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FB2021_04, released August 17, 2021

Gene: Dmel\Edc3

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General Information
Symbol
Dmel\Edc3
Species
D. melanogaster
Name
Enhancer of decapping 3
Annotation Symbol
CG6311
Feature Type
protein_coding_gene
FlyBase ID
FBgn0036735
Gene Model Status
Current
Stock Availability
7 publicly available
Gene Summary
In the process of mRNA degradation, may play a role in mRNA decapping. (UniProt, Q9VVI2)
Contribute a Gene Snapshot for this gene.
All Summaries
Also Known As

DmEDC3

Key Links
Genomic Location
Cytogenetic map
74D2-74D2
Sequence location
3L:17,525,333..17,529,861 [-]
Recombination map
3-45
RefSeq locus
NT_037436 REGION:17525333..17529861
Sequence
Get Decorated FASTA
Genomic Maps
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
NCBI
UCSC
Ensembl
PopFly
Function
GO Summary Ribbons
Gene Ontology (GO) Annotations (6 terms)
Molecular Function (2 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
enables protein binding
inferred from physical interaction with UniProtKB:Q7KQM6
(assigned by UniProt )
(Ruscica et al., 2019)
inferred from physical interaction with UniProtKB:P23128
(assigned by UniProt )
(Tritschler et al., 2007)
inferred from physical interaction with UniProtKB:Q5U127
(assigned by UniProt )
(Tritschler et al., 2007)
inferred from physical interaction with UniProtKB:Q9W1H5
(assigned by UniProt )
(Tritschler et al., 2007)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
enables mRNA binding
inferred from biological aspect of ancestor with PANTHER:PTN000341086
(assigned by GO_Central )
(Gaudet et al., 2011)
Biological Process (3 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
involved_in mRNA catabolic process
inferred from mutant phenotype
(assigned by UniProt )
(Tritschler et al., 2007)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
involved_in deadenylation-independent decapping of nuclear-transcribed mRNA
inferred from electronic annotation with InterPro:IPR034107
(assigned by InterPro )
(FlyBase Curators et al., 2004-)
involved_in P-body assembly
inferred from biological aspect of ancestor with PANTHER:PTN000341086
(assigned by GO_Central )
(Gaudet et al., 2011)
Cellular Component (1 term)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
located_in P-body
inferred from direct assay
(Eulalio et al., 2007, Tritschler et al., 2007)
Terms Based on Predictions or Assertions (0 terms)
Gene Group (FlyBase)
Protein Family (UniProt)
Belongs to the EDC3 family. (Q9VVI2)
Protein Signatures (InterPro)
Summaries
Protein Function (UniProtKB)
In the process of mRNA degradation, may play a role in mRNA decapping.
(UniProt, Q9VVI2)
Gene Model and Products
Number of Transcripts
1
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\Edc3 for information on other features

To submit a correction to a gene model please use the Contact FlyBase form

Protein Domains (via Pfam)
Isoform displayed:
Pfam protein domains
InterPro name
classification
start
end
Protein Domains (via SMART)
Isoform displayed:
SMART protein domains
InterPro name
classification
start
end
Comments on Gene Model

Gene model reviewed during 5.55

Low-frequency RNA-Seq exon junction(s) not annotated.

Gene model reviewed during 5.45

Gene model reviewed during 5.56

Sequence Ontology: Class of Gene
nuclear_gene
protein_coding_gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
Edc3-RB
FBtr0075208
NM_140735
4062
680
Additional Transcript Data and Comments
Reported size (kB)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
RefSeq ID
GenBank
Edc3-PB
FBpp0074970
73.4
680
8.59
NP_648992
AAF49329
Polypeptides with Identical Sequences

There is only one protein coding transcript and one polypeptide associated with this gene

Additional Polypeptide Data and Comments
Reported size (kDa)
Comments
External Data
Subunit Structure (UniProtKB)

Forms a complex with DCP1A, DCP2, Me31B/DDX6 and EDC4/HEDLS (By similarity). Within this complex directly interacts with DCP1A, DCP2 and Me31B/DDX6 (PubMed:17923697, PubMed:18765641, PubMed:19285948). Homooligomer (PubMed:17923697). Interacts with Gyf (PubMed:31114929).

