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XRN2 Gene

protein-coding   GIFtS: 62
GCID: GC20P021283

5'-3' Exoribonuclease 2

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(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
5'-3' Exoribonuclease 21 2
DHP Protein2 3
Dhm1-Like Protein (Mouse Homolog)2
EC 3.1.13.-3
DHM1-Like Protein3
EC 3.1.138

External Ids:    HGNC: 128361   Entrez Gene: 228032   Ensembl: ENSG000000889307   OMIM: 6088515   UniProtKB: Q9H0D63   

Export aliases for XRN2 gene to outside databases

Previous GC identifers: GC20P021272 GC20P021278 GC20P021231


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for XRN2 Gene:
This gene shares similarity with the mouse Dhm1 and the yeast dhp1 gene. The yeast gene is involved in homologous
recombination and RNA metabolism, such as RNA synthesis and RNA trafficking. Complementation studies show that
Dhm1 has a similar function in mouse as dhp1. The function of the human gene has not yet been determined.
Transcript variants encoding different isoforms have been noted for this gene; however, their full-length nature
is not known. (provided by RefSeq, Jul 2008)

GeneCards Summary for XRN2 Gene:
XRN2 (5'-3' exoribonuclease 2) is a protein-coding gene. GO annotations related to this gene include 5'-3' exonuclease activity and nucleic acid binding.

UniProtKB/Swiss-Prot: XRN2_HUMAN, Q9H0D6
Function: Possesses 5'->3' exoribonuclease activity (By similarity). May promote the termination of transcription
by RNA polymerase II. During transcription termination, cleavage at the polyadenylation site liberates a 5'
fragment which is subsequently processed to form the mature mRNA and a 3' fragment which remains attached to the
elongating polymerase. The processive degradation of this 3' fragment by this protein may promote termination of
transcription

Gene Wiki entry for XRN2 (5'-3' exoribonuclease 2) Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000020.10  NC_018931.2  NT_011387.9  
Regulatory elements:
   Regulatory transcription factor binding sites in the XRN2 gene promoter:
         AP-2rep   AML1a   C/EBPalpha   Egr-2   AREB6   CREB   NRF-2   deltaCREB   HSF2   c-Myb   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 4): XRN2 promoter sequence
   Search Chromatin IP Primers for XRN2

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat XRN2


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 20p11.2-p11.1   Ensembl cytogenetic band:  20p11.23   HGNC cytogenetic band: 20p11.2-p11.1

XRN2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
XRN2 gene location

GeneLoc information about chromosome 20         GeneLoc Exon Structure

GeneLoc location for GC20P021283:  view genomic region     (about GC identifiers)

Start:
21,283,942 bp from pter      End:
21,370,463 bp from pter
Size:
86,522 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: XRN2_HUMAN, Q9H0D6 (See protein sequence)
Recommended Name: 5'-3' exoribonuclease 2  
Size: 950 amino acids; 108582 Da
Sequence caution: Sequence=AAR24369.1; Type=Frameshift; Positions=73; Sequence=BAA90934.1; Type=Erroneous
initiation;
Secondary accessions: Q3L8N4 Q6KGZ9 Q9BQL1 Q9NTW0 Q9NXS6 Q9UL53
Alternative splicing: 2 isoforms:  Q9H0D6-1   Q9H0D6-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for XRN2: NX_Q9H0D6

Explore proteomics data for XRN2 at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys172, Lys517, Lys533
  • Modification sites at PhosphoSitePlus
  • Selected DME Specific Peptides for XRN2 (Q9H0D6) (see all 22)
     KECNGVK  PNTHHCL  DFYPEDF  EDEMMVA 


    See XRN2 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_036387.2  
    ENSEMBL proteins: 
     ENSP00000366396   ENSP00000441113   ENSP00000413548  
    Reactome Protein details: Q9H0D6

    XRN2 Human Recombinant Protein Products:

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    Novus Biologicals XRN2 Protein
    Novus Biologicals XRN2 Lysate
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    Cloud-Clone Corp. Proteins for XRN2

