FB2022_03, released June 9, 2022

Gene: Dmel\d4

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General Information
Symbol
Dmel\d4
Species
D. melanogaster
Name
d4
Annotation Symbol
CG2682
Feature Type
protein_coding_gene
FlyBase ID
FBgn0033015
Gene Model Status
Current
Stock Availability
9 publicly available
Gene Summary
Contribute a Gene Snapshot for this gene.
All Summaries
Also Known As

dd4

Key Links
Genomic Location
Cytogenetic map
Sequence location
Recombination map
2-55
RefSeq locus
NT_033778 REGION:5259004..5295965
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 (8 terms)
Molecular Function (3 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
enables histone binding
inferred from biological aspect of ancestor with PANTHER:PTN000064894
(assigned by GO_Central )
(Gaudet et al., 2011)
enables transcription coregulator activity
inferred from biological aspect of ancestor with PANTHER:PTN000064894
(assigned by GO_Central )
(Gaudet et al., 2011)
enables zinc ion binding
inferred from sequence model
(Ying et al., 2011)
Biological Process (3 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
involved_in negative regulation of transcription, DNA-templated
inferred from biological aspect of ancestor with PANTHER:PTN000064894
(assigned by GO_Central )
(Gaudet et al., 2011)
involved_in nervous system development
inferred from biological aspect of ancestor with PANTHER:PTN000064899
(assigned by GO_Central )
(Gaudet et al., 2011)
involved_in positive regulation of transcription by RNA polymerase II
inferred from biological aspect of ancestor with PANTHER:PTN000064894
(assigned by GO_Central )
(Gaudet et al., 2011)
Cellular Component (2 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
part_of brahma complex
inferred from direct assay
(Barish et al., 2020)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
part_of nBAF complex
inferred from biological aspect of ancestor with PANTHER:PTN000064899
(assigned by GO_Central )
(Gaudet et al., 2011)
Gene Group (FlyBase)
Protein Family (UniProt)
-
Protein Signatures (InterPro)
Summaries
Gene Group (FlyBase)
BRAHMA ASSOCIATED PROTEINS COMPLEX -
The Brahma associated proteins (BAP) complex is an ATP-dependent chromatin remodeling complex. (Adapted from FBrf0192510.)
Gene Model and Products
Number of Transcripts
4
Number of Unique Polypeptides
4

Please see the JBrowse view of Dmel\d4 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 New Section
Protein 3D structure   (Predicted by AlphaFold)   (AlphaFold entry Q7K3G5)

If you don't see the viewer to the right, 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.

Comments on Gene Model

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

Annotated transcripts do not represent all possible combinations of alternative exons and/or alternative promoters.

Gene model reviewed during 5.47

Sequence Ontology: Class of Gene
nuclear_gene
protein_coding_gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
d4-RA
FBtr0086082
NM_136319
1767
497
d4-RB
FBtr0111115
NM_165425
1850
339
d4-RC
FBtr0086083
NM_165424
1761
495
d4-RD
FBtr0335258
NM_001273778
1764
496
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
d4-PA
FBpp0085418
55.2
497
7.88
Q7K3G5
NP_610163
AAF57340
d4-PB
FBpp0110407
36.8
339
6.28
Q0E9P4
NP_724405
AAM68376
d4-PC
FBpp0085419
55.1
495
7.88
A1Z6E6
NP_724404
AAF57339
d4-PD
FBpp0307242
55.2
496
7.88
A0A0B4KEC3
NP_001260707
AGB93242
Polypeptides with Identical Sequences

None of the polypeptides share 100% sequence identity.

