FlyBase Gene Report: Dmel\eIF3d2

CYTOPLASMIC TRANSLATION INITIATION FACTORS -: Cytoplasmic (or eukaryotic) translation initiation factors function in the initiation stage of ribosome-mediated translation in the cytoplasm. (Adapted from FBrf0233552 and PMID:20094052).

Protein Function (UniProtKB)

mRNA cap-binding component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is involved in protein synthesis of a specialized repertoire of mRNAs and, together with other initiation factors, stimulates binding of mRNA and methionyl-tRNAi to the 40S ribosome. The eIF-3 complex specifically targets and initiates translation of a subset of mRNAs involved in cell proliferation. In the eIF-3 complex, eif3d specifically recognizes and binds the 7-methylguanosine cap of a subset of mRNAs.

(UniProt, Q9VGC7)

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the GBrowse view of Dmel\eIF3d2 or the JBrowse view of Dmel\eIF3d2 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 5.40

Gene model reviewed during 5.49

Sequence Ontology: Class of Gene

nuclear_gene

protein_coding_gene

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

eIF3d2-RA

FBtr0082546

NM_169456

2232

551

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

eIF3d2-PA

FBpp0082019

62.7

551

6.34

NP_731675

AAF54756

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)

Component of the eukaryotic translation initiation factor 3 (eIF-3) complex. The eIF-3 complex interacts with pix.

(UniProt, Q9VGC7)

Domain

The RNA gate region regulates mRNA cap recognition to prevent promiscuous mRNA-binding before assembly of eif3d into the full eukaryotic translation initiation factor 3 (eIF-3) complex.

(UniProt, Q9VGC7)

Crossreferences

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

Eukaryotic translation initiation factor 3 subunit D

Linkouts

Sequences Consistent with the Gene Model

Nucleotide / Polypeptide Records

UniProt

Q9VGC7

Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\eIF3d2 using the Feature Mapper tool.

External Data

Crossreferences

Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.

CG4810_1

Linkouts

Gene Ontology (4 terms)

Molecular Function (1 term)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

translation initiation factor activity

inferred from biological aspect of ancestor with PANTHER:PTN000273956

(assigned by GO_Central )

(Gaudet et al., 2011)

inferred from sequence or structural similarity with UniProtKB:Q9VCK0

(assigned by UniProt )

(UniProt Curators, 2002-)

Biological Process (2 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

regulation of translational initiation

inferred from sequence or structural similarity with UniProtKB:Q9VCK0

(assigned by UniProt )

(UniProt Curators, 2002-)

translational initiation

inferred from biological aspect of ancestor with PANTHER:PTN000273956

(assigned by GO_Central )

(Gaudet et al., 2011)

Cellular Component (1 term)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

eukaryotic translation initiation factor 3 complex

inferred from sequence or structural similarity with UniProtKB:Q9VCK0

(assigned by UniProt )

(UniProt Curators, 2002-)

inferred from biological aspect of ancestor with PANTHER:PTN000273956

(assigned by GO_Central )

(Gaudet et al., 2011)

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

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\eIF3d2 in GBrowse 2

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

View exonic expression by developmental stage for Dmel\eIF3d2

View exonic expression by tissue for Dmel\eIF3d2

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

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0037994

FLIGHT - Cell culture data for RNAi and other high-throughput technologies

FBgn0037994

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

CG4810-RA

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

CG4810

Flygut - An atlas of the Drosophila adult midgut

FBgn0037994

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, and Transgenic Constructs

Classical and Insertion Alleles ( 0 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 3 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of eIF3d2

Transgenic constructs containing regulatory region of eIF3d2

Deletions and Duplications ( 4 )

Disrupted in

Df(3R)ED5558

(Marygold et al., 2007)

Df(3R)ED5577

(Marygold et al., 2007)

Df(3R)Exel6162

(Ryder, 2004.4.26)

Df(3R)Exel7313

(Marygold et al., 2007, Ryder, 2004.4.26)

