FlyBase Gene Report: Dmel\TfIIB

General Information

Symbol

Dmel\TfIIB

Species

D. melanogaster

Name

Transcription factor IIB

Annotation Symbol

CG5193

Feature Type

protein_coding_gene

FlyBase ID

FBgn0004915

Gene Model Status

Current

Stock Availability

9 publicly available

Enzyme Name (EC)

histone acetyltransferase (2.3.1.48)

Gene Summary

Transcription factor IIB (TfIIB) encodes a basal transcription factor that binds to the TATA box-binding protein. It is required for the initiation of transcription by RNA polymerase II. [Date last reviewed: 2019-03-14] (FlyBase Gene Snapshot)

All Summaries

Gene Snapshot
Alliance
Auto summary
Gene Group
UniProtKB
Interactive Fly

Also Known As

dTFIIB, dmTFIIB

Key Links

Genomic Location

Cytogenetic map

31E2-31E2

Sequence location

2L:10,431,338..10,433,116 [+]

Recombination map

2-42

RefSeq locus

NT_033779 REGION:10431338..10433116

Sequence

Get Decorated FASTA

Genomic Maps

JBrowse

Other Genome Views

The following external sites may use different assemblies or annotations than FlyBase.

Function

Gene Ontology (GO) Annotations (11 terms)

Molecular Function (3 terms)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

enables TBP-class protein binding

inferred from physical interaction with FLYBASE:Trf; FB:FBgn0010287

(Hansen et al., 1997)

Terms Based on Predictions or Assertions (3 terms)

CV Term

Evidence

References

enables protein-lysine-acetyltransferase activity

inferred from sequence or structural similarity with UniProtKB:Q00403

(Gene Ontology Curators, 2002-)

enables RNA polymerase II general transcription initiation factor activity

inferred from biological aspect of ancestor with PANTHER:PTN000178620

(GO Reference Genome Project, 2011-)

enables TBP-class protein binding

inferred from biological aspect of ancestor with PANTHER:PTN000178620

(GO Reference Genome Project, 2011-)

inferred from electronic annotation with InterPro:IPR013150

(InterPro Project Members, 2004-)

Biological Process (6 terms)

Terms Based on Experimental Evidence (2 terms)

CV Term

Evidence

References

involved_in mRNA transcription by RNA polymerase II

inferred from direct assay

(Wampler and Kadonaga, 1992)

involved_in transcriptional start site selection at RNA polymerase II promoter

inferred from direct assay

(Wampler and Kadonaga, 1992)

Terms Based on Predictions or Assertions (5 terms)

CV Term

Evidence

References

involved_in DNA-templated transcription initiation

inferred from biological aspect of ancestor with PANTHER:PTN000178517

(GO Reference Genome Project, 2011-)

inferred from electronic annotation with InterPro:IPR000812

(InterPro Project Members, 2004-)

involved_in RNA polymerase II preinitiation complex assembly

inferred from biological aspect of ancestor with PANTHER:PTN000178621

(GO Reference Genome Project, 2011-)

involved_in transcription initiation at RNA polymerase II promoter

inferred from sequence or structural similarity with SGD:S000006290

(Aoyagi and Wassarman, 2000)

inferred from sequence or structural similarity with UniProtKB:Q00403

(Aoyagi and Wassarman, 2000)

involved_in transcription preinitiation complex assembly

inferred from electronic annotation with InterPro:IPR000812

(InterPro Project Members, 2004-)

involved_in transcriptional start site selection at RNA polymerase II promoter

inferred from biological aspect of ancestor with PANTHER:PTN000178621

(GO Reference Genome Project, 2011-)

Cellular Component (2 terms)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

located_in nucleus

inferred from direct assay

(Wampler and Kadonaga, 1992)

Terms Based on Predictions or Assertions (2 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 preinitiation complex

inferred from biological aspect of ancestor with PANTHER:PTN000178517

(GO Reference Genome Project, 2011-)