     
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    antibodies-online proteins for XRN2 (2 products) 

     
    antibodies-online peptides for XRN2

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    antibodies-online antibodies for XRN2 (24 products) 

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    antibodies-online kits for XRN2 (3 products) 


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    4 InterPro protein domains:
     IPR017151 5_3_exoribonuclease_2
     IPR004859 Put_53exo
     IPR027073 5_3_exoribonuclease
     IPR001878 Znf_CCHC

    Graphical View of Domain Structure for InterPro Entry Q9H0D6

    ProtoNet protein and cluster: Q9H0D6

    2 Blocks protein domains:
    IPB001878 C2HC-type zinc-finger signature
    IPB004859 Putative 5-3 exonuclease domain


    UniProtKB/Swiss-Prot: XRN2_HUMAN, Q9H0D6
    Similarity: Belongs to the 5'-3' exonuclease family. XRN2/RAT1 subfamily
    Similarity: Contains 1 CCHC-type zinc finger


    Find genes that share domains with XRN2           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: XRN2_HUMAN, Q9H0D6
    Function: Possesses 5'->3' exoribonuclease activity (By similarity). May promote the termination of transcription
    by RNA polymerase II. During transcription termination, cleavage at the polyadenylation site liberates a 5'
    fragment which is subsequently processed to form the mature mRNA and a 3' fragment which remains attached to the
    elongating polymerase. The processive degradation of this 3' fragment by this protein may promote termination of
    transcription
    Catalytic activity: Exonucleolytic cleavage in the 5'- to 3'-direction to yield nucleoside 5'-phosphates

         Genatlas biochemistry entry for XRN2:
    murine DHM1 gene homolog,5'-3' exoribonuclease 2,highly expressed in the testis,involved in homologous
    recomnbination

         Enzyme Numbers (IUBMB): EC 3.1.13.-1 EC 3.1.132

         Gene Ontology (GO): Selected molecular function terms (see all 8):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003676nucleic acid binding ----
    GO:0004518nuclease activity TAS10409438
    GO:0004527exonuclease activity ----
    GO:00045345'-3' exoribonuclease activity TAS10409438
    GO:0005515protein binding ----
         
    Find genes that share ontologies with XRN2           About GenesLikeMe


    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for XRN2

    miRNA
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    miRTarBase miRNAs that target XRN2:
    hsa-mir-186-5p (MIRT045038), hsa-mir-9-5p (MIRT021397), hsa-mir-760 (MIRT036710)

    Block miRNA regulation of human, mouse, rat XRN2 using miScript Target Protectors
    7 qRT-PCR Assays for microRNAs that regulate XRN2:
    hsa-miR-2052 hsa-miR-548am hsa-miR-548x hsa-miR-548c-3p hsa-miR-606 hsa-miR-3153 hsa-miR-3692
    SwitchGear 3'UTR luciferase reporter plasmidXRN2 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat XRN2

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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat XRN2

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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    XRN2_HUMAN, Q9H0D6: Nucleus, nucleolus
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5
    cytosol1
    mitochondrion1

    Gene Ontology (GO): 4 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005622intracellular ----
    GO:0005634nucleus IDA--
    GO:0005730nucleolus IDA--
    GO:0016235aggresome IDA--

    Find genes that share ontologies with XRN2           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    SuperPaths for XRN2 About    
    See pathways by source

    SuperPathContained pathways About
    1Protein folding
    Chaperonin-mediated protein folding0.91
    Association of TriC/CCT with target proteins during biosynthesis0.58
    Protein folding0.91
    2Deadenylation-dependent mRNA decay
    RNA degradation0.48
    3mRNA Splicing - Major Pathway
    mRNA processing0.44
    4Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein
    Metabolism of proteins0.30
    5Ribosome biogenesis in eukaryotes
    Ribosome biogenesis in eukaryotes


    Find genes that share SuperPaths with XRN2           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways


    1 BioSystems Pathway for XRN2
        mRNA processing

    1 Reactome Pathway for XRN2
        Association of TriC/CCT with target proteins during biosynthesis


    2 Kegg Pathways  (Kegg details for XRN2):
        Ribosome biogenesis in eukaryotes
    RNA degradation

        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for XRN2
    Interactions:

