Details for: COL13A1

Gene ID: 1305

Gene Type:  Protein-coding  - A gene that serves as a template for producing a messenger RNA (mRNA) molecule, which is then translated into a functional protein.

Symbol: COL13A1

Ensembl ID: ENSG00000197467

Description: collagen type XIII alpha 1 chain

Cell Significance Landscape

Associated with

Significant Cells

Cell Significance Index (CSI) scores for the chosen context(s)

  • cardiac muscle cell CL0000746
    CSI 5.7
    rCSI 8.18%
    PRS 82.64
  • interstitial cell of Cajal CL0002088
    CSI 3.98
    rCSI 5.06%
    PRS 93.77
  • fibroblast of lung CL0002553
    CSI 3.09
    rCSI 2.88%
    PRS 91.6
  • blood vessel endothelial cell CL0000071
    CSI 3.05
    rCSI 6.33%
    PRS 88.72
  • bronchus fibroblast of lung CL2000093
    CSI 2.83
    rCSI 2.3%
    PRS 89.65
  • vascular leptomeningeal cell CL4023051
    CSI 2.44
    rCSI 4.28%
    PRS 86.7
  • cerebellar granule cell CL0001031
    CSI 2.28
    rCSI 3.35%
    PRS 85.29
  • alveolar type 1 fibroblast cell CL4028004
    CSI 2.14
    rCSI 2.34%
    PRS 91.8
  • mesodermal cell CL0000222
    CSI 2.05
    rCSI 2.46%
    PRS 89.15
  • vascular associated smooth muscle cell CL0000359
    CSI 2.02
    rCSI 6.55%
    PRS 88.53
  • renal interstitial pericyte CL1001318
    CSI 1.56
    rCSI 4.29%
    PRS 87.74
  • enteric smooth muscle cell CL0002504
    CSI 1.52
    rCSI 2.17%
    PRS 90.47
  • mesenchymal cell CL0008019
    CSI 1.44
    rCSI 3.65%
    PRS 85.26
  • regular atrial cardiac myocyte CL0002129
    CSI 1.4
    rCSI 4.51%
    PRS 86.9
  • stromal cell CL0000499
    CSI 1.2
    rCSI 3.37%
    PRS 86.34
  • helper T cell CL0000912
    CSI 1.03
    rCSI 1.45%
    PRS 86.45
  • CD8-positive, alpha-beta memory T cell, CD45RO-positive CL0001203
    CSI 0.82
    rCSI 1%
    PRS 71.39

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this specific cell.

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this cell type. Calculated using techniques like effect size estimation and bootstrapping for reliability.

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this cell type. Calculated using techniques like effect size estimation and bootstrapping for reliability.
Network Configuration

Explore relationships of the current gene. Select an Interaction Source: 'ONTOLOGY' for shared pathways (GO/Reactome) or 'STRING' for protein-protein interactions. Further refine by selecting context genes and comparing Cell Significance Index (CSI) scores between baseline and target cell types and their specific contexts.

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Legend:
  • Query Gene
  • Node Color (Target Cell CSI, relative to current network):
    • Very High
    • High
    • Medium
    • Low
    • Very Low
    • CSI N/A
  • Node Size: Proportional to Target Cell CSI magnitude
  • STRING PPI Edge
  • Shared Pathway Edge (ONTOLOGY)

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Other Information

This section provides additional information about the gene, including a description generated by an AI language model and details about associated proteins.

