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

Gene ID: 57642, updated on 5-Aug-2022

Summary

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 and extracellular space. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in brain (RPKM 3.6) and testis (RPKM 0.8) See more
Orthologs
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Genomic context

See COL20A1 in Genome Data Viewer
Location:
20q13.33
Exon count:
38
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (63293186..63334806)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (65099069..65141009)
105.20220307 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 uncharacterized LOC100192386 Neighboring gene ADP ribosylation factor GTPase activating protein 1 Neighboring gene microRNA 4326 Neighboring gene RNA, U6 small nuclear 994, pseudogene Neighboring gene cholinergic receptor nicotinic alpha 4 subunit Neighboring gene uncharacterized LOC100130587

Genomic regions, transcripts, and products

Expression

  • Project title: 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • KIAA1510

Gene Ontology Provided by GOA

Component Evidence Code Pubs
part_of collagen trimer IEA
Inferred from Electronic Annotation
more info
 
is_active_in collagen-containing extracellular matrix IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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
 
is_active_in extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

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_020882.4NP_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
    Q9BQU7, Q9P218
    Related
    ENSP00000351767.6, ENST00000358894.11
    Conserved Domains (5) summary
    pfam01391
    Location:11111191
    Collagen; Collagen triple helix repeat (20 copies)
    cd00063
    Location:559644
    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:178341
    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:742821
    fn3; Fibronectin type III domain
    cl22861
    Location:8421036
    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: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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_011528937.2XP_011527239.1  collagen alpha-1(XX) chain isoform X1

    Conserved Domains (5) summary
    pfam01391
    Location:11331219
    Collagen; Collagen triple helix repeat (20 copies)
    cd00063
    Location:560645
    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:178341
    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:743822
    fn3; Fibronectin type III domain
    cl22861
    Location:8441038
    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_011528938.2XP_011527240.1  collagen alpha-1(XX) chain isoform X2

    Related
    ENST00000479501.5
    Conserved Domains (5) summary
    pfam01391
    Location:11451225
    Collagen; Collagen triple helix repeat (20 copies)
    cd00063
    Location:560645
    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:178341
    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:743822
    fn3; Fibronectin type III domain
    cl22861
    Location:8441038
    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)