        GeneGlobe Interaction Network for XRN2

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for XRN2 (Q9H0D62, 3 ENSP000003663964) via UniProtKB, MINT, STRING, and/or I2D (see all 1004)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    UPF2Q9HAU52, 3, ENSP000003487084MINT-7945693 MINT-7947479 I2D: score=4 STRING: ENSP00000348708
    EEF1A1P681042, 3, ENSP000003300544MINT-7945693 MINT-7947479 I2D: score=3 STRING: ENSP00000330054
    EIF3LQ9Y2622, 3, ENSP000004168924MINT-7945693 I2D: score=3 STRING: ENSP00000416892
    DXOO779323, ENSP000003377594I2D: score=4 STRING: ENSP00000337759
    ENSG00000236765O779323, ENSP000003911234I2D: score=4 STRING: ENSP00000391123
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 11):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000738DNA catabolic process, exonucleolytic IDA15565158
    GO:0006139nucleobase-containing compound metabolic process ----
    GO:0006353DNA-templated transcription, termination IEA--
    GO:0006355regulation of transcription, DNA-templated IEA--
    GO:0006396RNA processing TAS10409438

    Find genes that share ontologies with XRN2           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for XRN2



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for XRN2 gene: 
    NM_012255.3  

    Unigene Cluster for XRN2:

    5'-3' exoribonuclease 2
    Hs.255932  [show with all ESTs]
    Unigene Representative Sequence: BC142960
    3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000377191(uc002wsf.1 uc002wsg.1) ENST00000539513(uc010zsk.1 uc002wsh.1)
    ENST00000430571
    miRNA
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    7 qRT-PCR Assays for microRNAs that regulate XRN2:
    hsa-miR-2052 hsa-miR-548am hsa-miR-548x hsa-miR-548c-3p hsa-miR-606 hsa-miR-3153 hsa-miR-3692
    SwitchGear 3'UTR luciferase reporter plasmidXRN2 3' UTR sequence
    Inhib. RNA
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    Primer
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    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat XRN2
      QuantiTect SYBR Green Assays in human, mouse, rat XRN2
      QuantiFast Probe-based Assays in human, mouse, rat XRN2

    Additional mRNA sequence: 

    AF064257.1 AF152169.1 AK000084.1 AK001573.1 AK172858.1 AK302846.1 AK303312.1 AK314602.1 
    AL136841.1 AY382900.1 BC000315.2 BC006417.1 BC032075.2 BC131775.1 BC142960.1 

    24 DOTS entries:

    DT.101976662  DT.416242  DT.102832941  DT.97847492  DT.439293  DT.100808866  DT.92062355  DT.75101626 
    DT.75168600  DT.100810382  DT.91805915  DT.91858750  DT.92409492  DT.95185286  DT.95221799  DT.100810389 
    DT.102832940  DT.102832943  DT.120807525  DT.95218276  DT.95221798  DT.95221814  DT.99961805  DT.99982457 

    Selected AceView cDNA sequences (see all 379):

    BP364827 BX102929 CA775812 AU133908 CR607652 AI758685 BQ936061 AA323017 
    AL136841 AW250130 AA354795 BU186202 AU133886 AI796426 BM729186 AW196349 
    BX953011 AI372022 BU176486 AW242471 AK001573 BF446617 BM456556 BM821448 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for XRN2 (see all 7)    About this scheme

    ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3 ^ 4 ^ 5a · 5b ^ 6 ^ 7a · 7b ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15a · 15b ^ 16 ^ 17a · 17b ^ 18 ^ 19 ^
    SP1:                          -                       -                                                                                         -               
    SP2:                          -     -                 -                                                                                         -               
    SP3:                                                  -                                                                                                         
    SP4:                          -     -     -     -     -     -     -     -     -     -     -     -     -     -     -     -     -     -     -     -     -     -   
    SP5:                          -                                                                                                                                 

