Atlas of Genetics and Cytogenetics in Oncology and Haematology


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COL18A1 (collagen, type XVIII, alpha 1)

Identity

Other namesKNO
KNO1
KS
HGNC (Hugo) COL18A1
LocusID (NCBI) 80781
Atlas_Id 40123
Location 21q22.3
Location_base_pair Starts at 46875424 and ends at 46933634 bp from pter ( according to hg19-Feb_2009)
Fusion genes
(updated 2015)
COL18A1 21q22.3 / ADARB1 21q22.3COL18A1 21q22.3 / HSPA5 9q33.3

Note

Non-annotated gene. Preliminary data : if you are an author
who wish to write a full paper/card on this gene, go to  How to contribute

DNA/RNA

 


External links

Nomenclature
HGNC (Hugo)COL18A1   2195
Cards
Entrez_Gene (NCBI)COL18A1  80781  collagen, type XVIII, alpha 1
GeneCards (Weizmann)COL18A1
Ensembl hg19 (Hinxton)ENSG00000182871 [Gene_View]  chr21:46875424-46933634 [Contig_View]  COL18A1 [Vega]
Ensembl hg38 (Hinxton)ENSG00000182871 [Gene_View]  chr21:46875424-46933634 [Contig_View]  COL18A1 [Vega]
ICGC DataPortalENSG00000182871
TCGA cBioPortalCOL18A1
AceView (NCBI)COL18A1
Genatlas (Paris)COL18A1
WikiGenes80781
SOURCE (Princeton)COL18A1
Genomic and cartography
GoldenPath hg19 (UCSC)COL18A1  -     chr21:46875424-46933634 +  21q22.3   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)COL18A1  -     21q22.3   [Description]    (hg38-Dec_2013)
EnsemblCOL18A1 - 21q22.3 [CytoView hg19]  COL18A1 - 21q22.3 [CytoView hg38]
Mapping of homologs : NCBICOL18A1 [Mapview hg19]  COL18A1 [Mapview hg38]
OMIM120328   267750   
Gene and transcription
Genbank (Entrez)AF018081 AF018082 AF184060 AF333246 AF333247
RefSeq transcript (Entrez)NM_030582 NM_130444 NM_130445
RefSeq genomic (Entrez)NC_000021 NC_018932 NG_011903 NT_011512 NW_004929427
Consensus coding sequences : CCDS (NCBI)COL18A1
Cluster EST : UnigeneHs.517356 [ NCBI ]
CGAP (NCI)Hs.517356
Alternative Splicing : Fast-db (Paris)GSHG0019557
Alternative Splicing GalleryENSG00000182871
Gene ExpressionCOL18A1 [ NCBI-GEO ]     COL18A1 [ SEEK ]   COL18A1 [ MEM ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
BioGPS (Tissue expression)80781
Protein : pattern, domain, 3D structure
UniProt/SwissProtP39060 (Uniprot)
NextProtP39060  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP39060
Splice isoforms : SwissVarP39060 (Swissvar)
PhosPhoSitePlusP39060
Domaine pattern : Prosite (Expaxy)FZ (PS50038)   
Domains : Interpro (EBI)C-type_lectin-like    C-type_lectin_fold    COL18A1    Collagen    Collagenase_NC10/endostatin    ConA-like_dom    DUF959_COL18_N    Frizzled_dom    Laminin_G   
Domain families : Pfam (Sanger)Collagen (PF01391)    DUF959 (PF06121)    Endostatin (PF06482)    Fz (PF01392)   
Domain families : Pfam (NCBI)pfam01391    pfam06121    pfam06482    pfam01392   
Domain families : Smart (EMBL)FRI (SM00063)  LamG (SM00282)  TSPN (SM00210)  
DMDM Disease mutations80781
Blocks (Seattle)COL18A1
PDB (SRS)1BNL    3HON    3HSH   
PDB (PDBSum)1BNL    3HON    3HSH   
PDB (IMB)1BNL    3HON    3HSH   
PDB (RSDB)1BNL    3HON    3HSH   
Structural Biology KnowledgeBase1BNL    3HON    3HSH   
SCOP (Structural Classification of Proteins)1BNL    3HON    3HSH   
CATH (Classification of proteins structures)1BNL    3HON    3HSH   
Human Protein AtlasENSG00000182871
Peptide AtlasP39060
HPRD00382
IPIIPI00022822   IPI00414694   IPI00783931   IPI01014165   IPI00828004   IPI00479309   IPI00796842   
Protein Interaction databases
DIP (DOE-UCLA)P39060
IntAct (EBI)P39060
FunCoupENSG00000182871
BioGRIDCOL18A1
IntegromeDBCOL18A1
STRING (EMBL)COL18A1
ZODIACCOL18A1
Ontologies - Pathways
QuickGOP39060