## Summary [COL13A1](/details-gene/1305) encodes the alpha-1 chain of type XIII collagen, a transmembrane protein that functions as a structural component of the extracellular matrix (ECM). It plays a crucial role in cell-matrix and cell-cell adhesion, skeletal system development, and the organization of the ECM. Expression data highlights its high significance in cells requiring robust structural integrity and connectivity, particularly [cardiac muscle cell](/details-cell/CL0000746), [interstitial cell of Cajal](/details-cell/CL0002088), and various fibroblast populations. Clinically, mutations in [COL13A1](/details-gene/1305) are associated with congenital myasthenic syndrome type 19 ([OMIM:120350](https://omim.org/entry/120350)), underscoring its essential role at the neuromuscular junction. ## Cellular Roles and Expression Landscape The expression profile of [COL13A1](/details-gene/1305) indicates a primary role in structural and contractile tissues. **Overall**, its most significant expression is observed in [cardiac muscle cell](/details-cell/CL0000746) (CSI: 5.70), suggesting a fundamental function in maintaining the integrity and function of the myocardium. High significance is also noted in cell types associated with the gastrointestinal tract's muscularis externa, including [interstitial cell of Cajal](/details-cell/CL0002088) (CSI: 3.98) and [enteric smooth muscle cell](/details-cell/CL0002504) (CSI: 1.52), pointing to a role in gut motility and structure. Furthermore, [COL13A1](/details-gene/1305) is a key marker for various mesenchymal and stromal cell populations that are responsible for producing and organizing the ECM. This includes high significance in [fibroblast of lung](/details-cell/CL0002553) (CSI: 3.09), [bronchus fibroblast of lung](/details-cell/CL2000093) (CSI: 2.83), and [alveolar type 1 fibroblast cell](/details-cell/CL4028004) (CSI: 2.14). Its expression in [blood vessel endothelial cell](/details-cell/CL0000071) (CSI: 3.05) and [vascular associated smooth muscle cell](/details-cell/CL0000359) (CSI: 2.02) also highlights its contribution to vascular architecture. The notable expression in [cerebellar granule cell](/details-cell/CL0001031) (CSI: 2.28) is consistent with its established role in the nervous system, particularly at synaptic junctions. The widespread expression across these diverse muscle, fibroblast, and vascular cell types underscores its general importance in tissue cohesion and organization. ## Pathways and Molecular Function The functions of [COL13A1](/details-gene/1305) are tightly linked to the synthesis, organization, and degradation of the extracellular matrix. Gene Ontology annotations reveal its involvement in fundamental biological processes such as 'cell-matrix adhesion' ([GO:0007160](https://www.ebi.ac.uk/QuickGO/term/GO:0007160)), 'extracellular matrix organization' ([GO:0030198](https://www.ebi.ac.uk/QuickGO/term/GO:0030198)), and 'skeletal system development' ([GO:0001501](https://www.ebi.ac.uk/QuickGO/term/GO:0001501)). Its molecular function as an 'extracellular matrix structural constituent conferring tensile strength' ([GO:0030020](https://www.ebi.ac.uk/QuickGO/term/GO:0030020)) is consistent with its high expression in mechanically active tissues like cardiac muscle. Reactome pathways further specify its role within the collagen life cycle, including 'Collagen formation' ([R-HSA-1474290](https://reactome.org/content/detail/R-HSA-1474290)), 'Collagen chain trimerization' ([R-HSA-8948216](https://reactome.org/content/detail/R-HSA-8948216)), and 'Extracellular matrix organization' ([R-HSA-1474244](https://reactome.org/content/detail/R-HSA-1474244)). The GO Cellular Component annotation places the protein in the 'collagen-containing extracellular matrix' ([GO:0062023](https://www.ebi.ac.uk/QuickGO/term/GO:0062023)), the 'plasma membrane' ([GO:0005886](https://www.ebi.ac.uk/QuickGO/term/GO:0005886)), and importantly, the 'postsynaptic membrane' ([GO:0045211](https://www.ebi.ac.uk/QuickGO/term/GO:0045211)). This latter localization provides a direct molecular basis for its association with congenital myasthenic syndrome, a disorder of the neuromuscular junction ([Link](https://doi.org/10.1016/j.ajhg.2015.10.017)). ## Research Directions The specific expression patterns and known functions of [COL13A1](/details-gene/1305) suggest several avenues for future research. The clinical link to myasthenic syndrome has established its importance at the neuromuscular junction, yet its role in other tissues where it is highly expressed, such as the heart and gut, is less understood. Based on the available data, we can propose the following testable hypotheses: 1. **Hypothesis 1:** Given its exceptionally high significance in [cardiac muscle cell](/details-cell/CL0000746), [COL13A1](/details-gene/1305) is essential for maintaining the structural and functional integrity of the cardiac synapse and the surrounding ECM. Its dysregulation may be a contributing factor in the pathogenesis of certain inherited cardiomyopathies or cardiac fibrosis. 2. **Hypothesis 2:** The high significance of [COL13A1](/details-gene/1305) in both [interstitial cell of Cajal](/details-cell/CL0002088) and [enteric smooth muscle cell](/details-cell/CL0002504) suggests that it mediates the critical cell-cell and cell-matrix interactions required for synchronized gut peristalsis. Disruption of [COL13A1](/details-gene/1305) function could lead to disorders of gastrointestinal motility. To test the role of [COL13A1](/details-gene/1305) in cardiac function (Hypothesis 1), a key experiment would be to generate a cardiomyocyte-specific conditional knockout mouse model (e.g., using a *Myh6*-Cre driver). These animals could be subjected to cardiac stress models (e.g., transverse aortic constriction) and analyzed via echocardiography, histology, and single-cell RNA sequencing to assess the development of cardiac dysfunction, fibrosis, and altered gene expression networks in the absence of [COL13A1](/details-gene/1305). From a therapeutic perspective, [COL13A1](/details-gene/1305) is primarily associated with a loss-of-function rare disease. Therefore, it is not a conventional target for inhibition. Instead, its therapeutic potential lies in restoration strategies. For congenital myasthenic syndrome caused by [COL13A1](/details-gene/1305) mutations, therapeutic avenues could include gene replacement therapy to deliver a functional copy of the gene to affected neuromuscular junctions or the development of small molecules designed to stabilize the mutant protein or promote compensatory pathways.

