FB2024_03 , released June 25, 2024
Gene: Dmel\Taf4
Open Close
General Information
Symbol
Dmel\Taf4
Species
D. melanogaster
Name
TBP-associated factor 4
Annotation Symbol
CG5444
Feature Type
FlyBase ID
FBgn0010280
Gene Model Status
Stock Availability
Gene Summary
TBP-associated factor 4 (Taf4) encodes a protein that forms part of the multisubunit basal transcription factor TFIIID. It is important in maintaining TFIIID stability for activator dependent transcription. It forms a histone-like pair with the product of Taf12. [Date last reviewed: 2019-03-14] (FlyBase Gene Snapshot)
Also Known As

dTAFII110, TAFII110, TAF110, TAFII110, TFIID

Key Links
Genomic Location
Cytogenetic map
Sequence location
Recombination map
3-44
RefSeq locus
NT_037436 REGION:16113212..16121651
Sequence
Genomic Maps
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
Function
Gene Ontology (GO) Annotations (11 terms)
Molecular Function (5 terms)
Terms Based on Experimental Evidence (4 terms)
CV Term
Evidence
References
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
Biological Process (4 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
inferred from physical interaction with UniProtKB:P51123
inferred from physical interaction with UniProtKB:P51123
inferred from direct assay
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
inferred from sequence or structural similarity with HGNC:11537
inferred from sequence or structural similarity with SGD:S000004607
inferred from biological aspect of ancestor with PANTHER:PTN000388601
Cellular Component (2 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
located_in nucleus
inferred from direct assay
inferred from physical interaction with FLYBASE:Taf6; FB:FBgn0010417
inferred from physical interaction with UniProtKB:P51123
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN000388601
inferred from electronic annotation with InterPro:IPR007900, InterPro:IPR045144
inferred from sequence or structural similarity with HGNC:11537
inferred from sequence or structural similarity with SGD:S000004607
Gene Group (FlyBase)
Protein Family (UniProt)
Belongs to the TAF4 family. (P47825)
Summaries
Gene Snapshot
TBP-associated factor 4 (Taf4) encodes a protein that forms part of the multisubunit basal transcription factor TFIIID. It is important in maintaining TFIIID stability for activator dependent transcription. It forms a histone-like pair with the product of Taf12. [Date last reviewed: 2019-03-14]
Gene Group (FlyBase)
TRANSCRIPTION FACTOR II D -
The general transcription factor complex Transcription factor II D (TFIID) plays an important role in recruiting the transcription machinery to core promoters. TFIID is a complex composed of TBP and several TBP-associated factors. (Adapted from FBrf0125116 and FBrf0156065).
Protein Function (UniProtKB)
TFIID is a multimeric protein complex that plays a central role in mediating promoter responses to various activators and repressors. May function as a coactivator by serving as a site of protein-protein contact between activators like Sp1 (or btd) and TFIID complex.
(UniProt, P47825)
Gene Model and Products
Number of Transcripts
9
Number of Unique Polypeptides
5

Please see the JBrowse view of Dmel\Taf4 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 P47825)

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
Comments on Gene Model

Gene model reviewed during 5.55

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

Gene model reviewed during 5.46

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

Gene model reviewed during 5.56

Sequence Ontology: Class of Gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
FBtr0075448
4916
921
FBtr0075449
4574
921
FBtr0075450
4423
851
FBtr0075451
4166
851
FBtr0114589
5134
1088
FBtr0301911
4622
921
FBtr0333290
4756
962
FBtr0333291
5011
1047
FBtr0345951
4226
921
Additional Transcript Data and Comments
Reported size (kB)

4.615 (longest cDNA)

5.0 (northern blot)

Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
UniProt
RefSeq ID
GenBank
FBpp0075205
99.3
921
10.64
FBpp0075206
99.3
921
10.64
FBpp0075207
92.1
851
10.59
FBpp0089259
92.1
851
10.59
FBpp0113081
117.2
1088
10.86
FBpp0291125
99.3
921
10.64
FBpp0305485
103.5
962
10.68
FBpp0305486
113.1
1047
10.83
FBpp0311865
99.3
921
10.64
Polypeptides with Identical Sequences

The group(s) of polypeptides indicated below share identical sequence to each other.

