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    Col13a1 collagen, type XIII, alpha 1 [ Mus musculus (house mouse) ]

    Gene ID: 12817, updated on 23-Jun-2021

    Summary

    Official Symbol
    Col13a1provided by MGI
    Official Full Name
    collagen, type XIII, alpha 1provided by MGI
    Primary source
    MGI:MGI:1277201
    See related
    Ensembl:ENSMUSG00000058806
    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
    Expression
    Broad expression in lung adult (RPKM 5.8), limb E14.5 (RPKM 1.5) and 15 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See Col13a1 in Genome Data Viewer
    Location:
    10 32.29 cM; 10 B4
    Exon count:
    45
    Annotation release Status Assembly Chr Location
    109 current GRCm39 (GCF_000001635.27) 10 NC_000076.7 (61674013..61814985, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 10 NC_000076.6 (61838234..61979206, complement)
    Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 10 NC_000076.5 (61301246..61441856, complement)

    Chromosome 10 - NC_000076.7Genomic Context describing neighboring genes Neighboring gene macroH2A.2 histone Neighboring gene predicted gene 2137 Neighboring gene predicted gene, 51765 Neighboring gene predicted gene, 40674 Neighboring gene predicted gene, 30121 Neighboring gene predicted gene, 51766 Neighboring gene ribosomal protein L7A pseudogene Neighboring gene argininosuccinate synthase pseudogene Neighboring gene family with sequence similarity 241, member B

    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

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Variation

    Alleles

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

    Pathways from PubChem

    General gene information

    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables extracellular matrix structural constituent IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables extracellular matrix structural constituent conferring tensile strength RCA
    inferred from Reviewed Computational Analysis
    more info
    PubMed 
    enables heparin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables heparin binding ISO
    Inferred from Sequence Orthology
    more info
     
    Process Evidence Code Pubs
    acts_upstream_of_or_within cell adhesion IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cell-cell adhesion IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in cell-matrix adhesion IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in cell-matrix adhesion ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in collagen fibril organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    acts_upstream_of_or_within endochondral ossification IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in extracellular matrix organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in morphogenesis of a branching structure IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    acts_upstream_of_or_within morphogenesis of a branching structure IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    acts_upstream_of_or_within multicellular organism development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in notochord development IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    acts_upstream_of_or_within ossification IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in skeletal system development IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in cell junction IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in cell-cell junction IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    located_in cell-cell junction IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of collagen trimer IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    located_in collagen-containing extracellular matrix HDA PubMed 
    is_active_in extracellular matrix IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    is_active_in extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    located_in integral component of membrane IEA
    Inferred from Electronic Annotation
    more info
     
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
     
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
     
    located_in postsynaptic membrane IEA
    Inferred from Electronic Annotation
    more info
     
    located_in synapse IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    collagen alpha-1(XIII) chain
    Names
    procollagen, type XIII, alpha 1
    type XIII collagen

    NCBI Reference Sequences (RefSeq)

    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_001304757.1NP_001291686.1  collagen alpha-1(XIII) chain isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks three alternate in-frame exons in the coding region, compared to variant 1. The encoded isoform (2) is shorter, compared to isoform 1.
      Source sequence(s)
      AC122315, AC164702
      Consensus CDS
      CCDS78821.1
      UniProtKB/TrEMBL
      D3Z7B8
      Related
      ENSMUSP00000101093.2, ENSMUST00000105453.8
      Conserved Domains (1) summary
      pfam01391
      Location:571628
      Collagen; Collagen triple helix repeat (20 copies)
    2. NM_007731.3NP_031757.1  collagen alpha-1(XIII) chain isoform 1

      See identical proteins and their annotated locations for NP_031757.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AC122315, AC164702
      Consensus CDS
      CCDS35918.1
      UniProtKB/Swiss-Prot
      Q9R1N9
      Related
      ENSMUSP00000101094.3, ENSMUST00000105454.3
      Conserved Domains (1) summary
      pfam01391
      Location:534592
      Collagen; Collagen triple helix repeat (20 copies)

    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_000076.7 Reference GRCm39 C57BL/6J

      Range
      61674013..61814985 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011243333.3XP_011241635.1  collagen alpha-1(XIII) chain isoform X12

      Conserved Domains (1) summary
      pfam01391
      Location:515573
      Collagen; Collagen triple helix repeat (20 copies)
    2. XM_006513171.5XP_006513234.1  collagen alpha-1(XIII) chain isoform X21

      Conserved Domains (1) summary
      pfam01391
      Location:574631
      Collagen; Collagen triple helix repeat (20 copies)
    3. XM_006513170.4XP_006513233.1  collagen alpha-1(XIII) chain isoform X20

      Conserved Domains (1) summary
      pfam01391
      Location:613672
      Collagen; Collagen triple helix repeat (20 copies)
    4. XM_030244857.1XP_030100717.1  collagen alpha-1(XIII) chain isoform X25

      Related
      ENSMUSP00000101092.3, ENSMUST00000105452.9
      Conserved Domains (1) summary
      pfam01391
      Location:635694
      Collagen; Collagen triple helix repeat (20 copies)
    5. XM_011243342.2XP_011241644.1  collagen alpha-1(XIII) chain isoform X19