Genular Protein ID: 3697179409

Symbol: CODA1_HUMAN

Name: Collagen alpha-1(XIII) chain

UniProtKB Accession Codes:

Q5TAT6 A6NFR5 B9EGD2 E7EWL8 Q13992 Q13993 Q13994 Q13995 Q13996 Q5TAT4 Q5TAT5 Q7KZ33 Q7KZ49 Q99228 Q9NQ52

Database IDs:

AGR 1 AlphaFoldDB 1 Antibodypedia 1 Bgee 1 BioGRID 1 BioGRID-ORCS 1 BioMuta 1 CCDS 6 CTD 1 ChiTaRS 1 ComplexPortal 1 DMDM 1 DNASU 1 DisGeNET 1 EMBL 57 Ensembl 6 ExpressionAtlas 1 GO 17 GeneCards 1 GeneTree 1 GeneWiki 1 GenomeRNAi 1 HGNC 1 HOGENOM 1 HPA 1 InParanoid 1 IntAct 1 InterPro 2 KEGG 1 MIM 3 MalaCards 1 MassIVE 1 NCBI Taxonomy 1 OpenTargets 1 Orphanet 2 OrthoDB 1 PANTHER 2 PIR 1 PRO 1 PathwayCommons 1 PaxDb 1 PeptideAtlas 1 Pfam 1 PharmGKB 1 Pharos 1 PhosphoSitePlus 1 PhylomeDB 1 Proteomes 1 ProteomicsDB 11 RNAct 1 Reactome 4 RefSeq 6 STRING 1 SignaLink 1 SwissPalm 1 TreeFam 1 UCSC 1 VEuPathDB 1 eggNOG 1 iPTMnet 1 jPOST 1 neXtProt 1

Citations:

PubMed ID: 11013208

Title: A short sequence in the N-terminal region is required for the trimerization of type XIII collagen and is conserved in other collagenous transmembrane proteins.

PubMed ID: 11013208

DOI: 10.1093/emboj/19.19.5051

PubMed ID: 15164054

Title: The DNA sequence and comparative analysis of human chromosome 10.

PubMed ID: 15164054

DOI: 10.1038/nature02462

PubMed ID: 15489334

Title: The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).

PubMed ID: 15489334

DOI: 10.1101/gr.2596504

PubMed ID: 1698771

Title: The alpha 1 chain of type XIII collagen consists of three collagenous and four noncollagenous domains, and its primary transcript undergoes complex alternative splicing.

