U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from Nucleotide

    • Showing Current items.

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

    Gene ID: 12817, updated on 27-Nov-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    Col13a1provided by MGI
    Official Full Name
    collagen, type XIII, alpha 1provided by MGI
    Primary source
    MGI:MGI:1277201
    See related
    Ensembl:ENSMUSG00000058806 AllianceGenome:MGI:1277201
    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
    Summary
    Predicted to enable heparin binding activity. Predicted to be an extracellular matrix structural constituent conferring tensile strength. Involved in endochondral ossification and morphogenesis of a branching structure. Located in cell-cell junction. Is expressed in several structures, including central nervous system; genitourinary system; heart and pericardium; jaw; and musculoskeletal system. Used to study congenital myasthenic syndrome 19. Human ortholog(s) of this gene implicated in congenital myasthenic syndrome 19. Orthologous to human COL13A1 (collagen type XIII alpha 1 chain). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Broad expression in lung adult (RPKM 5.8), limb E14.5 (RPKM 1.5) and 15 other tissues See more
    Orthologs
    human all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See Col13a1 in Genome Data Viewer
    Location:
    10 32.29 cM; 10 B4
    Exon count:
    45
    Annotation release Status Assembly Chr Location
    RS_2024_02 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)

    Chromosome 10 - NC_000076.7Genomic Context describing neighboring genes Neighboring gene macroH2A.2 histone Neighboring gene predicted gene 2137 Neighboring gene STARR-seq mESC enhancer starr_26861 Neighboring gene predicted gene, 51765 Neighboring gene predicted gene, 40674 Neighboring gene STARR-seq mESC enhancer starr_26863 Neighboring gene STARR-seq mESC enhancer starr_26864 Neighboring gene predicted gene, 30121 Neighboring gene predicted gene, 51766 Neighboring gene ribosomal protein L7A pseudogene Neighboring gene STARR-seq mESC enhancer starr_26865 Neighboring gene STARR-seq mESC enhancer starr_26870 Neighboring gene STARR-seq mESC enhancer starr_26872 Neighboring gene argininosuccinate synthase pseudogene Neighboring gene family with sequence similarity 241, member B

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • 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

    Go to the top of the pageHelp

    Related articles in PubMed

    1. The CMS19 disease model specifies a pivotal role for collagen XIII in bone homeostasis. Kemppainen AV, et al. Sci Rep, 2022 Apr 7. PMID 35393492, Free PMC Article
    2. Alternative splicing of mouse alpha1(XIII) collagen RNAs results in at least 17 different transcripts, predicting alpha1(XIII) collagen chains with length varying between 651 and 710 amino acid residues. Peltonen S, et al. DNA Cell Biol, 1997 Feb. PMID 9052743
    3. Mapping of mouse alpha 1(XIII) collagen to chromosome 10 and its exclusion as a kd candidate gene. Mrug M, et al. Biochem Genet, 2000 Oct. PMID 11129527
    4. Lack of cytosolic and transmembrane domains of type XIII collagen results in progressive myopathy. Kvist AP, et al. Am J Pathol, 2001 Oct. PMID 11583983, Free PMC Article
    5. Cardiac dysfunction in transgenic mouse fetuses overexpressing shortened type XIII collagen. Tahkola J, et al. Cell Tissue Res, 2008 Jul. PMID 18481090

    See all (44) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The CMS19 disease model specifies a pivotal role for collagen XIII in bone homeostasis.
      Title: The CMS19 disease model specifies a pivotal role for collagen XIII in bone homeostasis.
    2. Overall, these results confirm the role of collagen XIII at the neuromuscular synapses and highlight the importance of its correct expression and localization for motor synapse formation and function.
      Title: Correct expression and localization of collagen XIII are crucial for the normal formation and function of the neuromuscular system.
    3. Alterations at the NMJ in Col13a1-/- mice contribute to impaired and incomplete NMJ regeneration and functional recovery after peripheral nerve injury.
      Title: Collagen XIII Is Required for Neuromuscular Synapse Regeneration and Functional Recovery after Peripheral Nerve Injury.
    4. Data show that the induction of collagen XIII in endothelial cells of Alport syndrome kidneys mediates the selective recruitment of alpha1beta1 integrin-positive monocytes.
      Title: Collagen XIII induced in vascular endothelium mediates alpha1beta1 integrin-dependent transmigration of monocytes in renal fibrosis.
    5. Collagen XIII plays an autocrine role in postsynaptic maturation, organization, and function of the vertebrate neuromuscular junction.
      Title: Muscle-derived collagen XIII regulates maturation of the skeletal neuromuscular junction.
    6. Cardiac dysfunction is reported in transgenic mouse fetuses overexpressing shortened type XIII collagen.
      Title: Cardiac dysfunction in transgenic mouse fetuses overexpressing shortened type XIII collagen.
    7. two widely separated coiled-coil domains of type XIII and related collagens function as independent oligomerization domains participating in the folding of distinct areas of the molecule.
      Title: Type XIII collagen and some other transmembrane collagens contain two separate coiled-coil motifs, which may function as independent oligomerization domains.
    Submit: New GeneRIF Correction

