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Aliases for COL13A1 Gene

Aliases for COL13A1 Gene

  • Collagen Type XIII Alpha 1 Chain 2 3 5
  • Collagen, Type XIII, Alpha 1 2 3
  • COLXIIIA1 3 4
  • Collagen Alpha-1(XIII) Chain 3
  • CMS19 3

External Ids for COL13A1 Gene

Previous GeneCards Identifiers for COL13A1 Gene

  • GC10P070372
  • GC10P070648
  • GC10P071454
  • GC10P070906
  • GC10P071231
  • GC10P071561
  • GC10P065553

Summaries for COL13A1 Gene

Entrez Gene Summary for COL13A1 Gene

  • This gene encodes the alpha chain of one of the nonfibrillar collagens. The function of this gene product is not known, however, it has been detected at low levels in all connective tissue-producing cells so it may serve a general function in connective tissues. Unlike most of the collagens, which are secreted into the extracellular matrix, collagen XIII contains a transmembrane domain and the protein has been localized to the plasma membrane. The transcripts for this gene undergo complex and extensive splicing involving at least eight exons. Like other collagens, collagen XIII is a trimer; it is not known whether this trimer is composed of one or more than one alpha chain isomer. A number of alternatively spliced transcript variants have been described, but the full length nature of some of them has not been determined. [provided by RefSeq, Jul 2008]

GeneCards Summary for COL13A1 Gene

COL13A1 (Collagen Type XIII Alpha 1 Chain) is a Protein Coding gene. Diseases associated with COL13A1 include Myasthenic Syndrome, Congenital, 19 and Col13a1-Related Congenital Myasthenic Syndrome. Among its related pathways are T Cell Co-Signaling Pathway: Ligand-Receptor Interactions and Degradation of the extracellular matrix. GO annotations related to this gene include heparin binding. An important paralog of this gene is COL25A1.

UniProtKB/Swiss-Prot for COL13A1 Gene

  • Involved in cell-matrix and cell-cell adhesion interactions that are required for normal development. May participate in the linkage between muscle fiber and basement membrane. May play a role in endochondral ossification of bone and branching morphogenesis of lung. Binds heparin. At neuromuscular junctions, may play a role in acetylcholine receptor clustering (PubMed:26626625).

Gene Wiki entry for COL13A1 Gene

Additional gene information for COL13A1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for COL13A1 Gene

Genomics for COL13A1 Gene

Regulatory Elements for COL13A1 Gene

Enhancers for COL13A1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH10H069861 1.4 Ensembl ENCODE dbSUPER 11.3 +59.9 59915 1 PKNOX1 NFIB KLF17 RAD21 ZNF366 ZSCAN5C FOS EGR2 CEBPB TSHZ1 COL13A1 LOC105378347 LOC102723350
GH10H069845 1.2 Ensembl ENCODE dbSUPER 11.7 +45.1 45119 3 SCRT1 MAFG ZIC2 ZKSCAN1 ZNF316 POLR2A GLIS1 FOS FOXP2 MAFK COL13A1 FAM241B LOC105378347 LOC102723350
GH10H069806 0.9 Ensembl ENCODE 14.2 +5.7 5673 1 KLF1 JUN ZMYM3 REST ZNF23 MLLT1 FOS NR2C2 COL13A1 LOC105378347
GH10H069854 1.1 ENCODE dbSUPER 11.4 +54.0 53984 3 HDAC1 PKNOX1 ATF1 TAL1 ZNF175 CEBPG FOSL1 CTBP1 GATA2 EGR1 COL13A1 LOC105378347 LOC102723350
GH10H069757 1.1 ENCODE dbSUPER 11.2 -43.9 -43858 1 ZSCAN26 NFIB ZNF473 ZNF195 ZIC2 ZFHX2 ZNF776 LCORL ZBTB48 POLR2A DDX50 CEP57L1P1 COL13A1 FAM241B PALD1 TSPAN15 RPL5P26 GC10P069687
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around COL13A1 on UCSC Golden Path with GeneCards custom track

Promoters for COL13A1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000029296 637 1801 PKNOX1 FEZF1 GLIS2 KLF7 SP3 ZNF610 GLIS1 WT1 PRDM4 SP7

