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

    Gene ID: 57642, updated on 18-Sep-2024

    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
    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

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General protein information

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

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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
      Q4VXQ4, Q6PI59, Q8WUT2, Q96CY9, Q9BQU6, 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: 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_011528937.2XP_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)

    mRNA and Protein(s)

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

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