Free for academic non-profit institutions. Other users need a Commercial license

Aliases for COL20A1 Gene

Aliases for COL20A1 Gene

  • Collagen Type XX Alpha 1 Chain 2 3 5
  • Collagen, Type XX, Alpha 1 2 3
  • Collagen Alpha-1(XX) Chain 3
  • Collagen-Like Protein 3
  • BA261N11.4 3
  • KIAA1510 4

External Ids for COL20A1 Gene

Previous GeneCards Identifiers for COL20A1 Gene

  • GC20P061398
  • GC20P061924
  • GC20P058649

Summaries for COL20A1 Gene

GeneCards Summary for COL20A1 Gene

COL20A1 (Collagen Type XX Alpha 1 Chain) is a Protein Coding gene. Among its related pathways are Phospholipase-C Pathway and Collagen chain trimerization. An important paralog of this gene is COL14A1.

UniProtKB/Swiss-Prot for COL20A1 Gene

  • Probable collagen protein.

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for COL20A1 Gene

Genomics for COL20A1 Gene

Regulatory Elements for COL20A1 Gene

Enhancers for COL20A1 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
GH20G063264 1.4 FANTOM5 Ensembl ENCODE 16.7 -26.0 -25985 5.4 RB1 ARID4B DMAP1 ZBTB7B RAD21 GLIS2 PCBP1 DEK EGR2 ZNF263 BIRC7 COL20A1 NKAIN4 ARFGAP1 RNU6-994P OGFR ENSG00000231977 ENSG00000237371 GC20P063264
GH20G063252 1.1 Ensembl ENCODE 11.7 -38.6 -38631 4.3 ZSCAN4 ZNF2 RAD21 ZEB1 ZNF335 SCRT2 ZNF143 ZNF207 CREM ZNF654 BIRC7 NKAIN4 COL20A1 RNU6-994P ENSG00000231977 MIR124-3 ARFGAP1 GC20M063249 FLJ16779
GH20G063393 1 ENCODE dbSUPER 12 +101.1 101102 0.9 CTCF MAX ARID4B RBBP5 RAD21 ZSCAN5C NR2F6 ZNF654 L3MBTL2 BHLHE40 RNU6-994P COL20A1 GC20M063393 CHRNA4
GH20G063258 0.9 ENCODE 11.5 -34.2 -34241 1.0 HDGF PKNOX1 NFIB ZNF473 ZNF195 BMI1 YBX1 PLRG1 ZBTB7B ZNF366 BIRC7 COL20A1 RNU6-994P ENSG00000231977 MIR124-3 TNFRSF6B ARFGAP1 GC20M063249 GC20P063264
GH20G063260 0.8 ENCODE 11.2 -31.7 -31674 1.7 FOXA2 SAP130 ZNF133 KLF17 NFXL1 YBX1 ZIC2 ZBTB40 ZKSCAN1 FOSL1 BIRC7 MIR647 UCKL1 LAMA5 NKAIN4 ENSG00000237371 COL20A1 RNU6-994P ENSG00000226332 PRPF6
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around COL20A1 on UCSC Golden Path with GeneCards custom track

Genomic Location for COL20A1 Gene

Chromosome:
20
Start:
63,293,169 bp from pter
End:
63,334,851 bp from pter
Size:
41,683 bases
Orientation:
Plus strand

Genomic View for COL20A1 Gene

Genes around COL20A1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
COL20A1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for COL20A1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for COL20A1 Gene

Proteins for COL20A1 Gene

  • Protein details for COL20A1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9P218-COKA1_HUMAN
    Recommended name:
    Collagen alpha-1(XX) chain
    Protein Accession:
    Q9P218
    Secondary Accessions:
    • Q4VXQ4
    • Q6PI59
    • Q8WUT2
    • Q96CY9
    • Q9BQU6
    • Q9BQU7