    Variation

    Go to the top of the page Help

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (2) 
    • Targeted (6)  1 citation

    Pathways from PubChem

    Go to the top of the page

    General gene information

    Go to the top of the page Help

    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables extracellular matrix structural constituent conferring tensile strength IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    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
    		  
    enables heparin binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables heparin binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in cell differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in cell-cell adhesion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in cell-cell adhesion ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in cell-matrix adhesion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in cell-matrix adhesion ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in cell-matrix adhesion ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in endochondral ossification IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    involved_in extracellular matrix organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in morphogenesis of a branching structure IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in morphogenesis of a branching structure IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    involved_in skeletal system development IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in basement membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in cell-cell junction IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cell-cell junction IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of collagen trimer IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of collagen type IX trimer IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in collagen-containing extracellular matrix HDA PubMed 
    is_active_in extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in postsynaptic membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

    Go to the top of the page Help
    Preferred Names
    collagen alpha-1(XIII) chain
    Names
    procollagen, type XIII, alpha 1
    type XIII collagen

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    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_001304757.1 → NP_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:571 → 628
      Collagen; Collagen triple helix repeat (20 copies)

    2. NM_007731.3 → NP_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:534 → 592
      Collagen; Collagen triple helix repeat (20 copies)

    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_000076.7 Reference GRCm39 C57BL/6J

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

    mRNA and Protein(s)

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

      Conserved Domains (1) summary
      pfam01391
      Location:515 → 573
      Collagen; Collagen triple helix repeat (20 copies)

    2. XM_006513171.5 → XP_006513234.1  collagen alpha-1(XIII) chain isoform X21

      Conserved Domains (1) summary
      pfam01391
      Location:574 → 631
      Collagen; Collagen triple helix repeat (20 copies)

    3. XM_006513170.4 → XP_006513233.1  collagen alpha-1(XIII) chain isoform X20

      Conserved Domains (1) summary
      pfam01391
      Location:613 → 672
      Collagen; Collagen triple helix repeat (20 copies)

    4. XM_030244857.1 → XP_030100717.1  collagen alpha-1(XIII) chain isoform X25

      UniProtKB/TrEMBL
      D3Z7B9
      Related
      ENSMUSP00000101092.3, ENSMUST00000105452.9
      Conserved Domains (1) summary
      pfam01391
      Location:635 → 694
      Collagen; Collagen triple helix repeat (20 copies)

    5. XM_011243342.2 → XP_011241644.1  collagen alpha-1(XIII) chain isoform X19

      Conserved Domains (1) summary
      pfam01391
      Location:625 → 684
      Collagen; Collagen triple helix repeat (20 copies)

    6. XM_011243339.2 → XP_011241641.1  collagen alpha-1(XIII) chain isoform X16

      Conserved Domains (1) summary
      pfam01391
      Location:515 → 573
      Collagen; Collagen triple helix repeat (20 copies)

    7. XM_011243332.3 → XP_011241634.1  collagen alpha-1(XIII) chain isoform X11

      Conserved Domains (1) summary
      pfam01391
      Location:515 → 573
      Collagen; Collagen triple helix repeat (20 copies)

    8. XM_036155571.1 → XP_036011464.1  collagen alpha-1(XIII) chain isoform X22

      Conserved Domains (1) summary
      pfam01391
      Location:555 → 609
      Collagen; Collagen triple helix repeat (20 copies)

    9. XM_011243341.3 → XP_011241643.1  collagen alpha-1(XIII) chain isoform X18

      Conserved Domains (1) summary
      pfam01391
      Location:468 → 526
      Collagen; Collagen triple helix repeat (20 copies)

