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SNRNP40 (small nuclear ribonucleoprotein U5 subunit 40)

Identity

Alias_namesWDR57
WD repeat domain 57 (U5 snRNP specific)
small nuclear ribonucleoprotein 40kDa (U5)
small nuclear ribonucleoprotein, U5 40kDa subunit
Alias_symbol (synonym)PRP8BP
SPF38
PRPF8BP
HPRP8BP
Other alias40K
HGNC (Hugo) SNRNP40
LocusID (NCBI) 9410
Atlas_Id 54648
Location 1p35.2  [Link to chromosome band 1p35]
Location_base_pair Starts at 31732415 and ends at 31769644 bp from pter ( according to hg19-Feb_2009)
Fusion genes
(updated 2016)
SNRNP40 (1p35.2) / ADGRB2 (1p35.2)SNRNP40 (1p35.2) / EPB41 (1p35.3)SNRNP40 (1p35.2) / PRDX1 (1p34.1)
SRSF4 (1p35.3) / SNRNP40 (1p35.2)SNRNP40 1p35.2 BAI2SNRNP40 1p35.2 / EPB41 1p35.3

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) [ 1 ]
  Lung: Translocations in Adenocarcinoma


External links

Nomenclature
HGNC (Hugo)SNRNP40   30857
Cards
Entrez_Gene (NCBI)SNRNP40  9410  small nuclear ribonucleoprotein U5 subunit 40
Aliases40K; HPRP8BP; PRP8BP; PRPF8BP; 
SPF38; WDR57
GeneCards (Weizmann)SNRNP40
Ensembl hg19 (Hinxton)ENSG00000060688 [Gene_View]  chr1:31732415-31769644 [Contig_View]  SNRNP40 [Vega]
Ensembl hg38 (Hinxton)ENSG00000060688 [Gene_View]  chr1:31732415-31769644 [Contig_View]  SNRNP40 [Vega]
ICGC DataPortalENSG00000060688
TCGA cBioPortalSNRNP40
AceView (NCBI)SNRNP40
Genatlas (Paris)SNRNP40
WikiGenes9410
SOURCE (Princeton)SNRNP40
Genetics Home Reference (NIH)SNRNP40
Genomic and cartography
GoldenPath hg19 (UCSC)SNRNP40  -     chr1:31732415-31769644 -  1p35.2   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)SNRNP40  -     1p35.2   [Description]    (hg38-Dec_2013)
EnsemblSNRNP40 - 1p35.2 [CytoView hg19]  SNRNP40 - 1p35.2 [CytoView hg38]
Mapping of homologs : NCBISNRNP40 [Mapview hg19]  SNRNP40 [Mapview hg38]
OMIM607797   
Gene and transcription
Genbank (Entrez)AF090988 AK074516 AK123103 AK298823 AK313800
RefSeq transcript (Entrez)NM_004814
RefSeq genomic (Entrez)NC_000001 NC_018912 NT_032977 NW_004929290
Consensus coding sequences : CCDS (NCBI)SNRNP40
Cluster EST : UnigeneHs.33962 [ NCBI ]
CGAP (NCI)Hs.33962
Alternative Splicing GalleryENSG00000060688
Gene ExpressionSNRNP40 [ NCBI-GEO ]   SNRNP40 [ EBI - ARRAY_EXPRESS ]   SNRNP40 [ SEEK ]   SNRNP40 [ MEM ]
Gene Expression Viewer (FireBrowse)SNRNP40 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)9410
GTEX Portal (Tissue expression)SNRNP40
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ96DI7   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ96DI7  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ96DI7
Splice isoforms : SwissVarQ96DI7
PhosPhoSitePlusQ96DI7
Domaine pattern : Prosite (Expaxy)WD_REPEATS_1 (PS00678)    WD_REPEATS_2 (PS50082)    WD_REPEATS_REGION (PS50294)   
Domains : Interpro (EBI)G-protein_beta_WD-40_rep    WD40/YVTN_repeat-like_dom    WD40_repeat    WD40_repeat_CS    WD40_repeat_dom   
Domain families : Pfam (Sanger)WD40 (PF00400)   
Domain families : Pfam (NCBI)pfam00400   
Domain families : Smart (EMBL)WD40 (SM00320)  
Conserved Domain (NCBI)SNRNP40
DMDM Disease mutations9410
Blocks (Seattle)SNRNP40
SuperfamilyQ96DI7
Human Protein AtlasENSG00000060688
Peptide AtlasQ96DI7