Phenotypes

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

Lethality

Allele

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

eIF3d2^GD11435

viable, with Scer\GAL4^Mef2.PR

eIF3d2^GD11435

viable, with Scer\GAL4^pnr-MD237

eIF3d2^GD11435

viable, with Scer\GAL4^tin.CΔ4

eIF3d2^GD11435

Phenotype manifest in

Allele

Orthologs

Downloads

Download All DIOPT Orthologs

Download All OrthoDB Orthologs

Human Orthologs (via DIOPT v7.1)

Homo sapiens (Human) (1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Hsap\EIF3D

13 of 15

Yes

Model Organism Orthologs (via DIOPT v7.1)

Mus musculus (laboratory mouse) (1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Mmus\Eif3d

12 of 15

Yes

Rattus norvegicus (Norway rat) (1)

Rnor\Eif3d

12 of 13

Yes

Xenopus tropicalis (Western clawed frog) (1)

Xtro\eif3d

12 of 12

Yes

Danio rerio (Zebrafish) (1)

Drer\eif3d

13 of 15

Yes

Caenorhabditis elegans (Nematode, roundworm) (1)

Cele\eif-3.D

12 of 15

Yes

Arabidopsis thaliana (thale-cress) (2)

Atha\AT4G20980

8 of 9

Yes

Atha\AT5G44320

8 of 9

Yes

Saccharomyces cerevisiae (Brewer's yeast) (0)

No records found.

Schizosaccharomyces pombe (Fission yeast) (1)

Spom\moe1

10 of 12

Yes

Orthologs in Drosophila Species (via OrthoDB v9.1) ( EOG091906DG )

Organism

Common Name

Gene

AAA Syntenic Ortholog

Multiple Dmel Genes in this Orthologous Group

Drosophila suzukii

Spotted wing Drosophila

Drosophila simulans

Drosophila sechellia

Drosophila erecta

Drosophila yakuba

Drosophila ananassae

Drosophila pseudoobscura pseudoobscura

Dpse\GA18448

Drosophila persimilis

Dper\GL21571

Drosophila willistoni

Dwil\GK11533

Drosophila virilis

Dvir\GJ10066

Drosophila mojavensis

Dmoj\GI22467

Drosophila grimshawi

Dgri\GH15488

Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( None identified )

No non-Drosophilid orthologies identified

Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W02SV )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Bombyx mori

Silkmoth

Bmor\BGIBMGA005592

Danaus plexippus

Monarch butterfly

Dple\DPOGS213311-PA

Heliconius melpomene

Postman butterfly

Hmel\HMEL003724

Apis florea

Little honeybee

Aflo\3139480772

Apis mellifera

Western honey bee

Amel\eIF-3p66

Bombus impatiens

Common eastern bumble bee

Bimp\BIMP19846

Bombus terrestris

Buff-tailed bumblebee

Bter\15211470

Linepithema humile

Argentine ant

Lhum\LH10791

Megachile rotundata

Alfalfa leafcutting bee

Mrot\MROTU:001e7e

Nasonia vitripennis

Parasitic wasp

Nvit\Nasvi2EG000312

Dendroctonus ponderosae

Mountain pine beetle

Dpod\YQE_12144

Tribolium castaneum

Red flour beetle

Tcas\TC016069

Tribolium castaneum

Red flour beetle

Tcas\TC005665

Tribolium castaneum

Red flour beetle

Tcas\TC033342

Pediculus humanus

Human body louse

Phum\PHUM423160

Rhodnius prolixus

Kissing bug

Rpro\RPRC014905

Cimex lectularius

Bed bug

Clec\CLEC000573

Acyrthosiphon pisum

Pea aphid

Apim\ACYPI061611

Acyrthosiphon pisum

Pea aphid

Apim\ACYPI003646

Zootermopsis nevadensis

Nevada dampwood termite

Znev\Znev_07952

Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X04LL )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Strigamia maritima

European centipede

Smar\SMAR009412

Ixodes scapularis

Black-legged tick

Isca\ISCW009510

Stegodyphus mimosarum

African social velvet spider

Smim\KFM56779.1

Tetranychus urticae

Two-spotted spider mite

Turt\tetur04g07570

Daphnia pulex

Water flea

Dpux\DAPPUDRAFT_215354

Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G07IK )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Strongylocentrotus purpuratus

