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Col20a1 collagen, type XX, alpha 1 [ Mus musculus (house mouse) ]

Gene ID: 73368, updated on 2-Nov-2024

Summary

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Official Symbol
Col20a1provided by MGI
Official Full Name
collagen, type XX, alpha 1provided by MGI
Primary source
MGI:MGI:1920618
See related
Ensembl:ENSMUSG00000016356 AllianceGenome:MGI:1920618
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
1700051I12Rik
Summary
Predicted to be located in extracellular matrix and extracellular region. Predicted to be part of collagen trimer. Predicted to be active in collagen-containing extracellular matrix. Is expressed in central nervous system; sensory organ; and skeleton. Orthologous to human COL20A1 (collagen type XX alpha 1 chain). [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in testis adult (RPKM 8.7), ovary adult (RPKM 3.1) and 26 other tissues See more
Orthologs
human all
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Genomic context

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See Col20a1 in Genome Data Viewer
Location:
2 H4; 2 103.53 cM
Exon count:
37
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 2 NC_000068.8 (180626629..180659338)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 2 NC_000068.7 (180983323..181017545)

Chromosome 2 - NC_000068.8Genomic Context describing neighboring genes Neighboring gene Na+/K+ transporting ATPase interacting 4 Neighboring gene STARR-seq mESC enhancer starr_06745 Neighboring gene ADP-ribosylation factor GTPase activating protein 1 Neighboring gene cholinergic receptor, nicotinic, alpha polypeptide 4 Neighboring gene potassium voltage-gated channel, subfamily Q, member 2

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Mouse ENCODE transcriptome data Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

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Related articles in PubMed

  1. Absence of canonical Smad signaling in ureteral and bladder mesenchyme causes ureteropelvic junction obstruction. Tripathi P, et al. J Am Soc Nephrol, 2012 Apr. PMID 22282597, Free PMC Article
  2. Genome engineering uncovers 54 evolutionarily conserved and testis-enriched genes that are not required for male fertility in mice. Miyata H, et al. Proc Natl Acad Sci U S A, 2016 Jul 12. PMID 27357688, Free PMC Article
  3. The Vertebrate Genome Annotation browser 10 years on. Harrow JL, et al. Nucleic Acids Res, 2014 Jan. PMID 24316575, Free PMC Article
  4. BGEM: an in situ hybridization database of gene expression in the embryonic and adult mouse nervous system. Magdaleno S, et al. PLoS Biol, 2006 Apr. PMID 16602821, Free PMC Article
  5. Genetic determinants of micronucleus formation in vivo. Adams DJ, et al. Nature, 2024 Mar. PMID 38355793, Free PMC Article

See all (17) citations in PubMed

GeneRIFs: Gene References Into Functions

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)

Pathways from PubChem

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General gene information

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Markers

Homology

Gene Ontology Provided by MGI

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 matrix IEA
Inferred from Electronic Annotation
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

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_028518.1 → NP_082794.1  collagen alpha-1(XX) chain precursor

    See identical proteins and their annotated locations for NP_082794.1

    Status: VALIDATED

    Source sequence(s)
    AL450341, BX649560
    Consensus CDS
    CCDS50844.1
    UniProtKB/Swiss-Prot
    A8WIS2, Q91WC4, Q923P0, Q923P1, Q923P2, Q9D9L7
    UniProtKB/TrEMBL
    F6UFI2
    Related
    ENSMUSP00000153871.2, ENSMUST00000228434.2
    Conserved Domains (4) summary
    pfam01391
    Location:1150 → 1221
    Collagen; Collagen triple helix repeat (20 copies)
    cd01482
    Location:176 → 339
    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:750 → 818
    fn3; Fibronectin type III domain
    cl22861
    Location:840 → 1034
    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_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000068.8 Reference GRCm39 C57BL/6J

    Range
    180626629..180659338
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_036162614.1 → XP_036018507.1  collagen alpha-1(XX) chain isoform X1

    UniProtKB/TrEMBL
    A0A2K6EDL8, F6UFI2
    Related
    ENSMUSP00000104484.3, ENSMUST00000108856.9
    Conserved Domains (4) summary
    cd01482
    Location:218 → 381
    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:792 → 860
    fn3; Fibronectin type III domain
    pfam01391
    Location:1195 → 1263
    Collagen; Collagen triple helix repeat (20 copies)
    cl22861
    Location:882 → 1076
    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_036162615.1 → XP_036018508.1  collagen alpha-1(XX) chain isoform X2

    UniProtKB/TrEMBL
    F6UFI2
    Conserved Domains (4) summary
    cd01482
    Location:218 → 381
    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:792 → 860
    fn3; Fibronectin type III domain
    pfam01391
    Location:1194 → 1262
    Collagen; Collagen triple helix repeat (20 copies)
    cl22861
    Location:881 → 1075
    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 ...

  3. XM_017319288.2 → XP_017174777.1  collagen alpha-1(XX) chain isoform X3

    Conserved Domains (3) summary
    pfam01391
    Location:805 → 876
    Collagen; Collagen triple helix repeat (20 copies)
    pfam00041
    Location:405 → 473
    fn3; Fibronectin type III domain
    cl22861
    Location:495 → 689
    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 ...
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q923P0.3 GenPept UniProtKB/Swiss-Prot:Q923P0

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