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NET1 (neuroepithelial cell transforming gene 1)

Written2008-04David Murray, Peter Doran
UCD School of Medicine, Medical Sciences, UCD-Mater Clinical Research Centre, Mater Misericordiae University Hospital, Dublin 7, Ireland

(Note : for Links provided by Atlas : click)

Identity

Alias_symbol (synonym)ARHGEF8
NET1A
Other aliasNAT1
SLC6A2
HGNC (Hugo) NET1
LocusID (NCBI) 10276
Atlas_Id 41526
Location 10p15.1  [Link to chromosome band 10p15]
Location_base_pair Starts at 5412551 and ends at 5459056 bp from pter ( according to hg19-Feb_2009)  [Mapping NET1.png]
Local_order The NET1 gene is located on chromosome 10 in a 11832 bp sequence (5478574 to 5490426).
Fusion genes
(updated 2017)
Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
FAM208B (10p15.1) / NET1 (10p15.1)NET1 (10p15.1) / ATRN (20p13)

DNA/RNA

Description This gene, found on chromosome 10 at location 10p15 (5,444,518-5,490,401) encompasses 11832bp of genomic DNA. The gene has 10 exons and the mRNA transcript is 3414 nucleotides in length.

Protein

Description The protein encoded by this gene acts as guanine nucleotide exchange factor (gef) for RhoA gtpase . This gene encodes for a protein of 596 amino acids with a molecular weight of 67.74 kDa.
The protein contains the following domains : a Rho guanine nucleotide exchange factor (RhoGEF) activity domain from amino acid 178 - 355 and a pleckstrin homology domain from amino acid 387 - 503.
The 596 amino acid sequence is :
1 mepelaaqkq prprrrsrra sglstegatg psadtsgsel dgrcslrrgs sftfltpgpn
61 wdftlkrkrr ekdddvvsls sldlkepsnk rvrplarvts lanlispvrn gavrrfgqti
121 qsftlrgdhr spasaqkfss rstvptpakr rssalwseml ditmkesltt reirrqeaiy
181 emsrgeqdli edlklarkay hdpmlklsim seeelthifg dldsyiplhe dlltrigeat
241 kpdgtveqig hilvswlprl nayrgycsnq laakalldqk kqdprvqdfl qrclespfsr
301 kldlwsfldi prsrlvkypl llkeilkhtp kehpdvqlle dailiiqgvl sdinlkkges
361 ecqyyidkle yldekqrdpr ieaskvllch gelrsksghk lyiflfqdil vltrpvtrne
421 rhsyqvyrqp ipvqelvled lqdgdvrmgg sfrgafsnse kaknifrirf hdpspaqsht
481 lqandvfhkq qwfnciraai apfqsagspp elqglpelhe ecegnhpsar kltaqrrast
541 vssvtqvevd enayrcgsgm qmaedskslk thqtqpgirr ardkalsggk rketlv
Expression This protein is widely expressed in mammalian tissue.
Localisation It is localized to both the cytoplasm and the nucleus.
Function Acts as guanine nucleotide exchange factor (GEF) for RhoA GTPase.
Homology Holomogy with Pan troglodytes (97%); Canis lupus familiaris (92%); Mus musculus (93%), Rattus norvegicus (92%), Gallus gallus (88%).

Mutations

Note NET1 is subject to the following misense mutations :







Source ID:rs34821922rs34658946rs34821949
Wild type nucleotide:ATA
Wild type amino acid: KIK
Variant nucleotide:GCG
Variant amino acid: RTE
Amino Acid Position:28363466

Implicated in

Note
  
Entity Gastric Cancer
Disease Gastric or stomach cancer is a malignant epithelial malignancy of the stomach mucosa. The vast majority of gastric carcinomas are adenocarcinomas, arising from the gastric glandular epithelium.
Prognosis Prognosis depends on the stage of the cancer. Because most stomach cancers are at an advanced stage upon diagnosis, the average 5 years survival rate is 12%. This is often due to the fact that the tumor has spread beyond the primary site.
Oncogenesis NET1 has been shown to be up-regulated in Gastric Cancer (Leyden J et al., 2006). NET1 is a GEF exchange factor for Rho GTPase proteins (Alberts AS et al., 1998) and is therefore implicated in Rho-mediated processes such as cytoskeletal organization and cell migration. NET1 has been shown to drive gastric tumor cell invasion (Leyden J et al., 2006). It is this aggressive phenotype of the disease that accounts for the dismal prognosis as the majority of gastric tumors are at an advanced stage upon diagnosis where they have spread beyond the primary site.
  

