V3 here soon-try beta now
Gene Search (GeneCards Home) | GeneCards Guide | User Feedback | Terms of Use | Notice about third-party sites
 

XRN1 Gene

protein-coding   GIFtS: 51

GC03M143508
5'-3' exoribonuclease 1
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database
Services    
(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc , and/or 7Ensembl, 8miRBase)
About This Section

Aliases
DKFZp434P0721 2
DKFZp686B22225 2
DKFZp686F19113 2
EC 3.1.11.- 3
FLJ41903 2
SEP1 1, 2, 3, 5
Descriptions
5'-3' exoribonuclease 1 2
Strand-exchange protein 1 homolog 3
strand-exchange protein 1 2
External Ids
HGNC: 306541
Entrez Gene: 544642
UniProtKB: Q8IZH23
Ensembl: ENSG000001141277
Search outside databases for aliases for XRN1 gene

Previous GC identifer: GC03M139058

(According to Entrez Gene, Wikipedia's Gene Wiki,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

EntrezGene summary for XRN1:
SEP1 localizes to cytoplasmic foci containing a complex of mRNA-degrading enzymes. In addition to
mRNA metabolism, yeast Sep1 has been implicated in a variety of nuclear and cytoplasmic functions,
including homologous recombination, meiosis, telomere maintenance, and microtubule
assembly.[supplied by OMIM]

UniProtKB/Swiss-Prot: XRN1_HUMAN, Q8IZH2
Function: Major 5'-3' exoribonuclease involved in mRNA decay. Required for the 5'-3'processing of
the G4 tetraplex-containing DNA and RNA substrates. The kinetic of hydrolysis is faster for G4 RNA
tetraplex than for G4 DNA tetraplex and monomeric RNA tetraplex. Binds to RNA and DNA (By
similarity). May act as a tumor suppressor protein in osteogenic sarcoma (OGS)

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 36),
and/or miRBase,
Genomic Views according to UCSC and Ensembl, Transcription factor binding sites according to SABiosciences)
About This Section

Genomic View:
UCSC Golden Path with GeneCards custom track

 Transcription factor binding sites upstream to the XRN1 gene  

Entrez Gene cytogenetic band: 3q23   Ensembl cytogenetic band:  3q23   HGNC cytogenetic band: 3q23

XRN1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)

GeneLoc gene densities for chromosome 3         GeneLoc Exon Structure

GeneLoc location for GC03M143508:     (about GC identifiers)

Start:
143,508,139 bp from pter
End:
143,649,543 bp from pter
Size:
141,405 bases
Orientation:
minus strand
RefSeq DNA sequence:
NC_000003.10  NT_005612.15  
(According to 1UniProtKB, and/or Ensembl, Phosphorylation sites according to 2Phosphosite, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Enzo Life Sciences, Abnova, OriGene and/or, Abcam,
Biochemical Assays by Invitrogen, Millipore, R&D Systems, Cell Signaling Technology, and/or Enzo Life Sciences, Ontologies according to Gene Ontology Consortium 01 Apr 2009 and Entrez Gene, Antibodies by Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Cell Signaling Technology, Abcam, Abnova, and/or Novus Biologicals)
About This Section

UniProtKB/Swiss-Prot: XRN1_HUMAN, Q8IZH2 (See protein sequence)
Recommended Name: 5'-3' exoribonuclease 1  
Size: 1706 amino acids; 194107 Da
Subunit: Associates with alpha and beta tubulins (By similarity). Found in a mRNP complex with
RENT1, RENT2, RENT3B and XRN1
Subcellular location: Cytoplasm. Note=Discrete foci at the inner surface of the cell membrane
Miscellaneous: Down-regulated in OGS biopsy
Secondary accessions: Q4G0S3 Q68D88 Q6AI24 Q6MZS8 Q86WS7 Q8N8U4 Q9UF39
Alternative splicing: 3 isoforms:  Q8IZH2-1   Q8IZH2-2   Q8IZH2-3   

