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Aliases for COL6A5 Gene

Aliases for COL6A5 Gene

  • Collagen, Type VI, Alpha 5 2 3
  • COL29A1 3 4 6
  • Von Willebrand Factor A Domain-Containing Protein 4 3 4
  • Collagen, Type XXIX, Alpha 1 2 3
  • VWA4 3 4
  • Von Willebrand Factor A Domain Containing 4 2
  • Collagen Alpha-1(XXIX) Chain 4
  • Collagen Alpha-5(VI) Chain 3

External Ids for COL6A5 Gene

Previous HGNC Symbols for COL6A5 Gene

  • COL29A1

Previous GeneCards Identifiers for COL6A5 Gene

  • GC03P130065
  • GC03P127449

Summaries for COL6A5 Gene

Entrez Gene Summary for COL6A5 Gene

  • This gene encodes a member of the collagen superfamily of proteins. The encoded protein contains multiple von Willebrand factor A-like domains and may interact with the alpha 1 and alpha 2 chains of collagen VI to form the complete collagen VI trimer. Polymorphisms in this gene may be linked to dermal phenotypes, such as eczema. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2013]

GeneCards Summary for COL6A5 Gene

COL6A5 (Collagen, Type VI, Alpha 5) is a Protein Coding gene. Diseases associated with COL6A5 include bethlem myopathy and ullrich congenital muscular dystrophy. Among its related pathways are Signaling by FGFR and Signaling by GPCR. An important paralog of this gene is SCARA3.

UniProtKB/Swiss-Prot for COL6A5 Gene

  • Collagen VI acts as a cell-binding protein.

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for COL6A5 Gene

Genomics for COL6A5 Gene

Genomic Location for COL6A5 Gene

Start:
130,345,516 bp from pter
End:
130,484,846 bp from pter
Size:
139,331 bases
Orientation:
Plus strand

Genomic View for COL6A5 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for COL6A5 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for COL6A5 Gene

No data available for Regulatory Elements for COL6A5 Gene

Proteins for COL6A5 Gene

  • Protein details for COL6A5 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    A8TX70-CO6A5_HUMAN
    Recommended name:
    Collagen alpha-5(VI) chain
    Protein Accession:
    A8TX70
    Secondary Accessions:
    • A9J6L2
    • A9J6L4
    • A9J6L6
    • A9J6L7
    • A9J6M0
    • A9J6M1
    • A9J6M2
    • B5MEA7
    • Q6ZW26
    • Q8NA36

    Protein attributes for COL6A5 Gene

    Size:
    2615 amino acids
    Molecular mass:
    289926 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).
    SequenceCaution:
    • Sequence=BAC04092.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=BAC04092.1; Type=Frameshift; Positions=2591; Evidence={ECO:0000305}; Sequence=BAC85681.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for COL6A5 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for COL6A5 Gene

Proteomics data for COL6A5 Gene at MOPED

Post-translational modifications for COL6A5 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 Asn201, Asn260, Asn835, and Asn2509
  • Modification sites at PhosphoSitePlus

Other Protein References for COL6A5 Gene

No data available for DME Specific Peptides for COL6A5 Gene

Domains for COL6A5 Gene

Gene Families for COL6A5 Gene

HGNC:

Protein Domains for COL6A5 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for COL6A5 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

A8TX70

UniProtKB/Swiss-Prot:

CO6A5_HUMAN :
  • A8TX70
Domain:
  • Contains 6 collagen-like domains.
  • Contains 10 VWFA domains.
Family:
  • Belongs to the type VI collagen family.
genes like me logo Genes that share domains with COL6A5: view

Function for COL6A5 Gene

Molecular function for COL6A5 Gene

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

Gene Ontology (GO) - Molecular Function for COL6A5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 19478074
genes like me logo Genes that share ontologies with COL6A5: view

Animal Model Products

CRISPR Products

miRNA for COL6A5 Gene

miRTarBase miRNAs that target COL6A5

No data available for Enzyme Numbers (IUBMB) , Phenotypes , Animal Models , Transcription Factor Targeting and HOMER Transcription for COL6A5 Gene

Localization for COL6A5 Gene

Subcellular locations from UniProtKB/Swiss-Prot for COL6A5 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 COL6A5 Gene COMPARTMENTS Subcellular localization image for COL6A5 gene
Compartment Confidence
extracellular 5
endoplasmic reticulum 3
plasma membrane 1

Gene Ontology (GO) - Cellular Components for COL6A5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS --
GO:0005578 proteinaceous extracellular matrix IEA --
GO:0005581 collagen trimer IEA --
GO:0031012 colocalizes_with extracellular matrix ISS 22261194
genes like me logo Genes that share ontologies with COL6A5: view

Pathways for COL6A5 Gene

genes like me logo Genes that share pathways with COL6A5: view

Pathways by source for COL6A5 Gene

Interacting Proteins for COL6A5 Gene

Gene Ontology (GO) - Biological Process for COL6A5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007155 cell adhesion IEA --
GO:0022617 extracellular matrix disassembly TAS --
GO:0030198 extracellular matrix organization TAS --
GO:0030574 collagen catabolic process TAS --
genes like me logo Genes that share ontologies with COL6A5: view

Transcripts for COL6A5 Gene

mRNA/cDNA for COL6A5 Gene

Unigene Clusters for COL6A5 Gene

Collagen, type VI, alpha 5:
Representative Sequences:

CRISPR Products

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for COL6A5

Primer Products

  • OriGene qSTAR qPCR primer pairs in human,mouse,rat for COL6A5
  • 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

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for COL6A5 Gene

ExUns: 1 ^ 2a · 2b ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9
SP1:
SP2: - -

