This gene encodes an alpha chain for one of the low abundance fibrillar collagens. Fibrillar collagen molecules are trimers that can be composed of one or more types of alpha chains. Type V collagen is found in tissues containing type I collagen and appears to regulate the assembly of heterotypic fibers composed of both type I and type V collagen. This gene product is closely r... See more...

Aliases for COL5A3 Gene

Aliases for COL5A3 Gene

  • Collagen Type V Alpha 3 Chain 2 3 5
  • Collagen Alpha-3(V) Chain 3 4
  • Collagen, Type V, Alpha 3 3
  • Pro-(Alpha)3(V) Collagen 3
  • Collagen Type V Alpha 3 2
  • COL5A3 5

External Ids for COL5A3 Gene

Previous GeneCards Identifiers for COL5A3 Gene

  • GC19M010191
  • GC19M010293
  • GC19M009916
  • GC19M010071
  • GC19M009650

Summaries for COL5A3 Gene

Entrez Gene Summary for COL5A3 Gene

  • This gene encodes an alpha chain for one of the low abundance fibrillar collagens. Fibrillar collagen molecules are trimers that can be composed of one or more types of alpha chains. Type V collagen is found in tissues containing type I collagen and appears to regulate the assembly of heterotypic fibers composed of both type I and type V collagen. This gene product is closely related to type XI collagen and it is possible that the collagen chains of types V and XI constitute a single collagen type with tissue-specific chain combinations. Mutations in this gene are thought to be responsible for the symptoms of a subset of patients with Ehlers-Danlos syndrome type III. Messages of several sizes can be detected in northern blots but sequence information cannot confirm the identity of the shorter messages. [provided by RefSeq, Jul 2008]

GeneCards Summary for COL5A3 Gene

COL5A3 (Collagen Type V Alpha 3 Chain) is a Protein Coding gene. Diseases associated with COL5A3 include Ehlers-Danlos Syndrome and Lactocele. Among its related pathways are Integrin Pathway and Collagen chain trimerization. Gene Ontology (GO) annotations related to this gene include heparin binding and extracellular matrix structural constituent. An important paralog of this gene is COL5A1.

UniProtKB/Swiss-Prot Summary for COL5A3 Gene

  • Type V collagen is a member of group I collagen (fibrillar forming collagen). It is a minor connective tissue component of nearly ubiquitous distribution. Type V collagen binds to DNA, heparan sulfate, thrombospondin, heparin, and insulin.

Gene Wiki entry for COL5A3 Gene

Additional gene information for COL5A3 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for COL5A3 Gene

Genomics for COL5A3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for COL5A3 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
GH19J010005 Promoter/Enhancer 1.7 EPDnew FANTOM5 Ensembl ENCODE 638.5 +2.2 2184 4.9 ARHGAP35 CREB1 TEAD4 PRDM10 ZNF629 REST ZNF692 PRDM1 ZIC2 ZNF776 COL5A3 LOC100419831 ZNF559 ZNF177 ILF3 KRI1 DNMT1 ZNF121 ZNF846 ZNF317
GH19J010012 Enhancer 0.5 Ensembl 624 -1.7 -1669 0.4 PRDM1 ZNF398 KLF1 ZNF121 EZH2 COL5A3 RDH8
GH19J009913 Promoter/Enhancer 1.8 FANTOM5 Ensembl ENCODE CraniofacialAtlas 11.2 +96.5 96505 2.5 CTCF KDM1A ZNF692 JUND LARP7 RXRB MTA1 PATZ1 REST ZNF501 OLFM2 RDH8 COL5A3 ENSG00000267273 ZNF266 FJ601684-214 piR-51671-046 PIN1
GH19J010235 Promoter/Enhancer 1.9 EPDnew FANTOM5 ENCODE CraniofacialAtlas dbSUPER 9.7 -226.8 -226816 4.4 SP1 GATAD2A ZNF629 TFE3 ZNF512 LEF1 IKZF1 RCOR2 POLR2A BACH1 MRPL4 HSALNG0123913 S1PR5 RDH8 COL5A3 S1PR2 ATG4D SHFL TYK2 DNM2
GH19J009986 Enhancer 0.6 Ensembl ENCODE 23.9 +23.7 23731 1.6 TEAD4 NR2F2 HNF4A ZMYM3 ESRRA COL5A3 OLFM2 RDH8 SHFL RF00017-2800 lnc-RDH8-4
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around COL5A3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for COL5A3