921 aa isoforms: Taf4-PA, Taf4-PB, Taf4-PF, Taf4-PI
851 aa isoforms: Taf4-PC, Taf4-PD
Additional Polypeptide Data and Comments
Reported size (kDa)

921 (aa); 99.4 (kD)

921 (aa); 110 (kD)

Comments
External Data
Subunit Structure (UniProtKB)

Belongs to the TFIID complex which is composed of TATA binding protein (Tbp) and a number of TBP-associated factors (TAFs). Interacts with TFIIA-L when in complex with Tbp. Interacts with Taf1, Taf5, Taf11 and Taf12.

(UniProt, P47825)
Linkouts
Sequences Consistent with the Gene Model
Nucleotide / Polypeptide Records
 
Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\Taf4 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
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).

0.34

Transcript Expression
in situ
Stage
Tissue/Position (including subcellular localization)
Reference
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
immunolocalization
Stage
Tissue/Position (including subcellular localization)
Reference
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
located_in nucleus
inferred from direct assay
inferred from physical interaction with FLYBASE:Taf6; FB:FBgn0010417
inferred from physical interaction with UniProtKB:P51123
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\Taf4 in JBrowse
RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region
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
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
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 19 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 6 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Taf4
Transgenic constructs containing regulatory region of Taf4
Aberrations (Deficiencies and Duplications) ( 12 )
Variants
Variant Molecular Consequences
Alleles Representing Disease-Implicated Variants
Phenotypes
Orthologs
Human Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
Homo sapiens (Human) (2)
12 of 14
Yes
Yes
11 of 14
No
Yes
Model Organism Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
Rattus norvegicus (Norway rat) (2)
12 of 14
Yes
Yes
7 of 14
No
Yes
Mus musculus (laboratory mouse) (2)
12 of 14
Yes
Yes
9 of 14
No
Yes
Xenopus tropicalis (Western clawed frog) (4)
10 of 13
Yes
Yes
7 of 13
No
Yes
7 of 13
No
Yes
1 of 13
No
No
Danio rerio (Zebrafish) (4)
10 of 14
Yes
Yes
10 of 14
Yes
Yes
10 of 14
Yes
Yes
1 of 14
No
Yes
Caenorhabditis elegans (Nematode, roundworm) (1)
9 of 14
Yes
Yes
Anopheles gambiae (African malaria mosquito) (2)
6 of 12
Yes
Yes
Arabidopsis thaliana (thale-cress) (2)
8 of 13
Yes
Yes
7 of 13
No
Yes
Saccharomyces cerevisiae (Brewer's yeast) (1)
4 of 13
Yes
Yes
Schizosaccharomyces pombe (Fission yeast) (1)
1 of 12
Yes
Yes
Escherichia coli (enterobacterium) (0)
Other Organism Orthologs (via OrthoDB)
Data provided directly from OrthoDB:Taf4. Refer to their site for version information.
Paralogs
Paralogs (via DIOPT v9.1)
Drosophila melanogaster (Fruit fly) (1)
4 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
    Modifiers Based on Experimental Evidence ( 0 )
    Allele
    Disease
    Interaction
    References
    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.
    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:
    Show/hide secondary interactors 
    (data from AllianceMine provided by esyN)
    Select Layout:
    Legend:
    Protein
    RNA
    Selected Interactor(s)
    Other Interaction Browsers

    Please see the Physical Interaction reports below for full details
    protein-protein
    Physical Interaction
    Assay
    References
    RNA-protein
    Physical Interaction
    Assay
    References
    Summary of Genetic Interactions
    esyN Network Diagram
    Show/hide secondary interactors 
    (data from AllianceMine provided by esyN)
    esyN Network Key:
    Suppression
    Enhancement
    Other Interaction Browsers