Gene Group (FlyBase)

TRANSCRIPTION FACTOR II B

UNCLASSIFIED PROTEIN-LYSINE ACETYLTRANSFERASES

Protein Family (UniProt)

Belongs to the TFIIB family. (P29052)

Protein Signatures (InterPro)

Catalytic Activity (EC/Rhea)

protein-lysine-acetyltransferase activity

L-lysyl-[protein] + acetyl-CoA = N(6)-acetyl-L-lysyl-[protein] + CoA + H(+) (2.3.1.48)

RHEA 45948:

Summaries

Gene Snapshot

Gene Group (FlyBase)

TRANSCRIPTION FACTOR II B -: The general transcription factor Transcription factor II B (TFIIB) is required for RNA Pol II recruitment to the promoter and facilitates TBP binding to DNA and DNA bending. (Adapted from PMID:25693126).
UNCLASSIFIED PROTEIN-LYSINE ACETYLTRANSFERASES -: This group comprises lysine N-acetyltransferases that do not classify under other groups in FlyBase.

Protein Function (UniProtKB)

General factor that plays a major role in the activation of eukaryotic genes transcribed by RNA polymerase II.

(UniProt, P29052)

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\TfIIB 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 P29052)

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 5.46

Tissue-specific extension of 3' UTRs observed during later stages (FBrf0218523, FBrf0219848); all variants may not be annotated

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

TfIIB-RA

FBtr0080025

NM_057540

1410

315

TfIIB-RB

FBtr0333489

NM_001273420

1604

315

Additional Transcript Data and Comments

Reported size (kB)

1.5, 1.3 (northern blot)

(Wampler and Kadonaga, 1992)

1.6, 1.3 (northern blot)

(Yamashita et al., 1992)

Comments

External Data

Crossreferences

Polypeptide Data

Annotated Polypeptides

Name

FlyBase ID

Predicted MW (kDa)

Length (aa)

Theoretical pI

UniProt

RefSeq ID

GenBank

TfIIB-PA

FBpp0079615

34.4

315

8.40

FBpp0305673

34.4

315

8.40

P29052

NP_001260349

AGB92884

Polypeptides with Identical Sequences

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

315 aa isoforms: TfIIB-PA, TfIIB-PB

Additional Polypeptide Data and Comments

Reported size (kDa)

315 (aa); 34 (kD predicted)

(Wampler and Kadonaga, 1992, Yamashita et al., 1992)

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). Associates with TFIID-IIA (DA complex) to form TFIID-IIA-IIB (DAB-complex) which is then recognized by polymerase II.

(UniProt, P29052)

Crossreferences

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

Linkouts

Sequences Consistent with the Gene Model

Nucleotide / Polypeptide Records

UniProt

Mapped Features

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

External Data

Crossreferences

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

TfIIB_1

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).

2.97

Transcript Expression

in situ

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 1 -- 3

organism

Comment: maternally deposited

(Fisher et al., 2012)

embryonic stage 4 -- 6

organism | ubiquitous

(Fisher et al., 2012)

embryonic stage 7 -- 8

organism | ubiquitous

(Fisher et al., 2012)

embryonic stage 9 -- 10

organism | ubiquitous

(Fisher et al., 2012)

embryonic stage 11 -- 12

anterior midgut primordium

(Fisher et al., 2012)

head mesoderm

(Fisher et al., 2012)

organism | faint | ubiquitous

(Fisher et al., 2012)

posterior midgut primordium

(Fisher et al., 2012)

trunk mesoderm

(Fisher et al., 2012)

embryonic stage 13 -- 16

embryonic/larval midgut

(Fisher et al., 2012)

larval visceral muscle cell

(Fisher et al., 2012)

organism | faint | ubiquitous

(Fisher et al., 2012)

organism | ubiquitous

(Fisher et al., 2012)

northern blot

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage

(Wampler and Kadonaga, 1992)

Additional Descriptive Data

TfIIB transcripts are expressed in embryos.