Top Transcription factor binding sites by QIAGEN in the COL5A3 gene promoter:
  • AML1a
  • ATF
  • Bach1
  • Bach2
  • HEN1
  • NRSF form 1
  • NRSF form 2
  • Sp1

Genomic Locations for COL5A3 Gene

Genomic Locations for COL5A3 Gene
chr19:9,959,561-10,010,532
(GRCh38/hg38)
Size:
50,972 bases
Orientation:
Minus strand
chr19:10,070,237-10,121,147
(GRCh37/hg19)
Size:
50,911 bases
Orientation:
Minus strand

Genomic View for COL5A3 Gene

Genes around COL5A3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
COL5A3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for COL5A3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for COL5A3 Gene

Proteins for COL5A3 Gene

  • Protein details for COL5A3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P25940-CO5A3_HUMAN
    Recommended name:
    Collagen alpha-3(V) chain
    Protein Accession:
    P25940
    Secondary Accessions:
    • Q9NZQ6

    Protein attributes for COL5A3 Gene

    Size:
    1745 amino acids
    Molecular mass:
    172121 Da
    Quaternary structure:
    • Trimers of two alpha 1(V) and one alpha 2(V) chains in most tissues and trimers of one alpha 1(V), one alpha 2(V), and one alpha 3(V) chains in placenta.

neXtProt entry for COL5A3 Gene

Post-translational modifications for COL5A3 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 Asn102 and Asn141
  • Modification sites at PhosphoSitePlus
  • Glycosylation from GlyConnect
    • CO5A3_HUMAN (1138)

Other Protein References for COL5A3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for COL5A3 Gene

Domains & Families for COL5A3 Gene

Gene Families for COL5A3 Gene

HGNC:
Human Protein Atlas (HPA):
  • Cancer-related genes
  • Predicted secreted proteins

Protein Domains for COL5A3 Gene

InterPro:
Blocks:
  • Collagen triple helix repeat
  • Collagen helix repeat
  • Thrombospondin, N-terminal
  • Laminin G
  • Fibrillar collagen, C-terminal
ProtoNet:

Suggested Antigen Peptide Sequences for COL5A3 Gene

GenScript: Design optimal peptide antigens:
  • Collagen alpha-3(V) chain (CO5A3_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P25940

UniProtKB/Swiss-Prot:

CO5A3_HUMAN :
  • Belongs to the fibrillar collagen family.
Family:
  • Belongs to the fibrillar collagen family.
genes like me logo Genes that share domains with COL5A3: view

Function for COL5A3 Gene

Molecular function for COL5A3 Gene

UniProtKB/Swiss-Prot Function:
Type V collagen is a member of group I collagen (fibrillar forming collagen). It is a minor connective tissue component of nearly ubiquitous distribution. Type V collagen binds to DNA, heparan sulfate, thrombospondin, heparin, and insulin.

Phenotypes From GWAS Catalog for COL5A3 Gene

Gene Ontology (GO) - Molecular Function for COL5A3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005201 extracellular matrix structural constituent NAS 10722718
GO:0005518 collagen binding NAS 10722718
GO:0008201 heparin binding IEA --
GO:0030020 extracellular matrix structural constituent conferring tensile strength RCA 27559042
GO:0043394 proteoglycan binding IEA --
genes like me logo Genes that share ontologies with COL5A3: view
genes like me logo Genes that share phenotypes with COL5A3: view

Animal Models for COL5A3 Gene

MGI Knock Outs for COL5A3:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for COL5A3

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for COL5A3 Gene

Localization for COL5A3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for COL5A3 Gene

Secreted, extracellular space, extracellular matrix.

