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Aliases for COL5A3 Gene

Aliases for COL5A3 Gene

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

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. Among its related pathways are ERK Signaling and Focal Adhesion. 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 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 , fRNAdb sequence ontologies and piRNA Summary for COL5A3 Gene

Genomics for COL5A3 Gene

GeneHancer (GH) Regulatory Elements for COL5A3 Gene

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 2.1 EPDnew FANTOM5 Ensembl ENCODE 688.6 +2.2 2225 4.8 HDGF PKNOX1 SIN3A FEZF1 GLI4 GLIS2 FOS SP3 MIER2 TSHZ1 COL5A3 LOC100419831 ZNF559 ZNF177 KRI1 ZNF121 ZNF846 LOC100418883 OR7D1P OR7E19P
GH19J010235 Promoter/Enhancer 2.2 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 9.7 -226.8 -226810 4.4 HDGF PKNOX1 FOXA2 SMAD1 MLX ARID4B SIN3A FEZF1 YBX1 IRF4 MRPL4 S1PR5 COL5A3 RDH8 S1PR2 ATG4D C19orf66 TYK2 DNM2 FBXL12
GH19J009913 Promoter/Enhancer 1.7 FANTOM5 Ensembl ENCODE 11.2 +96.1 96111 1.7 HDGF ATF1 ARNT SIN3A ZNF48 GLIS2 ZNF213 ZNF143 FOS ATF7 OLFM2 RDH8 COL5A3 ENSG00000267273 ZNF266 GC19P009927 PIR54152
GH19J009917 Enhancer 1 Ensembl ENCODE 11.9 +93.1 93055 0.2 HDAC1 ELF3 PKNOX1 RB1 ARNT ZBTB40 ETS1 ZNF335 GATA2 ZNF143 LOC100128428 COL5A3 RDH8 QTRT1 C19orf66 OR7D2 GC19P009927 OLFM2 PIR54152
GH19J009930 Enhancer 0.8 ENCODE 12 +79.5 79488 0.2 ELF3 CTCF RB1 MAX BACH1 EBF1 GLI4 RAD21 CC2D1A ZFHX2 COL5A3 RDH8 C19orf66 GC19P009927 OLFM2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around COL5A3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the COL5A3 gene promoter:

Genomic Locations for COL5A3 Gene

Genomic Locations for COL5A3 Gene
chr19:9,959,561-10,010,538
(GRCh38/hg38)
Size:
50,978 bases
Orientation:
Minus strand
chr19:10,070,237-10,121,147
(GRCh37/hg19)

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 posLast=141141 and posLast=102102
  • Modification sites at PhosphoSitePlus

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

Suggested Antigen Peptide Sequences for COL5A3 Gene

GenScript: Design optimal peptide antigens:

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: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

Clone Products

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 5
plasma membrane 3
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 NAS,IEA 1571108
GO:0005788 endoplasmic reticulum lumen TAS --
GO:0031012 extracellular matrix IDA,IEA 27559042
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

genes like me logo Genes that share pathways with COL5A3: view

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:0030574 collagen catabolic process TAS --
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

(72) Selected AceView cDNA sequences:
(2) Additional mRNA sequences :
(3) REFSEQ mRNAs :
(2) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for COL5A3 Gene

Collagen, type V, alpha 3:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

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

Clone Products

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
ECgene alternative splicing isoforms for
COL5A3

Expression for COL5A3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP 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



NURSA nuclear receptor signaling pathways regulating expression of COL5A3 Gene:

COL5A3

SOURCE GeneReport for Unigene cluster for COL5A3 Gene:

Hs.235368

Evidence on tissue expression from TISSUES for COL5A3 Gene

  • Heart(4.1)
  • Liver(4.1)
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 34 33
  • 95.98 (n)
OneToOne
dog
(Canis familiaris)
Mammalia COL5A3 34 33
  • 87.98 (n)
OneToOne
cow
(Bos Taurus)
Mammalia COL5A3 34 33
  • 85.97 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Col5a3 16 34 33
  • 80.77 (n)
rat
(Rattus norvegicus)
Mammalia Col5a3 33
  • 80.74 (n)
oppossum
(Monodelphis domestica)
Mammalia COL5A3 34
  • 73 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia COL5A3 34
  • 61 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia COL5A3 34
  • 71 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii col5a3a 34
  • 60 (a)
OneToMany
col5a3b 34
  • 56 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 55 (a)
OneToMany
Species where no ortholog for COL5A3 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)
  • 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 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

(13) SIMAP similar genes for COL5A3 Gene using alignment to 1 proteins:

  • CO5A3_HUMAN
genes like me logo Genes that share paralogs with COL5A3: view

Variants for COL5A3 Gene

Sequence variations from dbSNP and Humsavar for COL5A3 Gene

SNP ID Clin Chr 19 pos Variation AA Info Type
rs864309605 uncertain-significance, not specified 9,989,353(-) T/C coding_sequence_variant, genic_upstream_transcript_variant, missense_variant, upstream_transcript_variant
rs1000049048 -- 9,987,860(-) G/A intron_variant
rs1000146469 -- 9,971,975(-) C/T intron_variant
rs1000227999 -- 9,997,305(-) C/T genic_upstream_transcript_variant, intron_variant
rs1000488822 -- 9,998,712(-) T/G genic_upstream_transcript_variant, intron_variant

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

Additional Disease Information for COL5A3

No disorders were found for COL5A3 Gene.

No data available for MalaCards , 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 58
  2. Type V Collagen in Health, Disease, and Fibrosis. (PMID: 26910848) Mak KM … Lee DJ (Anatomical record (Hoboken, N.J. : 2007) 2016) 2 3 58
  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 58
  4. Glycoproteomics Reveals Decorin Peptides With Anti-Myostatin Activity in Human Atrial Fibrillation. (PMID: 27559042) Barallobre-Barreiro J … Mayr M (Circulation 2016) 3 58
  5. Proteomic analysis of podocyte exosome-enriched fraction from normal human urine. (PMID: 23376485) Prunotto M … Moll S (Journal of proteomics 2013) 3 58

Products for COL5A3 Gene

Sources for COL5A3 Gene

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