    Please look at the allele data for full details of the genetic interactions
    Starting gene(s)
    Interaction type
    Interacting gene(s)
    Reference
    Starting gene(s)
    Interaction type
    Interacting gene(s)
    Reference
    External Data
    Subunit Structure (UniProtKB)
    Belongs to the TFIID complex which is composed of TATA binding protein (Tbp) and a number of TBP-associated factors (TAFs). Interacts with TFIIA-L when in complex with Tbp. Interacts with Taf1, Taf5, Taf11 and Taf12.
    (UniProt, P47825 )
    Linkouts
    BioGRID - A database of protein and genetic interactions.
    DroID - A comprehensive database of gene and protein interactions.
    MIST (genetic) - An integrated Molecular Interaction Database
    MIST (protein-protein) - An integrated Molecular Interaction Database
    Pathways
    Signaling Pathways (FlyBase)
    Metabolic Pathways
    External Data
    Genomic Location and Detailed Mapping Data
    Chromosome (arm)
    3L
    Recombination map
    3-44
    Cytogenetic map
    Sequence location
    FlyBase Computed Cytological Location
    Cytogenetic map
    Evidence for location
    72D7-72D8
    Limits computationally determined from genome sequence between P{lacW}thj5C8&P{PZ}Mbs03802 and P{lacW}SsRβs1939
    Experimentally Determined Cytological Location
    Cytogenetic map
    Notes
    References
    72D4-72D5
    72D4-72D5
    (determined by in situ hybridisation)
    Experimentally Determined Recombination Data
    Location
    Left of (cM)
    Right of (cM)
    Notes
    Stocks and Reagents
    Stocks (15)
    Genomic Clones (13)
     

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

    cDNA Clones (150)
     

    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.

    cDNA Clones, End Sequenced (ESTs)
    RNAi and Array Information
    Linkouts
    DRSC - Results frm RNAi screens
    Antibody Information
    Laboratory Generated Antibodies
     

    monoclonal

    Commercially Available Antibodies
     
    Cell Line Information
    Publicly Available Cell Lines
     
      Other Stable Cell Lines
       
        Other Comments

        The 'l(3)72Dj' (Taf4) complementation group comprises 4 EMS-induced mutant alleles.

        dsRNA has been made from templates generated with primers directed against this gene.

        dsRNA has been made from templates generated with primers directed against this gene. RNAi of Taf4 results in dorsal overextension of primary dendrites and a reduction in lateral branching. RNAi also causes defects in muscle, defects in dendrite morphogenesis and reproducible defects in da dendrite development.

        The proteins encoded by Taf4, Taf5, Taf6, e(y)1 and Taf12 form a core sub-complex of TFIID. Of these, Taf4 protein plays the most critical role in maintaining stability of the TFIID complex.

        The C-terminal domain of the Taf4 protein is necessary and sufficient for nucleating a holo-TFIID complex.

        The proteins encoded by Taf1 and Taf4 have a specific role in transcription activation from TATA-less, downstream core promoter element (DPE)-containing promoters.

        Area matching Drosophila TAF110 gene, Acc. No. L06861. Probable intron.

        An interplay of dl and twi proteins with Taf4 protein is required for the activation of mesoderm-determining gene expression in the embryo.

        Interacts, in vitro, with human thryroid-hormone receptor-β.

        The products of the Taf4 and Taf6 loci serve as coactivators to mediate transcriptional activation by the bcd and hb enhancer binding proteins. A quadruple complex containing Tbp, Taf1, Taf4 and Taf6 mediates transcriptional synergism by bcd and hb, whereas triple Tbp-Taf complexes lacking one or other coactivator failed to support synergistic activation. The concerted action of multiple regulators with different coactivators helps to establish the pattern and level of segmentation gene transcription during development.

        Mutagenesis studies in combination with protein binding experiments and reconstituted transcription reactions identified two independent activation domains of bcd that target different coactivator subunits (Taf4 and Taf6). Both coactivators are required for bcd to recruit the Tbp-Taf complex to the promoter and direct synergistic activation of transcription. Contact between multiple activation domains for bcd and different targets within the TfIID complex can mediate transcriptional synergism.

        The assembly and purification of various functional Tbp TAF complexes demonstrate that Tbp plus the TAFs is sufficient to replace endogenous TFIID to support activated transcription in vitro.

        TFIID subunit proteins and the Tbp protein can interact in pairwise combinations with several subunits in a network of interactions within TFIID.

        The TFIID complex interacts with the promoters of Hsp70Bb, Hsp70Bc, Hsp26 and His3 making contacts at the TATA element, initiator, +18 and +28 regions.

        Purified TAF80 is unable to bind TBP directly or to interact strongly with the C-terminal domain of TAF250, but can only interact with a complex containing TBP, TAF250, TAF110 and TAF60.

        Cell culture studies suggest that TAF110 can functionally interact with Sp1 and serve as a coactivator of transcription.

        A number of polypeptides (encoded by Taf1, Taf4, Taf5, Taf6, e(y)1 and Taf12) that are tightly associated with Tbp and are native TFIID components have been purified. Protein blotting experiments suggest that one of these proteins, Taf1, interacts directly with Tbp, while the association between Tbp and the other proteins is either weak or is an indirect association via Taf1.

        In vitro expressed TAF110 interacts directly with the TAF250 which itself interacts with TBP, a complex of all three is suggested. Binding study with various mutants of Taf1 suggests that both TAF110 and TBP interact with the N-terminal 352-amino acid portion of TAF250.

        Tbp, Taf1, Taf4 and Taf6 products can assemble into a mini-complex in vitro, showing that Taf6 and Taf4 occupy distinct binding sites on the C terminal part of Taf1.

        The assembly of a partial complex containing recombinant TBF, TAF250 and TAF110 was reported. This triple complex supports activation of HeLa cell Sp1 and reveals specific interactions between Tbp, Taf1 and Taf4.

        Relationship to Other Genes
        Source for database merge of

        Source for merge of: Taf110 l(3)72Dj

        Additional comments
        Nomenclature History
        Source for database identify of
        Nomenclature comments
        Etymology
        Synonyms and Secondary IDs (31)
        Reported As
        Symbol Synonym
        SY3-2 TAF110
        TFIID 110
        Name Synonyms
        TATA-associated factor 110
        TBP associated factor 110
        TBP-associated factor
        TBP-associated factor 110
        TBP-associated factor 110kD
        TBP-associated factor 4
        lethal(3)72Dj
        Secondary FlyBase IDs
        • FBgn0005542
        • FBgn0010419
        • FBgn0013958
        Datasets (0)
        Study focus (0)
        Experimental Role
        Project
        Project Type
        Title
        Study result (0)
        Result
        Result Type
        Title
        External Crossreferences and Linkouts ( 77 )
        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/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information
        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.
        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
        FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
        FlyMine - An integrated database for Drosophila genomics
        KEGG Genes - Molecular building blocks of life in the genomic space.
        MARRVEL_MODEL - MARRVEL (model organism gene)
        Linkouts
        BioGRID - A database of protein and genetic interactions.
        Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
        DroID - A comprehensive database of gene and protein interactions.
        DRSC - Results frm RNAi screens
        Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
        FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
        FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
        Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
        Flygut - An atlas of the Drosophila adult midgut
        FlyMet - A comprehensive tissue-specific metabolomics resource for Drosophila.
        KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.
        MIST (genetic) - An integrated Molecular Interaction Database
        MIST (protein-protein) - An integrated Molecular Interaction Database
        References (174)