FB2019_05, released Oct 15, 2019

Gene: Dmel\bip2

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General Information
Symbol
Dmel\bip2
Species
D. melanogaster
Name
bip2
Annotation Symbol
CG2009
Feature Type
protein_coding_gene
FlyBase ID
FBgn0026262
Gene Model Status
Current
Stock Availability
9 publicly available
Gene Snapshot
bip2 (bip2) encodes a protein that interacts with the transcription factor encoded by Trl and is involved in transcriptional activation. [Date last reviewed: 2019-08-01]
Other Summaries
Also Known As
TAF3, TFIID, Bric-a-brac interacting protein 2, TAFII155, dTAFII155
Key Links
Genomic Location
Cytogenetic map
Sequence location
4:459,887..466,828 [-]
Recombination map
4-0
Sequence
Get Decorated FASTA
Genomic Maps
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
NCBI
UCSC
Ensembl
Function
GO Summary Ribbons
Gene Group (FlyBase)
Protein Family (UniProt)
-
Protein Signatures (InterPro)
Molecular Function (GO)
[Detailed GO annotations]
Experimental Evidence
chromatin binding; p53 binding; POZ domain binding; protein binding; transcription factor binding
Predictions / Assertions
protein heterodimerization activity
Summaries
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).
Gene Model and Products
Number of Transcripts
1
Number of Unique Polypeptides
1

Please see the GBrowse view of Dmel\bip2 or the JBrowse view of Dmel\bip2 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
Low-frequency RNA-Seq exon junction(s) not annotated.
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)
bip2-RA
FBtr0089110
NM_143666
4514
1406
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
bip2-PA
FBpp0088179
154.5
1406
9.85
NP_651923
AAF59342
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
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\bip2 using the Feature Mapper tool.

External Data
Crossreferences
Linkouts
Gene Ontology (9 terms)
Molecular Function (6 terms)
Terms Based on Experimental Evidence (5 terms)
CV Term
Evidence
References
chromatin binding
inferred from direct assay
(Chopra et al., 2008, Gangloff et al., 2001, Pointud et al., 2001)
p53 binding
inferred from physical interaction with FLYBASE:p53; FB:FBgn0039044
(Bereczki et al., 2008)
POZ domain binding
inferred from physical interaction with FLYBASE:bab1; FB:FBgn0004870
(Pointud et al., 2001)
inferred from physical interaction with FLYBASE:bab2; FB:FBgn0025525
(Pointud et al., 2001)
protein binding
inferred from physical interaction with FLYBASE:bab1; FB:FBgn0004870
(Pointud et al., 2001)
inferred from physical interaction with FLYBASE:bab2; FB:FBgn0025525
(Pointud et al., 2001)
transcription factor binding
inferred from physical interaction with FLYBASE:Taf10; FB:FBgn0028398
(Gangloff et al., 2001)
inferred from physical interaction with FLYBASE:Trl; FB:FBgn0013263
(Chopra et al., 2008)
inferred from physical interaction with FLYBASE:bab1; FB:FBgn0004870
(Pointud et al., 2001)
inferred from physical interaction with FLYBASE:bab2; FB:FBgn0025525
(Pointud et al., 2001)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
protein heterodimerization activity
inferred from electronic annotation with InterPro:IPR009072
(assigned by InterPro )
(FlyBase Curators et al., 2004-)
Biological Process (1 term)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
positive regulation of transcription by RNA polymerase II
inferred from mutant phenotype
(Chopra et al., 2008)
inferred from genetic interaction with FLYBASE:Trl; FB:FBgn0013263
(Chopra et al., 2008)
Terms Based on Predictions or Assertions (0 terms)
Cellular Component (2 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
nucleus
inferred from direct assay
(Chopra et al., 2008, Gangloff et al., 2001, Pointud et al., 2001)
transcription factor TFIID complex
inferred from direct assay
(Gangloff et al., 2001)
Terms Based on Predictions or Assertions (0 terms)
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
Polypeptide Expression
immunolocalization
Stage
Tissue/Position (including subcellular localization)
Reference
embryonic stage
cell
• nucleus
(Gangloff et al., 2001)
organism | ubiquitous
• nucleus
(Gangloff et al., 2001)
cell
(Gangloff et al., 2001)
western blot
Stage
Tissue/Position (including subcellular localization)
Reference
embryonic stage
organism
• nucleus
(Gangloff et al., 2001)
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
nucleus
inferred from direct assay
(Chopra et al., 2008, Gangloff et al., 2001, Pointud et al., 2001)
transcription factor TFIID complex
inferred from direct assay
(Gangloff et al., 2001)
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\bip2 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
FlyExpress - Embryonic expression images (BDGP data)
  • Stages(s) 1-3
  • Stages(s) 4-6
  • Stages(s) 7-8
  • Stages(s) 9-10
  • Stages(s) 13-16
FlyBase Wiki
Image Based Resources
Alleles, Insertions, and Transgenic Constructs
Classical and Insertion Alleles ( 4 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 8 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of bip2
Transgenic constructs containing regulatory region of bip2
Deletions and Duplications ( 7 )
Phenotypes
Orthologs
Downloads
Download All DIOPT Orthologs
Download All OrthoDB Orthologs
Human Orthologs (via DIOPT v7.1)
Homo sapiens (Human) (7)
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\TAF3
9 of 15
Yes
Yes
Hsap\ING1
1 of 15
No
No
Hsap\ING2
1 of 15
No
No
Hsap\ING3
1 of 15
No
No
Hsap\ING4
1 of 15
No
No
Hsap\ING5
1 of 15
No
No
 
