FB2026_01 , released March 12, 2026
FB2026_01 , released March 12, 2026
Gene: Dmel\Brf
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General Information
Symbol
Dmel\Brf
Species
D. melanogaster
Name
Brf RNA polymerase III subunit
Annotation Symbol
CG31256
Feature Type
protein_coding_gene
FlyBase ID
FBgn0038499
Gene Model Status
Current
Stock Availability
19 publicly available
Gene Summary
Brf (Brf) encodes a transcription factor binding protein involved in transcription mediated by RNA polymerase III. [Date last reviewed: 2019-09-19] (FlyBase Gene Snapshot)
All Summaries
Also Known As

Brf1

Key Links
Genomic Location
Cytogenetic map
90A3-90A5
Sequence location
Recombination map
3-60
RefSeq locus
NT_033777 REGION:17374833..17391337
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
Gene Ontology (GO) Annotations (11 terms)
Molecular Function (4 terms)
Terms Based on Experimental Evidence (3 terms)
CV Term
Evidence
References
contributes_to core promoter sequence-specific DNA binding
inferred from physical interaction with FLYBASE:Trf; FB:FBgn0010287
(Isogai et al., 2007)
enables RNA polymerase III type 3 promoter sequence-specific DNA binding
inferred from direct assay
(Kang et al., 2016)
enables TBP-class protein binding
inferred from physical interaction with FLYBASE:Trf; FB:FBgn0010287
(Takada et al., 2000)
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
enables RNA polymerase III general transcription initiation factor activity
inferred from biological aspect of ancestor with PANTHER:PTN000178519
(GO Reference Genome Project, 2011-)
enables RNA polymerase III type 3 promoter sequence-specific DNA binding
inferred from biological aspect of ancestor with PANTHER:PTN000178519
(GO Reference Genome Project, 2011-)
enables TBP-class protein binding
inferred from electronic annotation with InterPro:IPR013150
(InterPro Project Members, 2004-)
Biological Process (3 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
involved_in transcription by RNA polymerase III
inferred from direct assay
(Takada et al., 2000)
inferred from physical interaction with FLYBASE:Trf; FB:FBgn0010287
(Takada et al., 2000)
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
involved_in DNA-templated transcription initiation
inferred from electronic annotation with InterPro:IPR000812
(InterPro Project Members, 2004-)
inferred from biological aspect of ancestor with PANTHER:PTN000178517
(GO Reference Genome Project, 2011-)
involved_in transcription by RNA polymerase III
inferred from biological aspect of ancestor with PANTHER:PTN000178519
(GO Reference Genome Project, 2011-)
involved_in transcription preinitiation complex assembly
inferred from electronic annotation with InterPro:IPR000812
(InterPro Project Members, 2004-)
Cellular Component (4 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
part_of transcription factor TFIIIB complex
inferred from direct assay
(Kang et al., 2016)
part_of transcription regulator complex
inferred from physical interaction with FLYBASE:Trf; FB:FBgn0010287
(Takada et al., 2000)
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
is_active_in nucleus
inferred from biological aspect of ancestor with PANTHER:PTN000178518
(GO Reference Genome Project, 2011-)
part_of transcription factor TFIIIB complex
inferred from biological aspect of ancestor with PANTHER:PTN000178519
(GO Reference Genome Project, 2011-)
part_of transcription preinitiation complex
inferred from biological aspect of ancestor with PANTHER:PTN000178517
(GO Reference Genome Project, 2011-)
Gene Group (FlyBase)
Protein Family (UniProt)
-
Protein Signatures (InterPro)
Summaries
Gene Snapshot
Brf (Brf) encodes a transcription factor binding protein involved in transcription mediated by RNA polymerase III. [Date last reviewed: 2019-09-19]
Summary (Interactive Fly)

transcription factor TRF1 forms a complex with the TFIIB-related factor Brf that plays a major role in RNA pol III transcription - fatbody specific loss of Brf phenocopies nutrient limitation and TOR inhibition, leading to decreased systemic insulin signalling and reduced organismal growth

Gene Model and Products
Number of Transcripts
2
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\Brf 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 Q9VEL2)

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

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

Gene model reviewed during 5.49

Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
Brf-RA
FBtr0083452
NM_142359
2975
662
Brf-RB
FBtr0302317
NM_001170165
2262
662
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
Brf-PA
FBpp0082893
73.6
662
4.74
Q9VEL2
NP_650616
AAF55409
Brf-PB
FBpp0291523
73.6
662
4.74
Q9VEL2
NP_001163636
ACZ94932
Polypeptides with Identical Sequences

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

662 aa isoforms: Brf-PA, Brf-PB
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\Brf 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).

-0.30

Transcript Expression
Polypeptide Expression
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
part_of transcription factor TFIIIB complex
inferred from direct assay
(Kang et al., 2016)
part_of transcription regulator complex
inferred from physical interaction with FLYBASE:Trf; FB:FBgn0010287
(Takada et al., 2000)
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\Brf in JBrowse
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) 1-3
  • Stages(s) 4-6
  • Stages(s) 11-12
  • Stages(s) 13-16
FlyBase Wiki
Image Based Resources
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 9 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 5 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Brf
Transgenic constructs containing regulatory region of Brf
Aberrations (Deficiencies and Duplications) ( 0 )
Inferred from experimentation ( 0 )
Inferred from location ( 4 )
Variants
Variant Molecular Consequences
Alleles Representing Disease-Implicated Variants
Phenotypes
Orthologs
Downloads
Download All DIOPT Orthologs
Human Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
Domainoid
eggNOG
Hieranoid
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Complementation?
Transgene?
Homo sapiens (Human) (3)
Hsap\BRF1
13 of 14
Yes
Yes
1  
Hsap\BRF2
2 of 14
No
No
Hsap\GTF2B
2 of 14
No
No
Model Organism Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
Domainoid
eggNOG
Hieranoid
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Complementation?
Transgene?
Rattus norvegicus (Norway rat) (3)
Rnor\Brf1
14 of 14
Yes
Yes
Rnor\Brf2
2 of 14
No
No
Rnor\Gtf2b
2 of 14
No
No
Mus musculus (laboratory mouse) (3)
Mmus\Brf1
13 of 14
Yes
Yes
Mmus\Brf2
2 of 14
No
No
Mmus\Gtf2b
2 of 14
No
No
Xenopus tropicalis (Western clawed frog) (1)
Xtro\brf1
11 of 13
Yes
Yes
Danio rerio (Zebrafish) (5)
Drer\brf1b
14 of 14
Yes
Yes
Drer\brf1a
13 of 14
No
Yes
Drer\brf2
2 of 14
No
No
Drer\gtf2b
1 of 14
No
No
Drer\LOC100536580
1 of 14
No
Yes
Caenorhabditis elegans (Nematode, roundworm) (2)
Cele\brf-1
14 of 14
Yes
Yes
Cele\ttb-1
2 of 14
No
No
Anopheles gambiae (African malaria mosquito) (3)
Agam\AgaP_AGAP004233
12 of 12
Yes
Yes
Agam\AgaP_AGAP009558
2 of 12
No
No
Agam\AgaP_AGAP009559
2 of 12
No
No
Arabidopsis thaliana (thale-cress) (12)
Atha\AT2G45100
10 of 13
Yes
Yes
Atha\AT3G09360
10 of 13
Yes
Yes
Atha\MEE65
10 of 13
Yes
Yes
Atha\AT1G30455
6 of 13
No
Yes
Atha\AT3G57370
3 of 13
No
No
Atha\AT4G35540
3 of 13
No
Yes
Atha\AT3G10330
2 of 13
No
No
Atha\AT4G10680
2 of 13
No
No
Atha\pBRP2
2 of 13
No
No
Atha\PBRP
2 of 13
No
No
Atha\TFIIB
2 of 13
No
No
Atha\AT5G48630
1 of 13
No
No
Saccharomyces cerevisiae (Brewer's yeast) (2)
Scer\BRF1
12 of 13
Yes
Yes
Scer\SUA7
2 of 13
No
No
Schizosaccharomyces pombe (Fission yeast) (2)
Spom\brf1
11 of 12
Yes
Yes
Spom\SPAC16E8.16
2 of 12
No
No
Escherichia coli (enterobacterium) (0)
Other Organism Orthologs (via OrthoDB)
Data provided directly from OrthoDB:Brf. Refer to their site for version information.
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v9.1)
Gene Symbol
Score
Source
Compara
Domainoid
eggNOG
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Drosophila melanogaster (Fruit fly) (1)
TfIIB
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 )
    Modifiers Based on Experimental Evidence ( 1 )
    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?
    BRF1; BRF1 general transcription factor IIIB subunit
    13 of 14
    604902
     
    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
    Summary of Genetic Interactions
    Interaction Browsers
    Starting gene(s)
    Interaction type
    Interacting gene(s)
    Reference
    Starting gene(s)
    Interaction type
    Interacting gene(s)
    Reference
    External Data
    Linkouts
    BioGRID - A database of protein and genetic interactions.
    DroID - A comprehensive database of gene and protein interactions.
    MIST (protein-protein) - An integrated Molecular Interaction Database
    Pathways
    Signaling Pathways (FlyBase)
    Metabolic Pathways
    FlyBase
    External Links
    External Data
    Linkouts
    Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
    Class of Gene
    Genomic Location and Detailed Mapping Data
    Chromosome (arm)
    3R
    Recombination map
    3-60
    Cytogenetic map
    90A3-90A5
    Sequence location
    FlyBase Computed Cytological Location
    Cytogenetic map
    Evidence for location
    90A3-90A5
    Limits computationally determined from genome sequence between P{EP}CG5208EP562&P{EP}DadEP3196 and P{PZ}l(3)0788207882
    Experimentally Determined Cytological Location
    Cytogenetic map
    Notes
    References
    Experimentally Determined Recombination Data
    Location

    3-60

    (FlyBase, 2016)

    3-59.6

    (Comeron et al., 2012)
    Left of (cM)
    Right of (cM)
    Notes
    Stocks and Reagents
    Stocks (19)
    Genomic Clones (29)
    cDNA Clones (21)
     

    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)
    BDGP DGC clones
    Other clones
    RNAi and Array Information
    Linkouts
    DRSC - Results frm RNAi screens
    Antibody Information
    Laboratory Generated Antibodies
     

    polyclonal

    (Popova et al., 2018, Kang et al., 2016)
    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

        FlyBase curator comment: the insertion in the "e00975" Exelixis line (PBac{RB}sds22e00975) was originally assigned to the Brf gene in FBrf0179797, resulting in the "Brfe00975" (FBal0162762) allele. However, FBrf0184340 shows that the insertion is actually within sds22.

        (Bloomington Drosophila Stock Center, 2004.11.6)

        Annotations CG4155, CG5419 merged as CG31256 in release 3 of the genome annotation.

        (FlyBase Genome Annotators, 2002-2003)

        Source for identity of Brf CG4155 CG5419 was sequence comparison ( date:000529 ).

        (FlyBase, 1996-)
        Nomenclature History
        Source for database identify of

        Source for identity of: Brf CG4155 CG5419

        (FlyBase, 1996-)
        Nomenclature comments
        Etymology
        Synonyms and Secondary IDs (11)
        Datasets (0)
        Study focus (0)
        Experimental Role
        Project
        Project Type
        Title
        Study result (0)
        Result
        Result Type
        Title
        External Crossreferences and Linkouts ( 51 )
        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
        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
        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)
        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.
        iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
        Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution
        MIST (protein-protein) - An integrated Molecular Interaction Database
        Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
        References (79)