REFSEQ proteins (2 alternative transcripts): 
NP_001036069.1  NP_061874.3  


ENSEMBL proteins: 
ENSP00000376707 ENSP00000264951 


Human Recombinant Proteins 
Browse Drug Discovery Central at Invitrogen for human recombinant proteins
Browse Purified and Recombinant Proteins at Millipore
Browse Human Recombinant Proteins at Sigma-Aldrich  
Browse R&D Systems for human recombinant proteins
Browse recombinant and purified proteins available from Enzo Life Sciences
Recombinant Proteins from Abcam (Xrn1)
Human Recombinant Proteins from Abnova (XRN1)
                Browse Origene for full length recombinant human proteins expressed in human HEK293 cells 

2 Gene Ontology (GO) cellular component terms (links to tree view):

GO IDQualified GO termEvidencePubMed IDs
GO:0005622 intracellular IEA--
GO:0005737 cytoplasm IEA--
About this table

Antibodies for XRN1: 
Browse Antibodies Central at Invitrogen
Browse Millipore's Extensive Line of Mono- and Polyclonal Antibodies
Browse Antibodies at Sigma-Aldrich
Browse R&D Systems for Antibodies
Antibodies from Abcam (Xrn1), each with their AbpromiseSM
Monoclonal and Polyclonal Antibodies from Abnova (XRN1)
Novus Biologicals Antibody for XRN1

Assays for XRN1: 
Browse Invitrogen for biochemical assays
Browse Kits and Assays available from Millipore
Browse R&D Systems for biochemical assays
Browse biochemical assays available from Enzo Life Sciences

(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section

2 InterPro domains/families:
 IPR004859 Put_53exo
 IPR016494 5_3_exoribonuclease_1


   GeneDecks  XRN1 for the domains selected above  
About GeneDecksing

Graphical View of Domain Structure for InterPro Entry Q8IZH2

ProtoNet protein and cluster: Q8IZH2

1 Blocks protein family: IPB004859 Putative 5-3 exonuclease domain

UniProtKB/Swiss-Prot: XRN1_HUMAN, Q8IZH2
Similarity: Belongs to the 5'-3' exonuclease family

(According to MGI Jun 06 2009, UniProtKB, IUBMB,and/or Genatlas,
shRNA from OriGene, Sigma-Aldrich, RNAi from Sigma-Aldrich,
RNAi Products, Clones, and Q-PCR Products from Invitrogen, Millipore, OriGene, and/or Abnova, siRNAs from Applied Biosystems, SYBR primers from OriGene, Cell-based Assays from Millipore, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
About This Section

Inhib.
RNA:
Invitrogen RNAi Products for gene knock-down (XRN1)
Browse for Gene Knock-down Tools from Millipore
Browse Abnova for Chimera RNAi Products
               OriGene 29mer shRNA kit in GFP-retroviral vectors (see all 2): NM_001042604

              Applied Biosystems Silencer® siRNAs for XRN1

              Sigma-Aldrich siRNA for XRN1  
                     Sigma-Aldrich shRNA for XRN1  
                     Explore Sigma-Aldrich super-pooled esiRNAs  

Clones:Invitrogen Clones for XRN1
Browse Clones for the Expression of Recombinant Proteins Available from Millipore
               OriGene GFP tagged cDNA clones in CMV expression vector (see all 2): NM_001042604
                                 Myc/DDK tagged cDNA clones in CMV expression vector (see all 2): NM_001042604
                                 untagged cDNA clones in CMV expression vector (see all 3): AK096177 

Primers: Browse Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers
              OriGene genome-wide validated SYBR primer pairs: NM_019001