    ExUns: 20 ^ 21 ^ 22 ^ 23a · 23b ^ 24 ^ 25 ^ 26 ^ 27 ^ 28 ^ 29 ^ 30 ^ 31a · 31b
    SP1:                          -                                                         
    SP2:                          -                                                         
    SP3:                                                                                    
    SP4:  -     -     -     -     -     -     -     -     -     -                           
    SP5:                                                                                    


    ECgene alternative splicing isoforms for XRN2

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    XRN2 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: CTGATTTTTA
    XRN2 Expression
    About this image


    XRN2 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 7) fully expand
     
     Brain (Nervous System)    fully expand to see all 4 entries
             Cerebral Cortex
     
     Ovary (Reproductive System)    fully expand to see all 2 entries
             Ovarian Mesenchymal Stroma Cells Ovary Interstitium
             Oviduct
     
     Trophoblast (Extraembryonic Tissues)
             Trophoblast Cells Trophoblast
     
     Pancreas (Endocrine System)
             Islets of Langerhans
     
     Testis (Reproductive System)
             Leydig Cells Testis Interstitium
    XRN2 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    XRN2 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.255932

    UniProtKB/Swiss-Prot: XRN2_HUMAN, Q9H0D6
    Tissue specificity: Expressed in the spleen, thymus, prostate, testis, ovary, small intestine, colon, peripheral
    blood leukocytes, heart, brain, placenta, lung, liver, skeletal muscle, kidney, and pancreas. Isoform 2 is
    expressed predominantly in peripheral blood leukocytes

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    In Situ
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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of eukaryotes.

    Orthologs for XRN2 gene from Selected species (see all 25)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Xrn21 , 5 5'-3' exoribonuclease 21, 5 92.35(n)1
    96.11(a)1
      2 (72.63 cM)5
    241281  NM_011917.21  NP_036047.21 
     1470129965 
    chicken
    (Gallus gallus)
    Aves XRN21 5'-3' exoribonuclease 2 78.99(n)
    83.47(a)
      421236  NM_001031033.1  NP_001026204.1 
    lizard
    (Anolis carolinensis)
    Reptilia XRN26
    5'-3' exoribonuclease 2
    81(a)
    1 ↔ 1
    4(81316733-81372659)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia Str.12102 Transcribed sequence with moderate similarity to protein more 81.61(n)    142003644 
    zebrafish
    (Danio rerio)
    Actinopterygii idibd10902 Danio rerio mRNA similar to 5'-3' exoribonuclease 2 more 74.74(n)    BC047182.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG103543
    Rat11
    5'-3' exoribonuclease3
    Rat11
    44(a)
    (best of 2)3
    56.68(n)1
    59.82(a)1
      27C43
    339641  NM_001273237.11  NP_001260166.11 
    worm
    (Caenorhabditis elegans)
    Secernentea Y48B6A.33
    xrn-21
    xrn-21 54(a)
    (best of 2)3
    57.91(n)1
    58.96(a)1
      II(14155604-14158131)3
    1750711  NM_064557.51  NP_496958.21 
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes RAT1(YOR048C)4
    RAT11
    Nuclear 5' to 3' single-stranded RNA exonuclease, involved more4
    RAT11
    57.22(n)1
    54.43(a)1
      15(421650-418630)4
    8542131, 4  NP_014691.11, 4 
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons XRN31 XRN3 54.79(n)
    48.12(a)
      843900  NM_106217.2  NP_565114.1 
    rice
    (Oryza sativa)
    Liliopsida Os.193682 Oryza sativa (japonica cultivar-group) cDNA cloneJ more 73.93(n)    AK070933.1 


    ENSEMBL Gene Tree for XRN2 (if available)
    TreeFam Gene Tree for XRN2 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for XRN2 gene
    1 SIMAP similar gene for XRN2 using alignment to 3 protein entries:     XRN2_HUMAN (see all proteins):
    XRN1

