Atlas of Genetics and Cytogenetics in Oncology and Haematology


Home   Genes   Leukemias   Solid Tumors   Cancer-Prone   Deep Insight   Case Reports   Journals  Portal   Teaching   

X Y 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 NA

PARN (poly(A)-specific ribonuclease)

Identity

Alias_namespoly(A)-specific ribonuclease (deadenylation nuclease)
Alias_symbol (synonym)DAN
Other aliasDKCB6
PFBMFT4
HGNC (Hugo) PARN
LocusID (NCBI) 5073
Atlas_Id 55216
Location 16p13.12  [Link to chromosome band 16p13]
Location_base_pair Starts at 14435700 and ends at 14630271 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)
CFB (6p21.33) / PARN (16p13.12)MAP3K1 (5q11.2) / PARN (16p13.12)PARN (16p13.12) / ABCA3 (16p13.3)
PARN (16p13.12) / GOLPH3 (5p13.3)PARN (16p13.12) / MALAT1 (11q13.1)PARN (16p13.12) / PARN (16p13.12)
PARN (16p13.12) / RRN3 (16p13.11)ZNF587 (19q13.43) / PARN (16p13.12)MAP3K1 5q11.2 / PARN 16p13.12
PARN 16p13.12 / ABCA3 16p13.3PARN 16p13.12 / RRN3 16p13.11

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 Cancer prone implicated (Data extracted from papers in the Atlas) [ 1 ]
  Dyskeratosis congenita (DKC)


