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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

COL13A1 Gene

protein-coding   GIFtS: 55
GCID: GC10P071561

Collagen, Type XIII, Alpha 1

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(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

Aliases
Collagen, Type XIII, Alpha 11 2
COLXIIIA12 3
Collagen Alpha-1(XIII) Chain2

External Ids:    HGNC: 21901   Entrez Gene: 13052   Ensembl: ENSG000001974677   OMIM: 1203505   UniProtKB: Q5TAT63   

Export aliases for COL13A1 gene to outside databases

Previous GC identifers: GC10P070372 GC10P070648 GC10P071454 GC10P070906 GC10P071231 GC10P065553


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

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 fatty liver disease, and liver disease, and among its related super-pathways are Collagen biosynthesis and modifying enzymes and FAK1 Signaling. GO annotations related to this gene include extracellular matrix structural constituent and heparin binding. An important paralog of this gene is COL25A1.

UniProtKB/Swiss-Prot: CODA1_HUMAN, Q5TAT6
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

Gene Wiki entry for COL13A1 (Collagen, type XIII, alpha 1) Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000010.10  NC_018921.2  NT_030059.13  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the COL13A1 gene promoter:
         AhR   POU2F2 (Oct-2.1)   Oct-B1   oct-B3   oct-B2   Arnt   POU2F2   POU2F2C   POU2F1   POU2F1a   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidCOL13A1 promoter sequence
   Search SABiosciences Chromatin IP Primers for COL13A1

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat COL13A1


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 10q22   Ensembl cytogenetic band:  10q22.1   HGNC cytogenetic band: 10q22

COL13A1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
COL13A1 gene location

GeneLoc information about chromosome 10         GeneLoc Exon Structure

GeneLoc location for GC10P071561:  view genomic region     (about GC identifiers)

Start:
71,561,644 bp from pter      End:
71,724,031 bp from pter
Size:
162,388 bases      Orientation:
plus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: CODA1_HUMAN, Q5TAT6 (See protein sequence)
Recommended Name: Collagen alpha-1(XIII) chain  
Size: 717 amino acids; 69950 Da
Subunit: 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
Subcellular location: Cell membrane; Single-pass type II membrane protein
Sequence caution: Sequence=AAA51685.1; Type=Erroneous initiation;
Secondary accessions: A6NFR5 B9EGD2 E7EWL8 Q13992 Q13993 Q13994 Q13995 Q13996 Q5TAT4 Q5TAT5
Q7KZ33 Q7KZ49 Q99228 Q9NQ52
Alternative splicing: 11 isoforms:  Q5TAT6-1   Q5TAT6-2   Q5TAT6-3   Q5TAT6-4   Q5TAT6-5   Q5TAT6-6   Q5TAT6-7   Q5TAT6-8   
Q5TAT6-9   Q5TAT6-10   Q5TAT6-11   (Gene prediction based on EST data)

Explore the universe of human proteins at neXtProt for COL13A1: NX_Q5TAT6

Explore proteomics data for COL13A1 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q5TAT6

  • COL13A1 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    COL13A1 Protein Expression
    REFSEQ proteins (6 alternative transcripts): 
    NP_001123575.1  NP_542988.3  NP_542990.3  NP_542991.3  NP_542992.3  NP_542995.3  

    ENSEMBL proteins: 
     ENSP00000430089   ENSP00000381949   ENSP00000346553   ENSP00000350463   ENSP00000428057  
     ENSP00000430061   ENSP00000428342   ENSP00000430173   ENSP00000381947   ENSP00000388774  
     ENSP00000381946   ENSP00000381943   ENSP00000381940   ENSP00000381938   ENSP00000381936  
     ENSP00000381941   ENSP00000348695   ENSP00000381944   ENSP00000381945  
    Reactome Protein details: Q5TAT6
    Human Recombinant Protein Products for COL13A1: 
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    Novus Biologicals COL13A1 Lysates
    Browse Sino Biological Recombinant Proteins
    Browse Sino Biological Cell Lysates 
    Browse ProSpec Recombinant Proteins
    Browse Proteins at Cloud-Clone Corp. 