HPRD08481
IPIIPI00940685   IPI00006723   IPI00385642   
Protein Interaction databases
DIP (DOE-UCLA)Q96DI7
IntAct (EBI)Q96DI7
FunCoupENSG00000060688
BioGRIDSNRNP40
STRING (EMBL)SNRNP40
ZODIACSNRNP40
Ontologies - Pathways
QuickGOQ96DI7
Ontology : AmiGORNA splicing, via transesterification reactions  mRNA splicing, via spliceosome  mRNA splicing, via spliceosome  protein binding  nucleoplasm  nucleoplasm  U5 snRNP  small nucleolar ribonucleoprotein complex  cytoplasm  RNA processing  RNA splicing  poly(A) RNA binding  precatalytic spliceosome  catalytic step 2 spliceosome  
Ontology : EGO-EBIRNA splicing, via transesterification reactions  mRNA splicing, via spliceosome  mRNA splicing, via spliceosome  protein binding  nucleoplasm  nucleoplasm  U5 snRNP  small nucleolar ribonucleoprotein complex  cytoplasm  RNA processing  RNA splicing  poly(A) RNA binding  precatalytic spliceosome  catalytic step 2 spliceosome  
Pathways : KEGGSpliceosome   
NDEx NetworkSNRNP40
Atlas of Cancer Signalling NetworkSNRNP40
Wikipedia pathwaysSNRNP40
Orthology - Evolution
OrthoDB9410
GeneTree (enSembl)ENSG00000060688
Phylogenetic Trees/Animal Genes : TreeFamSNRNP40
HOVERGENQ96DI7
HOGENOMQ96DI7
Homologs : HomoloGeneSNRNP40
Homology/Alignments : Family Browser (UCSC)SNRNP40
Gene fusions - Rearrangements
Fusion : MitelmanSNRNP40/ADGRB2 [1p35.2/1p35.2]  
Fusion : MitelmanSNRNP40/EPB41 [1p35.2/1p35.3]  [t(1;1)(p35;p35)]  
Fusion : MitelmanSRSF4/SNRNP40 [1p35.3/1p35.2]  [t(1;1)(p35;p35)]  
Fusion: TCGASNRNP40 1p35.2 BAI2 BLCA
Fusion: TCGASNRNP40 1p35.2 EPB41 1p35.3 HNSC
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerSNRNP40 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)SNRNP40
dbVarSNRNP40
ClinVarSNRNP40
1000_GenomesSNRNP40 
Exome Variant ServerSNRNP40
ExAC (Exome Aggregation Consortium)SNRNP40 (select the gene name)
Genetic variants : HAPMAP9410
Genomic Variants (DGV)SNRNP40 [DGVbeta]
DECIPHER (Syndromes)1:31732415-31769644  ENSG00000060688
CONAN: Copy Number AnalysisSNRNP40 
Mutations
ICGC Data PortalSNRNP40 
TCGA Data PortalSNRNP40 
Broad Tumor PortalSNRNP40
OASIS PortalSNRNP40 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICSNRNP40  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDSNRNP40
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 SNRNP40
DgiDB (Drug Gene Interaction Database)SNRNP40
DoCM (Curated mutations)SNRNP40 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)SNRNP40 (select a term)
intoGenSNRNP40
Cancer3DSNRNP40(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM607797   
Orphanet
MedgenSNRNP40
Genetic Testing Registry SNRNP40
NextProtQ96DI7 [Medical]
TSGene9410
GENETestsSNRNP40
Huge Navigator SNRNP40 [HugePedia]
snp3D : Map Gene to Disease9410
BioCentury BCIQSNRNP40
ClinGenSNRNP40
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD9410
Chemical/Pharm GKB GenePA164726132
Clinical trialSNRNP40
Miscellaneous
canSAR (ICR)SNRNP40 (select the gene name)
Probes
Litterature
PubMed37 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineSNRNP40
EVEXSNRNP40
GoPubMedSNRNP40
iHOPSNRNP40
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Thu Mar 30 15:20:18 CEST 2017

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