Aliases for COL20A1 Gene

Aliases for COL20A1 Gene

  • Collagen Type XX Alpha 1 Chain 2 3 5
  • Collagen Alpha-1(XX) Chain 3 4
  • Collagen, Type XX, Alpha 1 2 3
  • Collagen-Like Protein 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. Diseases associated with COL20A1 include Striate Palmoplantar Keratoderma. Among its related pathways are ERK Signaling and Collagen chain trimerization. An important paralog of this gene is COL1A1.

UniProtKB/Swiss-Prot Summary for COL20A1 Gene

Additional gene information for COL20A1 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for COL20A1 Gene

Genomics for COL20A1 Gene

GeneHancer (GH) Regulatory Elements for COL20A1 Gene

Promoters and enhancers for COL20A1 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH20J063292 Enhancer 0.5 Ensembl 500.7 -0.9 -868 0.2 PCBP1 POLR2G CEBPB KLF1 AGO1 POLR2A AHR COL20A1 MIR4326 lnc-ARFGAP1-4
GH20J063293 Promoter 0.3 EPDnew 500.7 +0.0 27 0.1 COL20A1 lnc-ARFGAP1-4 piR-61757-001
GH20J063329 Promoter 0.3 EPDnew 500.3 +35.9 35946 0.1 COL20A1 piR-61757-001
GH20J063264 Enhancer 1.3 FANTOM5 Ensembl ENCODE CraniofacialAtlas 11.2 -26.5 -26491 5.4 TEAD4 TGIF2 TEAD1 HINFP ZBTB26 MYC RELA ZNF316 CTCF SAP130 BIRC7 ARFGAP1 DIDO1 GMEB2 NKAIN4 RTEL1 ZGPAT COL20A1 RNU6-994P ENSG00000231977
GH20J063252 Promoter/Enhancer 1.3 EPDnew Ensembl ENCODE 11.7 -39.0 -39001 2.3 GABPA ZBTB26 HDAC2 EZH2 SP2 POLR2A CTCF SMARCA4 ATF2 RBM39 NKAIN4 FLJ16779 BIRC7 RTEL1 ARFGAP1 COL20A1 RNU6-994P ENSG00000231977 MIR124-3 YTHDF1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around COL20A1 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for COL20A1

Top Transcription factor binding sites by QIAGEN in the COL20A1 gene promoter:
  • ATF-2
  • ATF6
  • c-Jun
  • CREB
  • Ik-3
  • IRF-7A
  • LCR-F1
  • MRF-2
  • STAT5A
  • STAT5B

Genomic Locations for COL20A1 Gene

Genomic Locations for COL20A1 Gene
41,683 bases
Plus strand
41,666 bases
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:
    Recommended name:
    Collagen alpha-1(XX) chain
    Protein Accession:
    Secondary Accessions:
    • Q4VXQ4
    • Q6PI59
    • Q8WUT2
    • Q96CY9
    • Q9BQU6
    • Q9BQU7

    Protein attributes for COL20A1 Gene

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

    Three dimensional structures from OCA and Proteopedia for COL20A1 Gene

    Alternative splice isoforms for COL20A1 Gene


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

Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted secreted proteins

Protein Domains for COL20A1 Gene

  • Collagen triple helix repeat
  • Collagen helix repeat
  • Von Willebrand factor type A domain signature
  • Thrombospondin, N-terminal

Suggested Antigen Peptide Sequences for COL20A1 Gene

GenScript: Design optimal peptide antigens:
  • Collagen, type XX, alpha 1 (B7ZBI4_HUMAN)
  • Collagen, type XX, alpha 1 (B7ZBI5_HUMAN)
  • Collagen alpha-1(XX) chain (COKA1_HUMAN)
genes like me logo Genes that share domains with COL20A1: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for COL20A1 Gene

Function for COL20A1 Gene

Molecular function for COL20A1 Gene

UniProtKB/Swiss-Prot Function:
Probable collagen protein.