(Wampler and Kadonaga, 1992)

The 1.3kb TfIIB transcript is a minor transcript expressed in embryos.

(Wampler and Kadonaga, 1992)

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Evidence

References

located_in nucleus

inferred from direct assay

(Wampler and Kadonaga, 1992)

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\TfIIB in JBrowse

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

View exonic expression by developmental stage for Dmel\TfIIB

View exonic expression by tissue for Dmel\TfIIB

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

FBgn0004915

DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species

34430/tissue=All

EMBL-EBI Single Cell Expression Atlas - Single cell expression across species

FBgn0004915

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0004915

FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data

FBgn0004915

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

CG5193

Flygut - An atlas of the Drosophila adult midgut

FBgn0004915

Images

FlyExpress - Embryonic expression images (BDGP data)

Show all FlyExpress processed images for Dmel\TfIIB

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 ( 3 )

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 TfIIB

Transgenic constructs containing regulatory region of TfIIB

Aberrations (Deficiencies and Duplications) ( 0 )

Inferred from experimentation ( 0 )

Inferred from location ( 9 )

Variants

Variant Molecular Consequences

Alleles Representing Disease-Implicated Variants

Phenotypes

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

Lethality

Allele

lethal - all die during P-stage, with Scer\GAL4^sr-md710

TfIIB^NIG.5193R

Phenotype manifest in

Allele

Orthologs

Downloads

Download All DIOPT Orthologs

Human Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Homo sapiens (Human) (11)

Hsap\GTF2B

14 of 14

Yes

Hsap\BRF2

3 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Model Organism Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Rattus norvegicus (Norway rat) (3)

Rnor\Gtf2b

14 of 14

Yes

Rnor\Brf2

3 of 14

Yes

Rnor\Brf1

2 of 14

Mus musculus (laboratory mouse) (3)

Mmus\Gtf2b

13 of 14

Yes

Mmus\Brf2

3 of 14

Yes

Mmus\Brf1

2 of 14

Xenopus tropicalis (Western clawed frog) (8)

Xtro\gtf2b

7 of 13

Yes

Xtro\tshz1

5 of 13

Yes

Xtro\brf1

1 of 13

Xtro\brf2

1 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

Danio rerio (Zebrafish) (5)

Drer\gtf2b

13 of 14

Yes

Drer\brf2

3 of 14

Yes

Drer\brf1a

2 of 14

Drer\brf1b

2 of 14

Drer\LOC100536580

1 of 14

Yes

Caenorhabditis elegans (Nematode, roundworm) (6)

Cele\ttb-1

14 of 14

Yes

2 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Anopheles gambiae (African malaria mosquito) (10)

Agam\AgaP_AGAP009558

12 of 12

Yes

Agam\AgaP_AGAP009559

7 of 12

Yes

2 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

Arabidopsis thaliana (thale-cress) (22)

Atha\AT3G10330

13 of 13

Yes

Atha\TFIIB

13 of 13

Yes

Atha\pBRP2

9 of 13

Yes

Atha\AT3G57370

4 of 13

Yes

Atha\AT4G10680

4 of 13

Yes

Atha\PBRP

4 of 13

Yes

Atha\AT5G39230

3 of 13

Yes

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Saccharomyces cerevisiae (Brewer's yeast) (5)

Scer\SUA7

13 of 13

Yes

2 of 13

1 of 13

1 of 13

1 of 13

Schizosaccharomyces pombe (Fission yeast) (2)

Spom\SPAC16E8.16

12 of 12

Yes

Spom\brf1

2 of 12

Escherichia coli (enterobacterium) (0)

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:TfIIB. Refer to their site for version information.

