FlyBase Gene Report: Dmel\Edc3

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

9 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

Alliance
Auto summary
UniProtKB
Interactive Fly

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

JBrowse

Other Genome Views

The following external sites may use different assemblies or annotations than FlyBase.

Function

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

(Ruscica et al., 2019)

inferred from physical interaction with UniProtKB:P23128

(Tritschler et al., 2007)

inferred from physical interaction with UniProtKB:Q5U127

(Tritschler et al., 2007)

inferred from physical interaction with UniProtKB:Q9W1H5

(Tritschler et al., 2007)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

enables mRNA binding

inferred from electronic annotation with InterPro:IPR034107

(InterPro Project Members, 2004-)

inferred from biological aspect of ancestor with PANTHER:PTN000341086

(GO Reference Genome Project, 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

(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 biological aspect of ancestor with PANTHER:PTN000341086

(GO Reference Genome Project, 2011-)

inferred from electronic annotation with InterPro:IPR034107

(InterPro Project Members, 2004-)

involved_in P-body assembly

inferred from biological aspect of ancestor with PANTHER:PTN000341086

(GO Reference Genome Project, 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 (1 term)

CV Term

Evidence

References

is_active_in P-body

inferred from biological aspect of ancestor with PANTHER:PTN000341086

(GO Reference Genome Project, 2011-)

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

Number of Unique Polypeptides

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

Structure

Protein 3D structure (Predicted by AlphaFold) (AlphaFold entry Q9VVI2)

If you don't see a structure in the viewer, refresh your browser.

Model Confidence:

Very high (pLDDT > 90)
Confident (90 > pLDDT > 70)
Low (70 > pLDDT > 50)
Very low (pLDDT < 50)

AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Some regions with low pLDDT may be unstructured in isolation.

Experimentally Determined Structures

Crossreferences

PDB - An information portal to biological macromolecular structures

2RM4

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

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

UniProt

RefSeq ID

GenBank

Edc3-PB

FBpp0074970

73.4

680

8.59

Q9VVI2

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

PDB - An information portal to biological macromolecular structures

2RM4

Linkouts

Sequences Consistent with the Gene Model

Nucleotide / Polypeptide Records

UniProt

Q9VVI2

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

Testis-specificity index

The testis specificity index was calculated from modENCODE tissue expression data by Vedelek et al., 2018 to indicate the degree of testis enrichment compared to other tissues. Scores range from -2.52 (underrepresented) to 5.2 (very high testis bias).

-0.55

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

JBrowse - Visual display of RNA-Seq signals

View Dmel\Edc3 in JBrowse

RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region

View exonic expression by developmental stage for Dmel\Edc3

View exonic expression by tissue for Dmel\Edc3

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 - A single-cell RNA-seq resource for data mining and data comparison across species

39957/tissue=All

EMBL-EBI Single Cell Expression Atlas - Single cell expression across species

FBgn0036735

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0036735

FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data

FBgn0036735

Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns

CG6311

Flygut - An atlas of the Drosophila adult midgut

FBgn0036735

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 ( 7 )

Variants

Variant Molecular Consequences

Alleles Representing Disease-Implicated Variants

Phenotypes

For more details about a specific phenotype click on the relevant allele symbol.

Lethality

Allele

viable

Edc3^CB04145

viable, with Dcr-2^UAS.cDa, Scer\GAL4^elav.PLu

Edc3^GD11886

viable, with Scer\GAL4^Mef2.PR

Edc3^GD11886

viable, with Scer\GAL4^pnr-MD237

Edc3^GD11886

viable, with Scer\GAL4^tin.CΔ4

Edc3^GD11886

Phenotype manifest in

Allele

Orthologs

Downloads

Download All DIOPT Orthologs

Human Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Homo sapiens (Human) (3)

Hsap\EDC3

12 of 14

Yes

Hsap\NAXE

1 of 14

Hsap\YJEFN3

1 of 14

Model Organism Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Rattus norvegicus (Norway rat) (2)

Rnor\Edc3

12 of 14

Yes

Rnor\Naxe

1 of 14

Mus musculus (laboratory mouse) (3)

Mmus\Edc3

11 of 14

Yes

Mmus\Naxe

1 of 14

Mmus\Yjefn3

1 of 14

Xenopus tropicalis (Western clawed frog) (2)

Xtro\edc3

7 of 13

Yes

Xtro\yes1

1 of 13

Danio rerio (Zebrafish) (3)

