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RAP1B (RAP1B, member of RAS oncogene family)

Written2001-05Jean de Gunzburg
Laboratoire de Signalisation Intracellulaire et Oncogenöse INSERM U-528 Institut Curie Section de Recherche 26, rue d'Ulm, 75248 Paris Cedex 05, France

(Note : for Links provided by Atlas : click)

Identity

HGNC (Hugo) RAP1B
LocusID (NCBI) 5908
Atlas_Id 273
Location 12q15  [Link to chromosome band 12q15]
Location_base_pair Starts at 69004619 and ends at 69054385 bp from pter ( according to hg19-Feb_2009)  [Mapping RAP1B.png]
Fusion genes
(updated 2016)
LSM14B (20q13.33) / RAP1B (12q15)NUP107 (12q15) / RAP1B (12q15)PPM1H (12q14.1) / RAP1B (12q15)
RAP1B (12q15) / CPM (12q15)RAP1B (12q15) / CTDSP2 (12q14.1)RAP1B (12q15) / GLIPR1L1 (12q21.2)
RAP1B (12q15) / HUWE1 (Xp11.22)RAP1B (12q15) / TUBGCP3 (13q34)TLCD2 (17p13.3) / RAP1B (12q15)

DNA/RNA

 
Description The gene emcompasses 7 codinng exons covering 10779 bp on chromosome 12

Protein

Description Rap1 is a member of the Ras superfamily of monomeric GTPases, closely related to Ras. There are two isoforms, Rap1Aand Rap1B that share 95% identity and are encoded by two different genes. Rap1 proteins share 50% identity with Ras proteins, including the regions involved in GDP/GTP binding (hence Rap1A has very similar biochemical properties to Ras), C-terminal CAAX domain leading to prenylation (geranylgeranylation in the case of Rap1A), and effector region identical to that of Ras proteins causing Ras and Rap1 to share some potential effectors.
Expression ubiquitous ; highest in platelets and neutrophils
Localisation Rap1 is bound to membranes. In many cell types, it is found in a perinuclear compartment overlapping the Golgi. Rap1 proteins (A and B) are phosphorylated near the C-ter by cAMP-dependent protein kinase. This results in translocation of part of the Rap1 pool to the cytosol.
Function The function of Rap1 is still a matter of debate. Its overexpression is able to compete with the activation of Raf-1 by active Ras. Active Rap1B has been shown to activate the B-Raf kinase and the MEK-ERK cascade. In several cellular models, Rap1 has been shown to be involved in the regulation of integrin-mediated cell adhesion.
Homology 98% identical to Rap1A, 60% identical to Rap2 , 50 % to Ras proteins

Mutations

Germinal unknown

Implicated in

Note
Entity no implication in pathologies characterized so far
  

To be noted

see also RAP family

Bibliography

Rap1 signalling: adhering to new models.
Bos JL, de Rooij J, Reedquist KA
Nature reviews. Molecular cell biology. 2001 ; 2 (5) : 369-377.
PMID 11331911
 

Citation

This paper should be referenced as such :
Gunzburg, J de
RAP1B (RAP1B, member of RAS oncogene family)
Atlas Genet Cytogenet Oncol Haematol. 2001;5(3):174-175.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/RAP1BID273.html


Other Leukemias implicated (Data extracted from papers in the Atlas) [ 2 ]
  t(4;11)(q21;p15) NUP98/RAP1GDS1
t(4;11)(q23;p15) NUP98/RAP1GDS1

