A Database of Drosophila Genes & Genomes

FB2008_07, released August 8, 2008
 

Gene Dmel\RpII15

General Information
SymbolDmel\RpII15SpeciesD. melanogaster
NameRNA polymerase II 15kD subunitAnnotation symbolCG3284
Feature typeprotein_coding_geneFlyBase IDFBgn0004855
Created / Updated2003-12-01/2003-12-01
Genomic Location
Chromosome (arm)3RRecombination map
Cytogenetic map88B3-88B3Sequence location3R:10,134,816..10,135,566 [+]
Map ( GBrowse ) detailed view
hide Summary Information
Automatically generated summary

See sections below for more information
The gene RNA polymerase II 15kD subunit is referred to in FlyBase by the symbol RpII15 (CG3284, FBgn0004855). It has the cytological map location 88B3. Its sequence location is 3R:10134816..10135566. Its molecular function is described as: DNA-directed RNA polymerase activity; DNA binding; zinc ion binding; transcription regulator activity. It is involved in the biological processes: transcription from RNA polymerase II promoter; regulation of transcription. 8 alleles are reported. The phenotype of these alleles is annotated with capitellum. It has one annotated transcript and one annotated polypeptide.

hide Detailed Mapping Data
FlyBase Computed Cytological Location
Cytogenetic map
Evidence for location
88B3-88B3  
Limits computationally determined from genome sequence between P{lacW}trxj14A6&P{PZ}trx00347 and P{PZ}cv-c06951  
Experimentally Determined Cytological Location
Cytogenetic map
Notes
References
Experimentally Determined Recombination Data
Location
Left of (cM)
Right of (cM)
Notes
Molecular Map Data
Gene Order (in direction of increasing cytology)
References
In direction of increasing cytology: su(Hw)? RpII15?
(Harrison et al., 1992)
In direction of increasing cytology: su(Hw)- RpII15+ anon-88Ba? anon-88Bb? anon-88Bc? CG3321+ spn-B+
(Ghabrial et al., 1998)
Gene Order (overall orientation not stated)
References
hide Gene Model & Products
Please see the GBrowse view of Dmel\RpII15 for information on other features
detailed view FBtr0082946 FBtr0082945 FBtr0082925 FBtr0082926 FBpp0082404 FBpp0082405 FBpp0082384 FBpp0082385 FBti0041782
Comments on Gene Model
hide Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Associated CDS (aa)
RpII15-RA
FBtr0082925
 NM_169575
  696
  129
Additional Transcript Data & Comments
Reported size (kB)
1.2, 0.85 (northern blot)
(Harrison et al., 1992)
Comments
External Data
Crossreferences
hide Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kD)
Length (aa)
Theoretical pI
RefSeq ID
GenBank protein
RpII15-PA  
FBpp0082384  
15.1  
129  
5.22  
  NP_731898
  AAF55045
Additional Polypeptide Data & Comments
Reported size (kD)
129 (aa); 15.1 (kD)
(Harrison et al., 1992)
Comments
External Data
Linkouts
PANTHER - Protein classification by function, families, and pathways
•
Crossreferences
InterPro domains - A database of protein families, domains, and functional sites
•
Zinc finger, TFIIS-type (IPR001222)
DNA-directed RNA polymerase, M/15 kDa subunit (IPR001529)
hide Sequences Consistent with the Gene Model
DDBJ /
EMBL /
GenBank
DNA sequence
Protein sequence
Name
AA141475
 
AA141895
 
AA141897
 
AA141898
 
AE003704
AAF55045
 
AI295488
 
BI357464
 
BP555628
 
BP555629
 
CK02668
 
CO302141
 
EC051142
 
EC054144
 
EC056161
 
EC056319
 
EC245921
 
S66940
AAB29028
 
S88139
AAB21674
 
 
UniProtKB/Swiss-Prot
UniProtKB/TrEMBL
    Maps to
    Does NOT map to
    Identified with
    (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
    aberration junction
    Df(3R)red-P52.bk2
    3R:10,135,368..10,137,917
    comment=The deficiency breakpoint maps to an EcoRI-EcoRI fragment; position of restriction fragment on reference sequence inferred by FlyBase curator.
    evidence=experimental
    linked_to=EcoRI-EcoRI_rfrag
    (Harrison et al., 1992)
    deletion
    Df(3R)su(Hw)V
    3R:10,133,214..10,134,960
    comment=A 1747bp deletion extending from the su(Hw) coding region to the first Cys residue of RpII15 which includes the 5' control region for both genes.
    evidence=experimental
    (Harrison et al., 1992)
    deletion
    RpII15[Z23]
    3R:10,135,115..10,135,288
    comment=deletion of 174bp
    evidence=experimental
    (Harrison et al., 1992)
    rescue fragment
    RpII15[+t5.3]
    3R:10,132,959..10,137,917
    comment=Position of restriction fragment on reference sequence inferred by FlyBase curator.
    evidence=experimental
    linked_to=XbaI-KpnI_rfrag
    (Harrison et al., 1992)
    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
     embryonic stage-adult stage
     
