A Database of Drosophila Genes & Genomes

FB2008_07, released August 8, 2008
 

Gene Dmel\U2A

General Information
SymbolDmel\U2ASpeciesD. melanogaster
NameU2AAnnotation symbolCG1406
Feature typeprotein_coding_geneFlyBase IDFBgn0033210
Created / Updated2003-12-02/2003-12-02
Genomic Location
Chromosome (arm)2RRecombination map
Cytogenetic map43E9-43E9Sequence location2R:3,562,866..3,563,857 [-]
Map ( GBrowse ) detailed view
hide Summary Information
Automatically generated summary

See sections below for more information
This gene is referred to in FlyBase by the symbol U2A (CG1406, FBgn0033210). It has the cytological map location 43E9. Its sequence location is 2R:3562866..3563857. Its molecular function is described as: RNA splicing factor activity, transesterification mechanism; mRNA binding; protein binding. It is involved in the biological processes: nuclear mRNA splicing, via spliceosome; mitotic spindle organization and biogenesis. 4 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
43E9-43E9  
Limits computationally determined from genome sequence between P{PZ}scra03427&P{EP}EP2179 and P{PZ}l(2)0849208492  
Experimentally Determined Cytological Location
Cytogenetic map
Notes
References
43E-43E
(determined by in situ hybridisation)  
(Nagengast and Salz, 2001)
Experimentally Determined Recombination Data
Location
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\U2A for information on other features
detailed view FBtr0088942 FBtr0088924 FBtr0088941 FBtr0088940 FBtr0088939 FBpp0088016 FBpp0087998 FBpp0088015 FBpp0088014 FBpp0088013 FBti0072535
Comments on Gene Model
hide Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Associated CDS (aa)
U2A-RA
FBtr0088941
 NM_136471
  992
  265
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
U2A-PA  
FBpp0088015  
29.7  
265  
8.78  
  NP_610315
  AAF59207
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
•
Leucine-rich repeat (IPR001611)
U2A'/phosphoprotein 32 family A, C-terminal (IPR003603)
hide Sequences Consistent with the Gene Model
DDBJ /
EMBL /
GenBank
DNA sequence
Protein sequence
Name
AA801988
 
AE003840
AAF59207
 
AY071516
AAL49138
 
BI354512
 
BI370373
 
BI632660
 
BI636618
 
CO293450
 
EC201242
 
 
UniProtKB/Swiss-Prot
UniProtKB/TrEMBL
    Maps to
    (Nagengast and Salz, 2001)
    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
    point mutation
    U2A[1]
    2R:3,563,654..3,563,654
    evidence=experimental
    na_change=T3187962A
    pr_change=Y29@|U2A-PA
    reported_na_change=T?A
    reported_pr_change=Y29@
    (Nagengast and Salz, 2001)
    rescue fragment
    U2A[+t2.8]
    2R:3,562,198..3,565,010
    comment=Rescue construct includes 1270bp upstream of translation start and ends 745 bases 3' of the coding sequence.
    evidence=experimental
    (Nagengast and Salz, 2001)
    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 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 | embryonic stage | recessive
        Other Phenotypes
        Allele
        wild-type
        Phenotype manifest in
        Allele
        hide Classical Alleles ( 1 )
        For All Classical Alleles Show

        Allele of U2AClassMutagenStocksKnown lesion
        U2A1loss of function1 Yes
        hide Alleles Carried on Transgenic Constructs ( 3 )
        For All Alleles Carried on Transgenic Constructs Show

        Allele of U2AClassMutagenStocksKnown lesion
        U2A+t2.80 Yes
        U2A+t40 Yes
        U2AGD82101 Yes
        hide Aneuploid Aberrations
        Useful deficiency
         
