FlyBase Gene Report: Dmel\Nipped-A

General Information

Symbol

Dmel\Nipped-A

Species

D. melanogaster

Name

Nipped-A

Annotation Symbol

CG33554

Feature Type

protein_coding_gene

FlyBase ID

FBgn0053554

Gene Model Status

Current

Stock Availability

14 publicly available

Gene Summary

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)

Contribute a Gene Snapshot for this gene.

All Summaries

Alliance
Auto summary
Gene Group
UniProtKB
Interactive Fly

Also Known As

Tra1, TRRAP, dTra1, l(2)41Ah, 41Ah

Key Links

Genomic Location

Cytogenetic map

Sequence location

2R:5,177,965..5,251,022 [-]

Recombination map

2-55

RefSeq locus

NT_033778 REGION:5177965..5251022

Sequence

Get Decorated FASTA

Genomic Maps

JBrowse GBrowse

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Other Genome Views

The following external sites may use different assemblies or annotations than FlyBase.

Function

GO Summary Ribbons

Gene Ontology (GO) Annotations (15 terms)

Molecular Function (2 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

enables transcription coregulator activity

inferred from biological aspect of ancestor with PANTHER:PTN000124276

(assigned by GO_Central )

(Gaudet et al., 2011)

NOT enables kinase activity

inferred from key residues

(Elías-Villalobos et al., 2019)

inferred from sequence or structural similarity with UniProtKB:Q9Y4A5

(FlyBase Curators, 2008-)

Biological Process (6 terms)

Terms Based on Experimental Evidence (5 terms)

CV Term

Evidence

References

involved_in histone acetylation

inferred from direct assay

(Kusch et al., 2004)

involved_in histone exchange

inferred from direct assay

(Kusch et al., 2004)

involved_in histone H3 acetylation

inferred from direct assay

(Guelman et al., 2006)

involved_in regulation of transcription, DNA-templated

inferred from direct assay

(assigned by UniProt )

(Kusch et al., 2003)

involved_in wing disc pattern formation

inferred from genetic interaction with FLYBASE:mam; FB:FBgn0002643

(Gause et al., 2006)

inferred from genetic interaction with FLYBASE:N; FB:FBgn0004647

(Gause et al., 2006)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

involved_in DNA repair

inferred from biological aspect of ancestor with PANTHER:PTN000124276

(assigned by GO_Central )

(Gaudet et al., 2011)

involved_in regulation of transcription, DNA-templated

inferred from biological aspect of ancestor with PANTHER:PTN000124276

(assigned by GO_Central )

(Gaudet et al., 2011)

Cellular Component (7 terms)

Terms Based on Experimental Evidence (7 terms)

CV Term

Evidence

References

located_in cytoplasm

inferred from direct assay

(Gause et al., 2006)

part_of histone acetyltransferase complex

inferred from direct assay

(assigned by UniProt )

(Kusch et al., 2003)

inferred from physical interaction with FLYBASE:pont; FB:FBgn0040078

(Kusch et al., 2004)

part_of NuA4 histone acetyltransferase complex

inferred from direct assay

(Kusch et al., 2004)

located_in nucleus

inferred from direct assay

(Weake et al., 2011, Gause et al., 2006, Guelman et al., 2006, Kusch et al., 2004)

located_in polytene chromosome puff

inferred from direct assay

(Gause et al., 2006)

located_in polytene chromosome

inferred from direct assay

(Gause et al., 2006)

part_of SAGA complex

inferred from direct assay

(Weake et al., 2011, Guelman et al., 2006)

Terms Based on Predictions or Assertions (3 terms)

CV Term

Evidence

References

part_of NuA4 histone acetyltransferase complex

inferred from biological aspect of ancestor with PANTHER:PTN000124276

(assigned by GO_Central )

(Gaudet et al., 2011)

is_active_in nucleus

inferred from biological aspect of ancestor with PANTHER:PTN000124197

(assigned by GO_Central )

(Gaudet et al., 2011)

part_of SAGA complex

inferred from biological aspect of ancestor with PANTHER:PTN000124276

(assigned by GO_Central )

(Gaudet et al., 2011)

Gene Group (FlyBase)

ATYPICAL PROTEIN KINASES

PUTATIVE PSEUDOKINASES

SAGA COMPLEX

TIP60 COMPLEX

Protein Family (UniProt)

Belongs to the PI3/PI4-kinase family. TRA1 subfamily. (Q8I8U7)

Protein Signatures (InterPro)

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.
PUTATIVE PSEUDOKINASES -: Pseudokinases have a kinase domain but lack key residue(s) classically required for phosphotransfer. Although potentially lacking catalytic activity, pseudokinases may still have roles in signalling cascades and complexes. (Adapted from FBrf0209106, PMID:21074407 and PMID:23863165).
SAGA COMPLEX -: 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).