External links

Nomenclature
HGNC (Hugo)RAP1B   9857
Cards
AtlasRAP1BID273
Entrez_Gene (NCBI)RAP1B  5908  RAP1B, member of RAS oncogene family
AliasesK-REV; RAL1B
GeneCards (Weizmann)RAP1B
Ensembl hg19 (Hinxton)ENSG00000127314 [Gene_View]  chr12:69004619-69054385 [Contig_View]  RAP1B [Vega]
Ensembl hg38 (Hinxton)ENSG00000127314 [Gene_View]  chr12:69004619-69054385 [Contig_View]  RAP1B [Vega]
ICGC DataPortalENSG00000127314
TCGA cBioPortalRAP1B
AceView (NCBI)RAP1B
Genatlas (Paris)RAP1B
WikiGenes5908
SOURCE (Princeton)RAP1B
Genomic and cartography
GoldenPath hg19 (UCSC)RAP1B  -     chr12:69004619-69054385 +  12q14   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)RAP1B  -     12q14   [Description]    (hg38-Dec_2013)
EnsemblRAP1B - 12q14 [CytoView hg19]  RAP1B - 12q14 [CytoView hg38]
Mapping of homologs : NCBIRAP1B [Mapview hg19]  RAP1B [Mapview hg38]
OMIM179530   
Gene and transcription
Genbank (Entrez)AA809981 AB062128 AF279894 AF493913 AJ420497
RefSeq transcript (Entrez)NM_001010942 NM_001251917 NM_001251918 NM_001251921 NM_001251922 NM_015646
RefSeq genomic (Entrez)NC_000012 NC_018923 NT_029419 NW_004929384
Consensus coding sequences : CCDS (NCBI)RAP1B
Cluster EST : UnigeneHs.369920 [ NCBI ]
CGAP (NCI)Hs.369920
Alternative Splicing GalleryENSG00000127314
Gene ExpressionRAP1B [ NCBI-GEO ]   RAP1B [ EBI - ARRAY_EXPRESS ]   RAP1B [ SEEK ]   RAP1B [ MEM ]
Gene Expression Viewer (FireBrowse)RAP1B [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)5908
GTEX Portal (Tissue expression)RAP1B
Protein : pattern, domain, 3D structure
UniProt/SwissProtP61224 (Uniprot)
NextProtP61224  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP61224
Splice isoforms : SwissVarP61224 (Swissvar)
PhosPhoSitePlusP61224
Domaine pattern : Prosite (Expaxy)RAS (PS51421)   
Domains : Interpro (EBI)P-loop_NTPase    Small_GTP-bd_dom    Small_GTPase    Small_GTPase_Ras   
Domain families : Pfam (Sanger)Ras (PF00071)   
Domain families : Pfam (NCBI)pfam00071   
Domain families : Smart (EMBL)RAS (SM00173)  
DMDM Disease mutations5908
Blocks (Seattle)RAP1B
PDB (SRS)3BRW    3CF6    4DXA    4HDO    4HDQ    4M8N    4MGI    4MGK    4MGY    4MGZ    4MH0   
PDB (PDBSum)3BRW    3CF6    4DXA    4HDO    4HDQ    4M8N    4MGI    4MGK    4MGY    4MGZ    4MH0   
PDB (IMB)3BRW    3CF6    4DXA    4HDO    4HDQ    4M8N    4MGI    4MGK    4MGY    4MGZ    4MH0   
PDB (RSDB)3BRW    3CF6    4DXA    4HDO    4HDQ    4M8N    4MGI    4MGK    4MGY    4MGZ    4MH0   
Structural Biology KnowledgeBase3BRW    3CF6    4DXA    4HDO    4HDQ    4M8N    4MGI    4MGK    4MGY    4MGZ    4MH0   
SCOP (Structural Classification of Proteins)3BRW    3CF6    4DXA    4HDO    4HDQ    4M8N    4MGI    4MGK    4MGY    4MGZ    4MH0   
CATH (Classification of proteins structures)3BRW    3CF6    4DXA    4HDO    4HDQ    4M8N    4MGI    4MGK    4MGY    4MGZ    4MH0   
SuperfamilyP61224
Human Protein AtlasENSG00000127314
Peptide AtlasP61224
HPRD01546
IPIIPI00015148   IPI00816182   IPI00796349   IPI01009583   IPI00941942   IPI01012401   IPI01011985   IPI01015962   IPI01013827   IPI01026172   IPI01013357   IPI00745127   IPI01016056   IPI01014435   IPI00908754   IPI01009293   IPI01012426   IPI01011891   IPI01014236   IPI01013855   IPI01013329   IPI01012887   
Protein Interaction databases
DIP (DOE-UCLA)P61224
IntAct (EBI)P61224
FunCoupENSG00000127314
BioGRIDRAP1B
STRING (EMBL)RAP1B
ZODIACRAP1B
Ontologies - Pathways
QuickGOP61224
Ontology : AmiGOGTPase activity  protein binding  GTP binding  intracellular  lipid particle  cytosol  plasma membrane  cell-cell junction  intracellular protein transport  nucleocytoplasmic transport  metabolic process  membrane  GDP binding  microvillus assembly  protein complex binding  Rap protein signal transduction  membrane raft  establishment of endothelial barrier  extracellular exosome  cellular response to cAMP  regulation of cell junction assembly  regulation of establishment of cell polarity  
