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

Gene ID: 12817, updated on 5-Mar-2024

Summary

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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. Acts upstream of or within endochondral ossification and morphogenesis of a branching structure. Located in cell-cell junction. Is expressed in several structures, including genitourinary system; heart and pericardium; jaw; musculoskeletal system; and respiratory 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, Apr 2022]
Expression
Broad expression in lung adult (RPKM 5.8), limb E14.5 (RPKM 1.5) and 15 other tissues See more
Orthologs
human all
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Genomic context

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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

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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. 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. Correct expression and localization of collagen XIII are crucial for the normal formation and function of the neuromuscular system. Härönen H, et al. Eur J Neurosci, 2019 Jun. PMID 30667565
  3. Collagen XIII Is Required for Neuromuscular Synapse Regeneration and Functional Recovery after Peripheral Nerve Injury. Zainul Z, et al. J Neurosci, 2018 Apr 25. PMID 29626165, Free PMC Article
  4. Collagen XIII secures pre- and postsynaptic integrity of the neuromuscular synapse. Härönen H, et al. Hum Mol Genet, 2017 Jun 1. PMID 28369367
  5. Muscle-derived collagen XIII regulates maturation of the skeletal neuromuscular junction. Latvanlehto A, et al. J Neurosci, 2010 Sep 15. PMID 20844119, Free PMC Article

See all (42) 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.
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Variation

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Alleles

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

Pathways from PubChem

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General gene information

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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 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
  
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 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 
acts_upstream_of_or_within multicellular organism development IEA
Inferred from Electronic Annotation
more info
  
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
  
Component Evidence Code Pubs
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
  
located_in collagen-containing extracellular matrix HDA PubMed 
is_active_in collagen-containing extracellular matrix IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in extracellular space IBA
Inferred from Biological aspect of Ancestor
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

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

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_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

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