         
        Disrupted in
        (Heitzler et al., 1993)
        (Heitzler et al., 1993)
        (Heitzler et al., 1993)
        (Heitzler et al., 1993)
        (Heitzler et al., 1993)
        (Heitzler et al., 1993)
        (Ryder, 2004.4.26)
        (Ryder, 2004.4.26)
        (Heitzler et al., 1993)
        (Eeken et al., 2001)
        (Eeken et al., 2001, Nagengast and Salz, 2001, Heitzler et al., 1993)
        (Heitzler et al., 1993)
        (Eeken et al., 2001)
        (Heitzler et al., 1993)
        (Heitzler et al., 1993)
        (Heitzler et al., 1993)
        (Heitzler et al., 1993)
        Not disrupted in
        (Heitzler et al., 1993)
        (Heitzler et al., 1993)
        (Heitzler et al., 1993)
        (Heitzler et al., 1993)
        (Heitzler et al., 1993)
        (Heitzler et al., 1993)
        (Heitzler et al., 1993)
        (Heitzler et al., 1993)
        (Heitzler et al., 1993)
        (Heitzler et al., 1993)
        (Heitzler et al., 1993)
        (Heitzler et al., 1993)
        (Heitzler et al., 1993)
        (Heitzler et al., 1993)
        (Heitzler et al., 1993)
        (Heitzler et al., 1993)
        (Heitzler et al., 1993)
        (Heitzler et al., 1993)
        (Heitzler et al., 1993)
        (Heitzler et al., 1993)
        (Heitzler et al., 1993)
        (Heitzler et al., 1993)
        (Heitzler et al., 1993)
        (Heitzler et al., 1993)
        hide Transgenic Constructs & Insertions
        Transgenic Constructs
        Type of construct
        Name
        Expression data
        UAS construct
        P{GD8210}
        NA
        characterization construct
        P{U2A.2.8.genomic}
        NA
        P{U2A.4.genomic}
        NA
        Insertions
        Type of insertions
        Name
        Expression data
        hide Related Comments
        Please look at the allele reports for the complete phenotype data
        Mutants are embryonic lethal.
        (Nagengast et al., 2001)
        Homozygous U2A mutants complete embryogenesis but do not hatch.
        (Nagengast and Salz, 2001)
        RNAi screen using dsRNA made from templates generated with primers directed against this gene results in a long metaphase spindle with misaligned chromosomes when assayed in S2 cells. This phenotype can be observed when the screen is performed with or without Cdc27 dsRNA.
        (Goshima et al., 2007)
        hide Gene Ontology: Function, Process & Cellular Component ( 7 )
        hide Molecular Function
        CV term
        Evidence
        References
        RNA splicing factor activity, transesterification mechanism
        inferred from sequence or structural similarity with SGD_LOCUS:LEA1; SGD:S0006134
        (Mount and Salz, 2000)
        mRNA binding
        inferred from sequence or structural similarity
        (Nagengast et al., 2001)
        protein binding
        inferred from electronic annotation with InterPro:IPR001611
        (FlyBase Curators et al., 2004-)
        hide Biological Process
        CV term
        Evidence
        References
        mitotic spindle organization and biogenesis
        inferred from mutant phenotype
        (Goshima et al., 2007)
        nuclear mRNA splicing, via spliceosome
        inferred from sequence or structural similarity with NCBI_NP:003081 AND inferred from sequence or structural similarity with SGD_LOCUS:LEA1; SGD:S0006134
        (Mount and Salz, 2000)
        inferred from sequence or structural similarity with UniProtKB:P09661
        (FlyBase, 1992-)
        hide Cellular Component
        CV term
        Evidence
        References
        small nuclear ribonucleoprotein complex
        inferred from sequence or structural similarity with NCBI_NP:003081 AND inferred from sequence or structural similarity with SGD_LOCUS:LEA1; SGD:S0006134
        (Mount and Salz, 2000)
        snRNP U2
        inferred from sequence or structural similarity with NCBI_NP:003081
        (Mount and Salz, 2000)
        inferred from sequence or structural similarity with UniProtKB:P09661
        (FlyBase, 1992-)
        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
        U2A allele
        Gene
        References
        hide External Data
        Linkouts
        BioGRID - Interaction data, including yeast 2-hybrid and genetic interactions
        •
        Drosophila PIMRider - The Drosophila Protein Interaction map
        •
        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 ( 2 )
        VDRC
        v17358
        w1118; P{GD8210}v17358/TM3
        Bloomington
        4127
        Dp(?;2)bwD, U2A1 bwD/CyO
        hide Genomic Clones ( 2 )
        hide cDNA Clones ( 6 )
        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 identity of: U2A' CG1406
        (Salz, 2001.3.5)
        Source for database merge of
        Source for merge of: U2A l(2)43Ee Source for identity of: U2A U2A'
        (Salz, 2001.7.18)
        Source for merge of: U2A BcDNA:RE56869 Source for merge of U2A BcDNA:RE56869 was a shared cDNA (date:030728).
        (FlyBase, 1996-)
        Additional comments
        hide Comments About Role
        hide Comments About Molecular Function
        The gene products of U2A and snf are co-immunoprecipitated by antibodies to either protein, demonstrating that, like their yeast and human counterparts, they heterodimerize in vivo. A mutation in the U2A binding motif of snf reduces the amount of heterodimer formation but does not abolish it completely. The U2A binding motif from snf is only essential for heterodimer formation in the absence of the C-terminal end of the protein. The RNA binding specificity domain of snf is essential for interaction with U2A. The U2A gene product incorporation into U2 snRNP does not depend on dimerization of the U2A and snf gene products.
        (Nagengast and Salz, 2001)
        hide Other Comments
        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
        •
        Leucine-rich repeat (IPR001611)
        U2A'/phosphoprotein 32 family A, C-terminal (IPR003603)
        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
        •
        Drosophila PIMRider - The Drosophila Protein Interaction map
        •
        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 ( 7 )
        Reported As
        Symbol Synonym
        BcDNA:RE56869
         