    Gene Ontology (GO): 5/6 cellular component terms (GO ID links to tree view) (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005576extracellular region TAS--
    GO:0005600collagen type XIII TAS2459707
    GO:0005788endoplasmic reticulum lumen TAS--
    GO:0005886plasma membrane TAS--
    GO:0005911cell-cell junction IEA--

    COL13A1 for ontologies           About GeneDecksing



    COL13A1 Antibody Products: 
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    LSBio Antibodies in human, mouse, rat for COL13A1 

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    Browse ELISAs at Cloud-Clone Corp. 
    Browse CLIAs at Cloud-Clone Corp.


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    HGNC Gene Families: 
    COLLAGEN: Collagens

    1 InterPro protein domain:
     IPR008160 Collagen

    Graphical View of Domain Structure for InterPro Entry Q5TAT6

    ProtoNet protein and cluster: Q5TAT6

    2 Blocks protein domains:
    IPB008160 Collagen triple helix repeat
    IPB008161 Collagen helix repeat



    COL13A1 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: CODA1_HUMAN, Q5TAT6
    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

         Genatlas biochemistry entry for COL13A1:
    collagen,type XIII,alpha 1,short chain

         Gene Ontology (GO): 3 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005201extracellular matrix structural constituent NAS--
    GO:0005515protein binding IPI11956183
    GO:0008201heparin binding IDA11956183
         
    COL13A1 for ontologies           About GeneDecksing


    Phenotypes:
         8 MGI mutant phenotypes (inferred from 3 alleles(MGI details for Col13a1):
     behavior/neurological  cellular  growth/size  homeostasis/metabolism  immune system 
     muscle  nervous system  other 

    COL13A1 for phenotypes           About GeneDecksing

    Animal Models:
         MGI mouse knock-outs for COL13A1: Col13a1tm3.1Pih Col13a1tm1Pih

       inGenious Targeting Laboratory - Custom generated mouse model solutions for COL13A1 
       inGenious Targeting Laboratory - Custom generated inducible mouse model solutions for COL13A1

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    SwitchGear 3'UTR luciferase reporter plasmidCOL13A1 3' UTR sequence
    Inhib. RNA
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for COL13A1


    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene).
    About This Section

    SuperPaths for COL13A1 About   (see all 7)                                                                                              See pathways by source

    SuperPathContained pathways About
    1Collagen biosynthesis and modifying enzymes
    Collagen biosynthesis and modifying enzymes0.74
    Extracellular matrix organization0.39
    Collagen formation0.74
    Blood Coagulation Cascade0.39
    Intrinsic Prothrombin Activation Pathway0.40
    2Integrin Pathway
    Integrin Pathway0.67
    UPA-UPAR Pathway0.56
    FAK1 Signaling0.67
    Inhibition of Angiogenesis by TSP10.50
    GnRH Signaling0.56
    Transendothelial Migration of Leukocytes0.38
    3Rho Family GTPases
    Rho Family GTPases0.61
    Molecular Mechanisms of Cancer0.51
    ERK Signaling0.61
    ILK Signaling0.49
    MAPK Signaling0.58
    4Degradation of the extracellular matrix
    Degradation of the extracellular matrix0.79
    Degradation of collagen0.79
    5PTEN Pathway
    PTEN Pathway0.56
    Phospholipase-C Pathway0.56

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    1 R&D Systems Pathway for COL13A1
        Articular Cartilage Extracellular Matrix

    5/15 Downloadable PowerPoint Slides of QIAGEN Pathway Central Maps for COL13A1 (see all 15)
        MAPK Signaling
    Molecular Mechanisms of Cancer
    PTEN Pathway
    Transendothelial Migration of Leukocytes
    UPA-UPAR Pathway