Protein Function (UniProtKB)

(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

Interactive Fly

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see 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

Structure New Section

Protein 3D structure (Predicted by AlphaFold) (AlphaFold entry Q8I8U7)

If you don't see the viewer to the right, refresh your browser.

Model Confidence:

Very high (pLDDT > 90)
Confident (90 > pLDDT > 70)
Low (70 > pLDDT > 50)
Very low (pLDDT < 50)

AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Some regions with low pLDDT may be unstructured in isolation.

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

nuclear_gene

protein_coding_gene

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

Nipped-A-RE

FBtr0303293

NM_001103722

11515

3790

Nipped-A-RF

FBtr0347556

NM_001316406

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

Nipped-A-PE

FBpp0292385

435.3

3790

7.79

NP_001097192

ABV53702

Nipped-A-PF

FBpp0312589

429.9

3741

7.83

NP_001303335

ABI31023

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)

Crossreferences

InterPro - A database of protein families, domains and functional sites

Linkouts

Sequences Consistent with the Gene Model

Nucleotide / Polypeptide Records

UniProt

Q8I8U7

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.

Nipped-A_1

Linkouts

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

embryonic stage 1 -- 2

pole plasm

(Yatsu et al., 2008)

embryonic stage 4 -- 5

primordial germ cell

(Yatsu et al., 2008)

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

mass spectroscopy

Stage

Tissue/Position (including subcellular localization)

Reference

day 5 of adulthood & male -- day 7 of adulthood & male

spermatozoon

(Wasbrough et al., 2010)

day 7 of adulthood -- day 49 of adulthood

adult heart

(Cammarato et al., 2011)

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Evidence

References

located_in cytoplasm

inferred from direct assay

(Gause et al., 2006)

part_of histone acetyltransferase complex

inferred from direct assay

(assigned by UniProt )

(Kusch et al., 2003)

inferred from physical interaction with FLYBASE:pont; FB:FBgn0040078

(Kusch et al., 2004)

part_of NuA4 histone acetyltransferase complex

inferred from direct assay

(Kusch et al., 2004)

located_in nucleus

inferred from direct assay

(Weake et al., 2011, Gause et al., 2006, Guelman et al., 2006, Kusch et al., 2004)

located_in polytene chromosome puff

inferred from direct assay

(Gause et al., 2006)

located_in polytene chromosome

inferred from direct assay

(Gause et al., 2006)

part_of SAGA complex

inferred from direct assay

(Weake et al., 2011, Guelman et al., 2006)

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

View exonic expression by developmental stage for Dmel\Nipped-A

View exonic expression by tissue for Dmel\Nipped-A

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

DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species

35483/tissue=All

EMBL-EBI Single Cell Expression Atlas - Single cell expression across species

FBgn0053554

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0053554

FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data

FBgn0053554

Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns

Flygut - An atlas of the Drosophila adult midgut

FBgn0053554

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 72 )

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

Aberrations (Deficiencies and Duplications) ( 64 )

Inferred from experimentation ( 64 )

Gene disrupted in

Df(2R)Exel9021

(Ryder, 2004.4.26)

Df(2R)M41A4

(Duffy et al., 1996, Koryakov and Zhimulev, 1996, Eberl et al., 1993, Ganetzky, 1977, Hilliker, 1976)

Df(2R)M41A8

(Gambetta and Müller, 2009.8.18, Myster et al., 2004, Rollins et al., 1999, Koryakov and Zhimulev, 1996)

Df(2R)M41A10

(Gambetta and Müller, 2009.8.18, Myster et al., 2004, Rollins et al., 1999, Duffy et al., 1996, Koryakov and Zhimulev, 1996, Eberl et al., 1993, Sharp et al., 1985, Ganetzky, 1977, Hilliker, 1976)

Df(2R)nap1

(Gambetta and Müller, 2009.8.18, Myster et al., 2004)

Df(2R)nap4

(Gambetta and Müller, 2009.8.18)

Df(2R)nap8

(Gambetta and Müller, 2009.8.18)

Df(2R)NC13

(Myster et al., 2004, Myster and Peifer, 2003.9.11)

Df(2R)NC31

(Sinclair et al., 2009)