UniProtKB/Swiss-Prot: XRN1_HUMAN, Q8IZH2
Function: Major 5'-3' exoribonuclease involved in mRNA decay. Required for the 5'-3'processing of
the G4 tetraplex-containing DNA and RNA substrates. The kinetic of hydrolysis is faster for G4 RNA
tetraplex than for G4 DNA tetraplex and monomeric RNA tetraplex. Binds to RNA and DNA (By
similarity). May act as a tumor suppressor protein in osteogenic sarcoma (OGS)
Induction: By GDNF
Enzyme Number (IUBMB): EC 3.1.11.- 

5 Gene Ontology (GO) molecular function terms (links to tree view):

GO IDQualified GO termEvidencePubMed IDs
GO:0003677 DNA binding IEA--
GO:0003723 RNA binding IEA--
GO:0005515 protein binding IPI15231747
GO:0008409 5'-3' exonuclease activity IEA--
GO:0016787 hydrolase activity IEA--
About this table

(Pathways according to Invitrogen (maps by GeneGo), Millipore, Cell Signaling Technology, Sigma-Aldrich, KEGG and/or UniProtKB,
Sets of similar genes according to GeneDecks, Proteins Network according to SABiosciences, Interactions according to 1UniProtKB, 2MINT, and/or 3STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
About This Section



5/42 Interacting proteins for XRN1 (ENSP000002649513 Q8IZH21) via UniProtKB, MINT, and/or STRING (see all 42 )
InteractantInteraction Details
GeneCardExternal ID(s)
ALDOAP040751EBI-372406, EBI-709613
AP1G2O758431EBI-372406, EBI-373637
BAT3P463791EBI-372406, EBI-347552
CCT5P486431EBI-372406, EBI-355710
CHD4Q148391EBI-372406, EBI-372916
About this table

2 Gene Ontology (GO) biological process terms (links to tree view):

GO IDQualified GO termEvidencePubMed IDs
GO:0006139 nucleobase, nucleoside, nucleotide and nucleic acid metabolic process IEA--
GO:0045786 negative regulation of cell cycle IEA--
About this table
(Chemical Compounds according to UniProtKB, Enzo Life Sciences, Sigma-Aldrich, Tocris Bioscience, and/or Novoseek and Drugs according to Enzo Life Sciences and/or PharmGKB)
About This Section

Browse drugs & compounds from Enzo Life Sciences
Browse Small Molecules at Sigma-Aldrich

Browse Tocris compounds for XRN1

(GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 219 Homo sapiens; Jun 2 2009) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView,
non coding RNAs according to RNAdb,
ESTs according to GeneTide,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from Invitrogen, Millipore, and/or Abnova,
siRNAs from Applied Biosystems, Sigma-Aldrich,
shRNA from Sigma-Aldrich, OriGene,
Tagged/untagged cDNA clones from OriGene,
Expression Assays from Applied Biosystems)
About This Section

Inhib.
RNA:
Invitrogen RNAi Products for gene knock-down (XRN1)
Browse for Gene Knock-down Tools from Millipore
Browse Abnova for Chimera RNAi Products
               OriGene 29mer shRNA kit in GFP-retroviral vectors (see all 2): NM_001042604

              Sigma-Aldrich siRNA for XRN1  
                     Sigma-Aldrich shRNA for XRN1  
                     Explore Sigma-Aldrich super-pooled esiRNAs  

Applied Biosystems Silencer® siRNAs: 

NM_001042604  NM_019001  

REFSEQ mRNAs for XRN1 gene (2 alternative transcripts): 

NM_001042604.1   NM_019001.3   

Applied Biosystems TaqMan ® Gene Expression Assays: 

NM_001042604  NM_019001  

               OriGene GFP tagged cDNA clones in CMV expression vector (see all 2): NM_001042604
                                 Myc/DDK tagged cDNA clones in CMV expression vector (see all 2): NM_001042604
                                 untagged cDNA clones in CMV expression vector (see all 3): AK096177 

Additional cDNA sequence: 

