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PARN Gene

protein-coding   GIFtS: 56

GC16M014437
poly(A)-specific ribonuclease (deadenylation nuclease)
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
DAN 1, 2, 3, 5
EC 3.1.13.4 3
Descriptions
Deadenylating nuclease 2, 3
Deadenylation nuclease 3
Polyadenylate-specific ribonuclease 3
poly(A)-specific ribonuclease (deadenylation nuclease) 2
External Ids
HGNC: 86091
Entrez Gene: 50732
UniProtKB: O954533
Ensembl: ENSG000001406947
Search outside databases for aliases for PARN gene

Previous GC identifers: GC16M014478 GC16P017836 GC16M014495

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

EntrezGene summary for PARN:
The protein encoded by this gene is a 3'-exoribonuclease, with similarity to the RNase D
family of 3'-exonucleases. It prefers poly(A) as the substrate, hence, efficiently degrades
poly(A) tails of mRNAs. Exonucleolytic degradation of the poly(A) tail is often the first step in
the decay of eukaryotic mRNAs. This protein is also involved in silencing of certain maternal
mRNAs during oocyte maturation and early embryonic development, as well as in nonsense-mediated
decay (NMD) of mRNAs that contain premature stop codons. Alternatively spliced transcript variants
encoding different isoforms have been found for this gene. [provided by RefSeq]

UniProtKB/Swiss-Prot: PARN_HUMAN, O95453
Function: 3'-exoribonuclease that has a preference for poly(A) tails of mRNAs, thereby efficiently
degrading poly(A) tails. Exonucleolytic degradation of the poly(A) tail is often the first step in
the decay of eukaryotic mRNAs and is also used to silence certain maternal mRNAs translationally
during oocyte maturation and early embryonic development. Interacts with both the 3'-end poly(A)
tail and the 5'-end cap structure during degradation, the interaction with the cap structure being
required for an efficient degradation of poly(A) tails. Involved in nonsense-mediated mRNA decay,
a critical process of selective degradation of mRNAs that contain premature stop codons. Also
involved in degradation of inherently unstable mRNAs that contain AU-rich elements (AREs) in their
3'-UTR, possibly via its interaction with KHSRP. Probably mediates the removal of poly(A) tails of
AREs mRNAs, which constitutes the first step of destabilization

Gene Wiki entry for PARN

(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 PARN gene  

Entrez Gene cytogenetic band: 16p13   Ensembl cytogenetic band:  16p13.12   HGNC cytogenetic band: 16p13

PARN 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 16         GeneLoc Exon Structure

GeneLoc location for GC16M014437:     (about GC identifiers)

Start:
14,437,060 bp from pter
End:
14,640,920 bp from pter
Size:
203,861 bases
Orientation:
minus strand
RefSeq DNA sequence:
NC_000016.8  NT_010393.15  
(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: PARN_HUMAN, O95453 (See protein sequence)
Recommended Name: Poly(A)-specific ribonuclease PARN  
Size: 639 amino acids; 73451 Da
Cofactor: Divalent metal cations. Mg(2+) is the most probable
Subunit: Homodimer. Interacts with KHSRP and CUGBP1. Found in a mRNA decay complex with RENT1,
RENT2 and RENT3B
Subcellular location: Nucleus. Cytoplasm. Nucleus, nucleolus. Note=Some nuclear fraction is
nucleolar
PDB structures from and Proteopedia :
2A1R (3D)    2A1S (3D)    3CTR (3D)    

Post-translational modifications:

  • View phosphorylation sites using PhosphoSite2


  • REFSEQ proteins (2 alternative transcripts): 
    NP_001127949.1  NP_002573.1  


    ENSEMBL proteins: 
    ENSP00000345456 


    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 (PARN)
    Human Recombinant Proteins from Abnova (PARN)
                  OriGene Purified Recombinant Human Protein: PARN 

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634 nucleus TAS9736620
    GO:0005737 cytoplasm TAS9736620
    About this table