    (Harrison et al., 1992)
     adult stage
     
    (Harrison et al., 1992)
     embryonic stage
     
    (Harrison et al., 1992)
     larval stage
     
    (Harrison et al., 1992)
    Marker for
      Subcellular Localization
      CV Term
      hide Summary of Polypeptide Expression
      Stage
      Tissue/Position
      Reference
      Marker for
        Subcellular Localization
        CV Term
        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
        •
        hide Alleles & Phenotypes
        hide Summary of Allele Phenotypes
        Lethality
        Allele
        lethal | recessive
        lethal | polyphasic | recessive
        Other Phenotypes
        Allele
        wild-type
        Phenotype manifest in
        Allele
        capitellum
        hide Classical Alleles ( 2 )
        For All Classical Alleles Show

        Allele of RpII15ClassMutagenStocksKnown lesion
        RpII15V0 Yes
        RpII15Z230 Yes
        hide Alleles Carried on Transgenic Constructs ( 6 )
        For All Alleles Carried on Transgenic Constructs Show

        Allele of RpII15ClassMutagenStocksKnown lesion
        RpII15+t5.30 Yes
        RpII15GD42341 Yes
        RpII15MtnA.T:Zzzz\FLAG0 Yes
        RpII15T:Zzzz\FLAG0 Yes
        RpII15tKa0 Yes
        RpII15tR144Xb140 Yes
        hide Aneuploid Aberrations
        Useful deficiency
         
        Disrupted in
        (Ryder, 2004.4.26)
        (Mortin et al., 1992)
        (Breen and Harte, 1991, Mortin et al., 1992)
        (Breen and Harte, 1991, Mortin et al., 1992)
        (Breen and Harte, 1991, Mortin et al., 1992)
        (Breen and Harte, 1991)
        (Breen and Harte, 1991, Mortin et al., 1992, Harrison et al., 1992)
        (Breen and Harte, 1991)
        Not disrupted in
        (Mortin et al., 1992)
        (Breen and Harte, 1991)
        (Breen and Harte, 1991)
        (Breen and Harte, 1991)
        hide Transgenic Constructs & Insertions
        Transgenic Constructs
        Type of construct
        Name
        Expression data
        UAS construct
        P{GD4234}
        NA
        characterization construct
        P{CaSX/K5.3}
        NA
        P{R144Xb14}
        NA
        P{su(Hw)wt}
        NA
        P{Δ2-203;673-943}
        NA
        P{Δ2-203}
        NA
        P{Δ656-705}
        NA
        P{Δ673-943}
        NA
        P{Δ706-736}
        NA
        P{Δ738-780}
        NA
        P{Δ782-944}
        NA
        P{Δ853-880}
        NA
        P{Δ881-944}
        NA
        Insertions
        Type of insertions
        Name
        Expression data
        insertion of enhancer trap binary system
        P{GawB}RpII215PG124
        No
        insertion of enhancer trap
        P{lacW}RpII215PL22
        No
        P{lacW}RpII215PL39
        No
        hide Related Comments
        Please look at the allele reports for the complete phenotype data
        RpII15 is an essential gene required maternally for embryogenesis.
        (Harrison et al., 1992)
        The technique of paramagnetic particle-mediated selection of terminated run-on transcripts was used to examine RNA polymerase II pausing and 5' cap formation at high resolution on the heat shock genes Hsp70A, Hsp70B, Hsp26 and Hsp27. Results demonstrate that polymerases pause over a narrow region of each heat shock gene, not at a defined point. 5' capping occurs over a region coincidental with that of pausing.
        (Rasmussen and Lis, 1993)
        Isolation of the coding sequence and immunoblotting experiments demonstrate the RpII15 gene codes for a small subunit of RNA polymerase II.
        (Liu et al., 1993)
        Protein complexes of RNA polymerase II localise to major developmental puffs and heat shock puffs.
        (Weeks et al., 1993)
        RNAi screen using dsRNA made from templates generated with primers directed against this gene results in aberrantly long spindles with misaligned chromosomes when assayed in S2 cells in the presence of Cdc27 dsRNA. This phenotype cannot be observed when the screen is performed without Cdc27 dsRNA.
        (Goshima et al., 2007)
        hide Gene Ontology: Function, Process & Cellular Component ( 7 )
        hide Molecular Function
        CV term
        Evidence
        References
        DNA binding
        inferred from electronic annotation with InterPro:IPR001529
        (FlyBase Curators et al., 2004-)
        DNA-directed RNA polymerase activity
        inferred from sequence or structural similarity with HGNC_gene:POLR2I; HGNC:9196; OMIM:180662 AND inferred from sequence or structural similarity with SGD_LOCUS:RPB9; SGD:S0003038
        (Aoyagi and Wassarman, 2000)
        non-traceable author statement
        (Swiss-Prot Project Members, 2001.8.20)
        transcription regulator activity
        inferred from electronic annotation with InterPro:IPR001222
        (FlyBase Curators et al., 2004-)
        zinc ion binding
        inferred from electronic annotation with InterPro:IPR001222
        (FlyBase Curators et al., 2004-)
        hide Biological Process
        CV term
        Evidence
        References
        regulation of transcription
        inferred from electronic annotation with InterPro:IPR001222
        (FlyBase Curators et al., 2004-)
        transcription from RNA polymerase II promoter
        inferred from sequence or structural similarity with HGNC_gene:POLR2I; HGNC:9196; OMIM:180662 AND inferred from sequence or structural similarity with SGD_LOCUS:RPB9; SGD:S0003038
        (Aoyagi and Wassarman, 2000)
        non-traceable author statement
        (Swiss-Prot Project Members, 2001.8.20)
        hide Cellular Component
        CV term
        Evidence
        References
        DNA-directed RNA polymerase II, core complex
        inferred from sequence or structural similarity with HGNC_gene:POLR2I; HGNC:9196; OMIM:180662 AND inferred from sequence or structural similarity with SGD_LOCUS:RPB9; SGD:S0003038
        (Aoyagi and Wassarman, 2000)
        non-traceable author statement
        (Swiss-Prot Project Members, 2001.8.20)
        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
        RpII15 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
         
