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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economic lay-off of all the team involved in the Atlas before the begining of April 2015 (a foundation having suddenly withdrawn its commitment to support the Atlas).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 jlhuret@AtlasGeneticsOncology.org
Donations are also welcome
If each casual visitor gives 3 Euros or Dollars, the Atlas is saved in a week !
If each professional gives 100 Euros or Dollars once a year (now), the Atlas is saved in 2 weeks !
Don't let the Atlas imminent demise
Note: we send fiscal receipts for donations equal or above 50 Euros or Dollars

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RAPGEF6 (Rap guanine nucleotide exchange factor (GEF) 6)

Identity

Other namesKIA001LB
PDZ-GEF2
PDZGEF2
RA-GEF-2
RAGEF2
HGNC (Hugo) RAPGEF6
LocusID (NCBI) 51735
Location 5q31.1
Location_base_pair Starts at 130759614 and ends at 130970929 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

 

External links

Nomenclature
HGNC (Hugo)RAPGEF6   20655
Cards
Entrez_Gene (NCBI)RAPGEF6  51735  Rap guanine nucleotide exchange factor (GEF) 6
GeneCards (Weizmann)RAPGEF6
Ensembl hg19 (Hinxton)ENSG00000158987 [Gene_View]  chr5:130759614-130970929 [Contig_View]  RAPGEF6 [Vega]
Ensembl hg38 (Hinxton)ENSG00000158987 [Gene_View]  chr5:130759614-130970929 [Contig_View]  RAPGEF6 [Vega]
ICGC DataPortalENSG00000158987
cBioPortalRAPGEF6
AceView (NCBI)RAPGEF6
Genatlas (Paris)RAPGEF6
WikiGenes51735
SOURCE (Princeton)RAPGEF6
Genomic and cartography
GoldenPath hg19 (UCSC)RAPGEF6  -     chr5:130759614-130970929 -  5q31.1   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)RAPGEF6  -     5q31.1   [Description]    (hg38-Dec_2013)
EnsemblRAPGEF6 - 5q31.1 [CytoView hg19]  RAPGEF6 - 5q31.1 [CytoView hg38]
Mapping of homologs : NCBIRAPGEF6 [Mapview hg19]  RAPGEF6 [Mapview hg38]
OMIM610499   
Gene and transcription
Genbank (Entrez)AF085846 AF394782 AF478468 AF478469 AF478567
RefSeq transcript (Entrez)NM_001164386 NM_001164387 NM_001164388 NM_001164389 NM_001164390 NM_016340
RefSeq genomic (Entrez)NC_000005 NC_018916 NT_034772 NW_004929323
Consensus coding sequences : CCDS (NCBI)RAPGEF6
Cluster EST : UnigeneHs.483329 [ NCBI ]
CGAP (NCI)Hs.483329
Alternative Splicing : Fast-db (Paris)GSHG0025041
Alternative Splicing GalleryENSG00000158987
Gene ExpressionRAPGEF6 [ NCBI-GEO ]     RAPGEF6 [ SEEK ]   RAPGEF6 [ MEM ]
SOURCE (Princeton)Expression in : [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ8TEU7 (Uniprot)
NextProtQ8TEU7  [Medical]
With graphics : InterProQ8TEU7
Splice isoforms : SwissVarQ8TEU7 (Swissvar)
Domaine pattern : Prosite (Expaxy)CNMP_BINDING_3 (PS50042)    PDZ (PS50106)    RA (PS50200)    RASGEF_CAT (PS50009)    RASGEF_NTER (PS50212)   
Domains : Interpro (EBI)cNMP-bd-like    cNMP-bd_dom    PDZ    Ras-assoc    Ras-like_Gua-exchang_fac_N    Ras_GEF_dom    RASGEF_cat_dom    RmlC-like_jellyroll   
Related proteins : CluSTrQ8TEU7
Domain families : Pfam (Sanger)cNMP_binding (PF00027)    PDZ (PF00595)    RA (PF00788)    RasGEF (PF00617)    RasGEF_N (PF00618)   
Domain families : Pfam (NCBI)pfam00027    pfam00595    pfam00788    pfam00617    pfam00618   
Domain families : Smart (EMBL)cNMP (SM00100)  PDZ (SM00228)  RA (SM00314)  RasGEF (SM00147)  RasGEFN (SM00229)  