Df(2R)NC50

(Myster et al., 2004)

Df(2R)NC68

(Myster et al., 2004)

Df(2R)NC125

(Myster et al., 2004)

Df(2R)NC167

(Myster et al., 2004)

Df(2R)NC191

(Myster et al., 2004)

Df(2R)NC202

(Myster et al., 2004)

Df(2R)NC218

(Myster et al., 2004)

Df(2R)NC228

(Myster et al., 2004, Myster and Peifer, 2003.9.11)

Df(2R)Nipped-C160.1

(Rollins et al., 1999)

Df(2R)Nipped-D263.3

(Rollins et al., 1999)

Df(2R)Nipped-D341.1

(Rollins et al., 1999)

Df(2R)Nipped-D

(Myster et al., 2004)

Df(2R)Nipped-E43

(Gause et al., 2006, Rollins et al., 1999)

Df(2R)Nipped-E299.1

(Rollins et al., 1999)

Df(2R)Nipped-E338

(Rollins et al., 1999)

T(2;3)Nipped-A^394.2

(Rollins et al., 1999)

T(2;3)Nipped-C138.2

(Rollins et al., 1999)

Gene not disrupted in

Df(2R)244

(Myster et al., 2004)

Df(2R)247

(Myster et al., 2004)

Df(2R)B

(Ganetzky, 1977, Hilliker, 1976)

Df(2R)Dark2

(Myster et al., 2004)

Df(2R)M41A2

(Myster et al., 2004)

Df(2R)nap11

(Gambetta and Müller, 2009.8.18)

Df(2R)NC32

(Gambetta and Müller, 2009.8.18, Myster et al., 2004)

Df(2R)NC73

(Myster et al., 2004)

Df(2R)NC98

(Myster et al., 2004)

Df(2R)NC168

(Myster et al., 2004)

Df(2R)NC195

(Myster et al., 2004)

Df(2R)NC207

(Myster et al., 2004)

Df(2R)NC219

(Myster et al., 2004)

Df(2R)NC1198

(Myster et al., 2004)

Df(2R)PR50

(Eberl et al., 1993)

Df(2R)PRB

(Eberl et al., 1993)

Df(2R)PRF

(Eberl et al., 1993)

Df(2R)rl-1G

(Ganetzky, 1977, Hilliker, 1976)

Df(2R)rl-2J

(Ganetzky, 1977, Hilliker, 1976)

Df(2R)rl-4J

(Ganetzky, 1977, Hilliker, 1976)

Df(2R)rl-5B

(Ganetzky, 1977, Hilliker, 1976)

Df(2R)rl-6C

(Ganetzky, 1977, Hilliker, 1976)

Df(2R)rl-9B

(Hilliker, 1976)

Df(2R)rl-10G

(Rollins et al., 1999, Ganetzky, 1977, Hilliker, 1976)

Df(2R)rl-12E

(Ganetzky, 1977, Hilliker, 1976)

Df(2R)rl-13D

(Ganetzky, 1977, Hilliker, 1976)

Df(2R)rl-14C

(Ganetzky, 1977, Hilliker, 1976)

(Hilliker, 1976)

(Hilliker, 1976)

(Hilliker, 1976)

(Ganetzky, 1977, Hilliker, 1976)

(Hilliker, 1976)

(Ganetzky, 1977)

(Ganetzky, 1977)

(Ganetzky, 1977)

(Dimitri, 1991)

Ts(Y;2Lt)C+Ts(Y;2Rt)A

(Dimitri, 1991)

Gene partially disrupted in

Df(2R)Nipped-A^C25

(Rollins et al., 1999)

Inferred from location ( 0 )

Alleles Representing Disease-Implicated Variants

Phenotypes

For more details about a specific phenotype click on the relevant allele symbol.

Lethality

Allele

lethal

lethal (with Df(2R)BSC630)

Nipped-A^{MI10513-TG4.0}

lethal | recessive

lethal - all die before end of larval stage | recessive

lethal - all die before end of pupal stage, with Scer\GAL4^pnr-MD237

Nipped-A^GD15595

lethal - all die before end of second instar larval stage (with Df(2R)Nipped-E43)

lethal - all die during embryonic stage | recessive

partially lethal | recessive

Nipped-A²²

viable, with Dcr-2^UAS.cDa, Scer\GAL4^elav.PLu

Nipped-A^GD15595

viable, with Scer\GAL4^tin.CΔ4

Sterility

Allele

female sterile, with Scer\GAL4^{VP16.mat.αTub67C}

Nipped-A^GL00432

Other Phenotypes

Allele

abnormal flight, with Scer\GAL4^Mef2.PR

Nipped-A^GD15595

abnormal locomotor rhythm, with Scer\GAL4^Pdf.PU

Nipped-A^GD9847

abnormal locomotor rhythm | adult stage, with Scer\GAL4^Pdf.PU

abnormal locomotor rhythm | adult stage, with Scer\GAL4^tim.PE

abnormal neuroanatomy | larval stage

Nipped-A^GD9847

increased cell death | third instar larval stage

Nipped-A^NC96

melanotic mass phenotype, with Scer\GAL4^{SPARC-MI00329-GAL4}

Nipped-A^HMS00167

some die during embryonic stage | recessive

some die during larval stage | recessive

some die during pupal stage, with Scer\GAL4^pnr-MD237

Nipped-A^GD15595

some die during second instar larval stage (with Df(2R)Nipped-E43)

visible, with Scer\GAL4^pnr-MD237

Nipped-A^GD15595

Phenotype manifest in

Allele

embryo | maternal effect, with Scer\GAL4^{VP16.mat.αTub67C}

Nipped-A^GL00432

embryonic/larval brain | larval stage

Nipped-A^GD15595

fat body, with Scer\GAL4^{SPARC-MI00329-GAL4}

Nipped-A^HMS00167

ganglion mother cell | larval stage

Nipped-A^GD9847

imaginal disc | third instar larval stage

Nipped-A^NC96

larval neuroblast | larval stage

Nipped-A^GD9847

melanotic mass, with Scer\GAL4^{SPARC-MI00329-GAL4}

Nipped-A^HMS00167

mesothoracic tergum, with Scer\GAL4^pnr-MD237

Nipped-A^GD15595

myofibril, with Scer\GAL4^Mef2.PR

Nipped-A^GD15595

ocellus

trichogen cell, with Scer\GAL4^pnr-MD237

Nipped-A^GD15595

wing

Orthologs

Downloads

Download All DIOPT Orthologs

Human Orthologs (via DIOPT v8.0)

Homo sapiens (Human) (20)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Hsap\TRRAP

13 of 15

Yes

1 of 15

1 of 15

1 of 15

1 of 15

Yes

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

Yes

Hsap\SH3PXD2B

1 of 15

Yes

Hsap\SMG1

1 of 15

Model Organism Orthologs (via DIOPT v8.0)

Mus musculus (laboratory mouse) (17)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Mmus\Trrap

14 of 15

Yes

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

Yes

Mmus\Sh3pxd2b

1 of 15

Yes

Mmus\Smg1

1 of 15

Rattus norvegicus (Norway rat) (12)

Rnor\Trrap

2 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Xenopus tropicalis (Western clawed frog) (12)

Xtro\trrap

8 of 12

Yes

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

Danio rerio (Zebrafish) (17)

Drer\trrap

11 of 15

Yes

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

Yes

Drer\si:rp71-17i16.5

1 of 15

Drer\smg1

1 of 15

Drer\zgc:158659

1 of 15

Caenorhabditis elegans (Nematode, roundworm) (9)

Cele\trr-1

13 of 15

Yes

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

Arabidopsis thaliana (thale-cress) (2)

Atha\AT2G17930

7 of 9

Yes

Atha\AT4G36080

7 of 9

Yes

Saccharomyces cerevisiae (Brewer's yeast) (7)

Scer\TRA1

14 of 15

Yes

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

Schizosaccharomyces pombe (Fission yeast) (3)

Spom\tra1

11 of 12

Yes

Spom\tra2

10 of 12

Yes

Spom\tel1

1 of 12

Other Organism Orthologs (via OrthoDB)

Paralogs

Downloads

Download All DIOPT Paralogs

Paralogs (via DIOPT v8.0)

Drosophila melanogaster (Fruit fly) (10)

Gene Symbol

Score

Source

Alignment

3 of 10

3 of 10

Tor

3 of 10

tefu

2 of 10

CG30184

1 of 10

fwd

1 of 10

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 ( 1 )

Human Ortholog

Disease

Evidence

References

TRRAP; transformation/transcription domain associated protein

model of autosomal dominant nonsyndromic deafness 75

IEA

(FlyBase, 2019-)

Modifiers Based on Experimental Evidence ( 3 )

Allele

Disease

Interaction

References

Nipped-A^NC116

ameliorates autosomal dominant cerebellar ataxia

modeled by Hsap\ATXN7^{102Q.T.UAS.Tag:NLS(SV40-largeT)}

(Latouche et al., 2007)

exacerbates neurodegenerative disease

modeled by Hsap\HTT^Q93.ex1.UAS

(Zhang et al., 2010)

Nipped-A^NC186

exacerbates neurodegenerative disease

modeled by Hsap\HTT^Q93.ex1.UAS

(Zhang et al., 2010)

Nipped-A^GD9847

ameliorates brain cancer

modeled by l(3)mbt^ts1

(Rossi et al., 2017)

Disease Associations of Human Orthologs (via DIOPT v8.0 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?

TRRAP; transformation/transcription domain associated protein

13 of 15

603015

autosomal dominant nonsyndromic deafness 75

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

Interactions Browser

View in Interactions Browser

Please see the Physical Interaction reports below for full details

protein-protein

Physical Interaction

Assay

References

Nipped-A - Ada1-2

anti tag coimmunoprecipitation, peptide massfingerprinting

(Weake et al., 2009)

Nipped-A - Ada2b

anti tag coimmunoprecipitation, peptide massfingerprinting, anti bait coimmunoprecipitation, western blot

(Popova et al., 2018, Weake et al., 2011, Weake et al., 2009, Kusch et al., 2003)

Nipped-A - Ada3

anti bait coimmunoprecipitation, western blot

(Kusch et al., 2003)

Nipped-A - Atxn7

anti tag coimmunoprecipitation, peptide massfingerprinting

(Mohan et al., 2014)

Nipped-A - Brf

anti bait coimmunoprecipitation, western blot

(Popova et al., 2018)

Nipped-A - CG12054

anti tag coimmunoprecipitation, peptide massfingerprinting, experimental knowledge based

(Rhee et al., 2014)

Nipped-A - Clk

anti tag coimmunoprecipitation, Identification by mass spectrometry, anti tag western blot

(Mahesh et al., 2020)

Nipped-A - Gcn5

anti bait coimmunoprecipitation, western blot

(Popova et al., 2018, Kurshakova et al., 2009, Kurshakova et al., 2007, Kusch et al., 2003)

Nipped-A - Pbp45

anti bait coimmunoprecipitation, western blot

(Popova et al., 2018)

Nipped-A - Saf6

anti tag coimmunoprecipitation, peptide massfingerprinting

(Weake et al., 2009)

Nipped-A - Sf3b5

anti tag coimmunoprecipitation, peptide massfingerprinting

(Stegeman et al., 2016)

Nipped-A - Sgf29

anti tag coimmunoprecipitation, peptide massfingerprinting

(Weake et al., 2009)

Nipped-A - Spt20

anti tag coimmunoprecipitation, peptide massfingerprinting

(Stegeman et al., 2016)

Nipped-A - Spt3

anti tag coimmunoprecipitation, peptide massfingerprinting, anti bait coimmunoprecipitation, western blot

(Stegeman et al., 2016, Kusch et al., 2003)

Nipped-A - Tip60

anti bait coimmunoprecipitation, western blot

(Kusch et al., 2004)

Nipped-A - Tti1

anti tag coimmunoprecipitation, peptide massfingerprinting

(Glatter et al., 2011)

Nipped-A - e(y)2

anti bait coimmunoprecipitation, western blot

(Kurshakova et al., 2009, Kurshakova et al., 2007)

Nipped-A - pont

anti tag coimmunoprecipitation, peptide massfingerprinting, western blot

(Kusch et al., 2004)

Nipped-A - wda

anti tag coimmunoprecipitation, peptide massfingerprinting

(Weake et al., 2009)

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

Chi

enhanceable

Nipped-A

(Rollins et al., 1999)

enhanceable

Nipped-A

(Rollins et al., 1999)

ct|su(Hw)

enhanceable

Nipped-A

(Rollins et al., 1999)

dom

enhanceable

Nipped-A

(Kwon et al., 2013)

mam

enhanceable

Nipped-A

(Gause et al., 2006, Rollins et al., 1999)

enhanceable

Nipped-A

(Gause et al., 2006, Rollins et al., 1999)

suppressible

Nipped-A

(Gause et al., 2006, Rollins et al., 1999)

run

enhanceable

Nipped-A

(Duffy et al., 1996)

enhanceable

Nipped-A

(Rollins et al., 1999)

External Data

Subunit Structure (UniProtKB)

(UniProt, Q8I8U7 )

Linkouts

BioGRID - A database of protein and genetic interactions.