Paralogs

Downloads

Download All DIOPT Paralogs

Paralogs (via DIOPT v9.1)

Gene Symbol

Score

Source

Alignment

Drosophila melanogaster (Fruit fly) (6)

Brf

4 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 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 ( 0 )

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.

Homo sapiens (Human)

Gene name

Score

OMIM

OMIM Phenotype

DO term

Complementation?

Transgene?

GTF2B; general transcription factor IIB

14 of 14

189963

BRF2; BRF2 general transcription factor IIIB subunit

3 of 14

607013

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

Interaction Browsers

View in FlyBase Interactions Browser View in MIST tool (external link)

Please see the Physical Interaction reports below for full details

protein-protein

Physical Interaction

Assay

References

TfIIB - Abd-B

bimolecular fluorescence complementation, fluorescence microscopy

(Baëza et al., 2015)

TfIIB - Antp

bimolecular fluorescence complementation, fluorescence microscopy

(Baëza et al., 2015)

TfIIB - Nelf-E

anti tag coimmunoprecipitation, peptide massfingerprinting, experimental knowledge based

(Rhee et al., 2014)

TfIIB - Pc

anti bait coimmunoprecipitation, western blot

(Breiling et al., 2001)

TfIIB - Scr

bimolecular fluorescence complementation, fluorescence microscopy

(Baëza et al., 2015)

TfIIB - Taf9

pull down, western blot

(Goodrich et al., 1993)

TfIIB - Trf2

pull down, western blot

(Rabenstein et al., 1999)

TfIIB - Ubx

bimolecular fluorescence complementation, fluorescence microscopy

(Baëza et al., 2015)

TfIIB - abd-A

bimolecular fluorescence complementation, fluorescence microscopy

(Baëza et al., 2015)

TfIIB - nej

anti bait coimmunoprecipitation, anti tag western blot

(Boija et al., 2017)

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

Subunit Structure (UniProtKB)

(UniProt, P29052 )

Linkouts

BioGRID - A database of protein and genetic interactions.

60511

DroID - A comprehensive database of gene and protein interactions.

FBgn0004915

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

34430

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyBase

External Links

External Data

Linkouts

KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.

Basal transcription factors

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

SignaLink - A signaling pathway resource with multi-layered regulatory networks.

P29052

Class of Gene

nuclear_gene

protein_coding_gene

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

2-42

Cytogenetic map

31E2-31E2

Sequence location

2L:10,431,338..10,433,116 [+]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

31E2-31E2

Limits computationally determined from genome sequence between P{lacW}KdelR^k00311 and P{lacW}l(2)k09116^k09116&P{lacW}Fatp^k10307

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

31F-31F

(determined by in situ hybridisation)

(Wampler and Kadonaga, 1992, Yamashita et al., 1992)

Experimentally Determined Recombination Data

Location

2-42

(FlyBase, 2016)

2-35.5

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (9)

Aberrations including deletions of this gene Aberrations including duplications of this gene

Bloomington

62165

y¹ sc^* v¹ sev²¹; P{TRiP.HMC05172}attP40

Kyoto

114592

y^d2 w¹¹¹⁸ P{ey-FLP.N}2; P{wHy}TfIIB^DG14311 P{neoFRT}40A/CyO y⁺

NIG-Fly

5193R-2

P{NIG.5193R}2

5193R-3

P{NIG.5193R}3

M2L-2493

y¹ w¹¹¹⁸; TfIIB^SK2 P{neoFRT}40A/CyO-Tb

M2L-2494

y¹ w¹¹¹⁸; TfIIB^SK3 P{neoFRT}40A/CyO-Tb

2LG-1982

y² VhaAC39-1^cho-1 v¹; P{U6-TfIIB.NIG.sgRNA}attP40/CyO

VDRC

v330122

P{VSH330122}attP40

v106688

P{KK102283}VIE-260B

Genomic Clones (25)

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

cDNA Clones (88)

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.

FBgn0004915

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0004915

Antibody Information

Laboratory Generated Antibodies

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

Antibodies are used to locate the TfIIB protein to polytene chromosomes.