        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 ( 1 )
        VDRC
        v11219
        w1118; P{GD4234}v11219
        hide Genomic Clones ( 2 )
        hide cDNA Clones ( 9 )
        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
        Additional comments
        hide Comments About Role
        hide Comments About Molecular Function
        hide Other Comments
        Designation as "RpII215" was in error.
        (Kim et al., 1996)
        Used in a phylogenetic analysis, the tree in inferred by parsimony method from RpoB sequences, or homologous, multiple alignment.
        (Mollet et al., 1998)
        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
        •
        Zinc finger, TFIIS-type (IPR001222)
        DNA-directed RNA polymerase, M/15 kDa subunit (IPR001529)
        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
        •
        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
        •
        hide Synonyms & Secondary IDs ( 20 )
        Reported As
        Symbol Synonym
        CG3284
        (Aoyagi and Wassarman, 2000, Goshima et al., 2007)
        dRPB9
        (Gu et al., 2002, Park et al., 2001)
        H5
        (Leatherman et al., 2002, Robertson et al., 1999)
        l(3)88Be
         
        l(3)Z23
        (Breen and Harte, 1991, )
        pol II
        (Zhang and Gilmour, 2006)
        Pol II
        (Kim, 2004, Armstrong et al., 2002, Kaplan et al., 2000, Boehm et al., 2003)
        PolII
        (Zhang et al., 2004, Andrulis et al., 2000, Chen et al., 2008, Piel et al., 2008)
        polII
        (Gu et al., 2002, Lis, 1998, Bentley, 1998)
        RNAP
        (Ma, 2005)
        RNAP II
        (Leatherman and Jongens, 2003, Mollet et al., 1998, Seydoux and Dunn, 1997)
        RNApolII
        (Martinho et al., 2004, Sauer et al., 1995, Sauer et al., 1995)
        RNA Pol II
        (Meehan et al., 2001, Mito et al., 2005)
        RNA pol II
        (Farkas et al., 2000, Gilfillan et al., 2006)
        RNA polII
        (Leclerc et al., 2000)
        RPII15
        (Liu, 1994.2.4, Liu et al., 1993)
        RpII15
        (Goshima et al., 2007)
        RpII215
        (Kim et al., 1996)
        Name Synonym
        RNA polymerase II
        (Heinkoff et al., 2004, Shore et al., 2003, Chao and Price, 2001, Mizuguchi et al., 2001, Chao et al., 2000, Mahowald, 2001, Kal et al., 2000, Reim et al., 1999, Pham et al., 1999, Schock et al., 1999, Gu, 1998, Peng et al., 1998, Peng et al., 1998, Sandaltzopoulos and Becker, 1998, Hansen et al., 1997, Kephart et al., 1992, Visa et al., 1991, Spencer and Groudine, 1990, Wampler et al., 1990, Visa et al., 1988, Morcillo and MacIntyre, 2001, Robertson et al., 1999, Bentley, 1998, Redhouse and White, 2007, Yao et al., 2006, Silverman et al., 2008, Ratnaparkhi and Courey, 2008)
        RNA polymerase II 15kD subunit
         
        Secondary FlyBase IDs
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