    5        Reactome Pathways for COL13A1
        Extracellular matrix organization
    Collagen biosynthesis and modifying enzymes
    Degradation of the extracellular matrix
    Collagen formation
    Degradation of collagen


    1         Kegg Pathway  (Kegg details for COL13A1):
        Protein digestion and absorption


    COL13A1 for pathways           About GeneDecksing

    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for COL13A1

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    5/46 Interacting proteins for COL13A1 (ENSP000003486954) via UniProtKB, MINT, STRING, and/or I2D (see all 46)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    COL10A1ENSP000002432224STRING: ENSP00000243222
    COL11A1ENSP000003511634STRING: ENSP00000351163
    COL12A1ENSP000003251464STRING: ENSP00000325146
    COL14A1ENSP000002978484STRING: ENSP00000297848
    COL15A1ENSP000003641404STRING: ENSP00000364140
    About this table

    Gene Ontology (GO): 5/8 biological process terms (GO ID links to tree view) (see all 8):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001763morphogenesis of a branching structure ISS--
    GO:0001958endochondral ossification ISS--
    GO:0007160cell-matrix adhesion IPI11956183
    GO:0016337cell-cell adhesion IEP10865988
    GO:0022617extracellular matrix disassembly TAS--

    COL13A1 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for COL13A1 (CODA1)

    2 HMDB Compounds for COL13A1    About this table
    CompoundSynonyms CAS #PubMed Ids
    AtorvastatinAtorvastatin acid (see all 4)134523-00-5--
    Simvastatin(+)-Simvastatin (see all 28)79902-63-9--

    Search CenterWatch for drugs/clinical trials and news about COL13A1 / CODA1

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for COL13A1 gene (20 alternative transcripts): 
    NM_001130103.1  NM_080798.3  NM_080800.3  NM_080801.3  NM_080802.3  NM_080805.3  NM_005203.3  NM_080799.2  
    NM_080803.2  NM_080804.2  NM_080806.2  NM_080807.2  NM_080808.2  NM_080809.2  NM_080810.2  NM_080811.2  
    NM_080812.2  NM_080813.2  NM_080814.2  NM_080815.2  

    Unigene Cluster for COL13A1:

    Collagen, type XIII, alpha 1
    Hs.695934  [show with all ESTs]
    Unigene Representative Sequence: NM_001130103
    18/22 Ensembl transcripts including schematic representations, and UCSC links where relevant (see all 22):
    ENST00000479733 ENST00000398978 ENST00000354547 ENST00000357811 ENST00000520267
    ENST00000517713 ENST00000522165 ENST00000520133 ENST00000484990 ENST00000398975
    ENST00000456019 ENST00000518052 ENST00000478219 ENST00000398974 ENST00000398971
    ENST00000398968(uc021psc.1 uc021psh.1) ENST00000398966(uc021prz.1 uc001jqk.2 uc021psd.1 uc021psg.1)
    ENST00000398964(uc021psa.1 uc021psb.1 uc010qjf.2 uc021pse.1)


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    Additional mRNA sequence: 

    AJ293624.1 BC136385.1 BC139913.1 M15524.1 M33653.1 M59217.1 

    15 DOTS entries:

    DT.92419152  DT.92419154  DT.101968808  DT.100025599  DT.100025594  DT.453365  DT.91854784  DT.100025597 
    DT.100025601  DT.101969412  DT.91707313  DT.97837183  DT.100811044  DT.121295186  DT.91900699 

    24/65 AceView cDNA sequences (see all 65):

    NM_080805 NM_080810 NM_080806 NM_080814 NM_080813 AI741175 NM_080809 BU616183 
    NM_080802 NM_080798 NM_080815 NM_080799 NM_080812 NM_005203 AW102575 AA470704 
    NM_080808 NM_080811 BM974395 NM_080803 NM_080804 NM_080800 NM_080807 NM_080801 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    COL13A1 expression in normal human tissues (normalized intensities)      COL13A1 embryonic expression: see
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    COL13A1 Expression
    About this image