Additional Polypeptide Data and Comments
Reported size (kDa)
Comments
External Data
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\d4 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 the Fly Cell Atlas project found the gene expressed in that cell type. Darker colors mean that more cells of that cell type express the gene:
 low
high 
Colorless tiles indicate that there is no scRNAseq data for the gene in that cell type.
Colored tiles in ribbon indicate that expression data (RNA and/or protein) has been curated by FlyBase for that anatomical location. Colorless tiles indicate that there is no curated data for that location.
Colored tiles in the ribbon indicate the average RNA expression level of the gene at the indicated stages:
 low
high 
as determined by RNA-seq (RPKM) using whole organism samples modENCODE, Brown et al., 2014. For complete stage-specific expression data, view the modENCODE Development RNA-Seq section under High-Throughput Expression below.
Transcript Expression
Polypeptide Expression
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
part_of brahma complex
inferred from direct assay
(Barish et al., 2020)
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\d4 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
DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
Flygut - An atlas of the Drosophila adult midgut
Images
FlyExpress - Embryonic expression images (BDGP data)
  • Stages(s) 9-10
  • Stages(s) 11-12
  • Stages(s) 13-16
FlyBase Wiki
Image Based Resources
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 2 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 11 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of d4
Transgenic constructs containing regulatory region of d4
Aberrations (Deficiencies and Duplications) ( 4 )
Inferred from experimentation ( 4 )
Gene disrupted in
Df(2R)M41A8
(Myster et al., 2004)
Gene not disrupted in
Df(2R)M41A2
(Myster et al., 2004)
Df(2R)M41A10
(Myster et al., 2004)
Df(2R)Nipped-D
(Myster et al., 2004)
Inferred from location ( 0 )
Alleles Representing Disease-Implicated Variants
Phenotypes
Orthologs
Downloads
Download All DIOPT Orthologs
Human Orthologs (via DIOPT v8.0)
Homo sapiens (Human) (8)
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\DPF1
12 of 15
Yes
Yes
1  
Hsap\DPF2
12 of 15
Yes
Yes
1  
Hsap\DPF3
12 of 15
Yes
Yes
Hsap\RSF1
2 of 15
No
No
Hsap\KAT5
1 of 15
No
No
Hsap\KAT6A
1 of 15
No
No
Hsap\KAT6B
1 of 15
No
No
Hsap\PHF10
1 of 15
No
No
Model Organism Orthologs (via DIOPT v8.0)
Mus musculus (laboratory mouse) (9)
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\Dpf2
12 of 15
Yes
Yes
Mmus\Dpf1
11 of 15
No
Yes
Mmus\Dpf3
11 of 15
No
Yes
Mmus\Rsf1
2 of 15
No
No
Mmus\Kat5
1 of 15
No
No
Mmus\Kat6a
1 of 15
No
No
Mmus\Kat6b
1 of 15
No
No
Mmus\Phf10
1 of 15
No
No
Mmus\Zfp748
1 of 15
No
No
Rattus norvegicus (Norway rat) (7)
Rnor\Dpf1
10 of 13
Yes
Yes
Rnor\Dpf2
10 of 13
Yes
Yes
Rnor\Dpf3
8 of 13
No
Yes
Rnor\Rsf1
2 of 13
No
No
Rnor\Kat5
1 of 13
No
No
Rnor\Kat6a
1 of 13
No
No
Rnor\Phf10
1 of 13
No
No
Xenopus tropicalis (Western clawed frog) (6)
Xtro\dpf2
9 of 12
Yes
Yes
Xtro\dpf3
7 of 12
No
Yes
Xtro\dpf1
2 of 12
No
Yes
Xtro\LOC448243
1 of 12
No
Yes
Xtro\phf10
1 of 12
No
No
Xtro\rsf1
1 of 12
No
No
Danio rerio (Zebrafish) (9)
Drer\dpf3
12 of 15
Yes
Yes
Drer\dpf2
11 of 15
No
Yes
Drer\dpf2l
11 of 15
No
Yes
Drer\dpf1
5 of 15
No
Yes
Drer\rsf1b.1
2 of 15
No
No
Drer\kat6a
1 of 15
No
No
Drer\kat6b
1 of 15
No
No
Drer\phf10
1 of 15
No
No
Drer\rsf1a
1 of 15
No
No
Caenorhabditis elegans (Nematode, roundworm) (1)
Cele\dpff-1
12 of 15
Yes
Yes
Arabidopsis thaliana (thale-cress) (5)
Atha\AT2G19260
1 of 9
Yes
Yes
Atha\AT3G08020
1 of 9
Yes
Yes
Atha\AT3G52100
1 of 9
Yes
Yes
Atha\ATXR5
1 of 9
Yes
Yes
Atha\ATXR6
1 of 9
Yes
Yes
Saccharomyces cerevisiae (Brewer's yeast) (1)
Scer\ESA1
1 of 15
Yes
No
Schizosaccharomyces pombe (Fission yeast) (0)
No records found.
Other Organism Orthologs (via OrthoDB)
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v8.0)
Drosophila melanogaster (Fruit fly) (8)
Gene Symbol
Score
Source
Compara
eggNOG
Homologene
Inparanoid
Isobase
OrthoDB
OrthoFinder
orthoMCL
Panther
RoundUp
Alignment
e(y)3
4 of 10
tth
4 of 10
CG1894
2 of 10
chm
2 of 10
enok
2 of 10
mof
2 of 10
Tip60
2 of 10
CG8677
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?
    DPF1; double PHD fingers 1
    12 of 15
    601670
         