    Find genes that share paralogs with XRN2           About GenesLikeMe



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for XRN2 (see all 1731)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 20 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs37612871,2
    C,F--21281988(+) GAATCG/ACTTGA 1 -- us2k16Minor allele frequency- A:0.50NA WA 12
    rs1845547321,2
    --21282213(+) TCTTAC/TCTTTT 1 -- us2k10--------
    rs1455442901,2
    C--21282226(+) CGTTCA/GCGCAC 1 -- us2k10--------
    rs1892496021,2
    --21282423(+) ATCAGC/TGGGGT 1 -- us2k10--------
    rs37612881,2
    C,F,A,H--21282545(+) CCTGGA/GTGACT 1 -- us2k17Minor allele frequency- G:0.24NA WA EA 370
    rs1488547691,2
    C--21282880(+) CTGTGA/CGGTAA 1 -- us2k10--------
    rs344591851,2
    C,F--21282895(+) GCGAAA/CTACTT 1 -- us2k11Minor allele frequency- C:0.03NA 120
    rs1812167451,2
    --21282920(+) TGAGGA/TGAGCA 1 -- us2k10--------
    rs1453247891,2
    --21283044(+) AAATTA/CGTTTG 1 -- us2k10--------
    rs1464335141,2
    --21283051(+) TTTGGA/GACCAC 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for XRN2 (21283942 - 21370463 bp)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for XRN2 (see all 13):    About this table    
    Variant IDTypeSubtypePubMed ID
    esv1596170CNV Deletion17803354
    esv2722286CNV Deletion23290073
    esv2458583CNV Deletion19546169
    esv2276285CNV Deletion18987734
    nsv820835CNV Deletion20802225
    esv1007546CNV Deletion20482838
    nsv179550CNV Loss16902084
    esv2579624CNV Loss19546169
    nsv912813CNV Loss21882294
    nsv512606CNV Loss21212237

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing XRN2
    DNA2.0 Custom Variant and Variant Library Synthesis for XRN2

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 608851    OMIM disorders: --


    Find genes that share disorders with XRN2           About GenesLikeMe


    Export disorders for XRN2 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for XRN2 gene, integrated from 10 sources (see all 54):
    (articles sorted by number of sources associating them with XRN2)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Cloning and mapping of the XRN2 gene to human chromosome 20p11.1- p11.2. (PubMed id 10409438)1, 2, 3, 9 Zhang M.... Zhao S.Y. (Genomics 1999)
    2. A novel splice variant of human XRN2 gene is mainly expressed in blood leukocyte. (PubMed id 16147866)1, 2, 9 Li J.... Mao Y. (DNA Seq. 2005)
    3. A probability-based approach for high-throughput protein phosphorylation analysis and site localization. (PubMed id 16964243)1, 2 Beausoleil S.A.... Gygi S.P. (Nat. Biotechnol. 2006)
    4. Pause sites promote transcriptional termination of mammalian RNA polymerase II. (PubMed id 16648491)1, 2 Gromak N.... Proudfoot N.J. (Mol. Cell. Biol. 2006)
    5. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PubMed id 17081983)1, 2 Olsen J.V....Mann M. (Cell 2006)
    6. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    7. Human 5' -> 3' exonuclease Xrn2 promotes transcription termination at co-transcriptional cleavage sites. (PubMed id 15565158)1, 2 West S.... Proudfoot N.J. (Nature 2004)
    8. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    9. Functional proteomic analysis of human nucleolus. (PubMed id 12429849)1, 2 Scherl A.... Diaz J.-J. (Mol. Biol. Cell 2002)
    10. The DNA sequence and comparative analysis of human chromosome 20. (PubMed id 11780052)1, 2 Deloukas P....Rogers J. (Nature 2001)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     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, Kegg, and/or H-InvDB)
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    Entrez Gene: 22803 HGNC: 12836 AceView: XRN2 Ensembl:ENSG00000088930 euGenes: HUgn22803
    ECgene: XRN2 Kegg: 22803 H-InvDB: XRN2

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for XRN2 Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for XRN2 Genetics and Cytogenetics in Oncology and Haematology

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for XRN2 gene:
    Search GeneIP for patents involving XRN2

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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