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Aliases for COL13A1 Gene

Aliases for COL13A1 Gene

  • Collagen Type XIII Alpha 1 2 3
  • Collagen, Type XIII, Alpha 1 2 3 5
  • COLXIIIA1 3 4
  • 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) is a Protein Coding gene. Diseases associated with COL13A1 include synaptic congenital myasthenic syndromes and congenital myasthenic syndrome. Among its related pathways are Degradation of the extracellular matrix and ERK Signaling. GO annotations related to this gene include heparin binding. An important paralog of this gene is COL21A1.

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.

Gene Wiki entry for COL13A1 Gene

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

Genomics for COL13A1 Gene

Regulatory Elements for COL13A1 Gene

Promoters for COL13A1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around COL13A1 on UCSC Golden Path with GeneCards custom track

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

Proteomics data for COL13A1 Gene at MOPED

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)

No data available for DME Specific Peptides for COL13A1 Gene

Domains & Families for COL13A1 Gene

Gene Families for COL13A1 Gene

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.
genes like me logo Genes that share phenotypes with COL13A1: view

Animal Models for COL13A1 Gene

MGI Knock Outs for COL13A1:

Animal Model Products

  • Taconic Biosciences Mouse Models for COL13A1

CRISPR Products

Inhibitory RNA Products

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , 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.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for COL13A1 Gene COMPARTMENTS Subcellular localization image for COL13A1 gene
Compartment Confidence
endoplasmic reticulum 5
extracellular 5
plasma membrane 5
cytosol 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for COL13A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005911 cell-cell junction IEA --
genes like me logo Genes that share ontologies with COL13A1: view

Pathways & Interactions for COL13A1 Gene

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

Interacting Proteins for COL13A1 Gene

Gene Ontology (GO) - Biological Process for COL13A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007160 cell-matrix adhesion IPI 11956183
GO:0016337 single organismal cell-cell adhesion IEP 10865988
GO:0022617 extracellular matrix disassembly TAS --
GO:0030574 collagen catabolic process TAS --
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 493
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:

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 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



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.
genes like me logo Genes that share expression patterns with COL13A1: view

Protein tissue co-expression partners for COL13A1 Gene

Primer Products

In Situ Assay Products

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 35
  • 99.18 (n)
  • 99.14 (a)
COL13A1 36
  • 98 (a)
OneToOne
cow
(Bos Taurus)
Mammalia COL13A1 36
  • 86 (a)
OneToOne
COL13A1 35
  • 88.46 (n)
  • 89.44 (a)
dog
(Canis familiaris)
Mammalia COL13A1 35
  • 90.57 (n)
  • 92.44 (a)
COL13A1 36
  • 86 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Col13a1 16
Col13a1 35
  • 87.43 (n)
  • 90.68 (a)
Col13a1 36
  • 86 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia COL13A1 36
  • 80 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 36
  • 81 (a)
OneToMany
-- 36
  • 91 (a)
OneToMany
rat
(Rattus norvegicus)
Mammalia Col13a1 35
  • 86.64 (n)
  • 89.64 (a)
chicken
(Gallus gallus)
Aves COL13A1 35
  • 70.88 (n)
  • 72.1 (a)
COL13A1 36
  • 72 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia COL13A1 36
  • 73 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100498211 35
  • 61.49 (n)
  • 61.6 (a)
zebrafish
(Danio rerio)
Actinopterygii COL13A1 36
  • 55 (a)
OneToOne
wu:fb83c11 35
  • 59.3 (n)
  • 59.74 (a)
worm
(Caenorhabditis elegans)
Secernentea col-135 36
  • 33 (a)
OneToMany
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.2697 35
Species with no ortholog for COL13A1:
  • 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

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
rs1061954 - 69,930,495(+) GGGCA(C/G/T)CCAGG reference, synonymous-codon, missense
rs723332 -- 69,901,307(+) GCTCC(A/G)GAGTG intron-variant
rs1149696 -- 69,909,647(+) GCCAC(C/G)AAGGA intron-variant
rs1149697 -- 69,908,640(+) TTAGG(A/G)TGTCC intron-variant
rs1149698 -- 69,907,739(+) AATCA(C/T)AAACC intron-variant

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

Variant ID Type Subtype PubMed ID
esv32737 CNV Gain+Loss 17666407
nsv428233 CNV Gain 18775914
nsv516370 CNV Gain 19592680
nsv7043 CNV Insertion 18451855
nsv519900 CNV Gain 19592680
nsv509358 CNV Insertion 20534489
nsv895699 CNV Loss 21882294
esv2604076 CNV Insertion 19546169
esv267404 CNV Insertion 20981092
esv273870 CNV Insertion 20981092
esv1107415 CNV Insertion 17803354
nsv470962 CNV Loss 18288195
nsv527896 CNV Loss 19592680
nsv520046 CNV Loss 19592680

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

HapMap Linkage Disequilibrium report
COL13A1

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

Disorders for COL13A1 Gene

MalaCards: The human disease database

(2) MalaCards diseases for COL13A1 Gene - From: Orphanet and DISEASES

Disorder Aliases PubMed IDs
synaptic congenital myasthenic syndromes
congenital myasthenic syndrome
  • familial infantile myasthenia 1
- elite association - COSMIC cancer census association via MalaCards

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 UniProtKB/Swiss-Prot and Genatlas for COL13A1 Gene

Publications for COL13A1 Gene

  1. Assessment of a polymorphism of SDK1 with hypertension in Japanese Individuals. (PMID: 19851296) Oguri M. … Yamada Y. (Am. J. Hypertens. 2010) 3 48 67
  2. A genome-wide association study identifies a novel locus at 6q22.1 associated with ulcerative colitis. (PMID: 25082827) JuliA A. … Marsal S. (Hum. Mol. Genet. 2014) 3
  3. Parkinson disease loci in the mid-western Amish. (PMID: 23793441) Davis M.F. … Haines J.L. (Hum. Genet. 2013) 3
  4. Association of genetic variants with hemorrhagic stroke in Japanese individuals. (PMID: 20198315) Yoshida T. … Yamada Y. (Int. J. Mol. Med. 2010) 3
  5. Genome-wide association study identifies variants associated with histologic features of nonalcoholic Fatty liver disease. (PMID: 20708005) Chalasani N. … Rotter J.I. (Gastroenterology 2010) 3

Products for COL13A1 Gene

Sources for COL13A1 Gene

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