Ontology : AmiGOangiogenesis  endothelial cell morphogenesis  structural molecule activity  protein binding  extracellular region  collagen trimer  basement membrane  extracellular space  endoplasmic reticulum lumen  cell adhesion  visual perception  positive regulation of cell proliferation  negative regulation of cell proliferation  organ morphogenesis  extracellular matrix disassembly  extracellular matrix organization  positive regulation of cell migration  collagen catabolic process  extracellular matrix  extracellular matrix  extracellular matrix  response to drug  identical protein binding  metal ion binding  response to hydrostatic pressure  extracellular exosome  positive regulation of endothelial cell apoptotic process  
Ontology : EGO-EBIangiogenesis  endothelial cell morphogenesis  structural molecule activity  protein binding  extracellular region  collagen trimer  basement membrane  extracellular space  endoplasmic reticulum lumen  cell adhesion  visual perception  positive regulation of cell proliferation  negative regulation of cell proliferation  organ morphogenesis  extracellular matrix disassembly  extracellular matrix organization  positive regulation of cell migration  collagen catabolic process  extracellular matrix  extracellular matrix  extracellular matrix  response to drug  identical protein binding  metal ion binding  response to hydrostatic pressure  extracellular exosome  positive regulation of endothelial cell apoptotic process  
Pathways : KEGGProtein digestion and absorption   
Protein Interaction DatabaseCOL18A1
Atlas of Cancer Signalling NetworkCOL18A1
Wikipedia pathwaysCOL18A1
Orthology - Evolution
OrthoDB80781
GeneTree (enSembl)ENSG00000182871
Phylogenetic Trees/Animal Genes : TreeFamCOL18A1
Homologs : HomoloGeneCOL18A1
Homology/Alignments : Family Browser (UCSC)COL18A1
Gene fusions - Rearrangements
Fusion: TCGACOL18A1 21q22.3 ADARB1 21q22.3 KIRC
Fusion: TCGACOL18A1 21q22.3 HSPA5 9q33.3 HNSC
Polymorphisms : SNP, variants
NCBI Variation ViewerCOL18A1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)COL18A1
dbVarCOL18A1
ClinVarCOL18A1
1000_GenomesCOL18A1 
Exome Variant ServerCOL18A1
Exome Aggregation Consortium (ExAC)ENSG00000182871
SNP (GeneSNP Utah)COL18A1
SNP : HGBaseCOL18A1
Genetic variants : HAPMAPCOL18A1
Genomic Variants (DGV)COL18A1 [DGVbeta]
Mutations
ICGC Data PortalCOL18A1 
TCGA Data PortalCOL18A1 
Tumor PortalCOL18A1
TCGA Copy Number PortalCOL18A1
Somatic Mutations in Cancer : COSMICCOL18A1 
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch COL18A1
DgiDB (Drug Gene Interaction Database)COL18A1
DoCM (Curated mutations)COL18A1 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)COL18A1 (select a term)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] 
Diseases
DECIPHER (Syndromes)21:46875424-46933634
CONAN: Copy Number AnalysisCOL18A1 
Mutations and Diseases : HGMDCOL18A1
OMIM120328    267750   
MedgenCOL18A1
NextProtP39060 [Medical]
TSGene80781
GENETestsCOL18A1
Huge Navigator COL18A1 [HugePedia]  COL18A1 [HugeCancerGEM]
snp3D : Map Gene to Disease80781
BioCentury BCIQCOL18A1
General knowledge
Chemical/Protein Interactions : CTD80781
Chemical/Pharm GKB GenePA26711
Clinical trialCOL18A1
Other databases
Probes
Litterature
PubMed183 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineCOL18A1
GoPubMedCOL18A1
iHOPCOL18A1
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

Search in all EBI   NCBI

© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Sat Jan 16 18:22:48 CET 2016

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