        CG1406
        (Goshima et al., 2007)
        dU2A'
        (Nagengast and Salz, 2001, Nagengast et al., 2001)
        l(2)43Ee
        (Nagengast and Salz, 2001, Eeken et al., 2001, Roote, 1995.9.26, Heitzler et al., 1993, )
        U2A
        (Goshima et al., 2007)
        U2A'
        (Johnson and Salz, 2003, Salz, 2001.3.5, Mount and Salz, 2000, Chaouki and Salz, 2006)
        Name Synonym
        lethal(2)43Ee
         
        U2A
         
        Secondary FlyBase IDs
        • FBgn0004136
        • FBgn0047086
        hide References ( 17 )
        Research paper
        Chaouki and Salz, 2006, PLoS Gen. 2(12):
        Drosophila SPF45: A Bifunctional Protein with Roles in Both Splicing and DNA Repair. [FBrf0192968]
        Eeken et al., 2001, Mutat. Res. 485(3): 237--253
        Isolation and genetic characterisation of the Drosophila homologue of (SCE)REV3, encoding the catalytic subunit of DNA polymerase . [FBrf0134782]
        Nagengast and Salz, 2001, Nucleic Acids Res. 29(18): 3841--3847
        The Drosophila U2 snRNP protein U2A' has an essential function that is SNF/U2B' independent. [FBrf0138511]
        Mount and Salz, 2000, J. Cell Biol. 150(2): F37--F43
        Pre-messenger RNA processing factors in the Drosophila genome. [FBrf0129982]
        Heitzler et al., 1993, Genetics 135(1): 105--115
        Genetic and cytogenetic analysis of the 43A-E region containing the segment polarity gene costa and the cellular polarity genes prickle and spiny-legs in Drosophila melanogaster. [FBrf0058613]
        Supplementary material
        Goshima et al., 2007, Science 316(5823):
        Supporting online material for Genes required for mitotic spindle assembly in Drosophila S2 cells. [FBrf0200397]
        Personal communication to FlyBase
        Dickson et al., 2007.7.18, RNAi construct and insertion data submitted by the Vienna Drosophila RNAi Center
        RNAi construct and insertion data submitted by the Vienna Drosophila RNAi Center [FBrf0200327]
        FlyBase Curators et al., 2004-, Gene Ontology annotation in FlyBase through association of InterPro records with GO terms.
        Gene Ontology annotation in FlyBase through association of InterPro records with GO terms. [FBrf0174215]
        Ryder, 2004.4.26, Exelixis CG deletion data.
        Exelixis CG deletion data. [FBrf0184335]
        Salz, 2001.3.5, Helping FlyBase: ADRC-10651.
        Helping FlyBase: ADRC-10651. [FBrf0135295]
        Salz, 2001.7.18, Naming snRNP proteins.
        Naming snRNP proteins. [FBrf0137503]
        Roote, 1995.9.26, 43 lethals.
        43 lethals. [FBrf0086245]
        Abstract
        Johnson and Salz, 2003, A. Dros. Res. Conf. 44: 375C
        A comparative functional analysis of the U2A'' spliceosomal protein in Drosophila and the yeast S. pombe. [FBrf0155052]
        Nagengast et al., 2001, A. Dros. Res. Conf. 42: 359B
        The Drosophila U2 snRNP-U2A' protein has essential functions that are SNF/U2B'' independent. [FBrf0134024]
        FlyBase analysis
        FlyBase, 1996-, FlyBase inference based on genome sequence analysis.
        FlyBase inference based on genome sequence analysis. [FBrf0104946]
        FlyBase, 1992-, FlyBase curation
        FlyBase curation. [FBrf0105495]
        Computer file
        BDGP Project Members, 2000-, Berkeley Drosophila Genome Project.
        Berkeley Drosophila Genome Project. [FBrf0125078]