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

    Assays for PARN: 
    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

    4 InterPro domains/families:
     IPR006941 RNase_CAF1
     IPR001374 R3H_ss_bd
     IPR014789 PolyA-riboNase_RNA_binding
     IPR012677 a_b_plait_nuc_bd


       GeneDecks  PARN for the domains selected above  
    About GeneDecksing

    Graphical View of Domain Structure for InterPro Entry O95453

    ProtoNet protein and cluster: O95453

    1 Blocks protein family: IPB001374 Single-stranded nucleic acid binding R3H

    UniProtKB/Swiss-Prot: PARN_HUMAN, O95453
    Similarity: Belongs to the CAF1 family
    Similarity: Contains 1 R3H domain

    (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 (PARN)
    Browse for Gene Knock-down Tools from Millipore
    Abnova Chimera RNAi Products for Gene knock-down (PARN)
                   OriGene 29mer shRNA kit in GFP-retroviral vectors (see all 2): NM_001134477

                  Applied Biosystems Silencer® siRNAs for PARN

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

    Clones:Invitrogen Clones for PARN
    Browse Clones for the Expression of Recombinant Proteins Available from Millipore
                   OriGene GFP tagged cDNA clones in CMV expression vector (see all 2): NM_001134477
                                     Myc/DDK tagged cDNA clones in CMV expression vector (see all 2): NM_001134477
                                     untagged cDNA clones in CMV expression vector (see all 2): NM_001134477 

    Primers: Browse Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers
                  OriGene genome-wide validated SYBR primer pairs: NM_002582

    UniProtKB/Swiss-Prot: PARN_HUMAN, O95453
    Function: 3'-exoribonuclease that has a preference for poly(A) tails of mRNAs, thereby efficiently
    degrading poly(A) tails. Exonucleolytic degradation of the poly(A) tail is often the first step in
    the decay of eukaryotic mRNAs and is also used to silence certain maternal mRNAs translationally
    during oocyte maturation and early embryonic development. Interacts with both the 3'-end poly(A)
    tail and the 5'-end cap structure during degradation, the interaction with the cap structure being
    required for an efficient degradation of poly(A) tails. Involved in nonsense-mediated mRNA decay,
    a critical process of selective degradation of mRNAs that contain premature stop codons. Also
    involved in degradation of inherently unstable mRNAs that contain AU-rich elements (AREs) in their
    3'-UTR, possibly via its interaction with KHSRP. Probably mediates the removal of poly(A) tails of
    AREs mRNAs, which constitutes the first step of destabilization
    Catalytic activity: Exonucleolytic cleavage of poly(A) to 5'-AMP
    Enzyme Number (IUBMB): EC 3.1.13.4 

    Genatlas biochemistry entry for PARN:
    poly A specific ribonuclease,deadenylation nuclease,ubiquitously expressed,degrading poly A tail of
    mRNA molecules

    5/8 Gene Ontology (GO) molecular function terms (links to tree view) (see all 8 ):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000166 nucleotide binding IEA--
    GO:0000287 magnesium ion binding IEA--
    GO:0003723 RNA binding IEA--
    GO:0003730 mRNA 3'-UTR binding TAS9736620
    GO:0004527 exonuclease 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


     Gene Network CentralTM Interacting Genes and Proteins Network for  PARN 


    5/11 Interacting proteins for PARN (O954531 ENSP000003454563) via UniProtKB, MINT, and/or STRING (see all 11 )
    InteractantInteraction Details
    GeneCardExternal ID(s)
    C21orf56Q9H0A91EBI-372832, EBI-372911
    MPHOSPH6Q995471EBI-372832, EBI-373187
    KHSRPENSP000002018863STRING (score=.94)
    CUGBP1ENSP000003514093STRING (score=.909)
    RNASENENSP000003398453STRING (score=.869)
    About this table

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay IEA--
    GO:0006402 mRNA catabolic process IEA--
    GO:0007292 female gamete generation TAS9736620
    GO:0009451 RNA modification TAS9736620
    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 PARN

