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General Information
Symbol
Dmel\Nipped-A
Species
D. melanogaster
Name
Nipped-A
Annotation Symbol
CG33554
Feature Type
FlyBase ID
FBgn0053554
Gene Model Status
Stock Availability
Gene Snapshot
In progress.Contributions welcome.
Also Known As
Tra1, TRRAP, dTra1, l(2)41Ah, dTRRAP
Key Links
Genomic Location
Cytogenetic map
Sequence location
2R:5,177,965..5,251,022 [-]
Recombination map
2-55
Sequence
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
Function
GO Summary Ribbons
Protein Family (UniProt)
Belongs to the PI3/PI4-kinase family. TRA1 subfamily. (Q8I8U7)
Molecular Function (GO)
[Detailed GO annotations]
Experimental Evidence
Predictions / Assertions
Summaries
Gene Group (FlyBase)
ATYPICAL PROTEIN KINASES -
Atypical kinases are protein kinases or putative protein kinases that do not share clear sequence similarity with conventional eukaryotic protein kinases, but they or their orthologs have been shown experimentally to have protein kinase activity. Atypical kinases are defined in FBrf0201870.
SPT-ADA-GCN5 ACETYLTRANSFERASE -
The Spt-Ada-Gcn5 Acetyltransferase (SAGA) complex is a chromatin modifying complex. SAGA can acetylate and deubiquitinate histone residues. Also SAGA has been shown to regulate the transcriptional activation of a subset of genes. (Adapted from FBrf0228923, FBrf0219841 and FBrf0233349).
TIP60 COMPLEX -
The Tip60 chromatin remodeling complex acetylates nucleosomal phospho-histone H2Av and exchanges it with unmodified H2Av. (Adapted from FBrf0185742).
HISTONE ACETYLTRANSFERASES -
Histone acetyltransferases catalyze the acetylation of conserved lysine residues on histone proteins by transferring an acetyl group from acetyl CoA to form ε-N-acetyl lysine. (Adapted from PMID:11395403).
Protein Function (UniProtKB)
Part of the Tip60 chromatin-remodeling complex which is involved in DNA repair (PubMed:15528408). Upon induction of DNA double-strand breaks, this complex acetylates phosphorylated H2AV in nucleosomes and exchanges it with unmodified H2AV (PubMed:15528408). During wing development, required for activity of Notch and its coactivator mam (PubMed:16508010). Function in promoting mam function is likely to involve both the Tip60 and SAGA complexes (PubMed:16508010).
(UniProt, Q8I8U7)
Summary (Interactive Fly)
Homologue of the yeast Tra1 and human TRRAP proteins - a key component of both the SAGA and Tip60 (NuA4) chromatin-modifying complexes - required for Mastermind function during wing development
Gene Model and Products
Number of Transcripts
2
Number of Unique Polypeptides
2

Please see the GBrowse view of Dmel\Nipped-A or the JBrowse view of Dmel\Nipped-A 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
Gene model reviewed during 6.02
Low-frequency RNA-Seq exon junction(s) not annotated.
Annotated transcripts do not represent all possible combinations of alternative exons and/or alternative promoters.
Gene model reviewed during 5.47
Gene model reviewed during 6.04
Sequence Ontology: Class of Gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
FBtr0303293
11515
3790
FBtr0347556
11368
3741
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
FBpp0292385
435.3
3790
7.79
FBpp0312589
429.9
3741
7.83
Polypeptides with Identical Sequences

None of the polypeptides share 100% sequence identity.

Additional Polypeptide Data and Comments
Reported size (kDa)
Comments
External Data
Subunit Structure (UniProtKB)
Component of the Tip60 chromatin-remodeling complex which contains the catalytic subunit Tip60 and the subunits Domino, Tra1, Brd8, E(Pc), DMAP1, Pontin, Reptin, Ing3, Act87E, BAP55, Mrg15, MrgBP, Gas41 and YL-1 (PubMed:15528408). Probable component of some SAGA complex (PubMed:12697829). Interacts with Spt3, Gcn5, Ada3 and Ada2b (PubMed:12697829).
(UniProt, Q8I8U7)
Linkouts
Sequences Consistent with the Gene Model
Nucleotide / Polypeptide Records
 