Purple sea urchin

Spur\SPU_001765gn

Strongylocentrotus purpuratus

Purple sea urchin

Spur\Sp-Eif3d

Ciona intestinalis

Vase tunicate

Cint\LOC100181450

Gallus gallus

Domestic chicken

Ggal\EIF3D

Paralogs

Downloads

Download All DIOPT Paralogs

Paralogs (via DIOPT v7.1)

Drosophila melanogaster (Fruit fly) (1)

Gene Symbol

Score

Source

Alignment

8 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 v7.1 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?

EIF3D; eukaryotic translation initiation factor 3 subunit D

13 of 15

603915

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

Interactions Browser

View in Interactions Browser

Please see the Physical Interaction reports below for full details

protein-protein

Physical Interaction

Assay

References

eIF3d2 - trbd

two hybrid

(Hu et al., 2017.6.13)

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)

Component of the eukaryotic translation initiation factor 3 (eIF-3) complex. The eIF-3 complex interacts with pix.

(UniProt, Q9VGC7 )

Linkouts

BioGRID - A database of protein and genetic interactions.

66589

DroID - A comprehensive database of gene and protein interactions.

FBgn0037994

InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.

41475

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

CG4810

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

External Data

Linkouts

KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.

RNA transport

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

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

3-52

Cytogenetic map

87B2-87B2

Sequence location

3R:12,192,703..12,195,011 [-]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

87B2-87B2

Limits computationally determined from genome sequence between P{EP}Lk6^EP886 and P{PZ}svp⁰⁷⁸⁴²

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

3-52

(FlyBase, 2016)

3-49.3

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (2)

VDRC

v104342

P{KK104006}VIE-260B

v26637

w¹¹¹⁸; P{GD11435}v26637

Genomic Clones (27)

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

cDNA Clones (4)

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 sequences

BDGP DGC clones

GH14470

Other clones

DPiM_GH14470

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.

FBgn0037994

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0037994

GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents

41475

Antibody Information

Laboratory Generated Antibodies

Commercially Available Antibodies

Other Information

Relationship to Other Genes

Source for database identify of

Source for identity of: eIF3d2 CG4810

(Marygold et al., 2017)

Source for database merge of

Additional comments

Other Comments

Origin and Etymology

Discoverer

Etymology

Identification

External Crossreferences and Linkouts ( 35 )

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.

41475

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

Q9VGC7

Other crossreferences

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0037994

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

FBgn0037994

Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.

CG4810_1

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

CG4810

Flygut - An atlas of the Drosophila adult midgut

FBgn0037994

GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents

41475

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

Eukaryotic translation initiation factor 3 subunit D

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

Dmel_CG4810

modMine - A data warehouse for the modENCODE project

FBgn0037994

Linkouts

BioGRID - A database of protein and genetic interactions.

66589

DPiM - Drosophila Protein interaction map

FBgn0037994

DroID - A comprehensive database of gene and protein interactions.

FBgn0037994

DRSC - Results frm RNAi screens

FBgn0037994

FLIGHT - Cell culture data for RNAi and other high-throughput technologies

FBgn0037994

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

CG4810-RA

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0037994

FlyMine - An integrated database for Drosophila genomics

FBgn0037994

InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.

41475

KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.

RNA transport

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

CG4810

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

Synonyms and Secondary IDs (5)

Reported As

Symbol Synonym

149735_at

(Kristensen et al., 2005)

CG4810

(Marygold et al., 2017, Kwon et al., 2013, Japanese National Institute of Genetics, 2012.5.21, Keleman et al., 2009.8.5, Marygold et al., 2007, Cho et al., 2005)

eIF3-S7

(Lasko, 2000)

eIF3d2

(Hu et al., 2017.6.13, Marygold et al., 2017)

Name Synonyms

eukaryotic translation initiation factor 3 subunit d2

Secondary FlyBase IDs

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

References (27)

Report Sections

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