AK096177.1 AK123897.1 AK304312.1 AL117516.1 AL133623.1 AY137776.1 BC039314.1 BC048104.1 
BC078146.1 BX640905.1 CR627160.1 CR627396.1 CR749518.1 

14 DOTS entries:

DT.97837164  DT.212252  DT.409733  DT.95263243  DT.99967252  DT.97817152  DT.100022124  DT.120912012 
DT.40128661  DT.99977621  DT.40236568  DT.75102786  DT.91666774  DT.91879839 

24/134 AceView cDNA sequences (see all 134 ):

AI017478 BM876356 BC039314 AA486772 BQ215043 AK123897 H68938 CN481808 
CK823327 BX640905 BM677611 CR627396 AI908208 AA382099 AL133623 AA504374 
AK096177 BC078146 BM457935 BM802012 BX954729 BQ433900 AI004667 AA953359 

highest scoring ESTs for XRN1:

AI004667 BI561044 BQ215043 N68610 W01997 AK096177 BC039314 AA410585 AA411620 AA486772 

Unigene Cluster for XRN1:

5'-3' exoribonuclease 1
Hs.435103  [show with all ESTs]
Unigene Representative Sequence: BX640905


GeneLoc Exon Structure

2 Ensembl transcripts including schematic representations:
ENST00000392981  ENST00000264951  
(Experimental results according to 1GeneNote and GNF BioGPS,
probe sets-to-genes annotations according to 2GeneAnnot , 3GeneTide , Sets of similar genes according to GeneDecks, Electronic Northern calculations according to data from UniGene (Build 219 Homo sapiens), SAGE tags according to CGAP, plus additional links to SOURCE, and/or GNF BioGPS, and/or EXPOLDB, and/or UniProtKB,
Expression Assays from Applied Biosystems )
About This Section

XRN1 expression in normal and diseased human tissues

 Applied Biosystems TaqMan ® Gene Expression Assays for XRN1

1 / 2 / 3

11 probe-sets matching XRN1 gene


Affymetrix
probe-set
Array  GeneAnnot data GeneNote data GeneTide data
# genes Sensitivity Specificity Correlation Length Gb_Accession Consensus Uniqueness Score Rank

86814_at2, 3 U95-D 1 1.00 1.00 0.40 0.54 AI620731 0.60 1.00 0.82 1

47090_at2, 3 U95-B 1 1.00 1.00 0.75 1.56 AI004667 0.80 1.00 0.91 1
46550_at2, 3 U95-B 1 0.94 1.00 0.75 1.00 W01997 0.80 1.00 0.91 1
64909_at2, 3 U95-C 2 0.75 0.75 0.59 1.20 AI341683 0.20 0.25 0.23 2

42920_at2, 3 U95-B 1 0.62 1.00 0.63 0.72 N68610 0.80 1.00 0.91 1

225814_at2, 3 U133-B 1 1.00 1.00 -- -- BG534738 0.60 1.00 0.82 1

233632_s_at2, 3 U133-B 1 1.00 1.00 -- -- AL117516 0.40 1.00 0.76 1

225814_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --

233632_s_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --

1570394_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --

1555785_a_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --
GeneDecks  XRN1 for binary patterns associated with the probe-sets selected above  
About GeneDecksing
About this table    
Data from (Publications) and GNF BioGPS
    About these images
About these images

CGAP SAGE TAG: TTAAATGCTC

SOURCE GeneReport for Unigene cluster: Hs.435103

UniProtKB/Swiss-Prot: XRN1_HUMAN, Q8IZH2
Tissue specificity: Expressed in heart, brain, pancreas, spleen, testis, osteogenic sarcoma (OGS)
biopsy and primary cell lines

(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD and/or 5MGI Jun 06 2009, with possible further links to Flybase and/or WormBase, Gene Trees according to Ensembl)
About This Section