Drer\edc3

11 of 14

Yes

Drer\naxe

1 of 14

Drer\yjefn3

1 of 14

Caenorhabditis elegans (Nematode, roundworm) (2)

Cele\edc-3

2 of 14

Yes

Cele\Y18D10A.3

1 of 14

Anopheles gambiae (African malaria mosquito) (2)

Agam\AgaP_AGAP003131

11 of 12

Yes

Agam\AgaP_AGAP003324

1 of 12

Arabidopsis thaliana (thale-cress) (1)

Atha\PPOX

1 of 13

Yes

Saccharomyces cerevisiae (Brewer's yeast) (2)

Scer\EDC3

4 of 13

Yes

Scer\NNR1

1 of 13

Schizosaccharomyces pombe (Fission yeast) (2)

Spom\edc3

5 of 12

Yes

Spom\mug182

1 of 12

Escherichia coli (enterobacterium) (1)

Ecol\nnr

1 of 11

Yes

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:Edc3. Refer to their site for version information.

Paralogs

Downloads

Download All DIOPT Paralogs

Paralogs (via DIOPT v9.1)

Gene Symbol

Score

Source

Alignment

Drosophila melanogaster (Fruit fly) (1)

Naxe

1 of 13

Human Disease Associations

FlyBase Human Disease Model Reports

Disease Ontology (DO) Annotations

Models Based on Experimental Evidence ( 0 )

Allele

Disease

Evidence

References

Potential Models Based on Orthology ( 1 )

Human Ortholog

Disease

Evidence

References

EDC3; enhancer of mRNA decapping 3

model of autosomal recessive intellectual developmental disorder 50

IEA

(FlyBase, 2019-)

Modifiers Based on Experimental Evidence ( 1 )

Allele

Disease

Interaction

References

Edc3^NIG.6311R

exacerbates frontotemporal dementia and/or amyotrophic lateral sclerosis 1

modeled by Zzzz\poly-PR^PO-36.UAS

(Park et al., 2021)

Disease Associations of Human Orthologs (via DIOPT v9.1 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

12 of 14

609842

INTELLECTUAL DEVELOPMENTAL DISORDER, AUTOSOMAL RECESSIVE 50; MRT50

autosomal recessive intellectual developmental disorder 50

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

esyN Network Diagram

Show neighbor-neighbor interactions:

Off

Show/hide secondary interactors
(data from AllianceMine provided by esyN)

Select Layout:

Force Directed

Circle

Concentric

Legend:

Protein

RNA

Selected Interactor(s)

Other Interaction Browsers

View in FlyBase Interactions Browser View in MIST tool (external link)

Please see the Physical Interaction reports below for full details

protein-protein

Physical Interaction

Assay

References

Edc3

anti tag coimmunoprecipitation, anti tag western blot

(Tritschler et al., 2007)

Edc3 - DCP1

anti tag coimmunoprecipitation, anti tag western blot, western blot

(Zekri et al., 2009, Tritschler et al., 2008, Tritschler et al., 2007)

Edc3 - DCP2

anti tag coimmunoprecipitation, anti tag western blot

(Tritschler et al., 2008, Tritschler et al., 2007)

Edc3 - Gyf

anti tag coimmunoprecipitation, anti tag western blot

(Ruscica et al., 2019)

Edc3 - me31B

anti tag coimmunoprecipitation, anti tag western blot, western blot

(Peter et al., 2019, Wang et al., 2017, Haas et al., 2010, Tritschler et al., 2009, Jinek et al., 2008, Tritschler et al., 2008, Tritschler et al., 2007)

Summary of Genetic Interactions

esyN Network Diagram

Other Interaction Browsers

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

External Data

Subunit Structure (UniProtKB)

(UniProt, Q9VVI2 )

Linkouts

BioGRID - A database of protein and genetic interactions.

65245

DroID - A comprehensive database of gene and protein interactions.

FBgn0036735

MIST (protein-protein) - An integrated Molecular Interaction Database

39957

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyBase

External Links

External Data

Linkouts

KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.

