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

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: mouse all
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Genomic context

Location:: 20q13.33

Exon count:: 38

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	20	NC_000020.11 (63293186..63334806)
RS_2023_10	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_000020.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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

D1S3693 (e-PCR)
- UniSTS:474271

RH67296 (e-PCR)
- UniSTS:86959

G32605 (e-PCR)
- UniSTS:117188

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
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)

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_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000020.11 Reference GRCh38.p14 Primary Assembly

Range

63293186..63334806

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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 ...
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 ...