    10. XM_011243337.3 → XP_011241639.1  collagen alpha-1(XIII) chain isoform X15

      Conserved Domains (1) summary
      pfam01391
      Location:477 → 535
      Collagen; Collagen triple helix repeat (20 copies)

    11. XM_030244856.2 → XP_030100716.1  collagen alpha-1(XIII) chain isoform X17

      Conserved Domains (1) summary
      pfam01391
      Location:474 → 532
      Collagen; Collagen triple helix repeat (20 copies)

    12. XM_011243328.3 → XP_011241630.1  collagen alpha-1(XIII) chain isoform X7

      Conserved Domains (1) summary
      pfam01391
      Location:494 → 552
      Collagen; Collagen triple helix repeat (20 copies)

    13. XM_011243336.3 → XP_011241638.1  collagen alpha-1(XIII) chain isoform X14

      Conserved Domains (1) summary
      pfam01391
      Location:480 → 538
      Collagen; Collagen triple helix repeat (20 copies)

    14. XM_011243331.3 → XP_011241633.1  collagen alpha-1(XIII) chain isoform X10

      Conserved Domains (1) summary
      pfam01391
      Location:489 → 547
      Collagen; Collagen triple helix repeat (20 copies)

    15. XM_011243324.3 → XP_011241626.1  collagen alpha-1(XIII) chain isoform X3

      Conserved Domains (1) summary
      pfam01391
      Location:506 → 564
      Collagen; Collagen triple helix repeat (20 copies)

    16. XM_011243326.4 → XP_011241628.1  collagen alpha-1(XIII) chain isoform X5

      Conserved Domains (1) summary
      pfam01391
      Location:503 → 561
      Collagen; Collagen triple helix repeat (20 copies)

    17. XM_011243325.4 → XP_011241627.1  collagen alpha-1(XIII) chain isoform X4

      Conserved Domains (1) summary
      pfam01391
      Location:506 → 564
      Collagen; Collagen triple helix repeat (20 copies)

    18. XM_011243329.3 → XP_011241631.1  collagen alpha-1(XIII) chain isoform X8

      Conserved Domains (1) summary
      pfam01391
      Location:493 → 551
      Collagen; Collagen triple helix repeat (20 copies)

    19. XM_011243335.3 → XP_011241637.1  collagen alpha-1(XIII) chain isoform X13

      Conserved Domains (1) summary
      pfam01391
      Location:625 → 676
      Collagen; Collagen triple helix repeat (20 copies)

    20. XM_011243327.3 → XP_011241629.1  collagen alpha-1(XIII) chain isoform X6

      Conserved Domains (1) summary
      pfam01391
      Location:515 → 573
      Collagen; Collagen triple helix repeat (20 copies)

    21. XM_011243322.3 → XP_011241624.1  collagen alpha-1(XIII) chain isoform X1

      Conserved Domains (1) summary
      pfam01391
      Location:515 → 573
      Collagen; Collagen triple helix repeat (20 copies)

    22. XM_011243323.3 → XP_011241625.1  collagen alpha-1(XIII) chain isoform X2

      Conserved Domains (1) summary
      pfam01391
      Location:512 → 570
      Collagen; Collagen triple helix repeat (20 copies)

    23. XM_030244858.2 → XP_030100718.1  collagen alpha-1(XIII) chain isoform X26

      Conserved Domains (1) summary
      pfam01391
      Location:474 → 532
      Collagen; Collagen triple helix repeat (20 copies)

    24. XM_011243344.3 → XP_011241646.1  collagen alpha-1(XIII) chain isoform X24

      Conserved Domains (1) summary
      pfam01391
      Location:394 → 452
      Collagen; Collagen triple helix repeat (20 copies)

    25. XM_011243343.3 → XP_011241645.1  collagen alpha-1(XIII) chain isoform X23

      Conserved Domains (1) summary
      pfam01391
      Location:403 → 461
      Collagen; Collagen triple helix repeat (20 copies)

    26. XM_011243330.3 → XP_011241632.1  collagen alpha-1(XIII) chain isoform X9

      Conserved Domains (1) summary
      pfam01391
      Location:515 → 573
      Collagen; Collagen triple helix repeat (20 copies)
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9R1N9.1 GenPept UniProtKB/Swiss-Prot:Q9R1N9

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Other Literature Sources
    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools
    Miscellaneous