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COL13A1 Gene

protein-coding   GIFtS: 50
GCID: GC10P071561

Collagen, Type XIII, Alpha 1

  Search for COL13A1
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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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, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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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. 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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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Regulatory elements:
   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 Chromatin IP Primers for COL13A1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing 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 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, 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, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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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
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


See COL13A1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

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

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LSBio Antibodies in human, mouse, rat for COL13A1

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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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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



Find genes that share domains with COL13A1           About GenesLikeMe


(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,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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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:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005201extracellular matrix structural constituent ----
GO:0005515protein binding IPI11956183
GO:0008201heparin binding IDA11956183
     
Find genes that share ontologies with COL13A1           About GenesLikeMe


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

Find genes that share phenotypes with COL13A1           About GenesLikeMe

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

   inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for COL13A1
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   genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for COL13A1

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SwitchGear 3'UTR luciferase reporter plasmidCOL13A1 3' UTR sequence
Inhib. RNA
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Predesigned siRNA for gene silencing in human, mouse, rat COL13A1

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GenScript: all cDNA clones in your preferred vector (see all 6): COL13A1 (NM_001130103)
Browse Sino Biological Human cDNA Clones
DNA2.0 Custom Codon Optimized Gene Synthesis Service for COL13A1
Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat COL13A1

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In Situ Assay
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Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for COL13A1


(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Subcellular locations from UniProtKB/Swiss-Prot
CODA1_HUMAN, Q5TAT6: Cell membrane; Single-pass type II membrane protein
Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
extracellular5
plasma membrane5
endoplasmic reticulum4
cytosol1
golgi apparatus1

Gene Ontology (GO): Selected cellular component terms (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--

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(SuperPaths according to PathCards, Pathways according to 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 QIAGEN, 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 Apr 2014 via Entrez Gene).
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SuperPaths for COL13A1 About   (see all 8)  
See pathways by source

SuperPathContained pathways About
1Collagen biosynthesis and modifying enzymes
Collagen biosynthesis and modifying enzymes0.75
Intrinsic Prothrombin Activation Pathway0.39
Collagen formation0.75
Blood Coagulation Cascade0.38
2Integrin Pathway
FAK1 Signaling0.67
UPA-UPAR Pathway0.56
Integrin Pathway0.67
Inhibition of Angiogenesis by TSP10.50
GnRH Signaling0.56
Transendothelial Migration of Leukocytes0.38
3ERK Signaling
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 matrix0.43
Extracellular matrix organization0.34
Collagen degradation0.43
5Phospholipase-C Pathway
Phospholipase-C Pathway0.56
PTEN Pathway0.56


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Pathways by source                                                                                                                                                                 See SuperPaths
Show all pathways

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

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

3 Reactome Pathways for COL13A1
    Integrin cell surface interactions
Collagen biosynthesis and modifying enzymes
Collagen degradation


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

    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for COL13A1
Interactions:

    Search GeneGlobe Interaction Network for COL13A1

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

Selected 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
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Gene Ontology (GO): Selected biological process terms (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--

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(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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Browse Small Molecules at EMD Millipore
   Browse drugs & compounds from Enzo Life Sciences
  Browse compounds at ApexBio 

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--



(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,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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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  

Selected 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)

miRNA
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hsa-miR-30c hsa-miR-3163 hsa-miR-1271 hsa-miR-30d hsa-miR-30a hsa-miR-96* hsa-miR-593* hsa-miR-30b
SwitchGear 3'UTR luciferase reporter plasmidCOL13A1 3' UTR sequence
Inhib. RNA
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Primer
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  QuantiTect SYBR Green Assays in human, mouse, rat COL13A1
  QuantiFast Probe-based Assays in human, mouse, rat COL13A1

Selected AceView cDNA sequences (see all 65):