DMDM Disease mutations51735
Blocks (Seattle)Q8TEU7
PDB (SRS)2D93    3LNY   
PDB (PDBSum)2D93    3LNY   
PDB (IMB)2D93    3LNY   
PDB (RSDB)2D93    3LNY   
Human Protein AtlasENSG00000158987
Peptide AtlasQ8TEU7
HPRD11483
IPIIPI00337694   IPI00291839   IPI00943807   IPI00337696   IPI00872771   IPI00968195   IPI00966410   IPI00966076   IPI00943887   IPI00968012   IPI00967155   
Protein Interaction databases
DIP (DOE-UCLA)Q8TEU7
IntAct (EBI)Q8TEU7
FunCoupENSG00000158987
BioGRIDRAPGEF6
IntegromeDBRAPGEF6
STRING (EMBL)RAPGEF6
Ontologies - Pathways
QuickGOQ8TEU7
Ontology : AmiGOguanyl-nucleotide exchange factor activity  protein binding  cytosol  plasma membrane  Ras protein signal transduction  apical plasma membrane  Ras GTPase binding  microvillus assembly  endocytic vesicle  GTP-dependent protein binding  regulation of GTPase activity  positive regulation of GTPase activity  phosphatidic acid binding  protein localization to plasma membrane  establishment of endothelial intestinal barrier  
Ontology : EGO-EBIguanyl-nucleotide exchange factor activity  protein binding  cytosol  plasma membrane  Ras protein signal transduction  apical plasma membrane  Ras GTPase binding  microvillus assembly  endocytic vesicle  GTP-dependent protein binding  regulation of GTPase activity  positive regulation of GTPase activity  phosphatidic acid binding  protein localization to plasma membrane  establishment of endothelial intestinal barrier  
Pathways : KEGGRap1 signaling pathway   
Protein Interaction DatabaseRAPGEF6
DoCM (Curated mutations)RAPGEF6
Wikipedia pathwaysRAPGEF6
Gene fusion - rearrangements
Polymorphisms : SNP, variants
NCBI Variation ViewerRAPGEF6 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)RAPGEF6
dbVarRAPGEF6
ClinVarRAPGEF6
1000_GenomesRAPGEF6 
Exome Variant ServerRAPGEF6
SNP (GeneSNP Utah)RAPGEF6
SNP : HGBaseRAPGEF6
Genetic variants : HAPMAPRAPGEF6
Genomic Variants (DGV)RAPGEF6 [DGVbeta]
Mutations
ICGC Data PortalENSG00000158987 
Somatic Mutations in Cancer : COSMICRAPGEF6 
CONAN: Copy Number AnalysisRAPGEF6 
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
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] 
Diseases
DECIPHER (Syndromes)5:130759614-130970929
Mutations and Diseases : HGMDRAPGEF6
OMIM610499   
MedgenRAPGEF6
NextProtQ8TEU7 [Medical]
GENETestsRAPGEF6
Disease Genetic AssociationRAPGEF6
Huge Navigator RAPGEF6 [HugePedia]  RAPGEF6 [HugeCancerGEM]
snp3D : Map Gene to Disease51735
DGIdb (Drug Gene Interaction db)RAPGEF6
General knowledge
Homologs : HomoloGeneRAPGEF6
Homology/Alignments : Family Browser (UCSC)RAPGEF6
Phylogenetic Trees/Animal Genes : TreeFamRAPGEF6
Chemical/Protein Interactions : CTD51735
Chemical/Pharm GKB GenePA134885793
Clinical trialRAPGEF6
Cancer Resource (Charite)ENSG00000158987
Other databases
Probes
Litterature
PubMed25 Pubmed reference(s) in Entrez
CoreMineRAPGEF6
GoPubMedRAPGEF6
iHOPRAPGEF6
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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Contributor(s)

Written09-2002Dessen P, Le Minor S
Updated02-2015Dessen P

© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Sat Mar 28 17:05:57 CET 2015

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For comments and suggestions or contributions, please contact us

jlhuret@AtlasGeneticsOncology.org.