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 COL5A3 gene
Compartment Confidence
extracellular 5
endoplasmic reticulum 4
plasma membrane 3
cytoskeleton 1
mitochondrion 1
nucleus 1
cytosol 1
lysosome 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for COL5A3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS --
GO:0005581 collagen trimer IEA --
GO:0005588 collagen type V trimer IEA,NAS 1571108
GO:0005594 collagen type IX trimer IBA --
GO:0005615 extracellular space IBA 21873635
genes like me logo Genes that share ontologies with COL5A3: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for COL5A3 Gene

Pathways & Interactions for COL5A3 Gene

PathCards logo

SuperPathways for COL5A3 Gene

SuperPathway Contained pathways
1 Collagen chain trimerization
.48
.46
2 Integrin Pathway
.67
.67
.56
.56
.50
.38
3 ERK Signaling
.61
.61
.58
.51
.49
4 Phospholipase-C Pathway
.56
.56
5 Degradation of the extracellular matrix
genes like me logo Genes that share pathways with COL5A3: view

Pathways by source for COL5A3 Gene

1 KEGG pathway for COL5A3 Gene
15 Qiagen pathways for COL5A3 Gene
  • Blood Coagulation Cascade
  • ERK Signaling
  • FAK1 Signaling
  • GnRH Signaling
  • ILK Signaling

Gene Ontology (GO) - Biological Process for COL5A3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007160 cell-matrix adhesion IEA --
GO:0030198 extracellular matrix organization TAS --
GO:0030199 collagen fibril organization NAS 10722718
GO:0043588 skin development NAS 10722718
genes like me logo Genes that share ontologies with COL5A3: view

No data available for SIGNOR curated interactions for COL5A3 Gene

Drugs & Compounds for COL5A3 Gene

No Compound Related Data Available

Transcripts for COL5A3 Gene

mRNA/cDNA for COL5A3 Gene

1 REFSEQ mRNAs :
3 NCBI additional mRNA sequence :
2 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for COL5A3

Alternative Splicing Database (ASD) splice patterns (SP) for COL5A3 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20 ^ 21 ^ 22 ^ 23 ^ 24 ^ 25 ^ 26 ^
SP1:
SP2:

ExUns: 27 ^ 28 ^ 29 ^ 30 ^ 31 ^ 32 ^ 33 ^ 34 ^ 35 ^ 36 ^ 37 ^ 38 ^ 39 ^ 40 ^ 41 ^ 42 ^ 43 ^ 44 ^ 45 ^ 46 ^ 47 ^ 48 ^ 49 ^ 50 ^ 51 ^ 52 ^
SP1:
SP2:

ExUns: 53 ^ 54 ^ 55 ^ 56 ^ 57 ^ 58a · 58b ^ 59 ^ 60 ^ 61a · 61b ^ 62 ^ 63 ^ 64 ^ 65 ^ 66 ^ 67
SP1: - -
SP2:

Relevant External Links for COL5A3 Gene

GeneLoc Exon Structure for
COL5A3

Expression for COL5A3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for COL5A3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for COL5A3 Gene

This gene is overexpressed in Brain (18.0), Adipocyte (16.1), Lung (8.9), and Bone marrow mesenchymal stem cell (6.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for COL5A3 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for COL5A3

SOURCE GeneReport for Unigene cluster for COL5A3 Gene:

Hs.235368

Evidence on tissue expression from TISSUES for COL5A3 Gene

  • Heart(4.3)
  • Liver(4.3)
  • Skin(2.2)
genes like me logo Genes that share expression patterns with COL5A3: view

No data available for mRNA differential expression in normal tissues , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for COL5A3 Gene

Orthologs for COL5A3 Gene

This gene was present in the common ancestor of chordates.