Bibliography

PAK1 negatively regulates the activity of the Rho exchange factor NET1.
Alberts AS, Qin H, Carr HS, Frost JA.
J Biol Chem. 2005 Apr 1;280(13):12152-61.
PMID 15684429
 
Isolation of a novel oncogene, NET1, from neuroepithelioma cells by expression cDNA cloning.
Chan AM, Takai S, Yamada K, Miki T.
Oncogene. 1996 Mar 21;12(6):1259-66.
PMID 8649828
 
Identification of mNET1 as a candidate ligand for the first PDZ domain of MAGI-1.
Dobrosotskaya IY.
Biochem Biophys Res Commun. 2001 May 18;283(4):969-75.
PMID 11350080
 
The nuclear RhoA exchange factor Net1 interacts with proteins of the Dlg family, affects their localization, and influences their tumor suppressor activity.
Garcia-Mata R, Dubash AD, Sharek L, Carr HS, Frost JA, Burridge K.
Mol Cell Biol. 2007 Dec;27(24):8683-97.
PMID 17938206
 
Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes.
Kimura K, Wakamatsu A, Suzuki Y, Ota T, Nishikawa T, Yamashita R, Yamamoto J, Sekine M, Tsuritani K, Wakaguri H, Ishii S, Sugiyama T, Saito K, Isono Y, Irie R, Kushida N, Yoneyama T, Otsuka R, Kanda K, Yokoi T, Kondo H, Wagatsuma M, Murakawa, K, Ishida S, Ishibashi T, Takahashi-Fujii A, Tanase T, Nagai K, Kikuchi H, Nakai K, Isogai T, Sugano S.
Genome Res. 2006 Jan;16(1):55-65.
PMID 16344560
 
Net1 and Myeov: computationally identified mediators of gastric cancer.
Leyden J, Murray D, Moss A, Arumuguma M, Doyle E, McEntee G, O'Keane C, Doran P, MacMathuna P.
Br J Cancer. 2006 Apr 24;94(8):1204-12.
PMID 16552434
 
Characterization of the biochemical and transforming properties of the neuroepithelial transforming protein 1.
Qin H, Carr HS, Wu X, Muallem D, Tran NH, Frost JA.
J Biol Chem. 2005 Mar 4;280(9):7603-13.
PMID 15611121
 
The activity of guanine exchange factor NET1 is essential for transforming growth factor-beta-mediated stress fiber formation.
Shen X, Li J, Hu PP, Waddell D, Zhang J, Wang XF.
J Biol Chem. 2001 May 4;276(18):15362-8.
PMID 11278519
 

Citation

This paper should be referenced as such :
Murray, D ; Doran, P
NET1 (neuroepithelial cell transforming gene 1)
Atlas Genet Cytogenet Oncol Haematol. 2009;13(3):213-214.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/NET1ID41526ch10p15.html