Mapped Features

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

External Data
Crossreferences
Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
Linkouts
Gene Ontology (17 terms)
Molecular Function (2 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
inferred from direct assay
(assigned by UniProt )
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN000124276
(assigned by GO_Central )
Biological Process (8 terms)
Terms Based on Experimental Evidence (7 terms)
CV Term
Evidence
References
inferred from direct assay
inferred from direct assay
inferred from direct assay
inferred from mutant phenotype
inferred from direct assay
(assigned by UniProt )
inferred from direct assay
(assigned by UniProt )
inferred from genetic interaction with FLYBASE:mam; FB:FBgn0002643
inferred from genetic interaction with FLYBASE:N; FB:FBgn0004647
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN000124276
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN000124276
(assigned by GO_Central )
Cellular Component (7 terms)
Terms Based on Experimental Evidence (7 terms)
CV Term
Evidence
References
inferred from direct assay
inferred from direct assay
(assigned by UniProt )
inferred from physical interaction with FLYBASE:pont; FB:FBgn0040078
inferred from direct assay
inferred from direct assay
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN000124276
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN000124197
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN000124276
(assigned by GO_Central )
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
in situ
Stage
Tissue/Position (including subcellular localization)
Reference
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
mass spectroscopy
Stage
Tissue/Position (including subcellular localization)
Reference
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
inferred from direct assay
inferred from direct assay
(assigned by UniProt )
inferred from physical interaction with FLYBASE:pont; FB:FBgn0040078
inferred from direct assay
inferred from direct assay
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\Nipped-A in GBrowse 2
RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region
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
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
Alleles, Insertions, and Transgenic Constructs
Classical and Insertion Alleles ( 71 )
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 Nipped-A
Transgenic constructs containing regulatory region of Nipped-A
Deletions and Duplications ( 64 )
Partially disrupted in
Phenotypes
For more details about a specific phenotype click on the relevant allele symbol.
Lethality
Allele
Sterility
Allele
Other Phenotypes
Allele
Phenotype manifest in
Allele
Orthologs
Human Orthologs (via DIOPT v7.1)
Homo sapiens (Human) (1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
14 of 15
Yes
Yes
Model Organism Orthologs (via DIOPT v7.1)
Mus musculus (laboratory mouse) (1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
14 of 15
Yes
Yes
Rattus norvegicus (Norway rat) (1)
2 of 13
Yes
Yes
Xenopus tropicalis (Western clawed frog) (1)
8 of 12
Yes
Yes
Danio rerio (Zebrafish) (1)
11 of 15
Yes
Yes
Caenorhabditis elegans (Nematode, roundworm) (1)
15 of 15
Yes
Yes
Arabidopsis thaliana (thale-cress) (2)
7 of 9
Yes
Yes
7 of 9
Yes
Yes
Saccharomyces cerevisiae (Brewer's yeast) (1)
15 of 15
Yes
Yes
Schizosaccharomyces pombe (Fission yeast) (3)
11 of 12
Yes
Yes
11 of 12
Yes
Yes
1 of 12
No
No
Orthologs in Drosophila Species (via OrthoDB v9.1) ( EOG0919001M )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
Drosophila melanogaster
fruit fly
Drosophila simulans
Drosophila simulans
Drosophila sechellia
Drosophila erecta
Drosophila yakuba
Drosophila ananassae
Drosophila pseudoobscura pseudoobscura
Drosophila pseudoobscura pseudoobscura
Drosophila pseudoobscura pseudoobscura
Drosophila persimilis
Drosophila willistoni
Drosophila virilis
Drosophila mojavensis
Drosophila grimshawi
Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG09150012 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Musca domestica
House fly
Glossina morsitans
Tsetse fly
Glossina morsitans
Tsetse fly
Lucilia cuprina
Australian sheep blowfly
Mayetiola destructor
Hessian fly
Aedes aegypti
Yellow fever mosquito
Anopheles darlingi
American malaria mosquito
Anopheles darlingi
American malaria mosquito
Anopheles darlingi
American malaria mosquito
Anopheles gambiae
Malaria mosquito
Culex quinquefasciatus
Southern house mosquito
Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W000T )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Bombyx mori
Silkmoth
Danaus plexippus
Monarch butterfly
Danaus plexippus
Monarch butterfly
Heliconius melpomene
Postman butterfly
Apis florea
Little honeybee
Apis mellifera
Western honey bee
Bombus impatiens
Common eastern bumble bee
Bombus terrestris
Buff-tailed bumblebee
Linepithema humile
Argentine ant
Megachile rotundata
Alfalfa leafcutting bee
Nasonia vitripennis
Parasitic wasp
Dendroctonus ponderosae
Mountain pine beetle
Dendroctonus ponderosae
Mountain pine beetle
Tribolium castaneum
Red flour beetle
Pediculus humanus
Human body louse
Rhodnius prolixus
Kissing bug
Rhodnius prolixus
Kissing bug
Cimex lectularius
Bed bug
Cimex lectularius
Bed bug
Acyrthosiphon pisum
Pea aphid
Acyrthosiphon pisum
Pea aphid
Acyrthosiphon pisum
Pea aphid
Acyrthosiphon pisum
Pea aphid
Acyrthosiphon pisum
Pea aphid
Zootermopsis nevadensis
Nevada dampwood termite
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X000R )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strigamia maritima
European centipede
Ixodes scapularis
Black-legged tick
Ixodes scapularis
Black-legged tick
Ixodes scapularis
Black-legged tick
Stegodyphus mimosarum
African social velvet spider
Stegodyphus mimosarum
African social velvet spider
Stegodyphus mimosarum
African social velvet spider
Stegodyphus mimosarum
African social velvet spider
Stegodyphus mimosarum
African social velvet spider
Tetranychus urticae
Two-spotted spider mite
Tetranychus urticae
Two-spotted spider mite
Daphnia pulex
Water flea
Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G0024 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strongylocentrotus purpuratus
Purple sea urchin
Strongylocentrotus purpuratus
Purple sea urchin
Strongylocentrotus purpuratus
Purple sea urchin
Strongylocentrotus purpuratus
Purple sea urchin
Ciona intestinalis
Vase tunicate
Ciona intestinalis
Vase tunicate
Gallus gallus
Domestic chicken
Paralogs
Paralogs (via DIOPT v7.1)
Drosophila melanogaster (Fruit fly) (4)
1 of 10
1 of 10
1 of 10
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 ( 2 )
    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?
    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
    esyN Network Diagram
    Show neighbor-neighbor interactions:
    Select Layout:
    Legend:
    Protein
    RNA
    Selected Interactor(s)
    Interactions Browser

    Please see the Physical Interaction reports below for full details
    protein-protein
    Physical Interaction
    Assay
    References
    Summary of Genetic Interactions
    esyN Network Diagram
    esyN Network Key:
    Suppression
    Enhancement

    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
    External Data
    Subunit Structure (UniProtKB)
    Component of the Tip60 chromatin-remodeling complex which contains the catalytic subunit Tip60 and the subunits Domino, Tra1, Brd8, E(Pc), DMAP1, Pontin, Reptin, Ing3, Act87E, BAP55, Mrg15, MrgBP, Gas41 and YL-1 (PubMed:15528408). Probable component of some SAGA complex (PubMed:12697829). Interacts with Spt3, Gcn5, Ada3 and Ada2b (PubMed:12697829).
    (UniProt, Q8I8U7 )
    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 (genetic) - An integrated Molecular Interaction Database
    MIST (protein-protein) - An integrated Molecular Interaction Database
    Pathways
    Gene Group - Pathway Membership (FlyBase)
    External Data
    Linkouts
    SignaLink - A signaling pathway resource with multi-layered regulatory networks.
    Genomic Location and Detailed Mapping Data
    Chromosome (arm)
    2R
    Recombination map
    2-55
    Cytogenetic map
    Sequence location
    2R:5,177,965..5,251,022 [-]
    FlyBase Computed Cytological Location
    Cytogenetic map
    Evidence for location
    41E1-41E3
    Experimentally Determined Cytological Location
    Cytogenetic map
    Notes
    References
    Experimentally Determined Recombination Data
    Left of (cM)
    Right of (cM)
    Notes
    Stocks and Reagents
    Stocks (16)
    Genomic Clones (28)
    cDNA Clones (206)
     

    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)
      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
      Commercially Available Antibodies
       
      Other Information
      Relationship to Other Genes
      Source for database identify of
      Source for database merge of
      Source for merge of: l(2)41Ah Nipped-A
      Source for merge of: Nipped-A Tra1
      Source for merge of: Tra1 CG2905 CG10549
      Additional comments
      Release 4.1 annotation CG33554 (which corresponds to Nipped-A) contains sequences corresponding to both release 3.2 annotation CG2905 and release 2 annotation CG10549.
      'Nipped' mutations disrupt one or more of four recessive lethal complementation groups: l(2)41Ae, RpL38, Nipped-A and Nipped-B.
      Source for merge of Tra1 CG2905 CG10549 was sequence comparison ( date:030120 ).
      Complementation map circular, with the majority of mutants falling into a single complementation group that is complemented by only three of the thirty alleles.
      Other Comments
      dsRNA has been made from templates generated with primers directed against this gene.
      S2 cells treated with dsRNA generated against this gene show reduced phagocytosis of Candida albicans compared to untreated cells.
      dsRNA directed against this gene causes defects in cytokinesis when tested in an RNAi screen in S2 cells.
      CG10549 was eliminated in release 3 of the genome annotation, January 2003.
      'Nipped' mutations identify four essential complementation groups, l(2)41Ae, RpL38, Nipped-A and Nipped-B, that play distinct roles in regulating ct and N signalling.
      Nipped-A influences N receptor signalling or N expression during development of the wing margin and wing veins.
      The Nipped-group genes regulate ct and Ubx.
      Nipped-A acts as a dosage sensitive maternal modifier of run.
      Nipped-A locus exhibits high EMS mutability and the lethal alleles exhibit a complex interallelic complementation.
      Origin and Etymology
      Discoverer
      Etymology
      Identification
      External Crossreferences and Linkouts ( 50 )
      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/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information
      Other crossreferences
      Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
      Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
      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
      iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
      KEGG Genes - Molecular building blocks of life in the genomic space.
      modMine - A data warehouse for the modENCODE project
      Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
      SignaLink - A signaling pathway resource with multi-layered regulatory networks.
      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
      Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution
      InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
      MIST (genetic) - An integrated Molecular Interaction Database
      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 (24)
      Reported As
      Symbol Synonym
      CG10549
      l(2)C123
      l(2)EMS34-12
      Secondary FlyBase IDs
      • FBan0002905
      • FBtr0086095
      • FBan0033554
      • FBgn0002067
      • FBgn0002172
      • FBgn0004661
      • FBgn0020393
      • FBgn0033013
      • FBgn0039989
      Datasets (0)
      Study focus (0)
      Experimental Role
      Project
      Project Type
      Title
      References (152)