Relevant External Links for COL6A5 Gene

GeneLoc Exon Structure for
COL6A5
ECgene alternative splicing isoforms for
COL6A5

Expression for COL6A5 Gene

mRNA expression in normal human tissues for COL6A5 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for COL6A5 Gene

This gene is overexpressed in Lung (24.1), Testis (10.1), and Skin - Not Sun Exposed (Suprapubic) (6.6).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, and MOPED for COL6A5 Gene

SOURCE GeneReport for Unigene cluster for COL6A5 Gene Hs.205403

mRNA Expression by UniProt/SwissProt for COL6A5 Gene

A8TX70-CO6A5_HUMAN
Tissue specificity: Expressed in skin, followed by lung, small intestine, colon and testis. In skin, it is expressed in the epidermis with strongest staining in suprabasal viable layers. In ATOD patients, it is absent in the most differentiated upper spinous and granular layers (at protein level).
genes like me logo Genes that share expressions with COL6A5: view

In Situ Assay Products

Orthologs for COL6A5 Gene

This gene was present in the common ancestor of chordates.

Orthologs for COL6A5 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia COL6A5 35
  • 99.12 (n)
  • 98.61 (a)
COL6A5 36
  • 99 (a)
OneToOne
cow
(Bos Taurus)
Mammalia COL6A5 36
  • 74 (a)
OneToOne
dog
(Canis familiaris)
Mammalia COL6A5 35
  • 83.55 (n)
  • 75.73 (a)
COL6A5 36
  • 75 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Col6a5 35
  • 78.89 (n)
  • 73.97 (a)
Col6a5 16
Col6a5 36
  • 73 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia COL6A5 36
  • 30 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 36
  • 51 (a)
OneToMany
-- 36
  • 48 (a)
OneToMany
-- 36
  • 54 (a)
OneToMany
rat
(Rattus norvegicus)
Mammalia Col6a5 35
  • 77.67 (n)
  • 71.99 (a)
chicken
(Gallus gallus)
Aves -- 36
  • 33 (a)
ManyToMany
lizard
(Anolis carolinensis)
Reptilia -- 36
  • 21 (a)
ManyToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia col6a6 35
  • 54.36 (n)
  • 43.1 (a)
zebrafish
(Danio rerio)
Actinopterygii col6a6 36
  • 30 (a)
ManyToMany
Species with no ortholog for COL6A5:
  • 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 COL6A5 Gene

ENSEMBL:
Gene Tree for COL6A5 (if available)
TreeFam:
Gene Tree for COL6A5 (if available)

Paralogs for COL6A5 Gene

Paralogs for COL6A5 Gene

Selected SIMAP similar genes for COL6A5 Gene using alignment to 6 proteins:

genes like me logo Genes that share paralogs with COL6A5: view

Variants for COL6A5 Gene

Sequence variations from dbSNP and Humsavar for COL6A5 Gene

SNP ID Clin Chr 03 pos Sequence Context AA Info Type MAF
rs172815 -- 130,451,928(-) attcc(C/T)gtcac intron-variant
rs184423 -- 130,451,897(-) tggta(A/C)ctgct intron-variant
rs186518 -- 130,450,057(-) tacaa(A/T)gcttg intron-variant
rs188913 -- 130,449,759(-) taata(C/T)cgttt intron-variant
rs191217 -- 130,471,212(+) CAAAA(A/G)TAGCC intron-variant

Structural Variations from Database of Genomic Variants (DGV) for COL6A5 Gene

Variant ID Type Subtype PubMed ID
nsv877494 CNV Gain 21882294
esv2665713 CNV Deletion 23128226
esv269755 CNV Insertion 20981092
esv34166 CNV Loss 18971310
nsv437854 CNV Loss 16327808
nsv515803 CNV Loss 19592680
nsv526814 CNV Gain 19592680
esv23758 CNV Loss 19812545
esv2662769 CNV Deletion 23128226
nsv437881 CNV Loss 16468122
dgv5258n71 CNV Loss 21882294
nsv460854 CNV Loss 19166990

Relevant External Links for COL6A5 Gene

HapMap Linkage Disequilibrium report
COL6A5
Human Gene Mutation Database (HGMD)
COL6A5

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for COL6A5 Gene

Disorders for COL6A5 Gene

MalaCards: The human disease database

MalaCards: The human disease database. (2) Diseases for COL6A5 Gene including...

Search for COL6A5 Gene in MalaCards »

UniProtKB/Swiss-Prot

CO6A5_HUMAN
  • Note=Patients affected by atopic dermatitis display an abnormal distribution of COL29A1 mRNA and protein in skin suggesting that COL29A1 may be involved in the pathogenesis of the disease.

(2) University of Copenhagen DISEASES for COL6A5 Gene

Relevant External Links for COL6A5

Genetic Association Database (GAD)
COL6A5
Human Genome Epidemiology (HuGE) Navigator
COL6A5
genes like me logo Genes that share disorders with COL6A5: view

Publications for COL6A5 Gene

  1. Variants in a novel epidermal collagen gene (COL29A1) are associated with atopic dermatitis. (PMID: 17850181) Soederhaell C. … Lee Y.-A. (PLoS Biol. 2007) 2 3 4
  2. 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
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4
  4. Three novel collagen VI chains, alpha4(VI), alpha5(VI), and alpha6(VI). (PMID: 18400749) Fitzgerald J. … Hansen U. (J. Biol. Chem. 2008) 3
  5. No association between the eczema genes COL29A1 and IL31 and inflammatory bowel disease. (PMID: 18839421) Zucchelli M. … D'Amato M. (Inflamm. Bowel Dis. 2009) 3

Products for COL6A5 Gene

Sources for COL6A5 Gene

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