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XRN1 (5'-3' exoribonuclease 1)

Identity

Alias_symbol (synonym)SEP1
Other alias
HGNC (Hugo) XRN1
LocusID (NCBI) 54464
Atlas_Id 54788
Location 3q23  [Link to chromosome band 3q23]
Location_base_pair Starts at 142306607 and ends at 142448062 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2016)
NQO1 (16q22.1) / XRN1 (3q23)XRN1 (3q23) / ATR (3q23)XRN1 (3q23) / GNPTAB (12q23.2)
XRN1 (3q23) / PIP4K2A (10p12.2)XRN1 (3q23) / PRKCE (2p21)XRN1 3q23 / PRKCE 2p21

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)XRN1   30654
Cards
Entrez_Gene (NCBI)XRN1  54464  5'-3' exoribonuclease 1
AliasesSEP1
GeneCards (Weizmann)XRN1
Ensembl hg19 (Hinxton)ENSG00000114127 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000114127 [Gene_View]  chr3:142306607-142448062 [Contig_View]  XRN1 [Vega]
ICGC DataPortalENSG00000114127
TCGA cBioPortalXRN1
AceView (NCBI)XRN1
Genatlas (Paris)XRN1
WikiGenes54464
SOURCE (Princeton)XRN1
Genetics Home Reference (NIH)XRN1
Genomic and cartography
GoldenPath hg38 (UCSC)XRN1  -     chr3:142306607-142448062 -  3q23   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)XRN1  -     3q23   [Description]    (hg19-Feb_2009)
EnsemblXRN1 - 3q23 [CytoView hg19]  XRN1 - 3q23 [CytoView hg38]
Mapping of homologs : NCBIXRN1 [Mapview hg19]  XRN1 [Mapview hg38]
OMIM607994   
Gene and transcription
Genbank (Entrez)AK096177 AK123897 AK304312 AL117516 AL133623
RefSeq transcript (Entrez)NM_001042604 NM_001282857 NM_001282859 NM_019001
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)XRN1
Cluster EST : UnigeneHs.435103 [ NCBI ]
CGAP (NCI)Hs.435103
Alternative Splicing GalleryENSG00000114127
Gene ExpressionXRN1 [ NCBI-GEO ]   XRN1 [ EBI - ARRAY_EXPRESS ]   XRN1 [ SEEK ]   XRN1 [ MEM ]
Gene Expression Viewer (FireBrowse)XRN1 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)54464
GTEX Portal (Tissue expression)XRN1
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ8IZH2   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ8IZH2  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ8IZH2
Splice isoforms : SwissVarQ8IZH2
Catalytic activity : Enzyme3.1.13.- [ Enzyme-Expasy ]   3.1.13.-3.1.13.- [ IntEnz-EBI ]   3.1.13.- [ BRENDA ]   3.1.13.- [ KEGG ]   
PhosPhoSitePlusQ8IZH2
Domains : Interpro (EBI)5_3_exoribonuclease    Put_53exo   
Domain families : Pfam (Sanger)XRN_N (PF03159)   
Domain families : Pfam (NCBI)pfam03159   
Conserved Domain (NCBI)XRN1
DMDM Disease mutations54464
Blocks (Seattle)XRN1
SuperfamilyQ8IZH2
Human Protein AtlasENSG00000114127
Peptide AtlasQ8IZH2
HPRD10470
IPIIPI00657805   IPI00657645   IPI00328115   IPI00792899   IPI00946262   IPI00979282   IPI00944901   
Protein Interaction databases
DIP (DOE-UCLA)Q8IZH2
IntAct (EBI)Q8IZH2
FunCoupENSG00000114127
BioGRIDXRN1
STRING (EMBL)XRN1
ZODIACXRN1
Ontologies - Pathways
QuickGOQ8IZH2
Ontology : AmiGOP-body  nuclear-transcribed mRNA catabolic process  G-quadruplex RNA binding  RNA binding  5'-3' exoribonuclease activity  5'-3' exoribonuclease activity  protein binding  nucleus  cytosol  cytosol  plasma membrane  membrane  rRNA catabolic process  negative regulation of translation  dendrite  negative regulation of telomere maintenance via telomerase  response to testosterone  neuronal cell body  regulation of mRNA stability  synapse  G-quadruplex DNA binding  telomerase RNA binding  nuclear mRNA surveillance  histone mRNA catabolic process  cellular response to cycloheximide  RNA phosphodiester bond hydrolysis, exonucleolytic  cellular response to puromycin  
Ontology : EGO-EBIP-body  nuclear-transcribed mRNA catabolic process  G-quadruplex RNA binding  RNA binding  5'-3' exoribonuclease activity  5'-3' exoribonuclease activity  protein binding  nucleus  cytosol  cytosol  plasma membrane  membrane  rRNA catabolic process  negative regulation of translation  dendrite  negative regulation of telomere maintenance via telomerase  response to testosterone  neuronal cell body  regulation of mRNA stability  synapse  G-quadruplex DNA binding  telomerase RNA binding  nuclear mRNA surveillance  histone mRNA catabolic process  cellular response to cycloheximide  RNA phosphodiester bond hydrolysis, exonucleolytic  cellular response to puromycin  
Pathways : KEGGRibosome biogenesis in eukaryotes    RNA degradation   
NDEx NetworkXRN1
Atlas of Cancer Signalling NetworkXRN1
Wikipedia pathwaysXRN1
Orthology - Evolution
OrthoDB54464
GeneTree (enSembl)ENSG00000114127
Phylogenetic Trees/Animal Genes : TreeFamXRN1
HOVERGENQ8IZH2
HOGENOMQ8IZH2
Homologs : HomoloGeneXRN1
Homology/Alignments : Family Browser (UCSC)XRN1
Gene fusions - Rearrangements
Fusion: TCGAXRN1 3q23 PRKCE 2p21 LUAD
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerXRN1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)XRN1
dbVarXRN1
ClinVarXRN1
1000_GenomesXRN1 
Exome Variant ServerXRN1
ExAC (Exome Aggregation Consortium)XRN1 (select the gene name)
Genetic variants : HAPMAP54464
Genomic Variants (DGV)XRN1 [DGVbeta]
DECIPHERXRN1 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisXRN1 
Mutations
ICGC Data PortalXRN1 
TCGA Data PortalXRN1 
Broad Tumor PortalXRN1
OASIS PortalXRN1 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICXRN1  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDXRN1
intOGen PortalXRN1
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 XRN1
DgiDB (Drug Gene Interaction Database)XRN1
DoCM (Curated mutations)XRN1 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)XRN1 (select a term)
intoGenXRN1
Cancer3DXRN1(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM607994   
Orphanet
MedgenXRN1
Genetic Testing Registry XRN1
NextProtQ8IZH2 [Medical]
TSGene54464
GENETestsXRN1
Target ValidationXRN1
Huge Navigator XRN1 [HugePedia]
snp3D : Map Gene to Disease54464
BioCentury BCIQXRN1
ClinGenXRN1
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD54464
Chemical/Pharm GKB GenePA134878471
Clinical trialXRN1
Miscellaneous
canSAR (ICR)XRN1 (select the gene name)
Probes
Litterature
PubMed53 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineXRN1
EVEXXRN1
GoPubMedXRN1
iHOPXRN1
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 : Wed Jun 7 13:03:07 CEST 2017

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