Atlas of Genetics and Cytogenetics in Oncology and Haematology


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RFX3 (regulatory factor X, 3 (influences HLA class II expression))

Identity

Alias_namesregulatory factor X, 3 (influences HLA class II expression)
Other alias-
HGNC (Hugo) RFX3
LocusID (NCBI) 5991
Atlas_Id 72600
Location 9p24.2  [Link to chromosome band 9p24]
Location_base_pair Starts at 3218297 and ends at 3526001 bp from pter ( according to hg19-Feb_2009)
Fusion genes
(updated 2016)
CNTLN (9p22.2) / RFX3 (9p24.2)KDM4C (9p24.1) / RFX3 (9p24.2)RFX3 (9p24.2) / GLDC (9p24.1)
RFX3 (9p24.2) / PABPC1 (8q22.3)RFX3 (9p24.2) / RELB (19q13.32)RFX3 (9p24.2) / SMARCA2 (9p24.3)
RFX3 SMARCA2RFX3 RELBRFX3 GLDC
CNTLN RFX3KDM4C RFX3

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)RFX3   9984
Cards
Entrez_Gene (NCBI)RFX3  5991  regulatory factor X, 3 (influences HLA class II expression)
Aliases
GeneCards (Weizmann)RFX3
Ensembl hg19 (Hinxton)ENSG00000080298 [Gene_View]  chr9:3218297-3526001 [Contig_View]  RFX3 [Vega]
Ensembl hg38 (Hinxton)ENSG00000080298 [Gene_View]  chr9:3218297-3526001 [Contig_View]  RFX3 [Vega]
ICGC DataPortalENSG00000080298
TCGA cBioPortalRFX3
AceView (NCBI)RFX3
Genatlas (Paris)RFX3
WikiGenes5991
SOURCE (Princeton)RFX3
Genetics Home Reference (NIH)RFX3
Genomic and cartography
GoldenPath hg19 (UCSC)RFX3  -     chr9:3218297-3526001 -  9p24.2   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)RFX3  -     9p24.2   [Description]    (hg38-Dec_2013)
EnsemblRFX3 - 9p24.2 [CytoView hg19]  RFX3 - 9p24.2 [CytoView hg38]
Mapping of homologs : NCBIRFX3 [Mapview hg19]  RFX3 [Mapview hg38]
OMIM601337   
Gene and transcription
Genbank (Entrez)AI811824 AK127804 AK289540 AK310956 AW152407
RefSeq transcript (Entrez)NM_001282116 NM_001282117 NM_002919 NM_134428
RefSeq genomic (Entrez)NC_000009 NC_018920 NT_008413 NW_004929342
Consensus coding sequences : CCDS (NCBI)RFX3
Cluster EST : UnigeneHs.734648 [ NCBI ]
CGAP (NCI)Hs.734648
Alternative Splicing GalleryENSG00000080298
Gene ExpressionRFX3 [ NCBI-GEO ]   RFX3 [ EBI - ARRAY_EXPRESS ]   RFX3 [ SEEK ]   RFX3 [ MEM ]
Gene Expression Viewer (FireBrowse)RFX3 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)5991
GTEX Portal (Tissue expression)RFX3
Protein : pattern, domain, 3D structure
UniProt/SwissProtP48380   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP48380  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP48380
Splice isoforms : SwissVarP48380
PhosPhoSitePlusP48380
Domaine pattern : Prosite (Expaxy)RFX_DBD (PS51526)   
Domains : Interpro (EBI)DNA-bd_RFX    RFX1_trans_act    WHTH_DNA-bd_dom   
Domain families : Pfam (Sanger)RFX1_trans_act (PF04589)    RFX_DNA_binding (PF02257)   
Domain families : Pfam (NCBI)pfam04589    pfam02257   
Conserved Domain (NCBI)RFX3
DMDM Disease mutations5991
Blocks (Seattle)RFX3
SuperfamilyP48380
Human Protein AtlasENSG00000080298
Peptide AtlasP48380
HPRD03215
IPIIPI00102829   IPI00009298   IPI00646621   IPI00640983   IPI00552669   IPI00641602   IPI00647026   IPI00640355   IPI00642487   IPI00644630   IPI00552513   
Protein Interaction databases
DIP (DOE-UCLA)P48380
IntAct (EBI)P48380
FunCoupENSG00000080298
BioGRIDRFX3
STRING (EMBL)RFX3
ZODIACRFX3
Ontologies - Pathways
QuickGOP48380