Genomic Location for COL13A1 Gene

Chromosome:
10
Start:
69,801,863 bp from pter
End:
69,964,275 bp from pter
Size:
162,413 bases
Orientation:
Plus strand

Genomic View for COL13A1 Gene

Genes around COL13A1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
COL13A1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for COL13A1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for COL13A1 Gene

Proteins for COL13A1 Gene

  • Protein details for COL13A1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q5TAT6-CODA1_HUMAN
    Recommended name:
    Collagen alpha-1(XIII) chain
    Protein Accession:
    Q5TAT6
    Secondary Accessions:
    • A6NFR5
    • B9EGD2
    • E7EWL8
    • Q13992
    • Q13993
    • Q13994
    • Q13995
    • Q13996
    • Q5TAT4
    • Q5TAT5
    • Q7KZ33
    • Q7KZ49
    • Q99228
    • Q9NQ52

    Protein attributes for COL13A1 Gene

    Size:
    717 amino acids
    Molecular mass:
    69950 Da
    Quaternary structure:
    • Homotrimer; disulfide-linked. Nucleation of the type XIII collagen triple helix is likely to occur at the N-terminal region with triple helix formation proceeding from the N- to the C-terminus. Interacts with FN1, perlecan/HSPG2 and NID2.
    SequenceCaution:
    • Sequence=AAA51685.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for COL13A1 Gene

neXtProt entry for COL13A1 Gene

Post-translational modifications for COL13A1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Antibody Products

  • R&D Systems Antibodies for COL13A1 (Collagen XIII alpha 1)
  • Abcam antibodies for COL13A1

No data available for DME Specific Peptides for COL13A1 Gene

Domains & Families for COL13A1 Gene

Gene Families for COL13A1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted membrane proteins

Protein Domains for COL13A1 Gene

Suggested Antigen Peptide Sequences for COL13A1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with COL13A1: view

No data available for UniProtKB/Swiss-Prot for COL13A1 Gene

Function for COL13A1 Gene

Molecular function for COL13A1 Gene

GENATLAS Biochemistry:
collagen,type XIII,alpha 1,short chain
UniProtKB/Swiss-Prot Function:
Involved in cell-matrix and cell-cell adhesion interactions that are required for normal development. May participate in the linkage between muscle fiber and basement membrane. May play a role in endochondral ossification of bone and branching morphogenesis of lung. Binds heparin. At neuromuscular junctions, may play a role in acetylcholine receptor clustering (PubMed:26626625).

Phenotypes From GWAS Catalog for COL13A1 Gene

Gene Ontology (GO) - Molecular Function for COL13A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 11956183
GO:0008201 heparin binding IEA,IDA 11956183
genes like me logo Genes that share ontologies with COL13A1: view
genes like me logo Genes that share phenotypes with COL13A1: view

Human Phenotype Ontology for COL13A1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for COL13A1 Gene

MGI Knock Outs for COL13A1:

Animal Model Products

  • Taconic Biosciences Mouse Models for COL13A1

CRISPR Products

Clone Products

  • Applied Biological Materials Clones for COL13A1
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for COL13A1 Gene

Localization for COL13A1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for COL13A1 Gene

Cell membrane; Single-pass type II membrane protein. Cell junction, synapse, postsynaptic cell membrane.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for COL13A1 gene
Compartment Confidence
plasma membrane 5
extracellular 5
endoplasmic reticulum 5
cytosol 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for COL13A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS --
GO:0005581 collagen trimer IEA --
GO:0005600 collagen type XIII trimer TAS 2459707
GO:0005788 endoplasmic reticulum lumen TAS --
GO:0005886 plasma membrane TAS --
genes like me logo Genes that share ontologies with COL13A1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for COL13A1 Gene

Pathways & Interactions for COL13A1 Gene

genes like me logo Genes that share pathways with COL13A1: view

Gene Ontology (GO) - Biological Process for COL13A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001763 morphogenesis of a branching structure ISS --
GO:0001958 endochondral ossification ISS --
GO:0007155 cell adhesion IEA --
GO:0007160 cell-matrix adhesion IPI 11956183
GO:0007275 multicellular organism development IEA --
genes like me logo Genes that share ontologies with COL13A1: view

