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EDC3 Gene

protein-coding   GIFtS: 51

GC15M072712
enhancer of mRNA decapping 3 homolog (S. cerevisiae)
(Previous names: yjeF domain containing (E.coli), LSM16 homolog (EDC3, S. cerevisiae) )
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database
(Previous symbols: YJDC, LSM16)
Services    
(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc , and/or 7Ensembl, 8miRBase)
About This Section

Aliases
FLJ21128 1, 2
FLJ31777 2
LSM16 2, 3
YJDC 2, 3
YJEFN2 1, 2, 3
YjeF_N2 3
hYjeF_N2 3
hYjeF_N2-15q23 1, 2
Descriptions
LSM16 homolog 3
LSM16 homolog (EDC3, S. cerevisiae) 1, 2
YjeF N-terminal domain-containing protein 2 3
YjeF domain-containing protein 1 3
enhancer of mRNA decapping 3 2
enhancer of mRNA decapping 3 homolog (S. cerevisiae) 2
yjeF domain containing 2
yjeF domain containing (E.coli) 1
External Ids
HGNC: 261141
Entrez Gene: 801532
UniProtKB: Q96F863
Ensembl: ENSG000001791517
Search outside databases for aliases for EDC3 gene

(According to Entrez Gene, Wikipedia's Gene Wiki,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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EntrezGene summary for EDC3:
EDC3 is associated with an mRNA-decapping complex required for removal of the 5-prime cap from mRNA
prior to its degradation from the 5-prime end (Fenger-Gron et al., 2005 [PubMed
16364915]).[supplied by OMIM]

UniProtKB/Swiss-Prot: EDC3_HUMAN, Q96F86
Function: In the process of mRNA degradation, may play a role in mRNA decapping. May play a role in
spermiogenesis and oogenesis

Gene Wiki entry for EDC3

(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 EDC3 gene  

Entrez Gene cytogenetic band: 15q24.1   Ensembl cytogenetic band:  15q24.1   HGNC cytogenetic band: 15q24.1

EDC3 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 15         GeneLoc Exon Structure

GeneLoc location for GC15M072712:     (about GC identifiers)

Start:
72,709,952 bp from pter
End:
72,775,413 bp from pter
Size:
65,462 bases
Orientation:
minus strand
RefSeq DNA sequence:
NC_000015.8  NT_010194.16  
(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: EDC3_HUMAN, Q96F86 (See protein sequence)
Recommended Name: Enhancer of mRNA-decapping protein 3  
Size: 508 amino acids; 56078 Da
Subunit: Forms a complex with DCP1A, DCP2, DDX6 and EDC4/HEDLS, within this complex directly
interacts with DCP1A and DDX6. Interacts with ZFP36
Subcellular location: Cytoplasm, P-body. Note=Processing bodies (PB)
PDB structures from and Proteopedia :
2VC8 (3D)    2WAX (3D)    2WAY (3D)    3D3J (3D)    3D3K (3D)    
Secondary accessions: Q9H797

Post-translational modifications:

  • View phosphorylation sites using PhosphoSite2


  • REFSEQ proteins (3 alternative transcripts): 
    NP_001135915.1  NP_001135916.1  NP_079359.2  


    ENSEMBL proteins: 
    ENSP00000320503 


    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 (EDC3)
    Human Recombinant Proteins from Abnova (LSM16)
                  OriGene Purified Recombinant Human Protein: EDC3 

    1 Gene Ontology (GO) cellular component term (links to tree view):

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

    Antibodies for EDC3: 
    Browse Antibodies Central at Invitrogen
    Browse Millipore's Extensive Line of Mono- and Polyclonal Antibodies
    Sigma-Aldrich Antibodies for EDC3
    Browse R&D Systems for Antibodies
    Antibodies from Abcam (EDC3), each with their AbpromiseSM
    Monoclonal and Polyclonal Antibodies from Abnova (LSM16)
    Novus Biologicals Antibodies for EDC3

    Assays for EDC3: 
    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:
     IPR004443 YjeF_N
     IPR019050 DFDF_motif