PubMed ID: 1698771

DOI: 10.1016/s0021-9258(17)44849-6

PubMed ID: 3547403

Title: Partial characterization of a low molecular weight human collagen that undergoes alternative splicing.

PubMed ID: 3547403

DOI: 10.1073/pnas.84.4.940

PubMed ID: 2459707

Title: Gene structure for the alpha 1 chain of a human short-chain collagen (type XIII) with alternatively spliced transcripts and translation termination codon at the 5' end of the last exon.

PubMed ID: 2459707

DOI: 10.1073/pnas.85.20.7491

PubMed ID: 1447209

Title: Characterization of the spectrum of alternative splicing of alpha 1 (XIII) collagen transcripts in HT-1080 cells and calvarial tissue resulted in identification of two previously unidentified alternatively spliced sequences, one previously unidentified exon, and nine new mRNA variants.

PubMed ID: 1447209

DOI: 10.1016/s0021-9258(18)35820-4

PubMed ID: 1447210

Title: Patterns of expression of the six alternatively spliced exons affecting the structures of the COL1 and NC2 domains of the alpha 1(XIII) collagen chain in human tissues and cell lines.

PubMed ID: 1447210

DOI: 10.1016/s0021-9258(18)35821-6

PubMed ID: 8246446

Title: Location and alternative splicing of type XIII collagen RNA in the early human placenta.

PubMed ID: 8246446

PubMed ID: 10865988

Title: Type XIII collagen is widely expressed in the adult and developing human eye and accentuated in the ciliary muscle, the optic nerve and the neural retina.

PubMed ID: 10865988

DOI: 10.1006/exer.1998.0826

PubMed ID: 11956183

Title: The type XIII collagen ectodomain is a 150-nm rod and capable of binding to fibronectin, nidogen-2, perlecan, and heparin.

PubMed ID: 11956183

DOI: 10.1074/jbc.m107583200

PubMed ID: 26626625

Title: Congenital myasthenic syndrome type 19 is caused by mutations in COL13A1, Encoding the atypical non-fibrillar collagen type XIII alpha1 chain.

PubMed ID: 26626625

DOI: 10.1016/j.ajhg.2015.10.017

Sequence Information:

  • Length: 717
  • Mass: 69950
  • Checksum: FD12CA80CC93540F
  • Sequence:
    • MVAERTHKAA ATGARGPGEL GAPGTVALVA ARAERGARLP SPGSCGLLTL ALCSLALSLL 
AHFRTAELQA RVLRLEAERG EQQMETAILG RVNQLLDEKW KLHSRRRREA PKTSPGCNCP 
PGPPGPTGRP GLPGDKGAIG MPGRVGSPGD AGLSIIGPRG PPGQPGTRGF PGFPGPIGLD 
GKPGHPGPKG DMGLTGPPGQ PGPQGQKGEK GQCGEYPHRE CLSSMPAALR SSQIIALKLL 
PLLNSVRLAP PPVIKRRTFQ GEQSQASIQG PPGPPGPPGP SGPLGHPGLP GPMGPPGLPG 
PPGPKGDPGI QGYHGRKGER GMPGMPGKHG AKGAPGIAVA GMKGEPGIPG TKGEKGAEGS 
PGLPGLLGQK GEKGDAGNSI GGGRGEPGPP GLPGPPGPKG EAGVDGQVGP PGQPGDKGER 
GAAGEQGPDG PKGSKGEPGK GEMVDYNGNI NEALQEIRTL ALMGPPGLPG QIGPPGAPGI 
PGQKGEIGLP GPPGHDGEKG PRGKPGDMGP PGPQGPPGKD GPPGVKGENG HPGSPGEKGE 
KGETGQAGSP GEKGEAGEKG NPGAEVPGLP GPEGPPGPPG LQGVPGPKGE AGLDGAKGEK 
GFQGEKGDRG PLGLPGASGL DGRPGPPGTP GPIGVPGPAG PKGERGSKGD PGMTGPTGAA 
GLPGLHGPPG DKGNRGERGK KGSRGPKGDK GDQGAPGLDA PCPLGEDGLP VQGCWNK