Atlas of Genetics and Cytogenetics in Oncology and Haematology

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Taking over the Atlas
Dear Colleagues,
The Atlas, once more, is in great danger, and I will have to proceed to a collective economic lay-off of all the team involved in the Atlas before the begining of April 2015 (a foundation having suddenly withdrawn its commitment to support the Atlas). I ask you herein if any Scientific Society (a Society of Cytogenetics, of Clinical Genetics, of Hematology, or a Cancer Society, or any other...), any University and/or Hospital, any Charity, or any database would be interested in taking over the Atlas, in whole or in part. If taking charge of the whole lot is too big, a consortium of various actors could be the solution (I am myself trying to find partners). Could you please spread the information, contact the relevant authorities, and find partners.
Survival of the Atlas will be critically dependant upon your ability to find solutions (and urgently!).
Kind regards.
Jean-Loup Huret
Donations are also welcome

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VCL (vinculin)

Identity

Other namesCMD1W
CMH15
HEL114
MV
MVCL
HGNC (Hugo) VCL
LocusID (NCBI) 7414
Location 10q22.2
Location_base_pair Starts at 75757872 and ends at 75879914 bp from pter ( according to hg19-Feb_2009)
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

 

Other Leukemias implicated (Data extracted from papers in the Atlas)

Leukemias 11q23ChildAMLID1615

External links

Nomenclature
HGNC (Hugo)VCL   12665
Cards
Entrez_Gene (NCBI)VCL  7414  vinculin
GeneCards (Weizmann)VCL
Ensembl hg19 (Hinxton)ENSG00000035403 [Gene_View]  chr10:75757872-75879914 [Contig_View]  VCL [Vega]
Ensembl hg38 (Hinxton)ENSG00000035403 [Gene_View]  chr10:75757872-75879914 [Contig_View]  VCL [Vega]
ICGC DataPortalENSG00000035403
cBioPortalVCL
AceView (NCBI)VCL
Genatlas (Paris)VCL
WikiGenes7414
SOURCE (Princeton)VCL
Genomic and cartography
GoldenPath hg19 (UCSC)VCL  -     chr10:75757872-75879914 +  10q22.2   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)VCL  -     10q22.2   [Description]    (hg38-Dec_2013)
EnsemblVCL - 10q22.2 [CytoView hg19]  VCL - 10q22.2 [CytoView hg38]
Mapping of homologs : NCBIVCL [Mapview hg19]  VCL [Mapview hg38]
OMIM193065   611407   613255   
Gene and transcription
Genbank (Entrez)AA368699 AI290052 AK126978 AK296509 AK300280
RefSeq transcript (Entrez)NM_003373 NM_014000
RefSeq genomic (Entrez)AC_000142 NC_000010 NC_018921 NG_008868 NT_030059 NW_001837987 NW_004929376
Consensus coding sequences : CCDS (NCBI)VCL
Cluster EST : UnigeneHs.643896 [ NCBI ]
CGAP (NCI)Hs.643896
Alternative Splicing : Fast-db (Paris)GSHG0003457
Alternative Splicing GalleryENSG00000035403
Gene ExpressionVCL [ NCBI-GEO ]     VCL [ SEEK ]   VCL [ MEM ]
SOURCE (Princeton)Expression in : [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
Protein : pattern, domain, 3D structure
UniProt/SwissProtP18206 (Uniprot)
NextProtP18206  [Medical]
With graphics : InterProP18206
Splice isoforms : SwissVarP18206 (Swissvar)
Domaine pattern : Prosite (Expaxy)VINCULIN_1 (PS00663)    VINCULIN_2 (PS00664)   
Domains : Interpro (EBI)Vinculin    Vinculin/catenin    Vinculin_CS   
Related proteins : CluSTrP18206
Domain families : Pfam (Sanger)Vinculin (PF01044)   
Domain families : Pfam (NCBI)pfam01044   
DMDM Disease mutations7414
Blocks (Seattle)P18206
PDB (SRS)1RKC    1RKE    1SYQ    1TR2    1YDI    2GWW    2HSQ    2IBF    3H2U    3H2V    3MYI    3RF3    3S90    3TJ5    3TJ6    3VF0    4DJ9    4EHP   
PDB (PDBSum)1RKC    1RKE    1SYQ    1TR2    1YDI    2GWW    2HSQ    2IBF    3H2U    3H2V    3MYI    3RF3    3S90    3TJ5    3TJ6    3VF0    4DJ9    4EHP   
PDB (IMB)1RKC    1RKE    1SYQ    1TR2    1YDI    2GWW    2HSQ    2IBF    3H2U    3H2V    3MYI    3RF3    3S90    3TJ5    3TJ6    3VF0    4DJ9    4EHP   
PDB (RSDB)1RKC    1RKE    1SYQ    1TR2    1YDI    2GWW    2HSQ    2IBF    3H2U    3H2V    3MYI    3RF3    3S90    3TJ5    3TJ6    3VF0    4DJ9    4EHP   
Human Protein AtlasENSG00000035403
Peptide AtlasP18206
HPRD01900
IPIIPI00307162   IPI00291175   IPI00384973   IPI00909711   IPI01011952   IPI00910496   IPI01014113   
