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CPSF6 (cleavage and polyadenylation specific factor 6)

Identity

Alias_namescleavage and polyadenylation specific factor 6, 68kD subunit
cleavage and polyadenylation specific factor 6, 68kDa
Alias_symbol (synonym)CFIM
HPBRII-4
HPBRII-7
CFIM68
Other alias
HGNC (Hugo) CPSF6
LocusID (NCBI) 11052
Atlas_Id 52984
Location 12q15  [Link to chromosome band 12q15]
Location_base_pair Starts at 69239537 and ends at 69274358 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2016)
CPSF6 (12q15) / C9orf3 (9q22.32)CPSF6 (12q15) / CHMP1A (16q24.3)CPSF6 (12q15) / CPSF6 (12q15)
CPSF6 (12q15) / FGFR1 (8p11.23)CPSF6 (12q15) / MDM1 (12q15)CPSF6 (12q15) / NAV3 (12q21.2)
CPSF6 (12q15) / OSBPL8 (12q21.2)CPSF6 (12q15) / PTPRB (12q15)CPSF6 (12q15) / SH3YL1 (2p25.3)
ZNF28 (19q13.41) / CPSF6 (12q15)CPSF6 12q15 / C9orf3 9q22.32CPSF6 12q15 / CHMP1A 16q24.3
CPSF6 12q15 / MDM1 12q15CPSF6 12q15 / NAV3 12q21.2CPSF6 12q15 / OSBPL8 12q21.2
CPSF6 12q15 / PTPRB 12q15CPSF6 12q15 / SH3YL1 2p25.3

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 Leukemias implicated (Data extracted from papers in the Atlas) [ 2 ]
  8p11 myeloproliferative syndrome (FGFR1)
t(8;12)(p12;q15) CPSF6/FGFR1


