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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 Integrin Pathway and ERK Signaling. An important paralog of this gene is COL14A1.

UniProtKB/Swiss-Prot for COL20A1 Gene

  • Probable collagen protein.

Additional gene information for COL20A1 Gene

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

GeneHancer (GH) Regulatory Elements for COL20A1 Gene

Promoters and enhancers for COL20A1 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
GH20I063291 Enhancer 0.8 ENCODE 550.8 -1.7 -1745 0.2 RB1 ZFP64 ARID4B DMAP1 ZNF2 ZNF48 RAD21 SLC30A9 GLIS2 ZNF143 COL20A1 MIR4326 GC20P063264
GH20I063293 Promoter 0.5 EPDnew 550.8 +0.0 27 0.1 COL20A1 GC20P063264 PIR56756
GH20I063264 Enhancer 1.2 FANTOM5 Ensembl ENCODE 16.7 -26.0 -25985 5.4 BCOR MXI1 SAP130 ARID4B BACH1 ZMYM3 DMAP1 TEAD3 ZNF335 ZFHX2 BIRC7 MIR647 COL20A1 DIDO1 UCKL1 LAMA5 NKAIN4 ENSG00000237371 ARFGAP1 RTEL1
GH20I063252 Promoter/Enhancer 1.3 EPDnew Ensembl ENCODE 11.7 -38.6 -38630 4.3 CTCF ZBTB6 ZBTB8A ATF2 POLR2A SCRT2 ZNF143 CTBP2 ZNF600 ZBTB26 NKAIN4 FLJ16779 GC20M063249 GC20M063246 BIRC7 COL20A1 RNU6-994P ENSG00000231977 MIR124-3 ARFGAP1
GH20I063271 Promoter/Enhancer 2.2 EPDnew FANTOM5 Ensembl ENCODE 6 -19.8 -19816 2.8 HDGF PKNOX1 ZFP64 ARID4B SIN3A FEZF1 DMAP1 ZBTB7B SLC30A9 ZNF143 NKAIN4 ARFGAP1 MRGBP GMEB2 FNDC11 DIDO1 ADRM1 COL20A1 GC20P063264 MIR4326
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around COL20A1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the COL20A1 gene promoter:

Genomic Locations for COL20A1 Gene

Genomic Locations for COL20A1 Gene
chr20:63,293,169-63,334,851
(GRCh38/hg38)
Size:
41,683 bases
Orientation:
Plus strand
chr20:61,924,538-61,966,203
(GRCh37/hg19)

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

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

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

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.

Phenotypes From GWAS Catalog for COL20A1 Gene

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

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

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

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:

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

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 33 34
  • 98.68 (n)
cow
(Bos Taurus)
Mammalia COL20A1 33 34
  • 83.33 (n)
dog
(Canis familiaris)
Mammalia COL20A1 33 34
  • 81.34 (n)
rat
(Rattus norvegicus)
Mammalia Col20a1 33
  • 77.25 (n)
mouse
(Mus musculus)
Mammalia Col20a1 33 16 34
  • 76.08 (n)
oppossum
(Monodelphis domestica)
Mammalia COL20A1 34
  • 58 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia COL20A1 34
  • 58 (a)
OneToOne
chicken
(Gallus gallus)
Aves COL20A1 33 34
  • 61.76 (n)
lizard
(Anolis carolinensis)
Reptilia COL20A1 34
  • 37 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii slc35c2 34
  • 29 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea CSA.10963 34
  • 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

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 Variation AA Info Type
rs1000003062 -- 63,299,787(+) T/C intron_variant
rs1000019703 -- 63,309,036(+) G/A intron_variant
rs1000022222 -- 63,293,780(+) CT/ intron_variant
rs1000073974 -- 63,305,109(+) G/A intron_variant
rs1000196661 -- 63,312,883(+) G/A coding_sequence_variant, synonymous_variant

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

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

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
COL20A1

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

Disorders for COL20A1 Gene

Additional Disease Information for 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 research : an international journal for rapid publication of reports on genes and genomes 2000) 2 3 4 58
  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 58
  3. The DNA sequence and comparative analysis of human chromosome 20. (PMID: 11780052) Deloukas P … Rogers J (Nature 2001) 3 4 58
  4. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58
  5. A proteome-scale map of the human interactome network. (PMID: 25416956) Rolland T … Vidal M (Cell 2014) 3 58

Products for COL20A1 Gene

Sources for COL20A1 Gene

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