Orthologs for XRN1 gene from 5/19 species (see all 19 )
Organism Gene Locus Description Human
Similarity
NCBI accessions
dog
(Canis familiaris)
XRN11   -- 5'-3' exoribonuclease 1 93.44(n)
93.79(a)
477100  XM_534294.2  XP_534294.2 
chimpanzee
(Pan troglodytes)
XRN11   -- 5'-3' exoribonuclease 1 99.65(n)
99.24(a)
460744  XM_001161640.1  XP_001161640.1 
cow
(Bos taurus)
XRN11   -- 5'-3' exoribonuclease 1 92.48(n)
92.13(a)
540834  XM_613358.3  XP_613358.3 
rat
(Rattus norvegicus)
Xrn11   -- 5'-3' exoribonuclease 1 88.05(n)
89.14(a)
300944  XM_217233.4  XP_217233.4 
mouse
(Mus musculus)
Xrn11, 5 95
5'-3' exoribonuclease 11, 5 88.01(n)1
88.61(a)1
241271  NM_011916.21  NP_036046.21 
 AK0521945  AK1423115  (see all 18)
About this table        Species with no ortholog for XRN1

ENSEMBL Gene Tree for XRN1
(Paralogs according to 1HomoloGene
and 2Ensembl, Pseudogenes according to 3Pseudogene.org)
About This Section

Paralogs for XRN1 gene
XRN22  

(According to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, and UniProtKB, Linkage Disequilibrium by HapMap, Genotyping Reagents from Applied Biosystems)
About This Section


10/496 NCBI SNPs in XRN1 are shown (see all 496 )
(Click for Applied Biosystems TaqMan ® Genotyping Assay)  (see all 99)
ABGenomic DataTranscription DataAllele Frequencies
SNP IDValidChr 3 posSequenceRecsAA
Chg
TypeMoreRecsAllele
freq
PopTotal
sample
More
------------
rs39240571,2
A,C,F,H143649732(+) GGTGTG/ATTGCA 2 -- ng317Minor allele frequency- A:0.05EU EA WA NA 550
rs37627991,2
C,F,H143510501(+) CAGATA/GTACTC 2 -- ut31 ese313Minor allele frequency- N:0.00EA NA EU WA 2250
rs359026611,2
C,F143548867(-) TGCAGT/CTCTAC 2 A/V mis15Minor allele frequency- C:0.00NA EU EA WA 488
rs168522631,2
F,H143512609(+) TATACT/CGGAGG 2 -- ut31 ese37Minor allele frequency- C:0.04NA EU EA WA 562
rs352145101,2
C,F143605289(-) AGAAAA/GGTGGT 2 S/G mis15Minor allele frequency- G:0.01NA EU EA WA 490
--
rs126957571,2
A,C143507926(+) aaATTA/Taaaaa 2 -- ng510--------
rs23067001,2
C,F,H143606531(+) AGGCAC/TTCACT 2 E/E syn1 ese313Minor allele frequency- T:0.12EA NA EU WA 2540
rs28627451,2
A,C,F,H,O143554622(-) ATATGC/TATTCC 2 -- int18Minor allele frequency- N:0.00EU EA WA NA 636
rs28627431,2
A,C,F,H,O143595262(-) ACAGTA/GAGATG 2 -- int17Minor allele frequency- G:0.37EA WA NA 514
rs76526871,2
A,C,F,H143605966(+) GGAAGA/GTGAGA 2 -- int17Minor allele frequency- G:0.48NA EU EA WA 550
About this table

HapMap Linkage Disequilibrium images for XRN1 (up to first 250kb)

(in which this Gene is Involved, According to OMIM, UniProtKB, PharmGKB, Genatlas, GeneTests, Blood group antigen gene mutations by BGMUT, HGMD, GAD, HuGE Navigator, BCGD, and/or TGDB.)
About This Section