       GeneDecks  EDC3 for the domains selected above  
    About GeneDecksing

    Graphical View of Domain Structure for InterPro Entry Q96F86

    ProtoNet protein and cluster: Q96F86

    1 Blocks protein family: IPB004443 YjeF-related protein

    UniProtKB/Swiss-Prot: EDC3_HUMAN, Q96F86
    Similarity: Belongs to the EDC3 family
    Similarity: Contains 1 YjeF N-terminal 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 (EDC3)
    Browse for Gene Knock-down Tools from Millipore
    Abnova Chimera RNAi Products for Gene knock-down (LSM16)
                   OriGene 29mer shRNA kit in GFP-retroviral vectors (see all 3): NM_025083

                  Applied Biosystems Silencer® siRNAs for EDC3

                  Sigma-Aldrich siRNA for EDC3  
                         Sigma-Aldrich shRNA for EDC3  
                         Explore Sigma-Aldrich super-pooled esiRNAs  

    Clones:Invitrogen Clones for EDC3
    Browse Clones for the Expression of Recombinant Proteins Available from Millipore
                   OriGene GFP tagged cDNA clones in CMV expression vector (see all 3): NM_001142443
                                     Myc/DDK tagged cDNA clones in CMV expression vector (see all 3): NM_001142443
                                     untagged cDNA clones in CMV expression vector (see all 4): NM_001142443 

    Primers: Browse Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers
                  OriGene genome-wide validated SYBR primer pairs: NM_001142444

    UniProtKB/Swiss-Prot: EDC3_HUMAN, Q96F86
    Function: In the process of mRNA degradation, may play a role in mRNA decapping. May play a role in
    spermiogenesis and oogenesis

    1 Gene Ontology (GO) molecular function term (links to tree view):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515 protein binding IPI16364915 17353931
    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



    5/16 Interacting proteins for EDC3 (Q96F861, 2 ENSP000003205033) via UniProtKB, MINT, and/or STRING (see all 16 )
    InteractantInteraction Details
    GeneCardExternal ID(s)
    DDX6P261961, ENSP000002640183EBI-997311, EBI-351257 STRING (score=.975)
    ZFP36P266511, ENSP000002486733EBI-997311, EBI-374248 STRING (score=.702)
    YWHABP319461, 2EBI-997311, EBI-359815 MINT-50962 EBI-997311, EBI-359815 MINT-50962
    YWHAGP619811, 2EBI-997311, EBI-359832 MINT-50853 EBI-997311, EBI-359832 MINT-50853
    YWHAZP631041, 2EBI-997311, EBI-347088 MINT-3320046 EBI-997311, EBI-347088 MINT-3320046
    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 EDC3

    (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 (EDC3)
    Browse for Gene Knock-down Tools from Millipore
    Abnova Chimera RNAi Products for Gene knock-down (LSM16)
                   OriGene 29mer shRNA kit in GFP-retroviral vectors (see all 3): NM_025083

                  Sigma-Aldrich siRNA for EDC3  
                         Sigma-Aldrich shRNA for EDC3  
                         Explore Sigma-Aldrich super-pooled esiRNAs  

    Applied Biosystems Silencer® siRNAs: 

    NM_001142443  NM_001142444  NM_025083  

    REFSEQ mRNAs for EDC3 gene (3 alternative transcripts): 

    NM_001142443.1   NM_001142444.1   NM_025083.3   

    Applied Biosystems TaqMan ® Gene Expression Assays: 

    NM_001142443  NM_001142444  NM_025083  

                   OriGene GFP tagged cDNA clones in CMV expression vector (see all 3): NM_001142443
                                     Myc/DDK tagged cDNA clones in CMV expression vector (see all 3): NM_001142443
                                     untagged cDNA clones in CMV expression vector (see all 4): NM_001142443 

    Additional cDNA sequence: 

    AF193058.1 AK024781.1 AK056339.1 AK225099.1 AL133447.1 BC011534.1 BC021271.2 

    15 DOTS entries:

    DT.414479  DT.100791674  DT.99941570  DT.100791663  DT.100791665  DT.92036559  DT.121044324  DT.97813442 
    DT.100791675  DT.95165071  DT.100744007  DT.121044342  DT.121044349  DT.91660427  DT.95165049 