No data available for SIGNOR curated interactions for COL13A1 Gene

Drugs & Compounds for COL13A1 Gene

(2) Drugs for COL13A1 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
atorvastatin Approved Pharma Competitive, Inhibitor 0
Simvastatin Approved Pharma Competitive, Inhibitor HMG-CoA reductase inhibitor 528
genes like me logo Genes that share compounds with COL13A1: view

Transcripts for COL13A1 Gene

Unigene Clusters for COL13A1 Gene

Collagen, type XIII, alpha 1:
Representative Sequences:

CRISPR Products

Clone Products

  • Applied Biological Materials Clones for COL13A1
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

Alternative Splicing Database (ASD) splice patterns (SP) for COL13A1 Gene

No ASD Table

Relevant External Links for COL13A1 Gene

GeneLoc Exon Structure for
COL13A1
ECgene alternative splicing isoforms for
COL13A1

Expression for COL13A1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for COL13A1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for COL13A1 Gene

This gene is overexpressed in Brain - Cerebellar Hemisphere (x11.5), Brain - Cerebellum (x10.8), and Artery - Aorta (x4.4).

Protein differential expression in normal tissues from HIPED for COL13A1 Gene

This gene is overexpressed in Breast (46.6), NK cells (8.7), and Pancreatic juice (8.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for COL13A1 Gene



Protein tissue co-expression partners for COL13A1 Gene

NURSA nuclear receptor signaling pathways regulating expression of COL13A1 Gene:

COL13A1

SOURCE GeneReport for Unigene cluster for COL13A1 Gene:

Hs.695934

mRNA Expression by UniProt/SwissProt for COL13A1 Gene:

Q5TAT6-CODA1_HUMAN
Tissue specificity: Widely expressed in both fetal and adult ocular tissues (at protein level). In the eye, expression is accentuated in the ciliary muscle, optic nerve and the neural retina. In early placenta, localized to fibroblastoid stromal cells of the placental villi, to endothelial cells of developing capillaries and to cells of the cytotrophoblastic columns. Also detected in large decidual cells of the decidual membrane and to stromal cells of the gestational endometrium, but not in the epithelial cells in the endometrial glands. Isoform 10: Expressed in muscle (PubMed:26626625).
genes like me logo Genes that share expression patterns with COL13A1: view

Primer Products

No data available for Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for COL13A1 Gene

Orthologs for COL13A1 Gene

This gene was present in the common ancestor of animals.

Orthologs for COL13A1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia COL13A1 33 34
  • 99.18 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 91 (a)
OneToMany
-- 34
  • 81 (a)
OneToMany
dog
(Canis familiaris)
Mammalia COL13A1 33 34
  • 90.57 (n)
cow
(Bos Taurus)
Mammalia COL13A1 33 34
  • 88.46 (n)
mouse
(Mus musculus)
Mammalia Col13a1 33 16 34
  • 87.43 (n)
rat
(Rattus norvegicus)
Mammalia Col13a1 33
  • 86.64 (n)
oppossum
(Monodelphis domestica)
Mammalia COL13A1 34
  • 80 (a)
OneToOne
chicken
(Gallus gallus)
Aves COL13A1 33 34
  • 70.88 (n)
lizard
(Anolis carolinensis)
Reptilia COL13A1 34
  • 73 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100498211 33
  • 61.49 (n)
zebrafish
(Danio rerio)
Actinopterygii wu:fb83c11 33
  • 59.3 (n)
COL13A1 34
  • 55 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea col-135 34
  • 33 (a)
OneToMany
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.2697 33
Species where no ortholog for COL13A1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for COL13A1 Gene

ENSEMBL:
Gene Tree for COL13A1 (if available)
TreeFam:
Gene Tree for COL13A1 (if available)

Paralogs for COL13A1 Gene

Paralogs for COL13A1 Gene

genes like me logo Genes that share paralogs with COL13A1: view

Variants for COL13A1 Gene

Sequence variations from dbSNP and Humsavar for COL13A1 Gene

SNP ID Clin Chr 10 pos Sequence Context AA Info Type
rs769426298 Pathogenic 69,802,694(+) TGGGA(C/G/T)GAGTC nc-transcript-variant, reference, missense, stop-gained, utr-variant-5-prime
rs864309662 Pathogenic 69,922,770(+) CCAGG(-/G)CTCCC nc-transcript-variant, reference, frameshift-variant
rs864309663 Pathogenic 69,888,303(+) TTTCA(-/G)GGTCC splice-acceptor-variant
rs886041849 Pathogenic 69,894,692(+) CAAAA(-/A)GGAGA nc-transcript-variant, reference, frameshift-variant
rs1000010846 -- 69,883,524(+) GCCCT(C/T)TGGGC intron-variant