    COL13A1 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database 
     5/15 selected tissues (see all 15) fully expand
     
     Tooth (Integumentary System)    fully expand to see all 4 entries
             visceral organ/oral region/upper jaw   
     
     Brain (Nervous System)    fully expand to see all 4 entries
             Human Cerebellar Astrocytes   
     
     Uncategorized (Uncategorized)    fully expand to see all 3 entries
             PureStem Progenitor EN7
     
     Smooth Muscle (Muscoskeletal System)    fully expand to see all 2 entries
             Human umbilical Smooth Muscle (HUSM)   
     
     Peripheral Nervous System (Nervous System)    fully expand to see all 2 entries
             Human Perineurial Cells (HPC)   

    See COL13A1 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for COL13A1

    SOURCE GeneReport for Unigene cluster: Hs.695934

    UniProtKB/Swiss-Prot: CODA1_HUMAN, Q5TAT6
    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

        SABiosciences Custom PCR Arrays for COL13A1
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    In Situ
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for COL13A1

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

    This gene was present in the common ancestor of animals.

    Orthologs for COL13A1 gene from 6/14 species (see all 14)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Col13a11 , 5 collagen, type XIII, alpha 11, 5 81.94(n)1
    84.97(a)1
      10 (32.29 cM)5
    128171  NM_007731.21  NP_031757.11 
     618382365 
    chicken
    (Gallus gallus)
    Aves COL13A16
    Uncharacterized protein
    72(a)
    1 ↔ 1
    6(10558568-10638887)
    lizard
    (Anolis carolinensis)
    Reptilia COL13A16
    Uncharacterized protein
    73(a)
    1 ↔ 1
    3(48844590-48958494)
    zebrafish
    (Danio rerio)
    Actinopterygii col19a16
    col4a36
    (see all 3)
    collagen, type IV, alpha 3
    (see all 3)
    25(a)
    15(a)
    (see all 3)
    possible ortholog
    possible ortholog
    (see all 3)
    13(39550948-39675972)
    15(35323158-35380622)
    fruit fly
    (Drosophila melanogaster)
    Insecta CG423421 CG42342 51.39(n)
    48.93(a)
      7354466  NM_001202305.1  NP_001189234.1 
    worm
    (Caenorhabditis elegans)
    Secernentea col-991 Protein COL-99 51.61(n)
    50(a)
      185112  NM_067468.3  NP_499869.2 


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for COL13A1 gene
    COL25A12  COL19A12  COL9A12  COL22A12  COL9A32  COL9A22  COL16A12  COL21A12  
    COL23A12  
    8 SIMAP similar genes for COL13A1 using alignment to 13 protein entries:     CODA1_HUMAN (see all proteins):
    MSR1    COL6A5    C1QB    GLDN    COL4A2    COLEC11
    COL6A2    COL6A6

    COL13A1 for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/3656 SNPs in COL13A1 are shown (see all 3656)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 10 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1903280791,2
    --71559679(+) GCCTCA/CGAGAT 6 -- us2k10--------
    rs26426081,2
    C,F,A,H--71559723(-) CCTGGG/ATGTAA 6 -- us2k111Minor allele frequency- A:0.13NS EA NA WA 786
    rs22474271,2
    C,F,A,H--71559748(-) CAGGGT/GGACTC 6 -- us2k115Minor allele frequency- G:0.24NS EA NA WA CSA 781
    rs1172236001,2
    C,F--71559778(+) TGCTGG/AGGCCA 6 -- us2k11Minor allele frequency- A:0.03NA 120
    rs1452400591,2
    --71559908(+) AAAGAA/TCAGTT 6 -- us2k10--------
    rs27045061,2
    C,F,A,H--71560033(-) TTTCTG/ACACTG 6 -- us2k119Minor allele frequency- A:0.15NS EA NA WA 2156
    rs777931741,2
    C,F--71560141(+) GAAAAC/GAGAGT 6 -- us2k12Minor allele frequency- G:0.11NA 122
    rs751513581,2
    C,F--71560259(+) CATAGT/CGGCTG 6 -- us2k13Minor allele frequency- C:0.08WA NA EA 358
    rs1825539911,2
    --71560269(+) GACTGG/TCCCAG 6 -- us2k10--------
    rs1409983191,2
    --71560298(+) TTACAG/TATGAT 6 -- us2k10--------

