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COL20A1 collagen type XX alpha 1 chain [ Homo sapiens (human) ]

Gene ID: 57642, updated on 14-Nov-2024

Summary

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Official Symbol
COL20A1provided by HGNC
Official Full Name
collagen type XX alpha 1 chainprovided by HGNC
Primary source
HGNC:HGNC:14670
See related
Ensembl:ENSG00000101203 MIM:619390; AllianceGenome:HGNC:14670
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
Predicted to be located in endoplasmic reticulum lumen and extracellular region. Predicted to be part of collagen trimer. Predicted to be active in collagen-containing extracellular matrix. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Biased expression in brain (RPKM 3.6) and testis (RPKM 0.8) See more
Orthologs
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Genomic context

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See COL20A1 in Genome Data Viewer
Location:
20q13.33
Exon count:
38
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (63293186..63334806)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (65099069..65141009)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (61924538..61966158)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene sodium/potassium transporting ATPase interacting 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:61885071-61885602 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:61885603-61886134 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:61889508-61890125 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:61891361-61891976 Neighboring gene uncharacterized LOC100192386 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13150 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13151 Neighboring gene ARF GTPase activating protein 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:61915538-61916038 Neighboring gene H3K4me1 hESC enhancers GRCh37_chr20:61922048-61922671 and GRCh37_chr20:61922672-61923296 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:61924431-61924932 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:61924933-61925432 Neighboring gene microRNA 4326 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:61952290-61952790 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr20:61971654-61972853 Neighboring gene RNA, U6 small nuclear 994, pseudogene Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_60863 Neighboring gene cholinergic receptor nicotinic alpha 4 subunit Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr20:61986832-61988031 Neighboring gene uncharacterized LOC100130587

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Type XX Collagen Is Elevated in Circulation of Patients with Solid Tumors. Thorlacius-Ussing J, et al. Int J Mol Sci, 2022 Apr 8. PMID 35456962, Free PMC Article
  2. Whole-exome sequencing analysis reveals co-segregation of a COL20A1 missense mutation in a Pakistani family with striate palmoplantar keratoderma. Khan MI, et al. Genes Genomics, 2018 Jul. PMID 29934816
  3. Proteomics analysis of cardiac extracellular matrix remodeling in a porcine model of ischemia/reperfusion injury. Barallobre-Barreiro J, et al. Circulation, 2012 Feb 14. PMID 22261194
  4. 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. Nagase T, et al. DNA Res, 2000 Apr 28. PMID 10819331
  5. The DNA sequence and comparative analysis of human chromosome 20. Deloukas P, et al. Nature, 2001 Dec 20-27. PMID 11780052

See all (14) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Type XX Collagen Is Elevated in Circulation of Patients with Solid Tumors.
    Title: Type XX Collagen Is Elevated in Circulation of Patients with Solid Tumors.
  2. Our study proposes COL20A1 gene as another potential candidate gene for striate palmoplantar keratoderma (PPKS)which expand the spectrum of collagen proteins in the pathogenicity of Palmoplantar keratoderma.
    Title: Whole-exome sequencing analysis reveals co-segregation of a COL20A1 missense mutation in a Pakistani family with striate palmoplantar keratoderma.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • KIAA1510

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Component Evidence Code Pubs
part_of collagen trimer IEA
Inferred from Electronic Annotation
more info
  
colocalizes_with collagen-containing extracellular matrix TAS
Traceable Author Statement
more info
 PubMed 
located_in endoplasmic reticulum lumen TAS
Traceable Author Statement
more info
  
located_in extracellular region TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
collagen alpha-1(XX) chain
Names
collagen, type XX, alpha 1
collagen-like protein

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_020882.4 → NP_065933.2  collagen alpha-1(XX) chain precursor

    See identical proteins and their annotated locations for NP_065933.2

    Status: VALIDATED

    Source sequence(s)
    AB040943, AL121827, BC041767, BC043183
    Consensus CDS
    CCDS46628.1
    UniProtKB/Swiss-Prot
    Q4VXQ4, Q6PI59, Q8WUT2, Q96CY9, Q9BQU6, Q9BQU7, Q9P218
    Related
    ENSP00000351767.6, ENST00000358894.11
    Conserved Domains (5) summary
    pfam01391
    Location:1111 → 1191
    Collagen; Collagen triple helix repeat (20 copies)
    cd00063
    Location:559 → 644
    FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
    cd01482
    Location:178 → 341
    vWA_collagen_alphaI-XII-like; Collagen: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different ...
    pfam00041
    Location:742 → 821
    fn3; Fibronectin type III domain
    cl22861
    Location:842 → 1036
    LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    63293186..63334806
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011528937.2 → XP_011527239.1  collagen alpha-1(XX) chain isoform X1

    Conserved Domains (5) summary
    pfam01391
    Location:1133 → 1219
    Collagen; Collagen triple helix repeat (20 copies)
    cd00063
    Location:560 → 645
    FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
    cd01482
    Location:178 → 341
    vWA_collagen_alphaI-XII-like; Collagen: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different ...
    pfam00041
    Location:743 → 822
    fn3; Fibronectin type III domain
    cl22861
    Location:844 → 1038
    LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...

  2. XM_011528938.2 → XP_011527240.1  collagen alpha-1(XX) chain isoform X2

    Related
    ENST00000479501.5
    Conserved Domains (5) summary
    pfam01391
    Location:1145 → 1225
    Collagen; Collagen triple helix repeat (20 copies)
    cd00063
    Location:560 → 645
    FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
    cd01482
    Location:178 → 341
    vWA_collagen_alphaI-XII-like; Collagen: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different ...
    pfam00041
    Location:743 → 822
    fn3; Fibronectin type III domain
    cl22861
    Location:844 → 1038
    LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    65099069..65141009
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054323777.1 → XP_054179752.1  collagen alpha-1(XX) chain isoform X1

  2. XM_054323778.1 → XP_054179753.1  collagen alpha-1(XX) chain isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9P218.4 GenPept UniProtKB/Swiss-Prot:Q9P218

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