    Protein attributes for COL20A1 Gene

    Size:
    1284 amino acids
    Molecular mass:
    135830 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=AAH19637.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for COL20A1 Gene

    Alternative splice isoforms for COL20A1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for COL20A1 Gene

Post-translational modifications for COL20A1 Gene

  • Glycosylation at Asn607
  • Modification sites at PhosphoSitePlus

Other Protein References for COL20A1 Gene

No data available for DME Specific Peptides for COL20A1 Gene

Domains & Families for COL20A1 Gene

Gene Families for COL20A1 Gene

Suggested Antigen Peptide Sequences for COL20A1 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with COL20A1: view

No data available for UniProtKB/Swiss-Prot for COL20A1 Gene

Function for COL20A1 Gene

Molecular function for COL20A1 Gene

UniProtKB/Swiss-Prot Function:
Probable collagen protein.
genes like me logo Genes that share phenotypes with COL20A1: view

Animal Model Products

  • Taconic Biosciences Mouse Models for COL20A1

Inhibitory RNA Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for COL20A1 Gene

Localization for COL20A1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for COL20A1 Gene

Secreted, extracellular space.

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 COL20A1 gene
Compartment Confidence
extracellular 5
endoplasmic reticulum 4
plasma membrane 1

Gene Ontology (GO) - Cellular Components for COL20A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS --
GO:0005581 collagen trimer IEA --
GO:0005615 extracellular space IEA --
GO:0005788 endoplasmic reticulum lumen TAS --
GO:0031012 colocalizes_with extracellular matrix TAS 22261194
genes like me logo Genes that share ontologies with COL20A1: view

Pathways & Interactions for COL20A1 Gene

genes like me logo Genes that share pathways with COL20A1: view

Gene Ontology (GO) - Biological Process for COL20A1 Gene

None

No data available for SIGNOR curated interactions for COL20A1 Gene

Drugs & Compounds for COL20A1 Gene

(2) Drugs for COL20A1 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(2) Additional Compounds for COL20A1 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with COL20A1: view

Transcripts for COL20A1 Gene

Unigene Clusters for COL20A1 Gene

Collagen, type XX, alpha 1:
Representative Sequences:

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for COL20A1 Gene

ExUns: 1 ^ 2a · 2b ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13a · 13b ^ 14 ^ 15a · 15b ^ 16 ^ 17 ^ 18 ^ 19a · 19b ^ 20a · 20b ^ 21 ^
SP1: - -
SP2:
SP3:
SP4: -
SP5:
SP6: -
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:

ExUns: 22 ^ 23 ^ 24a · 24b ^ 25 ^ 26 ^ 27a · 27b ^ 28a · 28b
SP1: - -
SP2: - -
SP3:
SP4:
SP5:
SP6:
SP7: -
SP8:
SP9:
SP10:
SP11:
SP12:

Relevant External Links for COL20A1 Gene

GeneLoc Exon Structure for
COL20A1
ECgene alternative splicing isoforms for
COL20A1

Expression for COL20A1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for COL20A1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for COL20A1 Gene

This gene is overexpressed in Brain - Anterior cingulate cortex (BA24) (x5.5), Brain - Amygdala (x5.0), Brain - Cortex (x4.9), Testis (x4.8), and Brain - Substantia nigra (x4.3).

Protein differential expression in normal tissues from HIPED for COL20A1 Gene

This gene is overexpressed in Heart (40.6), Peripheral blood mononuclear cells (14.8), and Liver (13.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for COL20A1 Gene



Protein tissue co-expression partners for COL20A1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of COL20A1 Gene:

COL20A1

SOURCE GeneReport for Unigene cluster for COL20A1 Gene:

Hs.271285

mRNA Expression by UniProt/SwissProt for COL20A1 Gene:

Q9P218-COKA1_HUMAN
Tissue specificity: High expression in heart, lung, liver, skeletal muscle, kidney, pancreas, spleen, testis, ovary, subthalamic nucleus and fetal liver. Weak expression in other tissues tested.