(UniProt, Q9VVI2)
Crossreferences
InterPro - A database of protein families, domains and functional sites
Linkouts
Sequences Consistent with the Gene Model
Nucleotide / Polypeptide Records
 
UniProt
Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\Edc3 using the Feature Mapper tool.

External Data
Crossreferences
Linkouts
Expression Data
Expression Summary Ribbons
Colored tiles in ribbon indicate that expression data has been curated by FlyBase for that anatomical location. Colorless tiles indicate that there is no curated data for that location.
For complete stage-specific expression data, view the modENCODE Development RNA-Seq section under High-Throughput Expression below.
Transcript Expression
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
located_in P-body
inferred from direct assay
(Eulalio et al., 2007, Tritschler et al., 2007)
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\Edc3 in GBrowse 2
RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region
Bulk Downloads
RNA-Seq RPKM values for all genes
Reference
See Gelbart and Emmert, 2013 for analysis details and data files for all genes.
Developmental Proteome: Life Cycle
Developmental Proteome: Embryogenesis
External Data and Images
Linkouts
DRscDB
EMBL-EBI Single Cell Expression Atlas
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
Flygut - An atlas of the Drosophila adult midgut
Images
FlyBase Wiki
Image Based Resources
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 4 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 4 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Edc3
Transgenic constructs containing regulatory region of Edc3
Aberrations (Deficiencies and Duplications) ( 2 )
Inferred from experimentation ( 2 )
Gene disrupted in
Df(3L)Exel6132
(Ryder, 2004.4.26)
Df(3L)Exel9005
(Ryder, 2004.4.26)
Inferred from location ( 0 )
Alleles Representing Disease-Implicated Variants
Phenotypes
For more details about a specific phenotype click on the relevant allele symbol.
Lethality
Allele
viable
viable, with Dcr-2UAS.cDa, Scer\GAL4elav.PLu
viable, with Scer\GAL4Mef2.PR
viable, with Scer\GAL4pnr-MD237
viable, with Scer\GAL4tin.CΔ4
Phenotype manifest in
Allele
Orthologs
Downloads
Download All DIOPT Orthologs
Download All OrthoDB Orthologs
Human Orthologs (via DIOPT v8.0)
Homo sapiens (Human) (3)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
eggNOG
Hieranoid
Homologene
Inparanoid
Isobase
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
RoundUp
TreeFam
ZFIN
Alignment
Complementation?
Transgene?
Hsap\EDC3
13 of 15
Yes
Yes
Hsap\NAXE
1 of 15
No
No
Hsap\YJEFN3
1 of 15
No
No
1  
Model Organism Orthologs (via DIOPT v8.0)
Mus musculus (laboratory mouse) (3)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
eggNOG
Hieranoid
Homologene
Inparanoid
Isobase
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
RoundUp
TreeFam
ZFIN
Alignment
Complementation?
Transgene?
Mmus\Edc3
12 of 15
Yes
Yes
Mmus\Naxe
1 of 15
No
No
Mmus\Yjefn3
1 of 15
No
No
Rattus norvegicus (Norway rat) (3)
Rnor\Edc3
11 of 13
Yes
Yes
Rnor\Naxe
1 of 13
No
No
Rnor\Yjefn3
1 of 13
No
No
Xenopus tropicalis (Western clawed frog) (2)
Xtro\edc3
8 of 12
Yes
Yes
Xtro\naxe
1 of 12
No
No
Danio rerio (Zebrafish) (3)
Drer\edc3
13 of 15
Yes
Yes
Drer\naxe
1 of 15
No
No
Drer\yjefn3
1 of 15
No
No
Caenorhabditis elegans (Nematode, roundworm) (2)
Cele\edc-3
2 of 15
Yes
Yes
Cele\Y18D10A.3
1 of 15
No
No
Arabidopsis thaliana (thale-cress) (0)
No records found.
Saccharomyces cerevisiae (Brewer's yeast) (2)
Scer\EDC3
5 of 15
Yes
Yes
Scer\NNR1
1 of 15
No
No
Schizosaccharomyces pombe (Fission yeast) (1)
Spom\edc3
4 of 12
Yes
Yes
Ortholog(s) in Drosophila Species (via OrthoDB v9.1) ( EOG0919084P )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
Drosophila suzukii
Spotted wing Drosophila
Dsuz\DS10_00010424
Drosophila simulans
Dsim\GD12399
Drosophila sechellia
Dsec\GM24326
Drosophila erecta
Dere\GG15804
Drosophila yakuba
Dyak\GE22142
Drosophila ananassae
Dana\GF23907
Drosophila pseudoobscura pseudoobscura
Dpse\GA19506
Drosophila persimilis
Dper\GL11915
Drosophila willistoni
Dwil\GK18045
Drosophila virilis
Dvir\GJ13102
Drosophila mojavensis
Dmoj\GI12959
Drosophila grimshawi
Dgri\GH15355
Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG09150536 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Musca domestica
House fly
Mdoa\17016114
Glossina morsitans
Tsetse fly
Gmor\GMOY007388
Lucilia cuprina
Australian sheep blowfly
Lcup\FF38_07537
Mayetiola destructor
Hessian fly
Mdes\Mdes002767
Aedes aegypti
Yellow fever mosquito
Aaeg\AAEL008375
Anopheles darlingi
American malaria mosquito
Adar\ADAC007236