OMIM: 607994

(Possibly Related Articles in Doctor's Guide)
About This Section

  --

(in PubMed. Associations of this gene to articles via 1Novoseek, 2HGNC, 3Entrez Gene, 4UniProtKB/Swiss-Prot, 5UniProtKB/TrEMBL, 6GAD, and/or 7PharmGKB)
About This Section

10/16 PubMed articles for XRN1 gene (see all 16 ):
(in PubMed, OMIM, and NCBI Bookshelf)
About This Section

 ANDOR
Aliases
Free Text  

  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)
(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, and/or H-InvDB)
About This Section

Entrez Gene: 54464 HGNC: 30654 AceView: XRN1 Ensembl:ENSG00000114127 euGenes: HUgn54464
ECgene: XRN1 H-InvDB: XRN1
(According to HUGE)
About This Section

  --
(According to ATLAS, HORDE, IMGT, MTDB, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section

  --
(Available from WIS Yeda, Salk, Tufts)
About This Section

  --
(Reagents available from Applied Biosystems, Antibodies and assays by Cell Signaling Technology, Abcam, Novus Biologicals,
Sigma-Aldrich, R&D Systems, Millipore, Abnova, and/or Invitrogen, Clones available from OriGene,and/or Invitrogen, Drugs and/or compounds by Sigma-Aldrich,
Enzo Life Sciences, and/or Tocris Bioscience)
About This Section



Products for XRN1:
 TaqMan ® Gene Expression Assays
 TaqMan ® Genotyping Assays
  Free SNP selection tool



  Invitrogen iPath Pathways  Invitrogen BLOCK-iT™ RNAi
  Invitrogen Antibodies  Invitrogen Assays
  Invitrogen Clones  Invitrogen Q-PCR Products
  Invitrogen Human Recombinant Kinases  Invitrogen Custom Antibody and Peptide Service
  Invitrogen Proteins / Assays / Screening Services  Search Invitrogen catalog for XRN1-related products

 Millipore Custom Antibody & Bulk Services
 Millipore Preclinical / Clinical Development Services
 Millipore Immunoassay Services
 Millipore Target Screening & Profiling Services


 Predesigned and custom siRNAs for XRN1 Browse antibodies at Sigma-Aldrich
 Explore super-pooled esiRNAs Browse proteins at Sigma-Aldrich
 Lentivirus-delivered shRNAs for XRN1 Browse small molecules at Sigma-Aldrich
 "Your Favorite Gene" Pathwaysfeedback


  
 Antibodies   Primer Pairs  
 Cell Culture Products   ELISAs  
 Flow Cytometry Kits   Protease Activity Assays & Reagents  
 Cell Selection/Detection Kits & Reagents   ELISA/Assay Development Kits & Reagents  
 Multiplex/Array Assay Kits & Reagents   ELISpot Kits & Development Modules  
 Recombinant & Natural Proteins  

 Recombinant Proteins (XRN1)
 Antibodies (XRN1)
 Search for Chimera RNAi
 Custom Service for Mouse Mab
 Custom Service for Rabbit Pab from Full-length Protein
  
 Search for Antibodies & Assays

 Recombinant Proteins
(Xrn1)
 Antibodies (Xrn1)
 Search OriGene for XRN1
 Search Tocris compounds for XRN1




 Search www.enzolifesicences.com for proteins, assays, substrates, inhibitors & antibodies
 Antibodies for XRN1

GeneCards Homepage    -    Last full update: 2 Jul 2009        Incremental update: 13 Oct 2009

Random Gene From GIFtS : about GIFtS

Gene Index:   3   5   A   B   C   D   E   F   G   H   I   J   K   L   M   N   O   P   Q   R   S   T   U   V   W   X   Y   Z

Developed at the Crown Human Genome Center & Weizmann Institute of Science



The GeneCards Human Gene Database: Copyright © 1996-2009, Weizmann Institute of Science. All Rights Reserved.
XRN1 Gene at Home site.
Version 2.41.1
server5.xennexinc.com