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Aliases & Descriptions for XRN1
(According to
1 HGNC ,
2 Entrez Gene ,
3 UniProtKB/Swiss-Prot ,
4 UniProtKB/TrEMBL , 5 OMIM , 6 GeneLoc
, and/or 7 Ensembl ,
8 miRBase )About This Section
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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
Search outside databases for aliases for XRN1 genePrevious GC identifer: GC03M139058
Summaries for XRN1 (According to Entrez Gene ,
Wikipedia's
Gene Wiki ,
UniProtKB/Swiss-Prot ,
and/or
UniProtKB/TrEMBL )
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EntrezGene summary for XRN1 : SEP1 localizes to cytoplasmic foci containing a complex of mRNA-degrading enzymes. In addition tomRNA metabolism, yeast Sep1 has been implicated in a variety of nuclear and cytoplasmic functions,including homologous recombination, meiosis, telomere maintenance, and microtubuleassembly.[supplied by OMIM] UniProtKB/Swiss-Prot: XRN1_HUMAN, Q8IZH2 Function : Major 5'-3' exoribonuclease involved in mRNA decay. Required for the 5'-3'processing ofthe G4 tetraplex-containing DNA and RNA substrates. The kinetic of hydrolysis is faster for G4 RNAtetraplex than for G4 DNA tetraplex and monomeric RNA tetraplex. Binds to RNA and DNA (Bysimilarity). May act as a tumor suppressor protein in osteogenic sarcoma (OGS)
Genomic Location for XRN1
(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
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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 Proteins for XRN1
(According to
1 UniProtKB ,
and/or Ensembl ,
Phosphorylation sites according to 2 Phosphosite ,
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 )
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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 withRENT1, 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 Q9UF39Alternative 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 Origene for full length recombinant human proteins expressed in human HEK293 cells 2 Gene Ontology (GO) cellular component terms (links to tree view) :
About this table Antibodies for XRN1: Assays for XRN1:
Protein
Domains/ Families for XRN1(According to InterPro , ProtoNet ,
UniProtKB , and/or BLOCKS ,
Sets of similar genes according to GeneDecks )
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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
Gene Function for XRN1
(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
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Millipore ,
OriGene , and/or
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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 .)
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               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                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 ofthe G4 tetraplex-containing DNA and RNA substrates. The kinetic of hydrolysis is faster for G4 RNAtetraplex than for G4 DNA tetraplex and monomeric RNA tetraplex. Binds to RNA and DNA (Bysimilarity). May act as a tumor suppressor protein in osteogenic sarcoma (OGS) Induction : By GDNFEnzyme Number (IUBMB): EC 3.1.11.-
5 Gene Ontology (GO) molecular function terms (links to tree view) :
About this table
Pathways & Interactions for XRN1
(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 1 UniProtKB ,
2 MINT , and/or
3 STRING ,
with links to IntAct and
Ensembl ,
Ontologies according to Gene Ontology Consortium 01 Apr 2009 via
Entrez Gene .)
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5/42 Interacting proteins for XRN1 (ENSP00000264951 3 Q8IZH2 1 ) via UniProtKB, MINT, and/or STRING (see all 42
)About this table 2 Gene Ontology (GO) biological process terms (links to tree view) :
GO ID Qualified GO term Evidence PubMed IDs GO:0006139 nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
IEA -- GO:0045786 negative regulation of cell cycle
IEA --
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Drugs & Compounds for XRN1 (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 )
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Browse Tocris compounds for XRN1
Transcripts 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
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               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
Expression for XRN1
(Experimental results according to
1 GeneNote
and GNF BioGPS ,
probe sets-to-genes annotations according to
2 GeneAnnot ,
3 GeneTide ,
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
)
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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 Data from
(Publications) and GNF BioGPS About these images About these images CGAP SAGE TAG: TTAAATGCTCSOURCE 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 for XRN1
(Orthologs according to
1,2 HomoloGene (2 older version, for species not in 1 newer version),
3 euGenes ,
4 SGD
and/or
5 MGI Jun 06 2009,
with possible further links to
Flybase
and/or
WormBase ,
Gene Trees according to Ensembl )
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Orthologs for XRN1 gene from 5/19 species (see all 19
)
About this table Species with no ortholog for XRN1 ENSEMBL Gene Tree for XRN1 Paralogs for XRN1 (Paralogs according to 1 HomoloGene and 2 Ensembl , Pseudogenes according to 3 Pseudogene.org )About This Section
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Paralogs for XRN1 gene XRN2 2
SNPs/Variants for XRN1 (According to the
1 NCBI SNP Database ,
2 Ensembl ,
3 PupaSUITE , and
UniProtKB ,
Linkage Disequilibrium by HapMap ,
Genotyping Reagents from
Applied Biosystems )
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HapMap Linkage Disequilibrium images for XRN1 (up to first 250kb)
Disorders & Mutations for XRN1
(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 .)
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OMIM: 607994
Medical News for XRN1 (Possibly Related Articles in
Doctor's Guide )
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--
Publications for XRN1 (in
PubMed .
Associations of this gene to articles via
1 Novoseek ,
2 HGNC ,
3 Entrez Gene ,
4 UniProtKB/Swiss-Prot ,
5 UniProtKB/TrEMBL ,
6 GAD , and/or
7 PharmGKB )
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10/16 PubMed articles for XRN1 gene (see all 16
): The human LSm1-7 proteins colocalize with the mRNA-degrading enzymes Dcp1/2 and Xrnl in distinct cytoplasmic foci. (PubMed id 12515382) 2, 3, 4 Ingelfinger D....Achsel T. (2002) Identification of human SEP1 as a glial cell line-derived neurotrophic factor-inducible protein and its expression in the nervous system. (PubMed id 14580940) 1, 3, 4 Shimoyama Y.... Takahashi M. (2003) Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PubMed id 17081983) 3, 4 Olsen J.V....Mann M. (2006) The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334) 3, 4 Gerhard D.S....Malek J. (2004) Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039) 3, 4 Ota T....Sugano S. (2004) Nonsense-mediated mRNA decay in mammalian cells involves decapping, deadenylating, and exonucleolytic activities. (PubMed id 14527413) 3, 4 Lejeune F.... Maquat L.E. (2003) The human homolog of yeast SEP1 is a novel candidate tumor suppressor gene in osteogenic sarcoma. (PubMed id 12426100) 3, 4 Zhang K....Sarkar G. (2002) Cloning and characterization of human Sep1 (hSEP1) gene and cytoplasmic localization of its product. (PubMed id 9802570) 3, 4 Sato Y....Furuichi Y. (1998) The full-ORF clone resource of the German cDNA Consortium. (PubMed id 17974005) 4 Bechtel S....Schupp I. (2007) A protein interaction framework for human mRNA degradation. (PubMed id 15231747) 3 Lehner B. and Sanderson C.M. (2004)
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Genome Databases showing XRN1
(According to
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Ensembl ,
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and/or
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(According to HUGE )
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Specialized Databases showing XRN1 (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
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-- Services for XRN1 (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
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