Anopheles gambiae
Malaria mosquito
Agam\AGAP003131
Culex quinquefasciatus
Southern house mosquito
Cqui\CPIJ011786
Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W067S )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Bombyx mori
Silkmoth
Bmor\BGIBMGA012610
Danaus plexippus
Monarch butterfly
Dple\DPOGS210509-PA
Heliconius melpomene
Postman butterfly
Hmel\HMEL004632
Apis florea
Little honeybee
Aflo\2800827508
Apis mellifera
Western honey bee
Amel\Ame.6424
Bombus impatiens
Common eastern bumble bee
Bimp\BIMP16427
Bombus terrestris
Buff-tailed bumblebee
Bter\15209183
Linepithema humile
Argentine ant
Lhum\LH16484
Megachile rotundata
Alfalfa leafcutting bee
Mrot\MROTU:0030c7
Nasonia vitripennis
Parasitic wasp
Nvit\Nasvi2EG018615
Dendroctonus ponderosae
Mountain pine beetle
Dpod\YQE_05416
Tribolium castaneum
Red flour beetle
Tcas\TC008899
Pediculus humanus
Human body louse
Phum\PHUM236510
Acyrthosiphon pisum
Pea aphid
Apim\ACYPI005303
Zootermopsis nevadensis
Nevada dampwood termite
Znev\Znev_13575
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X0639 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strigamia maritima
European centipede
Smar\SMAR001208
Ixodes scapularis
Black-legged tick
Isca\ISCW021548
Stegodyphus mimosarum
African social velvet spider
Smim\KFM61550.1
Daphnia pulex
Water flea
Dpux\DAPPUDRAFT_300044
Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G09C2 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strongylocentrotus purpuratus
Purple sea urchin
Spur\Sp-Lsm16
Ciona intestinalis
Vase tunicate
Cint\ENSCING00000022142
Gallus gallus
Domestic chicken
Ggal\EDC3
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v8.0)
Drosophila melanogaster (Fruit fly) (1)
Gene Symbol
Score
Source
Compara
eggNOG
Homologene
Inparanoid
Isobase
OrthoDB
OrthoFinder
orthoMCL
Panther
RoundUp
Alignment
Naxe
1 of 10
Human Disease Associations
FlyBase Human Disease Model Reports
    Disease Model Summary Ribbon
    Disease Ontology (DO) Annotations
    Models Based on Experimental Evidence ( 0 )
    Allele
    Disease
    Evidence
    References
    Potential Models Based on Orthology ( 0 )
    Human Ortholog
    Disease
    Evidence
    References
    Modifiers Based on Experimental Evidence ( 0 )
    Allele
    Disease
    Interaction
    References
    Disease Associations of Human Orthologs (via DIOPT v8.0 and OMIM)
    Note that ortholog calls supported by only 1 or 2 algorithms (DIOPT score < 3) are not shown.
    Homo sapiens (Human)
    Gene name
    Score
    OMIM
    OMIM Phenotype
    DO term
    Complementation?
    Transgene?
    EDC3; enhancer of mRNA decapping 3
    13 of 15
    609842
      Functional Complementation Data
      Functional complementation data is computed by FlyBase using a combination of the orthology data obtained from DIOPT and OrthoDB and the allele-level genetic interaction data curated from the literature.
      Interactions
      Summary of Physical Interactions
      Summary of Genetic Interactions
      esyN Network Diagram
      Starting gene(s)
      Interaction type
      Interacting gene(s)
      Reference
      Starting gene(s)
      Interaction type
      Interacting gene(s)
      Reference
      External Data
      Subunit Structure (UniProtKB)
      Forms a complex with DCP1A, DCP2, Me31B/DDX6 and EDC4/HEDLS (By similarity). Within this complex directly interacts with DCP1A, DCP2 and Me31B/DDX6 (PubMed:17923697, PubMed:18765641, PubMed:19285948). Homooligomer (PubMed:17923697). Interacts with Gyf (PubMed:31114929).
      (UniProt, Q9VVI2 )
      Linkouts
      BioGRID - A database of protein and genetic interactions.
      DroID - A comprehensive database of gene and protein interactions.
      MIST (protein-protein) - An integrated Molecular Interaction Database
      Pathways
      Signaling Pathways (FlyBase)
      Metabolic Pathways
      External Data
      Linkouts
      KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.
      Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
      Genomic Location and Detailed Mapping Data
      Chromosome (arm)
      3L
      Recombination map
      3-45
      Cytogenetic map
      74D2-74D2
      Sequence location
      3L:17,525,333..17,529,861 [-]
      FlyBase Computed Cytological Location
      Cytogenetic map
      Evidence for location
      74D2-74D2
      Limits computationally determined from genome sequence between P{PZ}frc00073&P{PZ}frc02619 and P{lacW}l(3)j11B2j11B2
      Experimentally Determined Cytological Location
      Cytogenetic map
      Notes
      References
      Experimentally Determined Recombination Data
      Location

