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

Gene ID: 73368, updated on 23-Jun-2021

Summary

Official Symbol
Col20a1provided by MGI
Official Full Name
collagen, type XX, alpha 1provided by MGI
Primary source
MGI:MGI:1920618
See related
Ensembl:ENSMUSG00000016356
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
Expression
Ubiquitous expression in testis adult (RPKM 8.7), ovary adult (RPKM 3.1) and 26 other tissues See more
Orthologs
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Genomic context

See Col20a1 in Genome Data Viewer
Location:
2; 2 H4
Exon count:
37
Annotation release Status Assembly Chr Location
109 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)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 2 NC_000068.6 (180721240..180752245)

Chromosome 2 - NC_000068.8Genomic Context describing neighboring genes Neighboring gene Na+/K+ transporting ATPase interacting 4 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

Expression

  • 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

Variation

Alleles

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

General gene information

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
PubMed 
located_in extracellular region IEA
Inferred from Electronic Annotation
more info
 
is_active_in extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

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_028518.1NP_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
    Q923P0
    Related
    ENSMUSP00000153871.2, ENSMUST00000228434.2
    Conserved Domains (4) summary
    pfam01391
    Location:11501221
    Collagen; Collagen triple helix repeat (20 copies)
    cd01482
    Location:176339
    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:750818
    fn3; Fibronectin type III domain
    cl22861
    Location:8401034
    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: Mus musculus Annotation Release 109 details...Open this link in a new tab

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_036162614.1XP_036018507.1  collagen alpha-1(XX) chain isoform X1

    Related
    ENSMUSP00000104484.3, ENSMUST00000108856.9
    Conserved Domains (4) summary
    cd01482
    Location:218381
    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:792860
    fn3; Fibronectin type III domain
    pfam01391
    Location:11951263
    Collagen; Collagen triple helix repeat (20 copies)
    cl22861
    Location:8821076
    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_036162615.1XP_036018508.1  collagen alpha-1(XX) chain isoform X2

    Conserved Domains (4) summary
    cd01482
    Location:218381
    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:792860
    fn3; Fibronectin type III domain
    pfam01391
    Location:11941262
    Collagen; Collagen triple helix repeat (20 copies)
    cl22861
    Location:8811075
    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_017319288.2XP_017174777.1  collagen alpha-1(XX) chain isoform X3

    Conserved Domains (3) summary
    pfam01391
    Location:805876
    Collagen; Collagen triple helix repeat (20 copies)
    pfam00041
    Location:405473
    fn3; Fibronectin type III domain
    cl22861
    Location:495689
    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 ...
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