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

    Gene ID: 73368, updated on 30-Apr-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 region. Predicted to be part of collagen trimer. Predicted to be active in collagen-containing extracellular matrix and extracellular space. 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, Apr 2022]
    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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    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
    • 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. A conditional knockout resource for the genome-wide study of mouse gene function. Skarnes WC, et al. Nature, 2011 Jun 15. PMID 21677750, Free PMC Article

    See all (16) 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 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

    Gene LinkOut

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