Phenotypes From GWAS Catalog for COL20A1 Gene

Gene Ontology (GO) - Molecular Function for COL20A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IEA --
genes like me logo Genes that share ontologies with COL20A1: view
genes like me logo Genes that share phenotypes with COL20A1: view

Animal Model Products

  • Taconic Biosciences Mouse Models for COL20A1

CRISPR Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , 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

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 4
endoplasmic reticulum 4
plasma membrane 1
cytoskeleton 1
nucleus 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 IBA 21873635
GO:0005788 endoplasmic reticulum lumen TAS --
GO:0031012 extracellular matrix IBA 21873635
genes like me logo Genes that share ontologies with COL20A1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for COL20A1 Gene

Pathways & Interactions for COL20A1 Gene

PathCards logo

SuperPathways for COL20A1 Gene

SuperPathway Contained pathways
1 Integrin Pathway
2 Collagen chain trimerization
3 ERK Signaling
4 Phospholipase-C Pathway
5 Degradation of the extracellular matrix
genes like me logo Genes that share pathways with COL20A1: view

Pathways by source for COL20A1 Gene

15 Qiagen pathways for COL20A1 Gene
  • Blood Coagulation Cascade
  • ERK Signaling
  • FAK1 Signaling
  • GnRH Signaling
  • ILK Signaling

Gene Ontology (GO) - Biological Process for COL20A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003429 growth plate cartilage chondrocyte morphogenesis IBA 21873635
genes like me logo Genes that share ontologies with COL20A1: view

No data available for SIGNOR curated interactions for COL20A1 Gene

Drugs & Compounds for COL20A1 Gene

(3) Drugs for COL20A1 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(1) 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

mRNA/cDNA for COL20A1 Gene

7 NCBI additional mRNA sequence :
8 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR 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: - -
SP4: -
SP6: -

ExUns: 22 ^ 23 ^ 24a · 24b ^ 25 ^ 26 ^ 27a · 27b ^ 28a · 28b
SP1: - -
SP2: - -
SP7: -

Relevant External Links for COL20A1 Gene

GeneLoc Exon Structure for

Expression for COL20A1 Gene

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

Protein tissue co-expression partners for COL20A1 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for COL20A1

SOURCE GeneReport for Unigene cluster for COL20A1 Gene:


mRNA Expression by UniProt/SwissProt for COL20A1 Gene:

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

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
(Pan troglodytes)
Mammalia COL20A1 31 30
  • 98.68 (n)
(Bos Taurus)
Mammalia COL20A1 31 30
  • 83.33 (n)
(Canis familiaris)
Mammalia COL20A1 31 30
  • 81.34 (n)
(Rattus norvegicus)
Mammalia Col20a1 30
  • 77.25 (n)
(Mus musculus)
Mammalia Col20a1 17 31 30
  • 76.08 (n)
(Monodelphis domestica)
Mammalia COL20A1 31
  • 58 (a)
(Ornithorhynchus anatinus)
Mammalia COL20A1 31
  • 58 (a)
(Gallus gallus)
Aves COL20A1 31 30
  • 61.76 (n)
(Anolis carolinensis)
Reptilia COL20A1 31
  • 37 (a)
(Danio rerio)
Actinopterygii slc35c2 31
  • 29 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.10963 31
  • 13 (a)
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

Gene Tree for COL20A1 (if available)
Gene Tree for COL20A1 (if available)
Evolutionary constrained regions (ECRs) for COL20A1: view image

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, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for COL20A1 Gene

SNP ID Clinical significance and condition Chr 20 pos Variation AA Info Type
752588 Benign: not provided 63,308,630(+) G/A SYNONYMOUS_VARIANT
787606 Benign: not provided 63,305,966(+) G/A SYNONYMOUS_VARIANT
rs753686 - p.Pro134Leu

Additional dbSNP identifiers (rs#s) for COL20A1 Gene

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)

Additional Variant Information for COL20A1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

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

Disorders for COL20A1 Gene

MalaCards: The human disease database

(1) MalaCards diseases for COL20A1 Gene - From: GeneCards

Disorder Aliases PubMed IDs
striate palmoplantar keratoderma
  • keratosis palmoplantaris striata
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for COL20A1

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

No data available for 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 research : an international journal for rapid publication of reports on genes and genomes 2000) 2 3 4 54
  2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 54
  3. The DNA sequence and comparative analysis of human chromosome 20. (PMID: 11780052) Deloukas P … Rogers J (Nature 2001) 3 4 54
  4. Whole-exome sequencing analysis reveals co-segregation of a COL20A1 missense mutation in a Pakistani family with striate palmoplantar keratoderma. (PMID: 29934816) Khan MI … Kang C (Genes & genomics 2018) 3 54
  5. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 54

Products for COL20A1 Gene

  • Boster Bio Antibodies for COL20A1
  • Boster Bio ELISA Kits for COL20A1

Sources for COL20A1 Gene