Evidence on tissue expression from TISSUES for COL20A1 Gene

  • Nervous system(4.5)
genes like me logo Genes that share expression patterns with COL20A1: view

Primer Products

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for COL20A1 Gene

Orthologs for COL20A1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for COL20A1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia COL20A1 34 35
  • 98.68 (n)
cow
(Bos Taurus)
Mammalia COL20A1 34 35
  • 83.33 (n)
dog
(Canis familiaris)
Mammalia COL20A1 34 35
  • 81.34 (n)
rat
(Rattus norvegicus)
Mammalia Col20a1 34
  • 77.25 (n)
mouse
(Mus musculus)
Mammalia Col20a1 34 16 35
  • 76.08 (n)
oppossum
(Monodelphis domestica)
Mammalia COL20A1 35
  • 58 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia COL20A1 35
  • 58 (a)
OneToOne
chicken
(Gallus gallus)
Aves COL20A1 34 35
  • 61.76 (n)
lizard
(Anolis carolinensis)
Reptilia COL20A1 35
  • 37 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii slc35c2 35
  • 29 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea CSA.10963 35
  • 13 (a)
OneToMany
Species where no ortholog for COL20A1 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 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 COL20A1 Gene

ENSEMBL:
Gene Tree for COL20A1 (if available)
TreeFam:
Gene Tree for COL20A1 (if available)

Paralogs for COL20A1 Gene

(5) SIMAP similar genes for COL20A1 Gene using alignment to 3 proteins:

genes like me logo Genes that share paralogs with COL20A1: view

Variants for COL20A1 Gene

Sequence variations from dbSNP and Humsavar for COL20A1 Gene

SNP ID Clin Chr 20 pos Sequence Context AA Info Type
rs1000003062 -- 63,299,787(+) AGTGA(C/T)TGATT intron-variant
rs1000019703 -- 63,309,036(+) CTGCT(A/G)TGCCC intron-variant
rs1000022222 -- 63,293,780(+) AATCC(-/CT)GATTT intron-variant
rs1000073974 -- 63,305,109(+) GGGCA(A/G)CCCTG intron-variant
rs1000196661 -- 63,312,883(+) GGCGT(A/G)CTTGT reference, synonymous-codon

Structural Variations from Database of Genomic Variants (DGV) for COL20A1 Gene

Variant ID Type Subtype PubMed ID
esv1600196 CNV deletion 17803354
esv2722904 CNV deletion 23290073
esv3646309 CNV loss 21293372
nsv470560 CNV loss 18288195
nsv525279 CNV loss 19592680
nsv586564 CNV loss 21841781
nsv834032 CNV loss 17160897
nsv953306 CNV deletion 24416366
nsv9825 CNV gain 18304495

Variation tolerance for COL20A1 Gene

Residual Variation Intolerance Score: 96.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.26; 76.33% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for COL20A1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
COL20A1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for COL20A1 Gene

Disorders for COL20A1 Gene

Relevant External Links for COL20A1

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
COL20A1

No disorders were found for COL20A1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for COL20A1 Gene

Publications for COL20A1 Gene

  1. Prediction of the coding sequences of unidentified human genes. XVII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PMID: 10819331) Nagase T. … Ohara O. (DNA Res. 2000) 2 3 4 64
  2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64
  3. The DNA sequence and comparative analysis of human chromosome 20. (PMID: 11780052) Deloukas P. … Rogers J. (Nature 2001) 3 4 64
  4. A proteome-scale map of the human interactome network. (PMID: 25416956) Rolland T. … Vidal M. (Cell 2014) 3 64
  5. Proteomics analysis of cardiac extracellular matrix remodeling in a porcine model of ischemia/reperfusion injury. (PMID: 22261194) Barallobre-Barreiro J. … Mayr M. (Circulation 2012) 3 64

Products for COL20A1 Gene

Sources for COL20A1 Gene

Content
Loading form....