    (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 (PARN)
    Browse for Gene Knock-down Tools from Millipore
    Abnova Chimera RNAi Products for Gene knock-down (PARN)
                   OriGene 29mer shRNA kit in GFP-retroviral vectors (see all 2): NM_001134477

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

    Applied Biosystems Silencer® siRNAs: 

    NM_001134477  NM_002582  

    REFSEQ mRNAs for PARN gene (2 alternative transcripts): 

    NM_001134477.1   NM_002582.2   

    Applied Biosystems TaqMan ® Gene Expression Assays: 

    NM_001134477  NM_002582  

                   OriGene GFP tagged cDNA clones in CMV expression vector (see all 2): NM_001134477
                                     Myc/DDK tagged cDNA clones in CMV expression vector (see all 2): NM_001134477
                                     untagged cDNA clones in CMV expression vector (see all 2): NM_001134477 

    Additional cDNA sequence: 

    AJ005698.1 AK023866.1 AK293189.1 AK299653.1 AK301648.1 AK303348.1 AK315020.1 BC044763.1 
    BC050029.1 

    15 DOTS entries:

    DT.313148  DT.100780890  DT.91654186  DT.100780883  DT.100650345  DT.86841429  DT.97798723  DT.102830660 
    DT.40203091  DT.91866628  DT.91922711  DT.91954948  DT.95256219  DT.95375836  DT.102830658 

    24/160 AceView cDNA sequences (see all 160 ):

    NM_002582 AU099466 BM993702 AI364427 BM975508 AW262009 CB143265 AI309002 
    BP358795 BU616576 AI337134 BM799843 CD518439 BQ679680 BM459206 BU629697 
    BP335321 AA447167 BQ000452 BX113575 AU141208 BU185252 BM546879 AU105744 

    highest scoring ESTs for PARN:

    AJ005698 AA206172 AA331829 AL042465 AU099466 BG719035 BG721126 BG721172 BM546879 BM799843 

    Unigene Cluster for PARN:

    Poly(A)-specific ribonuclease (deadenylation nuclease)
    Hs.253197  [show with all ESTs]
    Unigene Representative Sequence: NM_002582


    GeneLoc Exon Structure

    1 Ensembl transcript including schematic representation:
    ENST00000341484  
    (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

    PARN expression in normal and diseased human tissues

     Applied Biosystems TaqMan ® Gene Expression Assays for PARN

    1 / 2 / 3

    3 probe-sets matching PARN gene


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

    36003_at2, 3 U95-A 1 1.00 1.00 1.00 1.00 AJ005698 1.00 0.90 0.95 1

    203905_at2, 3 U133-A 1 1.00 1.00 -- -- NM_002582 0.60 1.00 0.82 1

    203905_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --
    About this table
    Data from (Publications) and GNF BioGPS
        About these images
    About these images

    CGAP SAGE TAG: GCGCTGCTTT

    SOURCE GeneReport for Unigene cluster: Hs.253197

    Expression variation in blood from EXPOLDB for PARN

    UniProtKB/Swiss-Prot: PARN_HUMAN, O95453
    Tissue specificity: Ubiquitous

    (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 PARN gene from 5/11 species (see all 11 )
    Organism Gene Locus Description Human
    Similarity
    NCBI accessions
    dog
    (Canis familiaris)
    PARN1   -- poly(A)-specific ribonuclease (deadenylation nuclease) 91.8(n)
    93.1(a)
    479839  XM_536966.2  XP_536966.2 
    chimpanzee
    (Pan troglodytes)
    PARN1   -- poly(A)-specific ribonuclease (deadenylation nuclease) 99.78(n)
    99.84(a)
    453936  XM_510832.2  XP_510832.2 
    cow
    (Bos taurus)
    PARN1   -- poly(A)-specific ribonuclease (deadenylation nuclease) 91.75(n)
    94.51(a)
    524155  XM_875720.2  XP_880813.2 
    rat
    (Rattus norvegicus)
    Parn1   -- poly(A)-specific ribonuclease (deadenylation nuclease) 82(n)
    83.01(a)
    360464  XM_340740.3  XP_340741.3 
    mouse
    (Mus musculus)
    Parn1, 5 165
    poly(A)-specific ribonuclease (deadenylation nuclease)1, 5 86.32(n)1
    88.46(a)1
    741081  NM_028761.21  NP_083037.11 
     AA2121065  AK0045725  (see all 13)
    About this table        Species with no ortholog for PARN