External links

Nomenclature
HGNC (Hugo)NET1   14592
Cards
AtlasNET1ID41526ch10p15
Entrez_Gene (NCBI)NET1  10276  neuroepithelial cell transforming 1
AliasesARHGEF8; NET1A
GeneCards (Weizmann)NET1
Ensembl hg19 (Hinxton)ENSG00000173848 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000173848 [Gene_View]  chr10:5412551-5459056 [Contig_View]  NET1 [Vega]
ICGC DataPortalENSG00000173848
TCGA cBioPortalNET1
AceView (NCBI)NET1
Genatlas (Paris)NET1
WikiGenes10276
SOURCE (Princeton)NET1
Genetics Home Reference (NIH)NET1
Genomic and cartography
GoldenPath hg38 (UCSC)NET1  -     chr10:5412551-5459056 +  10p15.1   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)NET1  -     10p15.1   [Description]    (hg19-Feb_2009)
EnsemblNET1 - 10p15.1 [CytoView hg19]  NET1 - 10p15.1 [CytoView hg38]
Mapping of homologs : NCBINET1 [Mapview hg19]  NET1 [Mapview hg38]
OMIM606450   
Gene and transcription
Genbank (Entrez)AB209852 AJ010046 AK024919 AK294244 AK299335
RefSeq transcript (Entrez)NM_001047160 NM_005863
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)NET1
Cluster EST : UnigeneHs.25155 [ NCBI ]
CGAP (NCI)Hs.25155
Alternative Splicing GalleryENSG00000173848
Gene ExpressionNET1 [ NCBI-GEO ]   NET1 [ EBI - ARRAY_EXPRESS ]   NET1 [ SEEK ]   NET1 [ MEM ]
Gene Expression Viewer (FireBrowse)NET1 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)10276
GTEX Portal (Tissue expression)NET1
Human Protein AtlasENSG00000173848-NET1 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ7Z628   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ7Z628  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ7Z628
Splice isoforms : SwissVarQ7Z628
PhosPhoSitePlusQ7Z628
Domaine pattern : Prosite (Expaxy)DH_1 (PS00741)    DH_2 (PS50010)    PH_DOMAIN (PS50003)   
Domains : Interpro (EBI)DH-domain    GDS_CDC24_CS    PH_dom-like    PH_domain   
Domain families : Pfam (Sanger)PH (PF00169)    RhoGEF (PF00621)   
Domain families : Pfam (NCBI)pfam00169    pfam00621   
Domain families : Smart (EMBL)PH (SM00233)  RhoGEF (SM00325)  
Conserved Domain (NCBI)NET1
DMDM Disease mutations10276
Blocks (Seattle)NET1
PDB (SRS)3EO2    4XH9   
PDB (PDBSum)3EO2    4XH9   
PDB (IMB)3EO2    4XH9   
PDB (RSDB)3EO2    4XH9   
Structural Biology KnowledgeBase3EO2    4XH9   
SCOP (Structural Classification of Proteins)3EO2    4XH9   
CATH (Classification of proteins structures)3EO2    4XH9   
SuperfamilyQ7Z628
Human Protein Atlas [tissue]ENSG00000173848-NET1 [tissue]
Peptide AtlasQ7Z628
HPRD07342
IPIIPI00385312   IPI00180559   IPI01013865   IPI00513813   
Protein Interaction databases
DIP (DOE-UCLA)Q7Z628
IntAct (EBI)Q7Z628
FunCoupENSG00000173848
BioGRIDNET1
STRING (EMBL)NET1
ZODIACNET1
Ontologies - Pathways
QuickGOQ7Z628
Ontology : AmiGOregulation of cell growth  guanyl-nucleotide exchange factor activity  Rho guanyl-nucleotide exchange factor activity  protein binding  nucleus  cytosol  plasma membrane  signal transduction  GTP-Rho binding  regulation of Rho protein signal transduction  intracellular signal transduction  positive regulation of apoptotic process  positive regulation of apoptotic process  positive regulation of GTPase activity  regulation of small GTPase mediated signal transduction  myoblast migration  cellular response to hydrogen peroxide  cellular response to ionizing radiation  positive regulation of substrate adhesion-dependent cell spreading  
Ontology : EGO-EBIregulation of cell growth  guanyl-nucleotide exchange factor activity  Rho guanyl-nucleotide exchange factor activity  protein binding  nucleus  cytosol  plasma membrane  signal transduction  GTP-Rho binding  regulation of Rho protein signal transduction  intracellular signal transduction  positive regulation of apoptotic process  positive regulation of apoptotic process  positive regulation of GTPase activity  regulation of small GTPase mediated signal transduction  myoblast migration  cellular response to hydrogen peroxide  cellular response to ionizing radiation  positive regulation of substrate adhesion-dependent cell spreading  
REACTOMEQ7Z628 [protein]
REACTOME PathwaysR-HSA-416482 [pathway]   
NDEx NetworkNET1
Atlas of Cancer Signalling NetworkNET1
Wikipedia pathwaysNET1
Orthology - Evolution
OrthoDB10276
GeneTree (enSembl)ENSG00000173848
Phylogenetic Trees/Animal Genes : TreeFamNET1
HOVERGENQ7Z628
HOGENOMQ7Z628
Homologs : HomoloGeneNET1
Homology/Alignments : Family Browser (UCSC)NET1
Gene fusions - Rearrangements
Fusion : MitelmanFAM208B/NET1 [10p15.1/10p15.1]  [t(10;10)(p15;p15)]  
Fusion: TCGA_MDACCC10orf18 NET1 10p15.1 BRCA
Tumor Fusion PortalNET1
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerNET1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)NET1
dbVarNET1
ClinVarNET1
1000_GenomesNET1 
Exome Variant ServerNET1
ExAC (Exome Aggregation Consortium)ENSG00000173848
GNOMAD BrowserENSG00000173848
Genetic variants : HAPMAP10276
Genomic Variants (DGV)NET1 [DGVbeta]
DECIPHERNET1 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisNET1 
Mutations
ICGC Data PortalNET1 
TCGA Data PortalNET1 
Broad Tumor PortalNET1
OASIS PortalNET1 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICNET1  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDNET1
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 NET1
DgiDB (Drug Gene Interaction Database)NET1
DoCM (Curated mutations)NET1 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)NET1 (select a term)
intoGenNET1
NCG5 (London)NET1
Cancer3DNET1(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM606450   
Orphanet
DisGeNETNET1
MedgenNET1
Genetic Testing Registry NET1
NextProtQ7Z628 [Medical]
TSGene10276
GENETestsNET1
Target ValidationNET1
Huge Navigator NET1 [HugePedia]
snp3D : Map Gene to Disease10276
BioCentury BCIQNET1
ClinGenNET1
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD10276
Chemical/Pharm GKB GenePA164742175
Clinical trialNET1
Miscellaneous
canSAR (ICR)NET1 (select the gene name)
Probes
Litterature
PubMed50 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineNET1
EVEXNET1
GoPubMedNET1
iHOPNET1
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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