      3-45

      (FlyBase, 2016)

      3-41.0

      (Comeron et al., 2012)
      Left of (cM)
      Right of (cM)
      Notes
      Stocks and Reagents
      Stocks (7)
      Genomic Clones (26)
      cDNA Clones (175)
       

      Please Note This section lists cDNAs and ESTs that fall within the genomic extent of the gene model, which may include cDNAs and ESTs of genes within introns, or of overlapping genes. Please see GBrowse for alignment of the cDNAs and ESTs to the gene model.

      cDNA clones, fully sequenced
      BDGP DGC clones
      Other clones
        Drosophila Genomics Resource Center cDNA clones

        For each fully sequenced cDNA the DGRC maintains various forms of the cDNA (e.g tagged or untagged) in several different host vectors for subsequent cloning and expression in Drosophila and Drosophila cell lines.

        cDNA Clones, End Sequenced (ESTs)
        BDGP DGC clones
        Other clones
        RNAi and Array Information
        Linkouts
        DRSC - Results frm RNAi screens
        GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
        Antibody Information
        Laboratory Generated Antibodies
         

        polyclonal

        (Tritschler et al., 2008)
        Commercially Available Antibodies
         
        Other Information
        Relationship to Other Genes
        Source for database identify of

        Source for identity of: Edc3 CG6311

        (Tritschler et al., 2007)
        Source for database merge of
        Additional comments

        snoRNA:Edc3-a is encoded in an intron of Edc3.

        (Graveley et al., 2011)
        Other Comments
        Origin and Etymology
        Discoverer
        Etymology
        Identification
        External Crossreferences and Linkouts ( 39 )
        Sequence Crossreferences
        NCBI Gene - Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.
        GenBank Nucleotide - A collection of sequences from several sources, including GenBank, RefSeq, TPA, and PDB.
        GenBank Protein - A collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB.
        RefSeq - A comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein.
        UniProt/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information
        Other crossreferences
        Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
        DRscDB
        EMBL-EBI Single Cell Expression Atlas
        Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
        Flygut - An atlas of the Drosophila adult midgut
        GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
        iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
        InterPro - A database of protein families, domains and functional sites
        KEGG Genes - Molecular building blocks of life in the genomic space.
        MARRVEL_MODEL
        modMine - A data warehouse for the modENCODE project
        Linkouts
        BioGRID - A database of protein and genetic interactions.
        DroID - A comprehensive database of gene and protein interactions.
        DRSC - Results frm RNAi screens
        FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
        FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
        FlyMine - An integrated database for Drosophila genomics
        KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.
        MIST (protein-protein) - An integrated Molecular Interaction Database
        Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
        Synonyms and Secondary IDs (9)
        Datasets (0)
        Study focus (0)
        Experimental Role
        Project
        Project Type
        Title
        References (53)