External links

Nomenclature
HGNC (Hugo)PARN   8609
Cards
Entrez_Gene (NCBI)PARN  5073  poly(A)-specific ribonuclease
AliasesDAN; DKCB6; PFBMFT4
GeneCards (Weizmann)PARN
Ensembl hg19 (Hinxton)ENSG00000140694 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000140694 [Gene_View]  chr16:14435700-14630271 [Contig_View]  PARN [Vega]
ICGC DataPortalENSG00000140694
TCGA cBioPortalPARN
AceView (NCBI)PARN
Genatlas (Paris)PARN
WikiGenes5073
SOURCE (Princeton)PARN
Genetics Home Reference (NIH)PARN
Genomic and cartography
GoldenPath hg38 (UCSC)PARN  -     chr16:14435700-14630271 -  16p13.12   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)PARN  -     16p13.12   [Description]    (hg19-Feb_2009)
EnsemblPARN - 16p13.12 [CytoView hg19]  PARN - 16p13.12 [CytoView hg38]
Mapping of homologs : NCBIPARN [Mapview hg19]  PARN [Mapview hg38]
OMIM604212   616353   616371   
Gene and transcription
Genbank (Entrez)AJ005698 AK023866 AK293189 AK299653 AK301648
RefSeq transcript (Entrez)NM_001134477 NM_001242992 NM_002582
RefSeq genomic (Entrez)NC_000016 NC_018927 NG_042871 NT_187607
Consensus coding sequences : CCDS (NCBI)PARN
Cluster EST : UnigeneHs.253197 [ NCBI ]
CGAP (NCI)Hs.253197
Alternative Splicing GalleryENSG00000140694
Gene ExpressionPARN [ NCBI-GEO ]   PARN [ EBI - ARRAY_EXPRESS ]   PARN [ SEEK ]   PARN [ MEM ]
Gene Expression Viewer (FireBrowse)PARN [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)5073
GTEX Portal (Tissue expression)PARN
Human Protein AtlasENSG00000140694-PARN [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtO95453   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtO95453  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProO95453
Splice isoforms : SwissVarO95453
Catalytic activity : Enzyme3.1.13.4 [ Enzyme-Expasy ]   3.1.13.43.1.13.4 [ IntEnz-EBI ]   3.1.13.4 [ BRENDA ]   3.1.13.4 [ KEGG ]   
PhosPhoSitePlusO95453
Domaine pattern : Prosite (Expaxy)R3H (PS51061)   
Domains : Interpro (EBI)Nucleotide-bd_a/b_plait    PARN_R3H    PolyA-riboNase_RNA_binding    R3H_dom    RNase_CAF1    RNaseH-like_dom    RRM_dom   
Domain families : Pfam (Sanger)CAF1 (PF04857)    R3H (PF01424)    RNA_bind (PF08675)   
Domain families : Pfam (NCBI)pfam04857    pfam01424    pfam08675   
Conserved Domain (NCBI)PARN
DMDM Disease mutations5073
Blocks (Seattle)PARN
PDB (SRS)2A1R    2A1S    3CTR   
PDB (PDBSum)2A1R    2A1S    3CTR   
PDB (IMB)2A1R    2A1S    3CTR   
PDB (RSDB)2A1R    2A1S    3CTR   
Structural Biology KnowledgeBase2A1R    2A1S    3CTR   
SCOP (Structural Classification of Proteins)2A1R    2A1S    3CTR   
CATH (Classification of proteins structures)2A1R    2A1S    3CTR   
SuperfamilyO95453
Human Protein Atlas [tissue]ENSG00000140694-PARN [tissue]
Peptide AtlasO95453
HPRD07250
IPIIPI00294744   IPI00976057   IPI00908419   IPI01009342   IPI00909122   
Protein Interaction databases
DIP (DOE-UCLA)O95453
IntAct (EBI)O95453
FunCoupENSG00000140694
BioGRIDPARN
STRING (EMBL)PARN
ZODIACPARN
Ontologies - Pathways
QuickGOO95453
Ontology : AmiGOnuclear-transcribed mRNA catabolic process, nonsense-mediated decay  nuclear-transcribed mRNA poly(A) tail shortening  RNA binding  mRNA 3'-UTR binding  nuclease activity  poly(A)-specific ribonuclease activity  poly(A)-specific ribonuclease activity  protein binding  nucleus  nucleolus  cytoplasm  cytosol  female gamete generation  RNA modification  protein kinase binding  positive regulation of telomere maintenance via telomerase  cation binding  regulation of mRNA stability  metal ion binding  positive regulation of telomerase activity  telomerase RNA binding  RNA phosphodiester bond hydrolysis, exonucleolytic  telomerase RNA stabilization  regulation of telomerase RNA localization to Cajal body  
Ontology : EGO-EBInuclear-transcribed mRNA catabolic process, nonsense-mediated decay  nuclear-transcribed mRNA poly(A) tail shortening  RNA binding  mRNA 3'-UTR binding  nuclease activity  poly(A)-specific ribonuclease activity  poly(A)-specific ribonuclease activity  protein binding  nucleus  nucleolus  cytoplasm  cytosol  female gamete generation  RNA modification  protein kinase binding  positive regulation of telomere maintenance via telomerase  cation binding  regulation of mRNA stability  metal ion binding  positive regulation of telomerase activity  telomerase RNA binding  RNA phosphodiester bond hydrolysis, exonucleolytic  telomerase RNA stabilization  regulation of telomerase RNA localization to Cajal body  
Pathways : KEGGRNA degradation   
NDEx NetworkPARN
Atlas of Cancer Signalling NetworkPARN
Wikipedia pathwaysPARN
Orthology - Evolution
OrthoDB5073
GeneTree (enSembl)ENSG00000140694
Phylogenetic Trees/Animal Genes : TreeFamPARN
HOVERGENO95453
HOGENOMO95453
Homologs : HomoloGenePARN
Homology/Alignments : Family Browser (UCSC)PARN
Gene fusions - Rearrangements
Fusion : MitelmanMAP3K1/PARN [5q11.2/16p13.12]  [t(5;16)(q11;p13)]  
Fusion : MitelmanPARN/ABCA3 [16p13.12/16p13.3]  [t(16;16)(p13;p13)]  
Fusion : MitelmanPARN/RRN3 [16p13.12/16p13.11]  [t(16;16)(p13;p13)]  
Fusion: TCGA_MDACCMAP3K1 5q11.2 PARN 16p13.12 BRCA
Fusion: TCGA_MDACCPARN 16p13.12 ABCA3 16p13.3 BRCA
Fusion: TCGA_MDACCPARN 16p13.12 RRN3 16p13.11 BRCA
Tumor Fusion PortalPARN
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerPARN [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)PARN
dbVarPARN
ClinVarPARN
1000_GenomesPARN 
Exome Variant ServerPARN
ExAC (Exome Aggregation Consortium)ENSG00000140694
GNOMAD BrowserENSG00000140694
Genetic variants : HAPMAP5073
Genomic Variants (DGV)PARN [DGVbeta]
DECIPHERPARN [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisPARN 
Mutations
ICGC Data PortalPARN 
TCGA Data PortalPARN 
Broad Tumor PortalPARN
OASIS PortalPARN [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICPARN  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDPARN
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch PARN
DgiDB (Drug Gene Interaction Database)PARN
DoCM (Curated mutations)PARN (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)PARN (select a term)
intoGenPARN
Cancer3DPARN(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM604212    616353    616371   
Orphanet477    2949    7029   
DisGeNETPARN
MedgenPARN
Genetic Testing Registry PARN
NextProtO95453 [Medical]
TSGene5073
GENETestsPARN
Target ValidationPARN
Huge Navigator PARN [HugePedia]
snp3D : Map Gene to Disease5073
BioCentury BCIQPARN
ClinGenPARN
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD5073
Chemical/Pharm GKB GenePA32949
Clinical trialPARN
Miscellaneous
canSAR (ICR)PARN (select the gene name)
Probes
Litterature
PubMed57 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMinePARN
EVEXPARN
GoPubMedPARN
iHOPPARN
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

Search in all EBI   NCBI

© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Tue Nov 21 14:27:47 CET 2017

Home   Genes   Leukemias   Solid Tumors   Cancer-Prone   Deep Insight   Case Reports   Journals  Portal   Teaching   

For comments and suggestions or contributions, please contact us

jlhuret@AtlasGeneticsOncology.org.