830494 - 130,643,012(+) TGTGC(A/G)AGACC nc-transcript-variant, reference, missense
rs7614116 - 130,649,225(+) AGCGC(A/G)CATCG intron-variant, nc-transcript-variant, reference, missense

Structural Variations from Database of Genomic Variants (DGV) for COL6A6 Gene

Variant ID Type Subtype PubMed ID
nsv877494 CNV Gain 21882294
esv34166 CNV Loss 18971310
nsv4003 CNV Insertion 18451855
nsv521211 CNV Loss 19592680
nsv508243 CNV Loss 20534489
nsv4004 CNV Loss 18451855
nsv4005 CNV Insertion 18451855
nsv460855 CNV Loss 19166990
esv2639906 CNV Loss 19546169
esv2450346 CNV Deletion 19546169
esv2271871 CNV Deletion 18987734
esv2725914 CNV Deletion 23290073
dgv83n16 CNV Deletion 17901297
esv4329 CNV Deletion 18987735
esv5883 CNV Loss 19470904
esv2725915 CNV Deletion 23290073

Variation tolerance for COL6A6 Gene

Residual Variation Intolerance Score: 98.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 14.65; 96.57% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for COL6A6 Gene

Human Gene Mutation Database (HGMD)
COL6A6

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for COL6A6 Gene

Disorders for COL6A6 Gene

Relevant External Links for COL6A6

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
COL6A6

No disorders were found for COL6A6 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for COL6A6 Gene

Publications for COL6A6 Gene

  1. Three novel collagen VI chains with high homology to the alpha 3 chain. (PMID: 18276594) Gara S.K. … Wagener R. (J. Biol. Chem. 2008) 3 4 67
  2. Defective collagen VI I+6 chain expression in the skeletal muscle of patients with collagen VI-related myopathies. (PMID: 24907562) Tagliavini F. … Sabatelli P. (Biochim. Biophys. Acta 2014) 3
  3. Expression of collagen VI I+5 and I+6 chains in human muscle and in Duchenne muscular dystrophy-related muscle fibrosis. (PMID: 22226732) Sabatelli P. … Wagener R. (Matrix Biol. 2012) 3
  4. Expression of the collagen VI I+5 and I+6 chains in normal human skin and in skin of patients with collagen VI-related myopathies. (PMID: 20882040) Sabatelli P. … Wagener R. (J. Invest. Dermatol. 2011) 3
  5. Collagen VI is a basement membrane component that regulates epithelial cell-fibronectin interactions. (PMID: 21406227) Groulx J.F. … Beaulieu J.F. (Matrix Biol. 2011) 3

Products for COL6A6 Gene

Sources for COL6A6 Gene

Content