Protein Interaction databases
DIP (DOE-UCLA)P18206
IntAct (EBI)P18206
FunCoupENSG00000035403
BioGRIDVCL
IntegromeDBVCL
STRING (EMBL)VCL
Ontologies - Pathways
QuickGOP18206
Ontology : AmiGOmorphogenesis of an epithelium  dystroglycan binding  platelet degranulation  actin binding  actin binding  structural molecule activity  protein binding  extracellular region  cytosol  cytoskeleton  plasma membrane  cell-cell junction  adherens junction  cell-cell adherens junction  fascia adherens  focal adhesion  focal adhesion  cellular component movement  muscle contraction  cell adhesion  cell-matrix adhesion  blood coagulation  beta-catenin binding  actin cytoskeleton  lamellipodium assembly  cell-substrate junction  platelet activation  negative regulation of cell migration  adherens junction assembly  protein localization to cell surface  costamere  costamere  protein complex  apical junction assembly  alpha-catenin binding  cadherin binding  extracellular vesicular exosome  epithelial cell-cell adhesion  
Ontology : EGO-EBImorphogenesis of an epithelium  dystroglycan binding  platelet degranulation  actin binding  actin binding  structural molecule activity  protein binding  extracellular region  cytosol  cytoskeleton  plasma membrane  cell-cell junction  adherens junction  cell-cell adherens junction  fascia adherens  focal adhesion  focal adhesion  cellular component movement  muscle contraction  cell adhesion  cell-matrix adhesion  blood coagulation  beta-catenin binding  actin cytoskeleton  lamellipodium assembly  cell-substrate junction  platelet activation  negative regulation of cell migration  adherens junction assembly  protein localization to cell surface  costamere  costamere  protein complex  apical junction assembly  alpha-catenin binding  cadherin binding  extracellular vesicular exosome  epithelial cell-cell adhesion  
Pathways : BIOCARTARho cell motility signaling pathway [Genes]    Integrin Signaling Pathway [Genes]    Cell to Cell Adhesion Signaling [Genes]   
Pathways : KEGGFocal adhesion    Adherens junction    Leukocyte transendothelial migration    Regulation of actin cytoskeleton    Bacterial invasion of epithelial cells    Shigellosis    Amoebiasis   
Protein Interaction DatabaseVCL
DoCM (Curated mutations)VCL
Wikipedia pathwaysVCL
Gene fusion - rearrangements
Rearrangement : COSMICVCL [10q22.2]  -  ALK [2p23.2]
Polymorphisms : SNP, variants
NCBI Variation ViewerVCL [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)VCL
dbVarVCL
ClinVarVCL
1000_GenomesVCL 
Exome Variant ServerVCL
SNP (GeneSNP Utah)VCL
SNP : HGBaseVCL
Genetic variants : HAPMAPVCL
Genomic Variants (DGV)VCL [DGVbeta]
Mutations
ICGC Data PortalENSG00000035403 
Somatic Mutations in Cancer : COSMICVCL 
CONAN: Copy Number AnalysisVCL 
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
LOVD (Leiden Open Variation Database)Zhejiang University Center for Genetic and Genomic Medicine (ZJU-CGGM)
LOVD (Leiden Open Variation Database)MSeqDR-LSDB Mitochondrial Disease Locus Specific Database
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] 
Diseases
DECIPHER (Syndromes)10:75757872-75879914
Mutations and Diseases : HGMDVCL
OMIM193065    611407    613255   
MedgenVCL
NextProtP18206 [Medical]
GENETestsVCL
Disease Genetic AssociationVCL
Huge Navigator VCL [HugePedia]  VCL [HugeCancerGEM]
snp3D : Map Gene to Disease7414
DGIdb (Drug Gene Interaction db)VCL
General knowledge
Homologs : HomoloGeneVCL
Homology/Alignments : Family Browser (UCSC)VCL
Phylogenetic Trees/Animal Genes : TreeFamVCL
Chemical/Protein Interactions : CTD7414
Chemical/Pharm GKB GenePA37288
Clinical trialVCL
Cancer Resource (Charite)ENSG00000035403
Other databases
Probes
Litterature
PubMed145 Pubmed reference(s) in Entrez
CoreMineVCL
GoPubMedVCL
iHOPVCL
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

Search in all EBI   NCBI

Contributor(s)

Written09-2002Dessen P, Le Minor S
Updated12-2014Dessen P

© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Sat Feb 14 19:19:56 CET 2015
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For comments and suggestions or contributions, please contact us

jlhuret@AtlasGeneticsOncology.org.