      Conserved Domains (1) summary
      pfam01391
      Location:625684
      Collagen; Collagen triple helix repeat (20 copies)
    6. XM_011243339.2XP_011241641.1  collagen alpha-1(XIII) chain isoform X16

      Conserved Domains (1) summary
      pfam01391
      Location:515573
      Collagen; Collagen triple helix repeat (20 copies)
    7. XM_011243332.3XP_011241634.1  collagen alpha-1(XIII) chain isoform X11

      Conserved Domains (1) summary
      pfam01391
      Location:515573
      Collagen; Collagen triple helix repeat (20 copies)
    8. XM_036155571.1XP_036011464.1  collagen alpha-1(XIII) chain isoform X22

      Conserved Domains (1) summary
      pfam01391
      Location:555609
      Collagen; Collagen triple helix repeat (20 copies)
    9. XM_011243341.3XP_011241643.1  collagen alpha-1(XIII) chain isoform X18

      Conserved Domains (1) summary
      pfam01391
      Location:468526
      Collagen; Collagen triple helix repeat (20 copies)
    10. XM_011243337.3XP_011241639.1  collagen alpha-1(XIII) chain isoform X15

      Conserved Domains (1) summary
      pfam01391
      Location:477535
      Collagen; Collagen triple helix repeat (20 copies)
    11. XM_030244856.2XP_030100716.1  collagen alpha-1(XIII) chain isoform X17

      Conserved Domains (1) summary
      pfam01391
      Location:474532
      Collagen; Collagen triple helix repeat (20 copies)
    12. XM_011243328.3XP_011241630.1  collagen alpha-1(XIII) chain isoform X7

      Conserved Domains (1) summary
      pfam01391
      Location:494552
      Collagen; Collagen triple helix repeat (20 copies)
    13. XM_011243336.3XP_011241638.1  collagen alpha-1(XIII) chain isoform X14

      Conserved Domains (1) summary
      pfam01391
      Location:480538
      Collagen; Collagen triple helix repeat (20 copies)
    14. XM_011243331.3XP_011241633.1  collagen alpha-1(XIII) chain isoform X10

      Conserved Domains (1) summary
      pfam01391
      Location:489547
      Collagen; Collagen triple helix repeat (20 copies)
    15. XM_011243324.3XP_011241626.1  collagen alpha-1(XIII) chain isoform X3

      Conserved Domains (1) summary
      pfam01391
      Location:506564
      Collagen; Collagen triple helix repeat (20 copies)
    16. XM_011243326.4XP_011241628.1  collagen alpha-1(XIII) chain isoform X5

      Conserved Domains (1) summary
      pfam01391
      Location:503561
      Collagen; Collagen triple helix repeat (20 copies)
    17. XM_011243325.4XP_011241627.1  collagen alpha-1(XIII) chain isoform X4

      Conserved Domains (1) summary
      pfam01391
      Location:506564
      Collagen; Collagen triple helix repeat (20 copies)
    18. XM_011243329.3XP_011241631.1  collagen alpha-1(XIII) chain isoform X8

      Conserved Domains (1) summary
      pfam01391
      Location:493551
      Collagen; Collagen triple helix repeat (20 copies)
    19. XM_011243335.3XP_011241637.1  collagen alpha-1(XIII) chain isoform X13

      Conserved Domains (1) summary
      pfam01391
      Location:625676
      Collagen; Collagen triple helix repeat (20 copies)
    20. XM_011243327.3XP_011241629.1  collagen alpha-1(XIII) chain isoform X6

      Conserved Domains (1) summary
      pfam01391
      Location:515573
      Collagen; Collagen triple helix repeat (20 copies)
    21. XM_011243322.3XP_011241624.1  collagen alpha-1(XIII) chain isoform X1

      Conserved Domains (1) summary
      pfam01391
      Location:515573
      Collagen; Collagen triple helix repeat (20 copies)
    22. XM_011243323.3XP_011241625.1  collagen alpha-1(XIII) chain isoform X2

      Conserved Domains (1) summary
      pfam01391
      Location:512570
      Collagen; Collagen triple helix repeat (20 copies)
    23. XM_030244858.2XP_030100718.1  collagen alpha-1(XIII) chain isoform X26

      Conserved Domains (1) summary
      pfam01391
      Location:474532
      Collagen; Collagen triple helix repeat (20 copies)
    24. XM_011243344.3XP_011241646.1  collagen alpha-1(XIII) chain isoform X24

      Conserved Domains (1) summary
      pfam01391
      Location:394452
      Collagen; Collagen triple helix repeat (20 copies)
    25. XM_011243343.3XP_011241645.1  collagen alpha-1(XIII) chain isoform X23

      Conserved Domains (1) summary
      pfam01391
      Location:403461
      Collagen; Collagen triple helix repeat (20 copies)
    26. XM_011243330.3XP_011241632.1  collagen alpha-1(XIII) chain isoform X9

      Conserved Domains (1) summary
      pfam01391
      Location:515573
      Collagen; Collagen triple helix repeat (20 copies)
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