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

Gene ID: 311716, updated on 17-Aug-2024

Summary

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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 part of collagen trimer. Predicted to be active in collagen-containing extracellular matrix and extracellular space. Orthologous to human COL20A1 (collagen type XX alpha 1 chain). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in Adrenal (RPKM 49.1), Spleen (RPKM 47.1) and 9 other tissues See more
Orthologs
human mouse all
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Genomic context

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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 ADP-ribosylation factor 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

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages 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

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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

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Markers

Homology

Gene Ontology Provided by RGD

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
  
located_in extracellular region IEA
Inferred from Electronic Annotation
more info
  

General protein information

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

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_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

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