FB2020_06, released Dec 22, 2020

Gene: Dmel\eIF3d2

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General Information
Symbol
Dmel\eIF3d2
Species
D. melanogaster
Name
eukaryotic translation initiation factor 3 subunit d2
Annotation Symbol
CG4810
Feature Type
protein_coding_gene
FlyBase ID
FBgn0037994
Gene Model Status
Current
Stock Availability
2 publicly available
Gene Snapshot
Contributions welcome
Other Summaries
Key Links
Genomic Location
Cytogenetic map
87B2-87B2
Sequence location
3R:12,192,703..12,195,011 [-]
Recombination map

3-52

RefSeq locus
NT_033777 REGION:12192703..12195011
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 (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
enables 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
involved_in regulation of translational initiation
inferred from sequence or structural similarity with UniProtKB:Q9VCK0
(assigned by UniProt )
(UniProt Curators, 2002-)
involved_in 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
part_of 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)
Gene Group (FlyBase)
Protein Family (UniProt)
Belongs to the eIF-3 subunit D family. (Q9VGC7)
Protein Signatures (InterPro)
Summaries
Gene Group (FlyBase)
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
1
Number of Unique Polypeptides
1

Please see 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
Linkouts
Sequences Consistent with the Gene Model
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.
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
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
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
FLIGHT - Cell culture data for RNAi and other high-throughput technologies
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, 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 )
Phenotypes
For more details about a specific phenotype click on the relevant allele symbol.
Lethality
Allele
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) (1)
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\EIF3D
13 of 15
Yes
No
Model Organism Orthologs (via DIOPT v8.0)
Mus musculus (laboratory mouse) (1)
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\Eif3d
12 of 15
Yes
No
Rattus norvegicus (Norway rat) (1)
Rnor\Eif3d
12 of 13
Yes
No
Xenopus tropicalis (Western clawed frog) (1)
Xtro\eif3d
12 of 12
Yes
No
Danio rerio (Zebrafish) (1)
Drer\eif3d
13 of 15
Yes
No
Caenorhabditis elegans (Nematode, roundworm) (1)
Cele\eif-3.D
12 of 15
Yes
No
Arabidopsis thaliana (thale-cress) (2)
Atha\AT4G20980
8 of 9
Yes
No
Atha\AT5G44320
8 of 9
Yes
No
Saccharomyces cerevisiae (Brewer's yeast) (0)
No records found.
Schizosaccharomyces pombe (Fission yeast) (1)
Spom\moe1
10 of 12
Yes
No
Ortholog(s) 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
Dsuz\DS10_00009382
Drosophila simulans
Dsim\GD20597
Drosophila sechellia
Dsec\GM26037
Drosophila erecta
Dere\GG17155
Drosophila yakuba
Dyak\GE24545
Drosophila ananassae
Dana\GF17742
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 v8.0)
Drosophila melanogaster (Fruit fly) (1)
Gene Symbol
Score
Source
Compara
eggNOG
Homologene
Inparanoid
Isobase
OrthoDB
OrthoFinder
orthoMCL
Panther
RoundUp
Alignment
eIF3d1
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 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?
    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
        Show neighbor-neighbor interactions:
        Select Layout:
        Legend:
        Protein
        RNA
        Selected Interactor(s)
        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.
        DroID - A comprehensive database of gene and protein interactions.
        InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
        MIST (protein-protein) - An integrated Molecular Interaction Database
        Pathways
        Signaling Pathways (FlyBase)
        Metabolic Pathways
        External Data
        Genomic Location and Detailed Mapping Data
        Chromosome (arm)
        3R
        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}Lk6EP886 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)
        Genomic Clones (27)
        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 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
           
          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.
          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
          BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
          Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
          Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
          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
          InterPro - A database of protein families, domains and functional sites
          KEGG Genes - Molecular building blocks of life in the genomic space.
          modMine - A data warehouse for the modENCODE project
          Linkouts
          BioGRID - A database of protein and genetic interactions.
          DPiM - Drosophila Protein interaction map
          DroID - A comprehensive database of gene and protein interactions.
          DRSC - Results frm RNAi screens
          FLIGHT - Cell culture data for RNAi and other high-throughput technologies
          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
          InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
          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 (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)