Ontology : EGO-EBIGTPase activity  protein binding  GTP binding  intracellular  lipid particle  cytosol  plasma membrane  cell-cell junction  intracellular protein transport  nucleocytoplasmic transport  metabolic process  membrane  GDP binding  microvillus assembly  protein complex binding  Rap protein signal transduction  membrane raft  establishment of endothelial barrier  extracellular exosome  cellular response to cAMP  regulation of cell junction assembly  regulation of establishment of cell polarity  
Pathways : BIOCARTASignaling of Hepatocyte Growth Factor Receptor [Genes]    Eph Kinases and ephrins support platelet aggregation [Genes]   
Pathways : KEGGMAPK signaling pathway    Ras signaling pathway    Rap1 signaling pathway    Chemokine signaling pathway    Focal adhesion    Leukocyte transendothelial migration    Long-term potentiation    Neurotrophin signaling pathway    Pancreatic secretion    Renal cell carcinoma   
REACTOMEP61224 [protein]
REACTOME PathwaysR-HSA-392517 Rap1 signalling [pathway]
REACTOME PathwaysR-HSA-5674135 MAP2K and MAPK activation [pathway]
REACTOME PathwaysR-HSA-372708 p130Cas linkage to MAPK signaling for integrins [pathway]
REACTOME PathwaysR-HSA-354192 Integrin alphaIIb beta3 signaling [pathway]
REACTOME PathwaysR-HSA-354194 GRB2:SOS provides linkage to MAPK signaling for Integrins [pathway]
NDEx Network
Atlas of Cancer Signalling NetworkRAP1B
Wikipedia pathwaysRAP1B
Orthology - Evolution
OrthoDB5908
GeneTree (enSembl)ENSG00000127314
Phylogenetic Trees/Animal Genes : TreeFamRAP1B
Homologs : HomoloGeneRAP1B
Homology/Alignments : Family Browser (UCSC)RAP1B
Gene fusions - Rearrangements
Fusion : MitelmanPPM1H/RAP1B [12q14.1/12q15]  [t(12;12)(q14;q15)]  
Fusion : MitelmanRAP1B/CTDSP2 [12q15/12q14.1]  [t(12;12)(q14;q15)]  
Fusion : MitelmanRAP1B/GLIPR1L1 [12q15/12q21.2]  [t(12;12)(q15;q21)]  
Fusion: TCGARAP1B 12q15 CPM 12q15 GBM
Fusion: TCGARAP1B 12q15 CTDSP2 12q14.1 GBM
Fusion: TCGARAP1B 12q15 GLIPR1L1 12q21.2 BRCA
Polymorphisms : SNP, variants
NCBI Variation ViewerRAP1B [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)RAP1B
dbVarRAP1B
ClinVarRAP1B
1000_GenomesRAP1B 
Exome Variant ServerRAP1B
ExAC (Exome Aggregation Consortium)RAP1B (select the gene name)
Genetic variants : HAPMAP5908
Genomic Variants (DGV)RAP1B [DGVbeta]
Mutations
ICGC Data PortalRAP1B 
TCGA Data PortalRAP1B 
Broad Tumor PortalRAP1B
OASIS PortalRAP1B [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICRAP1B 
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 RAP1B
DgiDB (Drug Gene Interaction Database)RAP1B
DoCM (Curated mutations)RAP1B (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)RAP1B (select a term)
intoGenRAP1B
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] 
Diseases
DECIPHER (Syndromes)12:69004619-69054385  ENSG00000127314
CONAN: Copy Number AnalysisRAP1B 
Mutations and Diseases : HGMDRAP1B
OMIM179530   
MedgenRAP1B
Genetic Testing Registry RAP1B
NextProtP61224 [Medical]
TSGene5908
GENETestsRAP1B
Huge Navigator RAP1B [HugePedia]
snp3D : Map Gene to Disease5908
BioCentury BCIQRAP1B
ClinGenRAP1B
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD5908
Chemical/Pharm GKB GenePA34219
Clinical trialRAP1B
Miscellaneous
canSAR (ICR)RAP1B (select the gene name)
Probes
Litterature
PubMed78 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineRAP1B
EVEXRAP1B
GoPubMedRAP1B
iHOPRAP1B
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Sat Jun 11 12:58:54 CEST 2016

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