A Database of Drosophila Genes & Genomes

FB2008_07, released August 8, 2008
 

Gene Dmel\TfIIFβ

General Information
SymbolDmel\TfIIFβSpeciesD. melanogaster
NameTranscription factor TFIIFβAnnotation symbolCG6538
Feature typeprotein_coding_geneFlyBase IDFBgn0010421
Created / Updated2003-12-01/2003-12-01
Genomic Location
Chromosome (arm)3RRecombination map3-
Cytogenetic map86C6-86C6Sequence location3R:6,592,342..6,593,668 [-]
Map ( GBrowse ) detailed view
hide Summary Information
Automatically generated summary

See sections below for more information
The gene Transcription factor TFIIFβ is referred to in FlyBase by the symbol TfIIFβ (CG6538, FBgn0010421). It has the cytological map location 86C6. Its sequence location is 3R:6592342..6593668. Its molecular function is described as: general RNA polymerase II transcription factor activity; ATP-dependent DNA helicase activity; transcription initiation factor activity; ATP binding; catalytic activity. It is involved in the biological processes: transcription initiation from RNA polymerase II promoter; transcription from RNA polymerase II promoter. 2 alleles are reported. No phenotypic data is available. It has one annotated transcript and one annotated polypeptide.

hide Detailed Mapping Data
FlyBase Computed Cytological Location
Cytogenetic map
Evidence for location
86C6-86C6  
Limits computationally determined from genome sequence between P{PZ}hth05745 and P{EP}EP3340EP3340  
Experimentally Determined Cytological Location
Cytogenetic map
Notes
References
86C4-86C4
(determined by in situ hybridisation)  
(Ranz et al., 2001)
86C-86C
 
(Gong, 1995.4.19)
86C3-86C4
(determined by in situ hybridisation)  
(Spradling et al., 1999)
86C-86C
(determined by in situ hybridisation)  
(Gong et al., 1995)
86C-86C
(determined by in situ hybridisation)  
(Frank et al., 1995)
86C3-86C4
 
(BDGP Project Members, 1994-1999)
Experimentally Determined Recombination Data
Location
3-
(Gong, 1995.4.19)
Left of (cM)
Right of (cM)
Notes
Molecular Map Data
Gene Order (in direction of increasing cytology)
References
Gene Order (overall orientation not stated)
References
hide Gene Model & Products
Please see the GBrowse view of Dmel\TfIIFβ for information on other features
detailed view FBtr0082270 FBtr0082271 FBtr0082273 FBtr0082272 FBtr0082310 FBtr0082307 FBpp0081747 FBpp0081748 FBpp0081750 FBpp0081749 FBpp0081786 FBpp0081783 FBti0004944
Comments on Gene Model
hide Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Associated CDS (aa)
TfIIFbeta-RA
FBtr0082310
 NM_079581
  1262
  277
Additional Transcript Data & Comments
Reported size (kB)
Comments
External Data
Crossreferences
hide Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kD)
Length (aa)
Theoretical pI
RefSeq ID
GenBank protein
TfIIFbeta-PA  
FBpp0081786  
32.1  
277  
9.44  
  NP_524305
  AAF54548
Additional Polypeptide Data & Comments
Reported size (kD)
Comments
External Data
Linkouts
PANTHER - Protein classification by function, families, and pathways
•
Crossreferences
InterPro domains - A database of protein families, domains, and functional sites
•
Transcription initiation factor IIF, beta subunit (IPR003196)
Transcription Factor IIF, Rap30/Rap74, interaction (IPR011039)
Winged helix repressor DNA-binding (IPR011991)
Transcription initiation factor IIF, beta subunit, subgroup (IPR016640)
TRANSFAC - Eukaryotic transcription factors, their genomic binding sites, and DNA-binding profiles
•
  • T02174
hide Sequences Consistent with the Gene Model
DDBJ /
EMBL /
GenBank
DNA sequence
Protein sequence
Name
AA391386
 