External links

Nomenclature
HGNC (Hugo)CPSF6   13871
Cards
Entrez_Gene (NCBI)CPSF6  11052  cleavage and polyadenylation specific factor 6
AliasesCFIM; CFIM68; HPBRII-4; HPBRII-7
GeneCards (Weizmann)CPSF6
Ensembl hg19 (Hinxton)ENSG00000111605 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000111605 [Gene_View]  chr12:69239537-69274358 [Contig_View]  CPSF6 [Vega]
ICGC DataPortalENSG00000111605
TCGA cBioPortalCPSF6
AceView (NCBI)CPSF6
Genatlas (Paris)CPSF6
WikiGenes11052
SOURCE (Princeton)CPSF6
Genetics Home Reference (NIH)CPSF6
Genomic and cartography
GoldenPath hg38 (UCSC)CPSF6  -     chr12:69239537-69274358 +  12q15   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)CPSF6  -     12q15   [Description]    (hg19-Feb_2009)
EnsemblCPSF6 - 12q15 [CytoView hg19]  CPSF6 - 12q15 [CytoView hg38]
Mapping of homologs : NCBICPSF6 [Mapview hg19]  CPSF6 [Mapview hg38]
OMIM604979   
Gene and transcription
Genbank (Entrez)AK021534 AK021833 AK098338 AK223568 AK292024
RefSeq transcript (Entrez)NM_001300947 NM_007007
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)CPSF6
Cluster EST : UnigeneHs.369606 [ NCBI ]
CGAP (NCI)Hs.369606
Alternative Splicing GalleryENSG00000111605
Gene ExpressionCPSF6 [ NCBI-GEO ]   CPSF6 [ EBI - ARRAY_EXPRESS ]   CPSF6 [ SEEK ]   CPSF6 [ MEM ]
Gene Expression Viewer (FireBrowse)CPSF6 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)11052
GTEX Portal (Tissue expression)CPSF6
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ16630   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ16630  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ16630
Splice isoforms : SwissVarQ16630
PhosPhoSitePlusQ16630
Domaine pattern : Prosite (Expaxy)RRM (PS50102)   
Domains : Interpro (EBI)Nucleotide-bd_a/b_plait    RRM_dom   
Domain families : Pfam (Sanger)RRM_1 (PF00076)   
Domain families : Pfam (NCBI)pfam00076   
Domain families : Smart (EMBL)RRM (SM00360)  
Conserved Domain (NCBI)CPSF6
DMDM Disease mutations11052
Blocks (Seattle)CPSF6
PDB (SRS)3P5T    3P6Y    3Q2S    3Q2T    4B4N    4U0A    4U0B    4WYM   
PDB (PDBSum)3P5T    3P6Y    3Q2S    3Q2T    4B4N    4U0A    4U0B    4WYM   
PDB (IMB)3P5T    3P6Y    3Q2S    3Q2T    4B4N    4U0A    4U0B    4WYM   
PDB (RSDB)3P5T    3P6Y    3Q2S    3Q2T    4B4N    4U0A    4U0B    4WYM   
Structural Biology KnowledgeBase3P5T    3P6Y    3Q2S    3Q2T    4B4N    4U0A    4U0B    4WYM   
SCOP (Structural Classification of Proteins)3P5T    3P6Y    3Q2S    3Q2T    4B4N    4U0A    4U0B    4WYM   
CATH (Classification of proteins structures)3P5T    3P6Y    3Q2S    3Q2T    4B4N    4U0A    4U0B    4WYM   
SuperfamilyQ16630
Human Protein AtlasENSG00000111605
Peptide AtlasQ16630
IPIIPI00012998   IPI00030654   IPI01025254   IPI00910864   IPI00647126   IPI01021069   IPI01021204   
Protein Interaction databases
DIP (DOE-UCLA)Q16630
IntAct (EBI)Q16630
FunCoupENSG00000111605
BioGRIDCPSF6
STRING (EMBL)CPSF6
ZODIACCPSF6
Ontologies - Pathways
QuickGOQ16630
Ontology : AmiGORNA binding  RNA binding  mRNA binding  protein binding  nucleus  nucleoplasm  mRNA cleavage factor complex  mRNA polyadenylation  mRNA processing  membrane  nuclear speck  intracellular ribonucleoprotein complex  paraspeckles  protein tetramerization  
Ontology : EGO-EBIRNA binding  RNA binding  mRNA binding  protein binding  nucleus  nucleoplasm  mRNA cleavage factor complex  mRNA polyadenylation  mRNA processing  membrane  nuclear speck  intracellular ribonucleoprotein complex  paraspeckles  protein tetramerization  
Pathways : KEGGmRNA surveillance pathway   
NDEx NetworkCPSF6
Atlas of Cancer Signalling NetworkCPSF6
Wikipedia pathwaysCPSF6
Orthology - Evolution
OrthoDB11052
GeneTree (enSembl)ENSG00000111605
Phylogenetic Trees/Animal Genes : TreeFamCPSF6
HOVERGENQ16630
HOGENOMQ16630
Homologs : HomoloGeneCPSF6
Homology/Alignments : Family Browser (UCSC)CPSF6
Gene fusions - Rearrangements
Fusion : MitelmanCPSF6/C9orf3 [12q15/9q22.32]  
Fusion : MitelmanCPSF6/CHMP1A [12q15/16q24.3]  [t(12;16)(q15;q24)]  
Fusion : MitelmanCPSF6/FGFR1 [12q15/8p11.23]  [t(8;12)(p11;q15)]  
Fusion : MitelmanCPSF6/NAV3 [12q15/12q21.2]  [t(12;12)(q15;q21)]  
Fusion : MitelmanCPSF6/OSBPL8 [12q15/12q21.2]  [t(12;12)(q15;q21)]  
Fusion : MitelmanCPSF6/SH3YL1 [12q15/2p25.3]  [t(2;12)(p25;q15)]  
Fusion: TCGACPSF6 12q15 C9orf3 9q22.32 HNSC LUAD
Fusion: TCGACPSF6 12q15 CHMP1A 16q24.3 BLCA
Fusion: TCGACPSF6 12q15 MDM1 12q15 BRCA
Fusion: TCGACPSF6 12q15 NAV3 12q21.2 BRCA
Fusion: TCGACPSF6 12q15 OSBPL8 12q21.2 BRCA
Fusion: TCGACPSF6 12q15 PTPRB 12q15 LGG
Fusion: TCGACPSF6 12q15 SH3YL1 2p25.3 LUAD
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerCPSF6 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)CPSF6
dbVarCPSF6
ClinVarCPSF6
1000_GenomesCPSF6 
Exome Variant ServerCPSF6
ExAC (Exome Aggregation Consortium)CPSF6 (select the gene name)
Genetic variants : HAPMAP11052
Genomic Variants (DGV)CPSF6 [DGVbeta]
DECIPHERCPSF6 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisCPSF6 
Mutations
ICGC Data PortalCPSF6 
TCGA Data PortalCPSF6 
Broad Tumor PortalCPSF6
OASIS PortalCPSF6 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICCPSF6  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDCPSF6
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 CPSF6
DgiDB (Drug Gene Interaction Database)CPSF6
DoCM (Curated mutations)CPSF6 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)CPSF6 (select a term)
intoGenCPSF6
Cancer3DCPSF6(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM604979   
Orphanet
MedgenCPSF6
Genetic Testing Registry CPSF6
NextProtQ16630 [Medical]
TSGene11052
GENETestsCPSF6
Target ValidationCPSF6
Huge Navigator CPSF6 [HugePedia]
snp3D : Map Gene to Disease11052
BioCentury BCIQCPSF6
ClinGenCPSF6
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD11052
Chemical/Pharm GKB GenePA26846
Clinical trialCPSF6
Miscellaneous
canSAR (ICR)CPSF6 (select the gene name)
Probes
Litterature
PubMed93 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineCPSF6
EVEXCPSF6
GoPubMedCPSF6
iHOPCPSF6
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Mon Sep 25 19:03:37 CEST 2017

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