Hsap\TAF8
1 of 15
No
No
Model Organism Orthologs (via DIOPT v7.1)
Mus musculus (laboratory mouse) (7)
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\Taf3
10 of 15
Yes
Yes
Mmus\Ing1
1 of 15
No
No
Mmus\Ing2
1 of 15
No
No
Mmus\Ing3
1 of 15
No
No
Mmus\Ing4
1 of 15
No
No
Mmus\Ing5
1 of 15
No
No
Mmus\Taf8
1 of 15
No
No
Rattus norvegicus (Norway rat) (5)
Rnor\Taf3
6 of 13
Yes
Yes
Rnor\Ing1
1 of 13
No
No
Rnor\Ing2
1 of 13
No
No
Rnor\Ing3
1 of 13
No
No
Rnor\Ing4
1 of 13
No
No
Xenopus tropicalis (Western clawed frog) (6)
Xtro\taf3
4 of 12
Yes
Yes
Xtro\ing1
1 of 12
No
No
Xtro\ing2
1 of 12
No
No
Xtro\ing3
1 of 12
No
No
Xtro\ing5
1 of 12
No
No
Xtro\taf8
1 of 12
No
No
Danio rerio (Zebrafish) (8)
Drer\taf3
9 of 15
Yes
Yes
Drer\ing1
1 of 15
No
No
Drer\ing2
1 of 15
No
No
Drer\ing3
1 of 15
No
No
Drer\ing4
1 of 15
No
No
Drer\ing5a
1 of 15
No
No
Drer\ing5b
1 of 15
No
No
Drer\taf8
1 of 15
No
No
Caenorhabditis elegans (Nematode, roundworm) (7)
Cele\taf-3
6 of 15
Yes
Yes
Cele\phf-34
2 of 15
No
Yes
Cele\athp-3
1 of 15
No
Yes
Cele\ing-3
1 of 15
No
No
Cele\lsy-13
1 of 15
No
No
Cele\phf-31
1 of 15
No
Yes
Cele\taf-8
1 of 15
No
No
Arabidopsis thaliana (thale-cress) (0)
No records found.
Saccharomyces cerevisiae (Brewer's yeast) (3)
Scer\PHO23
1 of 15
Yes
No
Scer\YNG1
1 of 15
Yes
No
Scer\YNG2
1 of 15
Yes
No
Schizosaccharomyces pombe (Fission yeast) (1)
Spom\taf8
1 of 12
Yes
No
Orthologs in Drosophila Species (via OrthoDB v9.1) ( EOG091900SP )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
Drosophila melanogaster
fruit fly
Dmel\bip2
Drosophila suzukii
Spotted wing Drosophila
Dsuz\DS10_00007105
Drosophila simulans
Dsim\GD15475
Drosophila sechellia
Dsec\GM26780
Drosophila erecta
Dere\GG16447
Drosophila yakuba
Dyak\GE14514
Drosophila ananassae
Dana\GF22835
Drosophila pseudoobscura pseudoobscura
Dpse\GA15182
Drosophila persimilis
Dper\GL18176
Drosophila willistoni
Dwil\GK13694
Drosophila virilis
Dvir\GJ14147
Drosophila mojavensis
Dmoj\GI14094
Drosophila grimshawi
Dgri\GH23929
Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG091500H2 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Musca domestica
House fly
Mdoa\17010416
Glossina morsitans
Tsetse fly
Gmor\GMOY009470
Lucilia cuprina
Australian sheep blowfly
Lcup\FF38_12376
Mayetiola destructor
Hessian fly
Mdes\Mdes001215
Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W00DH )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Acyrthosiphon pisum
Pea aphid
Apim\ACYPI002409
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( None identified )
No non-Insect Arthropod orthologies identified
Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( None identified )
No non-Arthropod Metazoa orthologies identified
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v7.1)
Drosophila melanogaster (Fruit fly) (5)
Gene Symbol
Score
Source
Compara
eggNOG
Homologene
Inparanoid
Isobase
OrthoDB
OrthoFinder
orthoMCL
Panther
RoundUp
Alignment
CG7379
1 of 10
Ing3
1 of 10
Ing5
1 of 10
MESR4
1 of 10
Taf8
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
    Comments on Models/Modifiers Based on Experimental Evidence ( 0 )
     