Orthologs for COL5A3 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia COL5A3 30 31
  • 95.98 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia COL5A3 30 31
  • 87.98 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia COL5A3 30 31
  • 85.97 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Col5a3 30 17 31
  • 80.77 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Col5a3 30
  • 80.74 (n)
Oppossum
(Monodelphis domestica)
Mammalia COL5A3 31
  • 73 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia COL5A3 31
  • 61 (a)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia COL5A3 31
  • 71 (a)
OneToOne
Zebrafish
(Danio rerio)
Actinopterygii col5a3a 31
  • 60 (a)
OneToMany
col5a3b 31
  • 56 (a)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 55 (a)
OneToMany
Species where no ortholog for COL5A3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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)
  • Chicken (Gallus gallus)
  • 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 Vase (Ciona intestinalis)
  • 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)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for COL5A3 Gene

ENSEMBL:
Gene Tree for COL5A3 (if available)
TreeFam:
Gene Tree for COL5A3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for COL5A3: view image

Paralogs for COL5A3 Gene

Variants for COL5A3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for COL5A3 Gene

SNP ID Clinical significance and condition Chr 19 pos Variation AA Info Type
714631 Benign: not provided 9,980,687(-) A/G SYNONYMOUS_VARIANT
724669 Likely Benign: not provided 9,996,111(-) G/A SYNONYMOUS_VARIANT
727368 Likely Benign: not provided 9,979,394(-) C/T SYNONYMOUS_VARIANT
768969 Benign: not provided 10,005,618(-) G/A SYNONYMOUS_VARIANT
770806 Benign: not provided 9,973,784(-) A/G MISSENSE_VARIANT

Additional dbSNP identifiers (rs#s) for COL5A3 Gene

Structural Variations from Database of Genomic Variants (DGV) for COL5A3 Gene

Variant ID Type Subtype PubMed ID
esv1171542 CNV insertion 17803354
esv1205344 CNV deletion 17803354
esv1756302 CNV deletion 17803354
esv2406867 CNV deletion 18987734
esv2659051 CNV deletion 23128226
esv2667691 CNV deletion 23128226
esv2718163 CNV deletion 23290073
esv2718164 CNV deletion 23290073
esv2718165 CNV deletion 23290073
esv2718166 CNV deletion 23290073
esv2718167 CNV deletion 23290073
esv3404998 CNV insertion 20981092
esv3449361 CNV duplication 20981092
esv3643646 CNV loss 21293372
nsv1059984 CNV gain 25217958
nsv1072321 CNV deletion 25765185
nsv1131398 CNV deletion 24896259
nsv520683 CNV loss 19592680
nsv833742 CNV loss 17160897

Variation tolerance for COL5A3 Gene

Residual Variation Intolerance Score: 66.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 27.12; 99.81% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for COL5A3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
COL5A3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for COL5A3 Gene

Disorders for COL5A3 Gene

MalaCards: The human disease database

(2) MalaCards diseases for COL5A3 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
ehlers-danlos syndrome
  • cutis hyperelastica
lactocele
  • galactocele
- elite association - COSMIC cancer census association via MalaCards
genes like me logo Genes that share disorders with COL5A3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for COL5A3 Gene

Publications for COL5A3 Gene

  1. The pro-alpha3(V) collagen chain. Complete primary structure, expression domains in adult and developing tissues, and comparison to the structures and expression domains of the other types V and XI procollagen chains. (PMID: 10722718) Imamura Y … Greenspan DS (The Journal of biological chemistry 2000) 2 3 4
  2. Type V Collagen in Health, Disease, and Fibrosis. (PMID: 26910848) Mak KM … Lee DJ (Anatomical record (Hoboken, N.J. : 2007) 2016) 2 3
  3. Isolation of the alpha 3-chain of human type V collagen and characterization by partial sequencing. (PMID: 1571108) Mann K (Biological chemistry Hoppe-Seyler 1992) 3 4
  4. Loss of ER retention motif of AGR2 can impact mTORC signaling and promote cancer metastasis. (PMID: 30575818) Tiemann K … Kani K (Oncogene 2019) 3
  5. The COL5A3 and MMP9 genes interact in eczema susceptibility. (PMID: 29168291) Margaritte-Jeannin P … Dizier MH (Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology 2018) 3

Products for COL5A3 Gene

Sources for COL5A3 Gene