AA940968
 
AA942308
 
AE003688
AAF54548
 
AI402703
 
AQ026313
 
AY071514
AAL49136
 
BE978582
 
BI214488
 
BI227683
 
BI372019
 
BI486494
 
BI486694
 
BI578480
 
BQ103162
 
CO297953
 
CO325487
 
EC202020
 
EC208544
 
EC244287
 
EC247740
 
U02461
AAA81888
 
U25188
AAA86888
 
 
UniProtKB/Swiss-Prot
UniProtKB/TrEMBL
    Maps to
    Does NOT map to
    Identified with
    (Spradling et al., 1999)
    (BDGP Project Members, 2000-)
    hide Mapped Features & Mutations
    Please see GBrowse or insertion reports for information on insertions of transgenic constructs and features not listed here
    Type
    Symbol & Location
    Additional Notes
    References
    hide External Data
    Linkouts
    DEDB - Drosophila exon database: splicing graphs
    •
    Crossreferences
    hide Expression Data
    FlyBase-Curated Data
    Transcript and
    Protein data     		Please see the FlyBase Gene Expression Report for details of gene expression from the literature.
    hide Summary of Transcript Expression
    Stage
    Tissue/Position
    Reference
    Marker for
      Subcellular Localization
      CV Term
      hide Summary of Polypeptide Expression
      Stage
      Tissue/Position
      Reference
      Marker for
        Subcellular Localization
        CV Term
        hide Microarray Data
        Developmental timecourse, Costello et al., 2008 (Original data from Arbeitman et al., 2002)
        Untitled Document detailed view FBtr0082270 FBtr0082271 FBtr0082273 FBtr0082272 FBtr0082310 FBtr0082307
        AA940968
        AI293309
        hide External Data & Images
        Linkouts
        FLIGHT - Cell culture data for RNAi and other high-throughput technologies
        •
        FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
        •
        GEO (NCBI) - Gene expression data: microarray and other high-throughput technologies
        •
        FlyExpress - Embryonic expression images (BDGP data)
        •
        Show all FlyExpress processed images for TfIIFβ
        hide Alleles & Phenotypes
        hide Summary of Allele Phenotypes
        Lethality
        Allele
        lethal | recessive
        Phenotype manifest in
        Allele
        hide Classical Alleles ( 1 )
        For All Classical Alleles Show

        Allele of TfIIFβClassMutagenStocksKnown lesion
        TfIIFβj3C11 --
        hide Alleles Carried on Transgenic Constructs ( 1 )
        For All Alleles Carried on Transgenic Constructs Show

        Allele of TfIIFβClassMutagenStocksKnown lesion
        TfIIFβGD40911 Yes
        hide Aneuploid Aberrations
        Useful deficiency
         
        Useful duplication
         
        Not disrupted in
        (Spradling et al., 1999, BDGP Project Members, 1994-1999)
        Disrupted in
        (Christensen et al., 2008.6.11)
        (Ryder, 2004.4.26)
        hide Transgenic Constructs & Insertions
        Transgenic Constructs
        Type of construct
        Name
        Expression data
        Insertions
        Type of insertions
        Name
        Expression data
        insertion of enhancer trap
        P{lacW}TfIIFβj3C1
        No
        hide Related Comments
        Please look at the allele reports for the complete phenotype data
        A TfIIFβ cDNA has been cloned and sequenced. Analysis of deletion constructs suggests that the N terminus of the TfIIFβ protein interacts with TFIIF74, and the C terminus interacts with RNA polymerase II to mediate basal transcription.
        (Frank et al., 1995)
        TfIIF has been purified and shown to include two subunits.
        (Austin and Biggin, 1996)
        hide Gene Ontology: Function, Process & Cellular Component ( 9 )
        hide Molecular Function
        CV term
        Evidence
        References
        ATP binding
        inferred from electronic annotation with InterPro:IPR003196
        (FlyBase Curators et al., 2004-)
        ATP-dependent DNA helicase activity
        non-traceable author statement
        (Swiss-Prot Project Members, 1995.6.1)
        catalytic activity
        inferred from electronic annotation with InterPro:IPR011039
        (FlyBase Curators et al., 2004-)
        general RNA polymerase II transcription factor activity
        non-traceable author statement
        (Spradling et al., 1999)
        inferred from sequence or structural similarity with HGNC_gene:GTF2F2; HGNC:4653; OMIM:189969 AND inferred from sequence or structural similarity with SGD_LOCUS:TFG2; SGD:S0003237
        (Aoyagi and Wassarman, 2000)
        transcription initiation factor activity
        non-traceable author statement
        (Swiss-Prot Project Members, 1995.6.1)
        hide Biological Process
        CV term
        Evidence
        References
        transcription from RNA polymerase II promoter
        non-traceable author statement
        (Swiss-Prot Project Members, 1995.6.1)
        transcription initiation from RNA polymerase II promoter
        inferred from sequence or structural similarity with HGNC_gene:GTF2F2; HGNC:4653; OMIM:189969 AND inferred from sequence or structural similarity with SGD_LOCUS:TFG2; SGD:S0003237
        (Aoyagi and Wassarman, 2000)
        hide Cellular Component
        CV term
        Evidence
        References
        nucleus
        non-traceable author statement
        (Swiss-Prot Project Members, 1995.6.1)
        transcription factor TFIIF complex
        non-traceable author statement
        (Spradling et al., 1999)
        inferred from sequence or structural similarity with HGNC_gene:GTF2F2; HGNC:4653; OMIM:189969 AND inferred from sequence or structural similarity with SGD_LOCUS:TFG2; SGD:S0003237
        (Aoyagi and Wassarman, 2000)
        hide Sequence Ontology: Class of Gene
        protein_coding_gene
         
        nuclear_gene
         
        hide Interactions & Pathways
        hide Summary of Genetic Interactions
        Interacts with
        Please look at the allele data for full details of the genetic interactions
        TfIIFβ allele
        Gene
        References
        hide External Data
        Linkouts
        BioGRID - Interaction data, including yeast 2-hybrid and genetic interactions
        •
        hide Orthologs
        Genome-wide drosophilid orthologs
        Curated drosophilid orthologs
         
        (Ranz et al., 2001, Ranz et al., 2001)
        Linkouts
        InParanoid orthologs - Eukaryotic orthologs
        •
        hide Functional Complementation between Species
        hide Inter-Species Misexpression Data
        Produces phenotype in
        Produces NO phenotype in
        hide Stocks & Reagents
        hide Stocks Listed in FlyBase ( 2 )
        VDRC
        v12602
        w1118; P{GD4091}v12602/CyO
        Bloomington
        10239
        y1 w1118; P{lacW}TfIIFβj3C1/TM3, Sb1
        hide Genomic Clones ( 2 )
        hide cDNA Clones ( 14 )
        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
        cDNA Clones, End Sequenced (ESTs)
        BDGP DGC clones
        Other clones
        hide RNAi & Array Information
        Affy Oligo
        Linkouts
        DRSC - RNAi screening (Harvard): high-throughput cell culture data and design
        •
        GenomeRNAi - RNAi phenotypes (Heidelberg): high-throughput cell culture data
        •
        hide Antibody Information
        hide Other Information
        hide Discoverer
        hide Etymology
        hide Identification
        hide Position Effect Variegation Data
        hide Relationship to Other Genes
        Source for database identity of
        Source for database merge of
        Source for merge of: TfIIFβ l(3)j3C1
        (Spradling et al., 1999)
        Additional comments
        hide Comments About Role
        TfIIFβ has been cloned and sequenced.
        (Gong et al., 1995)
        hide Comments About Molecular Function
        hide Other Comments
        Isolated by PCR with oligonucleotides corresponding to regions of TFII30 that are conserved in vertebrate TFII30 proteins.
        (Frank et al., 1995)
        Isolated from a Drosophila embryo cDNA library, using the entire coding sequence of human TFIIFβ as a probe, under low stringency conditions.
        (Gong et al., 1995)
        hide External Crossreferences & Linkouts
        Sequence Crossreferences
        RefSeq (Transcripts)
        •
        RefSeq (Proteins)
        •
        DDBJ / EMBL / GenBank
        •
        UniProtKB/Swiss-Prot
        •
        Other Crossreferences
        InterPro domains - A database of protein families, domains, and functional sites
        •
        Transcription initiation factor IIF, beta subunit (IPR003196)
        Transcription Factor IIF, Rap30/Rap74, interaction (IPR011039)
        Winged helix repressor DNA-binding (IPR011991)
        Transcription initiation factor IIF, beta subunit, subgroup (IPR016640)
        TRANSFAC - Eukaryotic transcription factors, their genomic binding sites, and DNA-binding profiles
        •
        • T02174
        Linkouts
        BioGRID - Interaction data, including yeast 2-hybrid and genetic interactions
        •
        DEDB - Drosophila exon database: splicing graphs
        •
        DRSC - RNAi screening (Harvard): high-throughput cell culture data and design
        •
        FLIGHT - Cell culture data for RNAi and other high-throughput technologies
        •
        FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
        •
        FlyExpress - Embryonic expression images (BDGP data)
        •
        FlyMine - Integrated genomics database for Drosophila, Anopheles, and C.elegans
        •
        GEO (NCBI) - Gene expression data: microarray and other high-throughput technologies
        •
        GenomeRNAi - RNAi phenotypes (Heidelberg): high-throughput cell culture data
        •
        InParanoid orthologs - Eukaryotic orthologs
        •
        PANTHER - Protein classification by function, families, and pathways
        •
        University of Chicago Dev. Expression
        •
        hide Synonyms & Secondary IDs ( 13 )
        Reported As
        Symbol Synonym
        CG6538
        (Aoyagi and Wassarman, 2000, )
        dTFIIF30
        (Frank, 1993.10.6, Li and Manley, 1999, Li and Manley, 1998, Frank et al., 1995)
        FS
        (Park et al., 2001)
        l(3)j3C1
        (BDGP Project Members, 1994-1999, )
        RAP30
        (Lebedeva, 2005, Lebedeva et al., 2005, Sandaltzopoulos and Becker, 1998)
        TFIIF
        (Lebedeva, 2005, Lebedeva et al., 2005, Gu et al., 2002, Breiling et al., 2001, Breiling et al., 2001, Mizuguchi et al., 2001, Pham et al., 1999, Schock et al., 1999, Hansen et al., 1997, Sauer et al., 1995, Sauer et al., 1995, ten Harmsel and Biggin, 1995, Kephart et al., 1992, Wampler et al., 1990)
        TfIIF
        (Dynan and Gilman, 1993)
        TfIIFbeta
        (Spradling et al., 1999)
        TFIIFβ
        (Gong et al., 1995)
        TfIIFβ
        (Christensen et al., 2008.6.11)
        Name Synonym
        factor 5
        (Kephart et al., 1992)
        TFIIF small subunit
        (Gong, 1995.4.19)
        Transcription factor TFIIFβ
         
        Secondary FlyBase IDs
        • FBgn0011350
        hide References ( 40 )
        Generate a list of
        List References by type
        hide Recent research papers (0)
        All research papers listed in FlyBase were published before 2006
        Show research papers ...
        hide Recent reviews (0)
        All reviews listed in FlyBase were published before 2006
        Show reviews ...