    Disease Associations of Human Orthologs (via DIOPT v7.1 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?
    TAF3; TATA-box binding protein associated factor 3
    9 of 15
    606576
        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
        esyN Network Diagram
        esyN Network Key:
        Suppression
        Enhancement
        View in Interactions Browser
        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
        Antp
        enhanceable
        bip2
        (Prince et al., 2008)
        N|Antp
        enhanceable
        bip2
        (Prince et al., 2008)
        Ubx|Trl
        enhanceable
        bip2
        (Chopra et al., 2008)
        External Data
        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
        Genomic Location and Detailed Mapping Data
        Chromosome (arm)
        4
        Recombination map
        4-0
        Cytogenetic map
        102C1-102C1
        Sequence location
        4:459,887..466,828 [-]
        FlyBase Computed Cytological Location
        Cytogenetic map
        Evidence for location
        102C1-102C1
        Experimentally Determined Cytological Location
        Cytogenetic map
        Notes
        References
        102B-102B
        (determined by in situ hybridisation)
        (Pointud et al., 2001)
        102B-102B
        (Pointud, 1997.9.26)
        Experimentally Determined Recombination Data
        Location
        4-0
        (FlyBase, 2016)
        Left of (cM)
        Right of (cM)
        Notes
        Stocks and Reagents
        Stocks (9)
        Genomic Clones (5)
         

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

        cDNA Clones (105)
         

        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 sequences
        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
           
          polyclonal
          (Gangloff et al., 2001)
          Commercially Available Antibodies
           
          Other Information
          Relationship to Other Genes
          Source for database identify of
          Source for identity of: bip2 CG2009
          (Zhong, 1999.11)
          Source for database merge of
          Additional comments
          Other Comments
          Origin and Etymology
          Discoverer
          Etymology
          Identification
          External Crossreferences and Linkouts ( 64 )
          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/TrEMBL - Automatically annotated and unreviewed 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
          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.
          KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.
          modMine - A data warehouse for the modENCODE project
          Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
          Linkouts
          BioGRID - A database of protein and genetic interactions.
          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
          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 (23)
          Reported As
          Symbol Synonym
          BIP2
          (Percival-Smith, 2017, Hudry et al., 2011, Bereczki et al., 2008, Prince et al., 2008, Kramps et al., 2002, Tora, 2002, Aoyagi and Wassarman, 2000)
          Bip2
          (Bienz, 2006)
          CG2009
          (Fan et al., 2017, Hosono et al., 2015, Ni et al., 2010.12.1, Keleman et al., 2009.8.5, Perkins et al., 2009, Bienz, 2006, Battersby et al., 2003, Aoyagi and Wassarman, 2000)
          DmTAF3
          (Bereczki et al., 2008)
          TAF155
          (Bienz, 2006)
          TAF3
          (Vorobyeva et al., 2009, Vorobyeva et al., 2009, Weake et al., 2009, Chopra et al., 2008, Soshnikova et al., 2008, Couderc et al., 2005, Tora, 2002)
          TAFII155
          (Tora, 2002)
          TAFII155
          (Prince et al., 2008, Davidson, 2001.1.18)
          TFIID
          (Zhou, 2005, Butler and Kadonaga, 2002, Gu et al., 2002, Hochheimer et al., 2002, Stathopoulos and Levine, 2002)
          Taf3
          (Neves and Eisenman, 2019)
          bip-II
          (Pointud et al., 1999)
          bip2
          (Neves and Eisenman, 2019, Fan et al., 2017, Takács et al., 2012, Friedman et al., 2011, Toku et al., 2011, Blanco et al., 2010, Prince, 2009.6.21, Chopra et al., 2008, Prince et al., 2008, Riddle et al., 2008, Yatsu et al., 2008)
          dBIP2
          (Veenstra and Wolffe, 2001)
          dTAFII155
          (Chopra et al., 2008, Veenstra and Wolffe, 2001)
          dTAFII3
          (Prince et al., 2008)
          dmTAF3
          (Chopra et al., 2008)
          i163
          (Battersby et al., 2003)
          i31
          (Battersby et al., 2003)
          taf3
          (Fan et al., 2017)
          Name Synonyms
          Bric a brac Interacting Protein 2
          (Chopra et al., 2008)
          Bric-a-brac interacting protein 2
          (Bereczki et al., 2008, Prince et al., 2008)
          TATA binding protein associated factor 3
          (Bereczki et al., 2008)
          bip2
          bric-a-brac interacting protein 2
          (Prince et al., 2008)
          Secondary FlyBase IDs
            Datasets (0)
            Study focus (0)
            Experimental Role
            Project
            Project Type
            Title
            References (69)