Atlas of Genetics and Cytogenetics in Oncology and Haematology

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RBFOX1 (RNA binding fox-1 homolog 1)

Identity

Alias_namesRNA binding protein
Alias_symbol (synonym)A2BP1
FOX-1
HRNBP1
Other alias2BP1
FOX1
HGNC (Hugo) RBFOX1
LocusID (NCBI) 54715
Atlas_Id 53438
Location 16p13.3  [Link to chromosome band 16p13]
Location_base_pair Starts at 7332750 and ends at 7713338 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2017)		Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
BRD8 (5q31.2) / RBFOX1 (16p13.3)CBX6 (22q13.1) / RBFOX1 (16p13.3)CRYL1 (13q12.11) / RBFOX1 (16p13.3)
CSDE1 (1p13.2) / RBFOX1 (16p13.3)DGKI (7q33) / RBFOX1 (16p13.3)HPS3 (3q24) / RBFOX1 (16p13.3)
MKL2 (16p13.12) / RBFOX1 (16p13.3)RBFOX1 (16p13.3) / SMYD3 (1q44)RBFOX1 (16p13.3) / SPG20 (13q13.3)
UBE2H (7q32.2) / RBFOX1 (16p13.3)VASN (16p13.3) / RBFOX1 (16p13.3)ZEB2 (2q22.3) / RBFOX1 (16p13.3)
CSDE1 1p13.2 / RBFOX1 16p13.3MKL2 16p13.12 / RBFOX1 16p13.3VASN 16p13.3 / RBFOX1 16p13.3

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

 

Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 3 ]
  t(1;16)(p13;p13) CSDE1/RBFOX1
MKL2/RBFOX1 (16p13)
VASN/RBFOX1 (16p13)

