U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    Col20a1 collagen type XX alpha 1 chain [ Rattus norvegicus (Norway rat) ]

    Gene ID: 311716, updated on 9-Dec-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    Col20a1provided by RGD
    Official Full Name
    collagen type XX alpha 1 chainprovided by RGD
    Primary source
    RGD:1563901
    See related
    EnsemblRapid:ENSRNOG00000043150 AllianceGenome:RGD:1563901
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    RGD1563901
    Summary
    Predicted to be located in extracellular region. Predicted to be part of collagen trimer. Predicted to be active in collagen-containing extracellular matrix. Orthologous to human COL20A1 (collagen type XX alpha 1 chain). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Adrenal (RPKM 49.1), Spleen (RPKM 47.1) and 9 other tissues See more
    Orthologs
    human mouse all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See Col20a1 in Genome Data Viewer
    Location:
    3q43
    Exon count:
    36
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 3 NC_086021.1 (188477663..188512326)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 3 NC_051338.1 (168102475..168134759)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 3 NC_005102.4 (176491292..176526009)

    Chromosome 3 - NC_086021.1Genomic Context describing neighboring genes Neighboring gene Sodium/potassium transporting ATPase interacting 4 Neighboring gene ARF GTPase activating protein 1 Neighboring gene cholinergic receptor nicotinic alpha 4 subunit Neighboring gene potassium voltage-gated channel subfamily Q member 2 Neighboring gene eukaryotic translation elongation factor 1 alpha 2

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

    Go to the top of the pageHelp

    Related articles in PubMed

    1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

    Go to the top of the page Help

    Markers

    Homology

    Gene Ontology Provided by RGD

    Component Evidence Code Pubs
    part_of collagen trimer IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in extracellular region IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

    Go to the top of the page Help
    Preferred Names
    collagen alpha-1(XX) chain
    Names
    collagen, type XX, alpha 1

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    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_001427704.1 → NP_001414633.1  collagen alpha-1(XX) chain precursor

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000003
      UniProtKB/TrEMBL
      D3ZII5
      Related
      ENSRNOP00000049790.5, ENSRNOT00000040270.8

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086021.1 Reference GRCr8

      Range
      188477663..188512326
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039106762.2 → XP_038962690.1  collagen alpha-1(XX) chain isoform X1

      UniProtKB/TrEMBL
      A6KM63
      Conserved Domains (4) summary
      cd01482
      Location:222 → 386
      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:423 → 501
      fn3; Fibronectin type III domain
      pfam01391
      Location:1172 → 1215
      Collagen; Collagen triple helix repeat (20 copies)
      cl22861
      Location:887 → 1081
      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_063283895.1 → XP_063139965.1  collagen alpha-1(XX) chain isoform X6

      UniProtKB/TrEMBL
      A6KM63

    3. XM_039106763.2 → XP_038962691.1  collagen alpha-1(XX) chain isoform X3

      UniProtKB/TrEMBL
      A6KM63
      Conserved Domains (4) summary
      cd01482
      Location:222 → 386
      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:423 → 501
      fn3; Fibronectin type III domain
      pfam01391
      Location:1171 → 1214
      Collagen; Collagen triple helix repeat (20 copies)
      cl22861
      Location:886 → 1080
      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 ...

    4. XM_017592316.3 → XP_017447805.1  collagen alpha-1(XX) chain isoform X2

      UniProtKB/TrEMBL
      A6KM63

    5. XM_017592315.3 → XP_017447804.2  collagen alpha-1(XX) chain isoform X4

      UniProtKB/TrEMBL
      A6KM63
      Conserved Domains (4) summary
      cd01482
      Location:222 → 385
      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:422 → 500
      fn3; Fibronectin type III domain
      pfam01391
      Location:1170 → 1213
      Collagen; Collagen triple helix repeat (20 copies)
      cl22861
      Location:885 → 1079
      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 ...

    6. XM_039106764.2 → XP_038962692.1  collagen alpha-1(XX) chain isoform X5

      UniProtKB/TrEMBL
      A6KM63
      Conserved Domains (4) summary
      cd01482
      Location:218 → 382
      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:419 → 497
      fn3; Fibronectin type III domain
      pfam01391
      Location:1168 → 1211
      Collagen; Collagen triple helix repeat (20 copies)
      cl22861
      Location:883 → 1077
      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 ...

    7. XM_008762603.4 → XP_008760825.2  collagen alpha-1(XX) chain isoform X8

      UniProtKB/TrEMBL
      A6KM63
      Related
      ENSRNOP00000110695.1, ENSRNOT00000163325.1

    8. XM_039106765.2 → XP_038962693.1  collagen alpha-1(XX) chain isoform X7

      UniProtKB/TrEMBL
      A6KM63
      Conserved Domains (4) summary
      cd01482
      Location:222 → 386
      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:423 → 501
      fn3; Fibronectin type III domain
      pfam01391
      Location:1172 → 1215
      Collagen; Collagen triple helix repeat (20 copies)
      cl22861
      Location:887 → 1081
      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 ...

    RNA

    1. XR_010064639.1 RNA Sequence

    2. XR_010064640.1 RNA Sequence

    3. XR_010064641.1 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools