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 )
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Aliases & Descriptions for EDC3
(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 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
Search outside databases for aliases for EDC3 gene
Summaries for EDC3 (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 mRNAprior to its degradation from the 5-prime end (Fenger-Gron et al., 2005 [PubMed16364915]).[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 inspermiogenesis and oogenesis
Gene Wiki entry for EDC3
Genomic Location 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
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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 Proteins for EDC3
(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: 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 directlyinteracts 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 PhosphoSite 2
REFSEQ proteins (3 alternative transcripts):
NP_001135915.1 NP_001135916.1 NP_079359.2 ENSEMBL proteins: ENSP00000320503 Human Recombinant Proteins               OriGene Purified Recombinant Human Protein: EDC3 1 Gene Ontology (GO) cellular component term (links to tree view) :
GO ID Qualified GO term Evidence PubMed IDs GO:0005737 cytoplasm
IEA --
About this table Antibodies for EDC3: Assays for EDC3:
Protein
Domains/ Families for EDC3(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 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 familySimilarity : Contains 1 YjeF N-terminal domain
Gene Function for EDC3
(According to MGI Jun 06 2009, UniProtKB ,
IUBMB ,and/or Genatlas ,
shRNA from
OriGene ,
Sigma-Aldrich , RNAi from
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Clones , and
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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 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                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 inspermiogenesis and oogenesis
1 Gene Ontology (GO) molecular function term (links to tree view) :
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Pathways & Interactions for EDC3
(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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5/16 Interacting proteins for EDC3 (Q96F86 1 , 2 ENSP00000320503 3 ) via UniProtKB, MINT, and/or STRING (see all 16
)Interactant Interaction Details GeneCard External ID(s) DDX6 P26196 1 , ENSP00000264018 3 EBI-997311, EBI-351257 STRING (score=.975 ) ZFP36 P26651 1 , ENSP00000248673 3 EBI-997311, EBI-374248 STRING (score=.702 ) YWHAB P31946 1 , 2 EBI-997311, EBI-359815 MINT-50962 EBI-997311, EBI-359815 MINT-50962 YWHAG P61981 1 , 2 EBI-997311, EBI-359832 MINT-50853 EBI-997311, EBI-359832 MINT-50853 YWHAZ P63104 1 , 2 EBI-997311, EBI-347088 MINT-3320046 EBI-997311, EBI-347088 MINT-3320046
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Drugs & Compounds for EDC3 (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 EDC3
Transcripts 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
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               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
Expression for EDC3
(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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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 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 themeiotic division part II and apical membrane of Sertoli cells in testis (at protein level). Alsoexpressed in brain and mammary gland
Orthologs for EDC3
(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 EDC3 gene from 5/8 species (see all 8
)
About this table Species with no ortholog for EDC3 ENSEMBL Gene Tree for EDC3 Paralogs for EDC3 (Paralogs according to 1 HomoloGene and 2 Ensembl , Pseudogenes according to 3 Pseudogene.org )About This Section
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--
SNPs/Variants for EDC3 (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 EDC3 (up to first 250kb)
Disorders & Mutations for EDC3
(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: 609842
Medical News for EDC3 (Possibly Related Articles in
Doctor's Guide )
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--
Publications for EDC3 (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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10/19 PubMed articles for EDC3 gene (see all 19
): ApoA-I-binding protein (AI-BP) and its homologues hYjeF_N2 and hYjeF_N3 comprise the YjeF_N domain protein family in humans with a role in spermiogenesis and oogenesis. (PubMed id 17533573) 2, 3, 4 Rudolph C....Schmitz G. (2007) A divergent Sm fold in EDC3 proteins mediates DCP1 binding and P-body targeting. (PubMed id 17923697) 3, 4 Tritschler F....Weichenrieder O. (2007) A probability-based approach for high-throughput protein phosphorylation analysis and site localization. (PubMed id 16964243) 3, 4 Beausoleil S.A.... Gygi S.P. (2006) Multiple processing body factors and the ARE binding protein TTP activate mRNA decapping. (PubMed id 16364915) 3, 4 Fenger-Groen M.... Lykke-Andersen J. (2005) Novel Sm-like proteins with long C-terminal tails and associated methyltransferases. (PubMed id 15225602) 2, 3 Albrecht M. and Lengauer T. (2004) Large-scale cDNA transfection screening for genes related to cancer development and progression. (PubMed id 15498874) 3, 4 Wan D....Gu J. (2004) 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) Structural basis for the mutually exclusive anchoring of P body components EDC3 and Tral to the DEAD box protein DDX6/Me31B. (PubMed id 19285948) 3 Tritschler F....Weichenrieder O. (2009) Combining protein-based IMAC, peptide-based IMAC, and MudPIT for efficient phosphoproteomic analysis. (PubMed id 18220336) 4 Cantin G.T....Yates J.R. III (2008)
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Genome Databases showing EDC3
(According to
Entrez Gene ,
HGNC ,
AceView ,
euGenes ,
Ensembl ,
miRBase ,
ECgene ,
and/or
H-InvDB )
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Other Databases showing EDC3
(According to HUGE )
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Specialized Databases showing EDC3 (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 EDC3 (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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Recombinant Proteins (EDC3 ) Antibodies (EDC3 )
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