External links

Nomenclature
HGNC (Hugo)RBFOX1   18222
Cards
Entrez_Gene (NCBI)RBFOX1  54715  RNA binding fox-1 homolog 1
Aliases2BP1; A2BP1; FOX-1; FOX1; 
HRNBP1
GeneCards (Weizmann)RBFOX1
Ensembl hg19 (Hinxton)ENSG00000078328 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000078328 [Gene_View]  ENSG00000078328 [Sequence]  chr16:7332750-7713338 [Contig_View]  RBFOX1 [Vega]
ICGC DataPortalENSG00000078328
TCGA cBioPortalRBFOX1
AceView (NCBI)RBFOX1
Genatlas (Paris)RBFOX1
WikiGenes54715
SOURCE (Princeton)RBFOX1
Genetics Home Reference (NIH)RBFOX1
Genomic and cartography
GoldenPath hg38 (UCSC)RBFOX1  -     chr16:7332750-7713338 +  16p13.3   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)RBFOX1  -     16p13.3   [Description]    (hg19-Feb_2009)
EnsemblRBFOX1 - 16p13.3 [CytoView hg19]  RBFOX1 - 16p13.3 [CytoView hg38]
Mapping of homologs : NCBIRBFOX1 [Mapview hg19]  RBFOX1 [Mapview hg38]
OMIM605104   
Gene and transcription
Genbank (Entrez)AB208826 AF094849 AF107203 AF109106 AF229057
RefSeq transcript (Entrez)NM_001142333 NM_001142334 NM_001308117 NM_001364800 NM_018723 NM_145891 NM_145892 NM_145893
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)RBFOX1
Cluster EST : UnigeneHs.459842 [ NCBI ]
CGAP (NCI)Hs.459842
Alternative Splicing GalleryENSG00000078328
Gene ExpressionRBFOX1 [ NCBI-GEO ]   RBFOX1 [ EBI - ARRAY_EXPRESS ]   RBFOX1 [ SEEK ]   RBFOX1 [ MEM ]
Gene Expression Viewer (FireBrowse)RBFOX1 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)54715
GTEX Portal (Tissue expression)RBFOX1
Human Protein AtlasENSG00000078328-RBFOX1 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ9NWB1   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ9NWB1  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ9NWB1
Splice isoforms : SwissVarQ9NWB1
PhosPhoSitePlusQ9NWB1
Domaine pattern : Prosite (Expaxy)RRM (PS50102)   
Domains : Interpro (EBI)Fox-1_C_dom    FOX1_RRM    Nucleotide-bd_a/b_plait_sf    RBD_domain_sf    RNA-bd_Fox-1    RRM_dom   
Domain families : Pfam (Sanger)Fox-1_C (PF12414)    RRM_1 (PF00076)   
Domain families : Pfam (NCBI)pfam12414    pfam00076   
Domain families : Smart (EMBL)RRM (SM00360)  
Conserved Domain (NCBI)RBFOX1
DMDM Disease mutations54715
Blocks (Seattle)RBFOX1
PDB (RSDB)2ERR    2N82    4ZKA   
PDB Europe2ERR    2N82    4ZKA   
PDB (PDBSum)2ERR    2N82    4ZKA   
PDB (IMB)2ERR    2N82    4ZKA   
Structural Biology KnowledgeBase2ERR    2N82    4ZKA   
SCOP (Structural Classification of Proteins)2ERR    2N82    4ZKA   
CATH (Classification of proteins structures)2ERR    2N82    4ZKA   
SuperfamilyQ9NWB1
Human Protein Atlas [tissue]ENSG00000078328-RBFOX1 [tissue]
Peptide AtlasQ9NWB1
HPRD16091
IPIIPI01021020   IPI00170678   IPI01022902   IPI00170712   IPI00152050   IPI00922501   IPI00385553   IPI00910807   IPI01022127   IPI01022282   IPI01022463   IPI01023064   IPI00164146   
Protein Interaction databases
DIP (DOE-UCLA)Q9NWB1
IntAct (EBI)Q9NWB1
FunCoupENSG00000078328
BioGRIDRBFOX1
STRING (EMBL)RBFOX1
ZODIACRBFOX1
Ontologies - Pathways
QuickGOQ9NWB1
Ontology : AmiGOregulation of alternative mRNA splicing, via spliceosome  RNA binding  mRNA binding  protein binding  nucleus  cytoplasm  cytoplasm  trans-Golgi network  mRNA processing  nervous system development  protein C-terminus binding  RNA splicing  RNA transport  
Ontology : EGO-EBIregulation of alternative mRNA splicing, via spliceosome  RNA binding  mRNA binding  protein binding  nucleus  cytoplasm  cytoplasm  trans-Golgi network  mRNA processing  nervous system development  protein C-terminus binding  RNA splicing  RNA transport  
NDEx NetworkRBFOX1
Atlas of Cancer Signalling NetworkRBFOX1
Wikipedia pathwaysRBFOX1
Orthology - Evolution
OrthoDB54715
GeneTree (enSembl)ENSG00000078328
Phylogenetic Trees/Animal Genes : TreeFamRBFOX1
HOGENOMQ9NWB1
Homologs : HomoloGeneRBFOX1
Homology/Alignments : Family Browser (UCSC)RBFOX1
Gene fusions - Rearrangements
Fusion : MitelmanCSDE1/RBFOX1 [1p13.2/16p13.3]  [t(1;16)(p13;p13)]  
Fusion : MitelmanMKL2/RBFOX1 [16p13.12/16p13.3]  [t(16;16)(p13;p13)]  
Fusion : MitelmanVASN/RBFOX1 [16p13.3/16p13.3]  [t(16;16)(p13;p13)]  
Fusion PortalCSDE1 1p13.2 RBFOX1 16p13.3 OV
Fusion PortalMKL2 16p13.12 RBFOX1 16p13.3 OV
Fusion PortalVASN 16p13.3 RBFOX1 16p13.3 GBM
Fusion : QuiverRBFOX1
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerRBFOX1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)RBFOX1
dbVarRBFOX1
ClinVarRBFOX1
1000_GenomesRBFOX1 
Exome Variant ServerRBFOX1
ExAC (Exome Aggregation Consortium)ENSG00000078328
GNOMAD BrowserENSG00000078328
Varsome BrowserRBFOX1
Genetic variants : HAPMAP54715
Genomic Variants (DGV)RBFOX1 [DGVbeta]
DECIPHERRBFOX1 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisRBFOX1 
Mutations
ICGC Data PortalRBFOX1 
TCGA Data PortalRBFOX1 
Broad Tumor PortalRBFOX1
OASIS PortalRBFOX1 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICRBFOX1  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDRBFOX1
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 RBFOX1
DgiDB (Drug Gene Interaction Database)RBFOX1
DoCM (Curated mutations)RBFOX1 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)RBFOX1 (select a term)
intoGenRBFOX1
Cancer3DRBFOX1(select the gene name)
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM605104   
Orphanet
DisGeNETRBFOX1
MedgenRBFOX1
Genetic Testing Registry RBFOX1
NextProtQ9NWB1 [Medical]
TSGene54715
GENETestsRBFOX1
Target ValidationRBFOX1
Huge Navigator RBFOX1 [HugePedia]
snp3D : Map Gene to Disease54715
BioCentury BCIQRBFOX1
ClinGenRBFOX1 (curated)
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD54715
Chemical/Pharm GKB GenePA166048951
Clinical trialRBFOX1
Miscellaneous
canSAR (ICR)RBFOX1 (select the gene name)
DataMed IndexRBFOX1
Probes
Litterature
PubMed82 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineRBFOX1
EVEXRBFOX1
GoPubMedRBFOX1
iHOPRBFOX1
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

Search in all EBI   NCBI

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indexed on : Thu Feb 14 16:53:36 CET 2019
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