    24/340 AceView cDNA sequences (see all 340 ):

    AI692578 AI653427 BC011534 D81794 AA302883 BQ944676 BQ944680 BP351702 
    BU543885 BP337315 BQ218764 BQ935576 BE743563 BE388280 CA430814 BQ936767 
    BU543570 BU543582 NM_025083 BQ931302 BU542106 CB128393 BQ219763 BQ895881 

    highest scoring ESTs for EDC3:

    AF193058 AI436560 AK024781 AK056339 AL530931 AL596992 AW016187 AW250096 BC011534 BC021271 

    Unigene Cluster for EDC3:

    Enhancer of mRNA decapping 3 homolog (S. cerevisiae)
    Hs.96852  [show with all ESTs]
    Unigene Representative Sequence: NM_001142443


    GeneLoc Exon Structure

    5/13 Alternative Splicing Database (ASD) splice patterns (SP) for EDC3 (see all 13 )

    ExUns: 1a · 1b · 1c · 1d · 1e ^ 2a · 2b · 2c · 2d · 2e ^ 3 ^ 4a · 4b ^ 5 ^ 6 ^ 7 ^ 8a · 8b · 8c · 8d · 8e ^ 9 ^ 10a · 10b ^ 11 ^ 12a ·
    SP1:                                -     -     -     -     -                       -                                               -                       -   
    SP2:                                -     -     -     -     -     -                 -     -                                         -                       -   
    SP3:                                -     -     -     -     -     -     -     -     -     -                                         -                       -   
    SP4:                                -     -     -     -     -     -                 -                                                                           
    SP5:                                -     -     -     -     -     -     -     -     -                                               -                           

    ExUns: 12b · 12c ^ 13a · 13b · 13c · 13d
    SP1:                                    
    SP2:                                    
    SP3:                                    
    SP4:                                    
    SP5:                                    

    About this scheme

    ECgene alternative splicing isoforms for EDC3

    1 Ensembl transcript including schematic representation:
    ENST00000315127  
    (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

    EDC3 expression in normal and diseased human tissues

     Applied Biosystems TaqMan ® Gene Expression Assays for EDC3

    1 / 2 / 3

    7 probe-sets matching EDC3 gene


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

    54839_at2, 3 U95-C 1 1.00 1.00 0.58 1.12 N51702 0.80 1.00 0.91 1

    56298_at2, 3 U95-B 1 1.00 1.00 0.88 0.88 AI436560 0.80 1.00 0.91 1

    43416_s_at2, 3 U95-B 2 1.00 0.97 0.81 0.99 AW016187 0.80 1.00 0.91 1

    226042_at2, 3 U133-B 1 1.00 1.00 -- -- AL563608 0.60 1.00 0.82 1

    219207_at2, 3 U133-A 1 1.00 1.00 -- -- NM_025083 0.60 1.00 0.82 1

    226042_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --

    219207_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: --

    SOURCE GeneReport for Unigene cluster: Hs.96852

    UniProtKB/Swiss-Prot: EDC3_HUMAN, Q96F86
    Tissue specificity: Expressed in theca and granulosa cells in ovary, and in spermatids of the
    meiotic division part II and apical membrane of Sertoli cells in testis (at protein level). Also
    expressed in brain and mammary gland

    (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 EDC3 gene from 5/8 species (see all 8 )
    Organism Gene Locus Description Human
    Similarity
    NCBI accessions
    dog
    (Canis familiaris)
    EDC31   -- enhancer of mRNA decapping 3 homolog (S. cerevisiae) 91.73(n)
    96.46(a)
    487647  XM_861987.1  XP_867080.1 
    cow
    (Bos taurus)
    EDC31   -- enhancer of mRNA decapping 3 homolog (S. cerevisiae) 93.8(n)
    95.81(a)
    517979  NM_001031758.1  NP_001026928.1 
    mouse
    (Mus musculus)
    Edc31, 5 95
    enhancer of mRNA decapping 3 homolog (S. cerevisiae)1, 5 89.63(n)1
    95.67(a)1
    3531901  NM_153799.21  NP_722494.11 
     AA5178535  AI4508255  (see all 20)
    chicken
    (Gallus gallus)
    EDC31   -- enhancer of mRNA decapping 3 homolog (S. cerevisiae) 80.79(n)
    88.91(a)
    415294  NM_001030385.1  NP_001025556.1 
    zebrafish
    (Danio rerio)
    Dr.53502   -- Transcribed sequences 75.46(n)  BG729698.1 
    About this table        Species with no ortholog for EDC3

