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Aliases for COL6A6 Gene

Aliases for COL6A6 Gene

  • Collagen Type VI Alpha 6 Chain 2 3 5
  • Collagen, Type VI, Alpha 6 2 3
  • Collagen Alpha-6(VI) Chain 3

External Ids for COL6A6 Gene

Previous GeneCards Identifiers for COL6A6 Gene

  • GC03P131715
  • GC03P130280
  • GC03P127663

Summaries for COL6A6 Gene

Entrez Gene Summary for COL6A6 Gene

  • This gene encodes a large protein that contains multiple von Willebrand factor domains and forms a component of the basal lamina of epithelial cells. This protein may regulate epithelial cell-fibronectin interactions. Variation in this gene may be implicated in skin diseases. [provided by RefSeq, May 2017]

GeneCards Summary for COL6A6 Gene

COL6A6 (Collagen Type VI Alpha 6 Chain) is a Protein Coding gene. Among its related pathways are Collagen chain trimerization and Developmental Biology. An important paralog of this gene is COL6A5.

UniProtKB/Swiss-Prot for COL6A6 Gene

  • Collagen VI acts as a cell-binding protein.

Additional gene information for COL6A6 Gene

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

Genomics for COL6A6 Gene

GeneHancer (GH) Regulatory Elements for COL6A6 Gene

Promoters and enhancers for COL6A6 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH03J130516 Enhancer 0.6 ENCODE 650.7 +0.2 245 1.3 SP3 SUZ12 ZIC2 ZNF335 SP1 ZFHX2 GLIS2 GMEB1 ZNF341 PRDM10 COL6A6 GC03P130592
GH03J130582 Enhancer 0.4 ENCODE 11.8 +65.3 65330 0.9 JUNB BATF IRF4 COL6A6 GC03P130592
GH03J130508 Enhancer 0.4 ENCODE 9.5 -8.1 -8060 0.8 MAX NR2F2 COL6A6 GC03M130467
GH03J130576 Enhancer 0.2 ENCODE 11.8 +59.6 59615 0.2 COL6A6 GC03P130592
GH03J130600 Enhancer 0.6 ENCODE 0.2 +84.3 84343 1.9 ZNF146 PKNOX1 ZNF362 ZBTB21 YY2 GFI1B ZNF518A PRDM6 ZBTB48 TRIM28 GC03P130602 GC03M130583 COL6A6
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around COL6A6 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the COL6A6 gene promoter:

Genomic Locations for COL6A6 Gene

Genomic Locations for COL6A6 Gene
chr3:130,517,177-130,678,155
(GRCh38/hg38)
Size:
160,979 bases
Orientation:
Plus strand
chr3:130,279,178-130,396,999
(GRCh37/hg19)

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

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 Asn2034, Asn1290, Asn988, Asn930, posLast=520520, posLast=347347, posLast=298298, Asn288, posLast=275275, and posLast=198198
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for COL6A6 Gene

Domains & Families for COL6A6 Gene

Gene Families for COL6A6 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted secreted proteins

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 :
  • Belongs to the type VI collagen family.
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 From GWAS Catalog for COL6A6 Gene

Phenotypes for COL6A6 Gene

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

Animal Model Products

CRISPR Products

miRNA for COL6A6 Gene

miRTarBase miRNAs that target COL6A6

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for 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
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
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 --
GO:0005581 collagen trimer IEA --
GO:0031012 extracellular matrix IDA 27559042
genes like me logo Genes that share ontologies with COL6A6: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for COL6A6 Gene

Pathways & Interactions for COL6A6 Gene

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

Gene Ontology (GO) - Biological Process for COL6A6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007155 cell adhesion IEA --
GO:0030574 collagen catabolic process 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

mRNA/cDNA for COL6A6 Gene

Unigene Clusters for COL6A6 Gene

Collagen, type VI, alpha 6:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for COL6A6

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 from GTEx, Illumina, BioGPS, and CGAP SAGE 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 and MOPED for COL6A6 Gene



NURSA nuclear receptor signaling pathways regulating expression of COL6A6 Gene:

COL6A6

SOURCE GeneReport for Unigene cluster for COL6A6 Gene:

Hs.591282

Evidence on tissue expression from TISSUES for COL6A6 Gene

  • Liver(4.2)
  • Lymph node(4)
genes like me logo Genes that share expression patterns with COL6A6: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer 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
chimpanzee
(Pan troglodytes)
Mammalia COL6A6 34 33
  • 99.4 (n)
OneToOne
dog
(Canis familiaris)
Mammalia COL6A6 34 33
  • 87.37 (n)
OneToOne
cow
(Bos Taurus)
Mammalia COL6A6 34 33
  • 83.87 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Col6a6 16 34 33
  • 83.03 (n)
rat
(Rattus norvegicus)
Mammalia Col6a6 33
  • 83.02 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 67 (a)
ManyToMany
oppossum
(Monodelphis domestica)
Mammalia -- 34
  • 51 (a)
ManyToMany
chicken
(Gallus gallus)
Aves COL6A6 33
  • 51.86 (n)
-- 34
  • 21 (a)
ManyToMany
lizard
(Anolis carolinensis)
Reptilia -- 34
  • 50 (a)
ManyToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100486063 33
  • 52.3 (n)
zebrafish
(Danio rerio)
Actinopterygii col6a6 33
  • 49.18 (n)
zmp:0000000759 34
  • 24 (a)
ManyToMany
Species where no ortholog for COL6A6 was found in the sources mined by GeneCards:
  • 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)
Aminode:
Evolutionary constrained regions (ECRs) for COL6A6: view image

Paralogs for COL6A6 Gene

Paralogs for COL6A6 Gene

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

  • CO6A6_HUMAN
  • F8W6Y7_HUMAN
  • H0Y940_HUMAN
  • H0YA33_HUMAN

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 Variation AA Info Type
rs1064797298 uncertain-significance, not provided 130,649,243(+) A/G coding_sequence_variant, genic_downstream_transcript_variant, intron_variant, missense_variant, non_coding_transcript_variant
rs111457392 uncertain-significance, not provided 130,571,225(+) C/T coding_sequence_variant, missense_variant, non_coding_transcript_variant
rs371413939 uncertain-significance, not provided 130,649,420(+) G/C coding_sequence_variant, genic_downstream_transcript_variant, intron_variant, missense_variant, non_coding_transcript_variant
rs140872639 uncertain-significance, not specified 130,592,568(+) G/T coding_sequence_variant, non_coding_transcript_variant, stop_gained
rs200960657 uncertain-significance, not specified 130,581,896(+) C/T coding_sequence_variant, non_coding_transcript_variant, stop_gained

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

Variant ID Type Subtype PubMed ID
dgv2597n106 CNV deletion 24896259
dgv2598n106 CNV deletion 24896259
dgv83n16 CNV deletion 17901297
esv2271871 CNV deletion 18987734
esv2450346 CNV deletion 19546169
esv2639906 CNV loss 19546169
esv2725914 CNV deletion 23290073
esv2725915 CNV deletion 23290073
esv34166 CNV loss 18971310
esv3562539 CNV deletion 23714750
esv3575605 CNV gain 25503493
esv4329 CNV loss 18987735
esv5883 CNV loss 19470904
nsv1073679 CNV deletion 25765185
nsv4003 CNV insertion 18451855
nsv4004 CNV deletion 18451855
nsv4005 CNV insertion 18451855
nsv460855 CNV loss 19166990
nsv508243 CNV deletion 20534489
nsv521211 CNV loss 19592680
nsv956800 CNV deletion 24416366

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)

Additional Variant Information for COL6A6 Gene

Human Gene Mutation Database (HGMD)
COL6A6
SNPedia medical, phenotypic, and genealogical associations of SNPs for
COL6A6

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

Disorders for COL6A6 Gene

Additional Disease Information for 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. The expanded collagen VI family: new chains and new questions. (PMID: 23869615) Fitzgerald J … Hansen U (Connective tissue research 2013) 2 3 58
  2. Three novel collagen VI chains with high homology to the alpha3 chain. (PMID: 18276594) Gara SK … Wagener R (The Journal of biological chemistry 2008) 3 4 58
  3. The DNA sequence, annotation and analysis of human chromosome 3. (PMID: 16641997) Muzny DM … Gibbs RA (Nature 2006) 3 4 58
  4. Identification of novel candidate variants including COL6A6 polymorphisms in early-onset atopic dermatitis using whole-exome sequencing. (PMID: 28125976) Heo WI … Seo SJ (BMC medical genetics 2017) 3 58
  5. Glycoproteomics Reveals Decorin Peptides With Anti-Myostatin Activity in Human Atrial Fibrillation. (PMID: 27559042) Barallobre-Barreiro J … Mayr M (Circulation 2016) 3 58

Products for COL6A6 Gene

Sources for COL6A6 Gene

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