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

    Paralogs for PARN gene
    PNLDC12  

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


    10/568 NCBI SNPs in PARN are shown (see all 568 )
    (Click for Applied Biosystems TaqMan ® Genotyping Assay)  (see all 114)
    ABGenomic DataTranscription DataAllele Frequencies
    SNP IDValidChr 16 posSequenceRecsAA
    Chg
    TypeMoreRecsAllele
    freq
    PopTotal
    sample
    More
    ------------
    --
    rs75011191,2
    C,F,H14632090(+) gaagaG/Attcga 1 -- ng318Minor allele frequency- A:0.10EU EA WA 794
    rs7324591,2
    A,C,F,H14535195(+) ACCTGC/TCTGCA 1 -- int14Minor allele frequency- T:0.12EU EA WA 420
    rs129336371,2
    A,C,F,H14605199(+) TAGACG/ATTGCA 1 -- int119Minor allele frequency- A:0.14EU EA WA NA 1762
    --
    rs42386651,2
    A,C,F,H14444322(+) AAACAC/TTCACC 1 -- int17Minor allele frequency- T:0.43EU EA WA NA 558
    rs125989861,2
    A,C,F,H14449285(+) TGGGTA/GCTTTT 1 -- int14Minor allele frequency- G:0.18EU EA WA 418
    rs71856891,2
    A,C,F,H14539432(+) gatcaT/Cgtgtc 1 -- int14Minor allele frequency- C:0.08EU EA WA 420
    rs43950941,2
    A,C,F,H14516760(+) ATATGT/CAGATG 1 -- int14Minor allele frequency- C:0.09EU EA WA 418
    rs72002721,2
    A,C,F,H14572980(+) TCTGTC/TCCCCA 1 -- int14Minor allele frequency- T:0.13EU EA WA 420
    rs124469211,2
    A,C,F,H14536989(+) tatctA/Gtgatt 1 -- int14Minor allele frequency- G:0.12EU EA WA 420
    rs23790961,2
    A,C,F,H14543372(-) aaaaaG/Atcatt 1 -- int17Minor allele frequency- A:0.47EU EA WA NA 544
    About this table

    HapMap Linkage Disequilibrium images for PARN (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: 604212

    (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

    10/46 PubMed articles for PARN gene (see all 46 ):
    (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: 5073 HGNC: 8609 AceView: PARN Ensembl:ENSG00000140694 euGenes: HUgn5073
    ECgene: PARN H-InvDB: PARN
    (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 PARN:
     TaqMan ® Gene Expression Assays
     TaqMan ® Genotyping Assays
      Free SNP selection tool



      Invitrogen iPath Pathways  Invitrogen BLOCK-iT™ RNAi
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     Predesigned and custom siRNAs for PARN Antibodies for PARN
     Explore super-pooled esiRNAs Browse proteins at Sigma-Aldrich
     Lentivirus-delivered shRNAs for PARN Browse small molecules at Sigma-Aldrich
     "Your Favorite Gene" Pathwaysfeedback


      
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     Recombinant & Natural Proteins  

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     Recombinant Proteins
    (PARN)
     Antibodies (PARN)
     Tagged/untagged cDNA clones
     Validated SYBR primer pairs
     Purified proteins from HEK293T cells
     Western blot validated antibodies
     shRNA in GFP-retroviral vector
     Search Tocris compounds for PARN




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

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