    ENSEMBL Gene Tree for EDC3
    (Paralogs according to 1HomoloGene
    and 2Ensembl, Pseudogenes according to 3Pseudogene.org)
    About This Section

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


    10/180 NCBI SNPs in EDC3 are shown (see all 180 )
    (Click for Applied Biosystems TaqMan ® Genotyping Assay)  (see all 21)
    ABGenomic DataTranscription DataAllele Frequencies
    SNP IDValidChr 15 posSequenceRecsAA
    Chg
    TypeMoreRecsAllele
    freq
    PopTotal
    sample
    More
    ------------
    rs11286281,2
    C,F,H72710388(-) CCTCTC/GTTGGC 1 -- ut31 ese312Minor allele frequency- G:0.19MN NA EU EA WA 1150
    --
    rs71707341,2
    A,C72776459(+) actctC/Tggtgt 1 -- ng310--------
    rs41284361,2
    A,C,F,H72722947(-) ACTGCG/ATCCCA 1 -- int17Minor allele frequency- A:0.13NA EU EA WA 546
    rs110724981,2
    A,C,F,H72741240(+) GGAAAG/TGAGTA 1 -- int1 trp36Minor allele frequency- T:0.45EU EA WA 598
    rs74973421,2
    A,C,F,H72735116(+) ACCTGA/GTGCAA 1 -- int17Minor allele frequency- G:0.40NA EU EA WA 560
    rs71619031,2
    A,C,F,H72727323(+) AGAATA/GACATC 1 -- int18Minor allele frequency- G:0.41EU EA WA 838
    rs110724971,2
    A,C,F,H72738410(+) CACAGC/ACAGCT 1 -- int14Minor allele frequency- A:0.41EU EA WA 416
    rs64951191,2
    A,C,F,H72721493(+) GGCTAT/CAGCTT 1 -- int14Minor allele frequency- C:0.26EU EA WA 420
    rs110724991,2
    C,F,H72755926(+) GACATC/TATAGA 1 -- int14Minor allele frequency- T:0.21EU EA WA 416
    rs74977491,2
    C,F,H72729812(+) GAATAT/CCTTCC 1 -- int1 trp34Minor allele frequency- C:0.06EU EA WA 416
    About this table

    HapMap Linkage Disequilibrium images for EDC3 (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: 609842

    (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

    10/19 PubMed articles for EDC3 gene (see all 19 ):
    (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: 80153 HGNC: 26114 AceView: FLJ21128 Ensembl:ENSG00000179151 euGenes: HUgn80153
    ECgene: EDC3 H-InvDB: EDC3
    (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 EDC3:
     TaqMan ® Gene Expression Assays
     TaqMan ® Genotyping Assays
      Free SNP selection tool



      Invitrogen iPath Pathways  Invitrogen BLOCK-iT™ RNAi
      Invitrogen Antibodies  Invitrogen Assays
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      Invitrogen Human Recombinant Kinases  Invitrogen Custom Antibody and Peptide Service
      Invitrogen Proteins / Assays / Screening Services  Search Invitrogen catalog for EDC3-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 EDC3 Antibodies for EDC3
     Explore super-pooled esiRNAs Browse proteins at Sigma-Aldrich
     Lentivirus-delivered shRNAs for EDC3 Browse small molecules at Sigma-Aldrich
     "Your Favorite Gene" Pathwaysfeedback


      
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     Recombinant & Natural Proteins  

     Recombinant Proteins (LSM16)
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    (EDC3)
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     Validated SYBR primer pairs
     Purified proteins from HEK293T cells
     Western blot validated antibodies
     shRNA in GFP-retroviral vector
     Search Tocris compounds for EDC3




     Search www.enzolifesicences.com for proteins, assays, substrates, inhibitors & antibodies
     Antibodies for EDC3

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