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Aliases for COL6A5 Gene

Aliases for COL6A5 Gene

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

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 Chain) is a Protein Coding gene. Diseases associated with COL6A5 include Ullrich Congenital Muscular Dystrophy 1 and Bethlem Myopathy 1. Among its related pathways are Collagen chain trimerization and Developmental Biology. An important paralog of this gene is COL6A6.

UniProtKB/Swiss-Prot for COL6A5 Gene

  • Collagen VI acts as a cell-binding protein.

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

Genomics for COL6A5 Gene

Regulatory Elements for COL6A5 Gene

Enhancers for COL6A5 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH03G130395 0.7 ENCODE 4.8 +50.4 50411 1.7 ESRRA RFX1 TEAD4 ZNF398 OSR2 JUND ATF3 BCL6B FOSL2 FOS COL6A5 PIR62051
GH03G130354 0.9 FANTOM5 Ensembl 0.4 +9.1 9121 0.7 PKNOX1 SMAD5 PBX2 ZNF512 FOXP2 ATP2C1 COL6A5 PIR62051
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around COL6A5 on UCSC Golden Path with GeneCards custom track

Genomic Location for COL6A5 Gene

Chromosome:
3
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

Genes around COL6A5 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
COL6A5 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for COL6A5 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence 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

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 posLast=201201, posLast=260260, posLast=835835, and Asn2509
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for COL6A5 Gene

Domains & Families for COL6A5 Gene

Gene Families for COL6A5 Gene

Protein Domains for COL6A5 Gene

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 :
  • Belongs to the type VI collagen family.
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
genes like me logo Genes that share phenotypes with COL6A5: view

Animal Model Products

CRISPR Products

miRNA for COL6A5 Gene

miRTarBase miRNAs that target COL6A5

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets 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
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 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 IEA,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 & Interactions for COL6A5 Gene

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

Gene Ontology (GO) - Biological Process for COL6A5 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 COL6A5: view

No data available for SIGNOR curated interactions for COL6A5 Gene

Transcripts for COL6A5 Gene

mRNA/cDNA for COL6A5 Gene

Unigene Clusters for COL6A5 Gene

Collagen, type VI, alpha 5:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

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 from GTEx, Illumina, BioGPS, and CGAP SAGE 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 (x24.1), Testis (x10.1), and Skin - Not Sun Exposed (Suprapubic) (x6.6).

Protein differential expression in normal tissues from HIPED for COL6A5 Gene

This gene is overexpressed in Bone marrow mesenchymal stem cell (57.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for COL6A5 Gene



NURSA nuclear receptor signaling pathways regulating expression of COL6A5 Gene:

COL6A5

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).

Evidence on tissue expression from TISSUES for COL6A5 Gene

  • Lung(4.4)
  • Skin(4.3)
genes like me logo Genes that share expression patterns with COL6A5: view

Primer Products

No data available for Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for COL6A5 Gene

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 34 35
  • 99.12 (n)
dog
(Canis familiaris)
Mammalia COL6A5 34 35
  • 83.55 (n)
mouse
(Mus musculus)
Mammalia Col6a5 34 16 35
  • 78.89 (n)
rat
(Rattus norvegicus)
Mammalia Col6a5 34
  • 77.67 (n)
cow
(Bos Taurus)
Mammalia COL6A5 35
  • 74 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 54 (a)
OneToMany
-- 35
  • 51 (a)
OneToMany
-- 35
  • 48 (a)
OneToMany
oppossum
(Monodelphis domestica)
Mammalia COL6A5 35
  • 30 (a)
OneToOne
chicken
(Gallus gallus)
Aves -- 35
  • 33 (a)
ManyToMany
lizard
(Anolis carolinensis)
Reptilia -- 35
  • 21 (a)
ManyToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia col6a6 34
  • 54.36 (n)
zebrafish
(Danio rerio)
Actinopterygii col6a6 35
  • 30 (a)
ManyToMany
Species where no ortholog for COL6A5 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 COL6A5 Gene

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

Paralogs for COL6A5 Gene

(8) 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
rs1000011069 -- 130,477,402(+) TTTCA(C/T)CTGTC intron-variant
rs1000030150 -- 130,459,395(+) GGAAG(A/G)GTATT intron-variant
rs1000049763 -- 130,368,547(+) AGAGA(-/GTGT)GTGTG intron-variant
rs1000055271 -- 130,392,593(+) CTTCC(G/T)CCCTC intron-variant
rs1000058199 -- 130,452,890(+) TTCTC(A/G)GGGAT intron-variant

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

Variant ID Type Subtype PubMed ID
dgv301e215 CNV deletion 23714750
dgv8588n54 CNV loss 21841781
dgv8589n54 CNV loss 21841781
dgv8590n54 CNV loss 21841781
esv23758 CNV loss 19812545
esv2662769 CNV deletion 23128226
esv2665713 CNV deletion 23128226
esv3305478 CNV mobile element insertion 20981092
esv3376350 CNV insertion 20981092
esv34166 CNV loss 18971310
esv3597762 CNV loss 21293372
esv3597766 CNV loss 21293372
esv3597767 CNV loss 21293372
esv3597769 CNV loss 21293372
esv3597770 CNV loss 21293372
nsv1005410 CNV loss 25217958
nsv437854 CNV loss 16327808
nsv437881 CNV loss 16468122
nsv460854 CNV loss 19166990
nsv515803 CNV loss 19592680
nsv526814 CNV gain 19592680
nsv591719 CNV loss 21841781
nsv591722 CNV loss 21841781
nsv591723 CNV loss 21841781

Variation tolerance for COL6A5 Gene

Gene Damage Index Score: 24.99; 99.68% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for COL6A5 Gene

Human Gene Mutation Database (HGMD)
COL6A5
SNPedia medical, phenotypic, and genealogical associations of SNPs for
COL6A5

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

Disorders for COL6A5 Gene

MalaCards: The human disease database

(3) MalaCards diseases for COL6A5 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
ullrich congenital muscular dystrophy 1
  • ullrich congenital muscular dystrophy
bethlem myopathy 1
  • bethlem myopathy
atopic dermatitis
  • allergic eczema
- elite association - COSMIC cancer census association via 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.

Relevant External Links for COL6A5

Genetic Association Database (GAD)
COL6A5
Human Genome Epidemiology (HuGE) Navigator
COL6A5
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
COL6A5
genes like me logo Genes that share disorders with COL6A5: view

No data available for Genatlas for COL6A5 Gene

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 64
  2. The expanded collagen VI family: new chains and new questions. (PMID: 23869615) Fitzgerald J. … Hansen U. (Connect. Tissue Res. 2013) 2 3 64
  3. 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 64
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 64
  5. EMR-linked GWAS study: investigation of variation landscape of loci for body mass index in children. (PMID: 24348519) Namjou B. … Harley J.B. (Front Genet 2013) 3 64

Products for COL6A5 Gene

Sources for COL6A5 Gene

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