(Morris et al., 1997)

Tbp and TfIIB genes are sequenced and characterised revealing common features in the promoter regions.

(Lira-De Vito et al., 1995)

Kr monomer (the activator) interacts with TfIIB, Kr dimers do not (FBrf0082559). Kr dimers engage in protein-protein interaction with TfIIEβ (FBrf0082559). Kr monomer-dimer transition alters Krs ability to interact with the general transcription machinery (FBrf0082559).

(Roberts and Green, 1995)

Activity of the glutamine rich ftz activation domain is blocked by truncated TfIIB derivatives in Schneider L2 cells suggesting the block is mediated by interactions with TfIIB.

(Colgan et al., 1993)

Isolated from a cDNA library using the human TFIIB gene as a probe.

(Wampler and Kadonaga, 1992)

TfIIB has been isolated, sequenced and characterised in vitro.

(Wampler and Kadonaga, 1992)

TfIIB has been cloned and sequenced.

(Yamashita et al., 1992)

Relationship to Other Genes

Source for database merge of

Additional comments

Nomenclature History

Source for database identify of

Nomenclature comments

Etymology

Synonyms and Secondary IDs (10)

Reported As

Symbol Synonym

CG5193

(National Institute of Genetics Fly Stocks, 2022-, Meadows, 2017.1.11, Çiçek et al., 2016, Rosa-Ferreira et al., 2015, Tiwari et al., 2015, Ardehali et al., 2009, Keleman et al., 2009.8.5, Perkins et al., 2009, Aoyagi and Wassarman, 2000)

TFIIB

TfIIB

(Kögler et al., 2021, Vo Ngoc et al., 2019, Japanese National Institute of Genetics, 2012.5.21, Andersen et al., 2010, Turner et al., 2008)

Tfiib

(Joshi and Nguyen, 1995)

TfllB

(Pruteanu-Malinici et al., 2011)

dTFIIB

(Li and Manley, 1999, Li and Manley, 1998, Morris et al., 1997, Frank et al., 1995)

dTfIIB

(Wampler and Kadonaga, 1992)

dmTFIIB

(Lebedeva, 2005, Lebedeva et al., 2005)

tfIIb

(Tiwari et al., 2015)

Name Synonyms

Transcription factor IIB

Secondary FlyBase IDs

FBgn0023206

Datasets (1)

Study focus (1)

Experimental Role

Project

Project Type

Title

bait_protein

BDTNP_TFBS

genome binding

ChIP characterization of transcription factor genome binding, Berkeley Drosophila Transcription Factor Network Project.

Study result (0)

Result

Result Type

Title

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.

34430

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.

P29052

UniProt/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information

P29052

UniProt/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information

M9PCM4

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.

P29052

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0004915

DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species

34430/tissue=All

EMBL-EBI Single Cell Expression Atlas - Single cell expression across species

FBgn0004915

FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data

FBgn0004915

FlyMine - An integrated database for Drosophila genomics

FBgn0004915

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

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

dme:Dmel_CG5193

MARRVEL_MODEL - MARRVEL (model organism gene)

34430

Linkouts

BioGRID - A database of protein and genetic interactions.

60511

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

FBgn0004915

DroID - A comprehensive database of gene and protein interactions.

FBgn0004915

DRSC - Results frm RNAi screens

FBgn0004915

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

TfIIB_1

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0004915

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0004915

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

CG5193

Flygut - An atlas of the Drosophila adult midgut

FBgn0004915

FlyMet - A comprehensive tissue-specific metabolomics resource for Drosophila.

FBgn0004915

iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)

TC010900

KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.

Basal transcription factors

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

34430

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

SignaLink - A signaling pathway resource with multi-layered regulatory networks.

P29052

References (104)

The following external sites may use different assemblies or annotations than FlyBase.

2.97

Report Sections