Ontology : AmiGOnuclear chromatin  RNA polymerase II core promoter proximal region sequence-specific DNA binding  DNA binding  sequence-specific DNA binding transcription factor activity  RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity  protein binding  nucleus  transcription factor complex  transcription, DNA-templated  regulation of transcription, DNA-templated  regulation of transcription from RNA polymerase II promoter  endocrine pancreas development  cilium assembly  cilium assembly  transcription regulatory region DNA binding  negative regulation of transcription, DNA-templated  positive regulation of transcription, DNA-templated  positive regulation of transcription from RNA polymerase II promoter  cell maturation  regulation of insulin secretion  cilium-dependent cell motility  epithelial cilium movement involved in determination of left/right asymmetry  type B pancreatic cell maturation  positive regulation of type B pancreatic cell development  
Ontology : EGO-EBInuclear chromatin  RNA polymerase II core promoter proximal region sequence-specific DNA binding  DNA binding  sequence-specific DNA binding transcription factor activity  RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity  protein binding  nucleus  transcription factor complex  transcription, DNA-templated  regulation of transcription, DNA-templated  regulation of transcription from RNA polymerase II promoter  endocrine pancreas development  cilium assembly  cilium assembly  transcription regulatory region DNA binding  negative regulation of transcription, DNA-templated  positive regulation of transcription, DNA-templated  positive regulation of transcription from RNA polymerase II promoter  cell maturation  regulation of insulin secretion  cilium-dependent cell motility  epithelial cilium movement involved in determination of left/right asymmetry  type B pancreatic cell maturation  positive regulation of type B pancreatic cell development  
NDEx NetworkRFX3
Atlas of Cancer Signalling NetworkRFX3
Wikipedia pathwaysRFX3
Orthology - Evolution
OrthoDB5991
GeneTree (enSembl)ENSG00000080298
Phylogenetic Trees/Animal Genes : TreeFamRFX3
HOVERGENP48380
HOGENOMP48380
Homologs : HomoloGeneRFX3
Homology/Alignments : Family Browser (UCSC)RFX3
Gene fusions - Rearrangements
Fusion: TCGARFX3 SMARCA2
Fusion: TCGARFX3 RELB
Fusion: TCGARFX3 GLDC
Fusion: TCGACNTLN RFX3
Fusion: TCGAKDM4C RFX3
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerRFX3 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)RFX3
dbVarRFX3
ClinVarRFX3
1000_GenomesRFX3 
Exome Variant ServerRFX3
ExAC (Exome Aggregation Consortium)RFX3 (select the gene name)
Genetic variants : HAPMAP5991
Genomic Variants (DGV)RFX3 [DGVbeta]
DECIPHER (Syndromes)9:3218297-3526001  ENSG00000080298
CONAN: Copy Number AnalysisRFX3 
Mutations
ICGC Data PortalRFX3 
TCGA Data PortalRFX3 
Broad Tumor PortalRFX3
OASIS PortalRFX3 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICRFX3  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDRFX3
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch RFX3
DgiDB (Drug Gene Interaction Database)RFX3
DoCM (Curated mutations)RFX3 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)RFX3 (select a term)
intoGenRFX3
Cancer3DRFX3(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM601337   
Orphanet
MedgenRFX3
Genetic Testing Registry RFX3
NextProtP48380 [Medical]
TSGene5991
GENETestsRFX3
Huge Navigator RFX3 [HugePedia]
snp3D : Map Gene to Disease5991
BioCentury BCIQRFX3
ClinGenRFX3
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD5991
Chemical/Pharm GKB GenePA34354
Clinical trialRFX3
Miscellaneous
canSAR (ICR)RFX3 (select the gene name)
Probes
Litterature
PubMed22 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineRFX3
EVEXRFX3
GoPubMedRFX3
iHOPRFX3
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 : Tue Mar 14 12:40:57 CET 2017

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