AA235687 NM_080809 NM_080801 NM_080811 BM744248 NM_080805 BM974395 NM_080812 
NM_080814 AA243649 NM_080799 NM_080815 AW102575 NM_080813 NM_080804 NM_080802 
NM_080800 AI741175 NM_005203 BU616183 NM_080810 AA470704 NM_080803 NM_080806 

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™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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COL13A1 expression in normal human tissues (normalized intensities)
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
 selected tissues (see all 8) fully expand
 
 Bone (Muscoskeletal System)    fully expand to see all 2 entries
         Zeugopod Periosteum
 
 Dermis (Integumentary System)    fully expand to see all 2 entries
         Zigzag Dermal Papilla Cells Dermal Papilla
 
 Neural Crest (Gastrulation Derivatives)
         PureStem SM30, NCr-fac & Meso-latp Progenitor
 
 Endothelium (Cardiovascular System)
         Human umbilical vein endothelial cells (HUVEC)
 
 Blood (Hematopoietic System)
         Natural Killer Cells Peripheral Blood
COL13A1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

COL13A1 Protein Expression

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

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In Situ
Assay Products:
 

 
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)
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This gene was present in the common ancestor of animals.

Orthologs for COL13A1 gene from Selected species (see all 13)    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 87.43(n)1
90.68(a)1
  10 (32.29 cM)5
128171  NM_007731.21  NP_031757.11 
 618382365 
chicken
(Gallus gallus)
Aves COL13A11 collagen, type XIII, alpha 1 70.88(n)
72.1(a)
  769037  XM_004942004.1  XP_004942061.1 
lizard
(Anolis carolinensis)
Reptilia COL13A16
collagen, type XIII, alpha 1
73(a)
1 ↔ 1
3(48844590-48958494)
tropical clawed frog
(Xenopus tropicalis)
Amphibia LOC1004982111 collagen alpha-1(XIII) chain-like 61.49(n)
61.6(a)
  100498211  XM_002935770.2  XP_002935816.2 
zebrafish
(Danio rerio)
Actinopterygii wu:fb83c111 wu:fb83c11 59.3(n)
59.74(a)
  323154  XM_003199698.2  XP_003199746.2 
worm
(Caenorhabditis elegans)
Secernentea col-1356
Protein COL-135, isoform a (col-135) mRNA, complet...
33(a)
1 → many
IV(15129662-15131786) WBGene00000708


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)
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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

Find genes that share paralogs with COL13A1           About GenesLikeMe



(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), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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Selected SNPs for COL13A1 (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) Selected 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

Site Specific Mutation Identification with PCR Assays
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, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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OMIM gene information: 120350    OMIM disorders: --


Find genes that share disorders with COL13A1           About GenesLikeMe

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)
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PubMed articles for COL13A1 gene, integrated from 10 sources (see all 27):
(articles sorted by number of sources associating them with COL13A1)
    Utopia: connect your pdf to the dynamic
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  1. Assessment of a polymorphism of SDK1 with hypertension in Japanese Individuals. (PubMed id 19851296)1, 4 Oguri M....Yamada Y. (Am. J. Hypertens. 2010)
  2. Genome-wide association study identifies variants associated with histologic features of nonalcoholic Fatty liver disease. (PubMed id 20708005)1, 4 Chalasani N....Rotter J.I. (Gastroenterology 2010)
  3. Association of genetic variants with hemorrhagic stroke in Japanese individuals. (PubMed id 20198315)1, 4 Yoshida T....Yamada Y. (Int. J. Mol. Med. 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. (Am. J. Hum. Genet. 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. (J. Biol. Chem. 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. (Exp. Eye Res. 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. (Lab. Invest. 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. (J. Biol. Chem. 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. (J. Biol. Chem. 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. (J. Biol. Chem. 1990)

(in PubMed, OMIM, and NCBI Bookshelf)
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 ANDOR
Aliases
Free Text  

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

(According to HUGE)
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  --

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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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.)
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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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Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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