RNA degradation

Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.

mRNA decay by 5' to 3' exoribonuclease

Class of Gene

nuclear_gene

protein_coding_gene

Genomic Location and Detailed Mapping Data

Chromosome (arm)

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)j11B2^j11B2

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 (9)

Aberrations including deletions of this gene Aberrations including duplications of this gene

Bloomington

33229

w^*; P{ID.GAL4DBD}Edc3^F32.1

28584

y¹ v¹; P{TRiP.HM05072}attP2

13433

y¹ w^67c23; P{SUPor-P}Edc3^KG01392 ry⁵⁰⁶

34953

y¹ sc^* v¹ sev²¹; P{TRiP.HMS00392}attP2

51130

y¹ w^*; Mi{MIC}Edc3^MI08930/TM3, Sb¹ Ser¹

NIG-Fly

6311R-2

P{NIG.6311R}2

HMS00392

y¹ sc^* v¹ sev²¹; P{TRiP.HMS00392}attP2

VDRC

v30149

w¹¹¹⁸; P{GD11886}v30149

v30150

w¹¹¹⁸; P{GD11886}v30150

Genomic Clones (26)

Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete

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 JBrowse 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.

FBgn0036735

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0036735

Antibody Information

Laboratory Generated Antibodies

polyclonal

(Buddika et al., 2022, Tritschler et al., 2008)

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

Relationship to Other Genes

Source for database merge of

Additional comments

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

(Graveley et al., 2011)

Nomenclature History

Source for database identify of

Source for identity of: Edc3 CG6311

(Tritschler et al., 2007)

Nomenclature comments

Etymology

Synonyms and Secondary IDs (10)

Reported As

Symbol Synonym

CG6311

(Çiçek et al., 2016, Japanese National Institute of Genetics, 2012.5.21, Lindquist et al., 2011, Ni et al., 2011.7.19, Jäger and Dorner, 2010, Li et al., 2010, Müller et al., 2010, Perkins et al., 2009, Haussmann et al., 2008, Hughes et al., 2008, Buszczak et al., 2007, Yi et al., 2007, Molnar et al., 2006)

DmEDC3

(Tritschler et al., 2009, Tritschler et al., 2007)

EDC3

(Ruscica et al., 2019, Wang et al., 2017, Braun et al., 2012, Haas et al., 2010, Jäger and Dorner, 2010, Zekri et al., 2009, Jinek et al., 2008, Tritschler et al., 2008, Eulalio et al., 2007, Eulalio et al., 2007)

Edc3

(Wilby and Weil, 2023, Sankaranarayanan and Weil, 2020, Cao et al., 2016, Sopko et al., 2015, Gonzalez et al., 2014, Kwon et al., 2013, Graveley et al., 2011, Lindquist et al., 2011, Müller et al., 2010, Temme et al., 2010)

LSM16

(Lindquist et al., 2011)

LSm16

(Eulalio et al., 2007)

Lsm16

(Park et al., 2021)

Name Synonyms

CG6311

Enhancer of decapping 3

(Temme et al., 2010)

enhancer of decapping 3

(Tritschler et al., 2007)

enhancer of decapping-3

(Tritschler et al., 2008)

Secondary FlyBase IDs

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 43 )

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.

39957

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/GCRP - The gene-centric reference proteome (GCRP) provides a 1:1 mapping between genes and UniProt accessions in which a single 'canonical' isoform represents the product(s) of each protein-coding gene.

Q9VVI2

UniProt/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information

Q9VVI2

Other crossreferences

AlphaFold DB - AlphaFold provides open access to protein structure predictions for the human proteome and other key proteins of interest, to accelerate scientific research.

Q9VVI2

DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species

39957/tissue=All

EMBL-EBI Single Cell Expression Atlas - Single cell expression across species

FBgn0036735

FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data

FBgn0036735

FlyMine - An integrated database for Drosophila genomics

FBgn0036735

InterPro - A database of protein families, domains and functional sites

KEGG Genes - Molecular building blocks of life in the genomic space.

dme:Dmel_CG6311

MARRVEL_MODEL - MARRVEL (model organism gene)

39957

PDB - An information portal to biological macromolecular structures

2RM4

Linkouts

BioGRID - A database of protein and genetic interactions.

65245

Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones

FBgn0036735

DroID - A comprehensive database of gene and protein interactions.

FBgn0036735

DRSC - Results frm RNAi screens

FBgn0036735

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0036735

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0036735

Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns

CG6311

Flygut - An atlas of the Drosophila adult midgut

FBgn0036735

FlyMet - A comprehensive tissue-specific metabolomics resource for Drosophila.

FBgn0036735

iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)

TC008899

KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.

RNA degradation

MIST (protein-protein) - An integrated Molecular Interaction Database

39957

Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.

mRNA decay by 5' to 3' exoribonuclease

References (60)

The following external sites may use different assemblies or annotations than FlyBase.

-0.55

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