    HapMap Linkage Disequilibrium report for COL13A1 (71561644 - 71724031 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 10/14 variations for COL13A1 (see all 14):    About this table     
    Variant IDTypeSubtypePubMed ID
    esv1107415CNV Insertion17803354
    esv2604076CNV Insertion19546169
    nsv509358CNV Insertion20534489
    esv273870CNV Insertion20981092
    esv267404CNV Insertion20981092
    nsv7043CNV Insertion18451855
    nsv520046CNV Loss19592680
    nsv527896CNV Loss19592680
    nsv470962CNV Loss18288195
    nsv895699CNV Loss21882294

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    SeqTarget long-range PCR primers for resequencing COL13A1
    DNA2.0 Custom Variant and Variant Library Synthesis for COL13A1

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    OMIM gene information: 120350    OMIM disorders: --

    5 diseases for COL13A1:    About MalaCards
    fatty liver disease    liver disease    alzheimer's disease    gastric cancer
    endotheliitis


    COL13A1 for disorders           About GeneDecksing


    Congresses - knowledge worth sharing:  
    Alzheimer's & Parkinson's Diseases Congress (ADPD) 18 - 22 March 2015
    Genetic Association Database (GAD): COL13A1
    Human Genome Epidemiology (HuGE) Navigator: COL13A1 (4 documents)

    Export disorders for COL13A1 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for COL13A1 gene, integrated from 9 sources (see all 26):
    (articles sorted by number of sources associating them with COL13A1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Assessment of a polymorphism of SDK1 with hypertensio n in Japanese Individuals. (PubMed id 19851296)1, 4 Oguri M....Yamada Y. (2010)
    2. Genome-wide association study identifies variants ass ociated with histologic features of nonalcoholic Fatty liver disease. (PubMed id 20708005)1, 4 Chalasani N....Rotter J.I. (2010)
    3. Association of genetic variants with hemorrhagic stro ke in Japanese individuals. (PubMed id 20198315)1, 4 Yoshida T....Yamada Y. (2010)
    4. A scan of chromosome 10 identifies a novel locus showing strong association with late-onset Alzheimer disease. (PubMed id 16385451)1, 4 Grupe A....Goate A. (2006)
    5. The type XIII collagen ectodomain is a 150-nm rod and capable of binding to fibronectin, nidogen-2, perlecan, and heparin. (PubMed id 11956183)1, 2 Tu H....Pihlajaniemi T. (2002)
    6. 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)1, 2 Sandberg-Lall M.... Pihlajaniemi T. (2000)
    7. Location and alternative splicing of type XIII collagen RNA in the early human placenta. (PubMed id 8246446)1, 2 Juvonen M.... Autio-Harmainen H. (1993)
    8. 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)1, 2 Juvonen M. and Pihlajaniemi T. (1992)
    9. 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)1, 2 Juvonen M.... Pihlajaniemi T. (1992)
    10. 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)1, 2 Pihlajaniemi T. and Tamminen M. (1990)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
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      Query String
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 1305 HGNC: 2190 AceView: COL13A1 Ensembl:ENSG00000197467 euGenes: HUgn1305
    ECgene: COL13A1 Kegg: 1305 H-InvDB: COL13A1

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for COL13A1 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for COL13A1 gene:
    Search GeneIP for patents involving COL13A1

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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    GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 4 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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