        DPF2; double PHD fingers 2
        12 of 15
        601671
           
          DPF3; double PHD fingers 3
          12 of 15
          601672
              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
              d4 - Ada2b
              anti tag coimmunoprecipitation, peptide massfingerprinting
              (Weake et al., 2011)
              d4 - Bap111
              anti tag coimmunoprecipitation, protein cross-linking with a bifunctional reagent, Identification by mass spectrometry
              (Barish et al., 2020, Mashtalir et al., 2018)
              d4 - Bap55
              anti tag coimmunoprecipitation, Identification by mass spectrometry
              (Barish et al., 2020)
              d4 - Bdp1
              two hybrid array
              (Shokri et al., 2019)
              d4 - Blos1
              two hybrid array
              (Shokri et al., 2019)
              d4 - CG12075
              two hybrid array
              (Shokri et al., 2019)
              d4 - CG12299
              two hybrid array
              (Shokri et al., 2019)
              d4 - CG2116
              two hybrid array
              (Shokri et al., 2019)
              d4 - CG30431
              two hybrid array
              (Shokri et al., 2019)
              d4 - Eip78C
              two hybrid array
              (Shokri et al., 2019)
              d4 - Ets65A
              two hybrid array
              (Shokri et al., 2019)
              d4 - Hr78
              two hybrid array
              (Shokri et al., 2019)
              d4 - Hsp67Bc
              two hybrid
              (Hu et al., 2017.6.13)
              d4 - Kr
              two hybrid array
              (Shokri et al., 2019)
              d4 - Lpt
              two hybrid array
              (Shokri et al., 2019)
              d4 - PolE4
              two hybrid array
              (Shokri et al., 2019)
              d4 - Pph13
              two hybrid array
              (Shokri et al., 2019)
              d4 - Rel
              two hybrid array
              (Shokri et al., 2019)
              d4 - Snr1
              anti tag coimmunoprecipitation, protein cross-linking with a bifunctional reagent, Identification by mass spectrometry
              (Mashtalir et al., 2018)
              d4 - Ubx
              bimolecular fluorescence complementation, fluorescence microscopy
              (Bischof et al., 2018)
              d4 - abd-A
              bimolecular fluorescence complementation, fluorescence microscopy
              (Bischof et al., 2018)
              d4 - brm
              anti tag coimmunoprecipitation, Identification by mass spectrometry, anti bait coimmunoprecipitation
              (Tilly et al., 2021, Barish et al., 2020)
              d4 - eg
              two hybrid array
              (Shokri et al., 2019)
              d4 - mor
              anti tag coimmunoprecipitation, Identification by mass spectrometry
              (Barish et al., 2020)
              d4 - osa
              anti tag coimmunoprecipitation, protein cross-linking with a bifunctional reagent, Identification by mass spectrometry
              (Barish et al., 2020, Mashtalir et al., 2018)
              d4 - polybromo
              anti tag coimmunoprecipitation, protein cross-linking with a bifunctional reagent, Identification by mass spectrometry
              (Mashtalir et al., 2018)
              d4 - prg
              two hybrid array
              (Shokri et al., 2019)
              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
              Linkouts
              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
              Genomic Location and Detailed Mapping Data
              Chromosome (arm)
              2R
              Recombination map
              2-55
              Cytogenetic map
              41E3-41E4
              Sequence location
              FlyBase Computed Cytological Location
              Cytogenetic map
              Evidence for location
              41E3-41E4
              Experimentally Determined Cytological Location
              Cytogenetic map
              Notes
              References
              Experimentally Determined Recombination Data
              Location

              2-55

              (FlyBase, 2016)

              2-55.5

              (Comeron et al., 2012)
              Left of (cM)
              Right of (cM)
              Notes
              Stocks and Reagents
              Stocks (9)
              Genomic Clones (24)
              cDNA Clones (87)
               

              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: dd4 CG2682

                (FlyBase, 1996-)
                Source for database merge of
                Additional comments

                Source for identity of dd4 CG2682 was sequence comparison ( date:011027 ).

                (FlyBase, 1996-)
                Other Comments

                dsRNA has been made from templates generated with primers directed against this gene. RNAi of d4 results in reduced arborization of ddaD and ddaE neurons, defects in muscle and defects in dendrite morphogenesis.

                (Parrish et al., 2006)
                Origin and Etymology
                Discoverer
                Etymology
                Identification
                External Crossreferences and Linkouts ( 56 )
                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/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.
                UniProt/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information
                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.
                BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
                Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
                DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
                EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
                Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
                FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
                FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
                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 - MARRVEL (model organism gene)
                modMine - A data warehouse for the modENCODE project
                Linkouts
                DroID - A comprehensive database of gene and protein interactions.
                DRSC - Results frm RNAi screens
                FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
                FlyMine - An integrated database for Drosophila genomics
                MIST (protein-protein) - An integrated Molecular Interaction Database
                Synonyms and Secondary IDs (5)
                Datasets (0)
                Study focus (0)
                Experimental Role
                Project
                Project Type
                Title
                Study result (0)
                Result
                Result Type
                Title
                References (67)