Structural Variations from Database of Genomic Variants (DGV) for COL13A1 Gene

Variant ID Type Subtype PubMed ID
esv1107415 CNV insertion 17803354
esv2604076 CNV insertion 19546169
esv2761603 CNV gain 21179565
esv32737 CNV gain+loss 17666407
esv3623757 CNV gain 21293372
esv3623758 CNV loss 21293372
nsv428233 CNV gain 18775914
nsv470962 CNV loss 18288195
nsv509358 CNV insertion 20534489
nsv516370 CNV gain 19592680
nsv519900 CNV gain 19592680
nsv520046 CNV loss 19592680
nsv527896 CNV loss 19592680
nsv551478 CNV loss 21841781
nsv7043 CNV insertion 18451855

Variation tolerance for COL13A1 Gene

Residual Variation Intolerance Score: 46.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.41; 54.42% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for COL13A1 Gene

Human Gene Mutation Database (HGMD)
COL13A1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
COL13A1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for COL13A1 Gene

Disorders for COL13A1 Gene

MalaCards: The human disease database

(6) MalaCards diseases for COL13A1 Gene - From: HGMD, OMIM, ClinVar, GeneTests, Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
myasthenic syndrome, congenital, 19
  • congenital myasthenic syndrome 19
col13a1-related congenital myasthenic syndrome
  • myasthenic syndrome, congenital, 19
postsynaptic congenital myasthenic syndromes
  • congenital myasthenic syndromes, postsynaptic
presynaptic congenital myasthenic syndromes
  • congenital myasthenic syndromes, presynaptic
congenital myasthenic syndrome
  • familial limb-girdle myasthenia
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

CODA1_HUMAN
  • Myasthenic syndrome, congenital, 19 (CMS19) [MIM:616720]: A form of congenital myasthenic syndrome, a group of disorders characterized by failure of neuromuscular transmission, including pre-synaptic, synaptic, and post-synaptic disorders that are not of autoimmune origin. Clinical features are easy fatigability and muscle weakness affecting the axial and limb muscles (with hypotonia in early-onset forms), the ocular muscles (leading to ptosis and ophthalmoplegia), and the facial and bulbar musculature (affecting sucking and swallowing, and leading to dysphonia). The symptoms fluctuate and worsen with physical effort. {ECO:0000269 PubMed:26626625}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for COL13A1

Genetic Association Database (GAD)
COL13A1
Human Genome Epidemiology (HuGE) Navigator
COL13A1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
COL13A1
genes like me logo Genes that share disorders with COL13A1: view

No data available for Genatlas for COL13A1 Gene

Publications for COL13A1 Gene

  1. Congenital Myasthenic Syndrome Type 19 Is Caused by Mutations in COL13A1, Encoding the Atypical Non-fibrillar Collagen Type XIII α1 Chain. (PMID: 26626625) Logan CV … Beeson D (American journal of human genetics 2015) 3 4 60
  2. Assessment of a polymorphism of SDK1 with hypertension in Japanese Individuals. (PMID: 19851296) Oguri M … Yamada Y (American journal of hypertension 2010) 3 45 60
  3. Association of genetic variants with hemorrhagic stroke in Japanese individuals. (PMID: 20198315) Yoshida T … Yamada Y (International journal of molecular medicine 2010) 3 45 60
  4. Genome-wide association study identifies variants associated with histologic features of nonalcoholic Fatty liver disease. (PMID: 20708005) Chalasani N … Nonalcoholic Steatohepatitis Clinical Research Network (Gastroenterology 2010) 3 45 60
  5. A scan of chromosome 10 identifies a novel locus showing strong association with late-onset Alzheimer disease. (PMID: 16385451) Grupe A … Goate A (American journal of human genetics 2006) 3 45 60

Products for COL13A1 Gene

Sources for COL13A1 Gene

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