61398

DroID - A comprehensive database of gene and protein interactions.

FBgn0053554

MIST (genetic) - An integrated Molecular Interaction Database

Nipped-A

MIST (protein-protein) - An integrated Molecular Interaction Database

Nipped-A

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

External Data

Linkouts

Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

2-55

Cytogenetic map

41E1-41E3

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

41A-41A

(Dorsett, 1999.3.3)

Experimentally Determined Recombination Data

Location

2-55

(FlyBase, 2016)

2-55.5

(Comeron et al., 2012)

(Rollins et al., 1998, Rollins et al., 1997)

2-55.1

Left of (cM)

(Dorsett, 1999.3.3)

Right of (cM)

RpL38

(Dorsett, 1999.3.3)

Notes

Stocks and Reagents

Stocks (14)

Aberrations including deletions of this gene Aberrations including duplications of this gene

Bloomington

31255

y¹ v¹; P{TRiP.JF01196}attP2

16514

y¹; P{SUPor-P}Nipped-A^KG10162/CyO

30971

y¹ w^*; Mi{MIC}Nipped-A^MI00364/CyO

37234

y¹ w^*; Mi{MIC}Nipped-A^MI04079/SM6a

54566

y¹ w^*; Mi{MIC}Nipped-A^MI10513/SM6a

91657

w^*; TI{TI}Nipped-A^HA; TM2/TM6B, Tb¹

76723

y¹ w^*; Mi{Trojan-GAL4.0}Nipped-A^{MI10513-TG4.0}

35595

y¹ sc^* v¹ sev²¹; P{TRiP.GL00432}attP2

34849

y¹ sc^* v¹ sev²¹; P{TRiP.HMS00167}attP2

65337

y¹ w^*; Mi{PT-GFSTF.0}Nipped-A^{MI10513-GFSTF.0}/CyO

VDRC

v52486

w¹¹¹⁸ P{GD9847}v52486

v40789

w¹¹¹⁸; P{GD15595}v40789/TM3

More stocks available...

Genomic Clones (28)

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

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 sequenced

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.

FBgn0053554

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0053554

GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents

35483

Antibody Information

Laboratory Generated Antibodies

polyclonal

(Gause et al., 2006, Kusch et al., 2003)

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

(Dorsett, 1999.3.3)

Source for merge of: Nipped-A Tra1

(Myster et al., 2004)

Source for merge of: Tra1 CG2905 CG10549

(FlyBase, 1996-)

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.

(FlyBase Genome Annotators, 2005)

'Nipped' mutations disrupt one or more of four recessive lethal complementation groups: l(2)41Ae, RpL38, Nipped-A and Nipped-B.

(Rollins et al., 1999)

Source for merge of Tra1 CG2905 CG10549 was sequence comparison ( date:030120 ).

(FlyBase, 1996-)

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.

(Marr et al., 2006)

S2 cells treated with dsRNA generated against this gene show reduced phagocytosis of Candida albicans compared to untreated cells.

(Stroschein-Stevenson et al., 2006)

dsRNA directed against this gene causes defects in cytokinesis when tested in an RNAi screen in S2 cells.

(Echard et al., 2004)

CG10549 was eliminated in release 3 of the genome annotation, January 2003.

(FlyBase Genome Annotators, 2002-2003)

'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.

(Rollins et al., 1999)

Nipped-A influences N receptor signalling or N expression during development of the wing margin and wing veins.

(Rollins et al., 1999)

The Nipped-group genes regulate ct and Ubx.

(Rollins et al., 1997)

Nipped-A acts as a dosage sensitive maternal modifier of run.

(Duffy et al., 1996)

Nipped-A locus exhibits high EMS mutability and the lethal alleles exhibit a complex interallelic complementation.

(Hilliker, 1976)

Origin and Etymology

Discoverer

Etymology

Identification

External Crossreferences and Linkouts ( 54 )

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.

35483

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/GCRP - The gene-centric reference proteome (GCRP) provides a 1:1 mapping between genes and UniProt accessions in which a single 'canonical' isoform represents the product(s) of each protein-coding gene.

Q8I8U7

UniProt/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information

Q8I8U7

Other crossreferences

AlphaFold DB - AlphaFold provides open access to protein structure predictions for the human proteome and other key proteins of interest, to accelerate scientific research.

Q8I8U7

Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones

FBgn0053554

DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species

35483/tissue=All

EMBL-EBI Single Cell Expression Atlas - Single cell expression across species

FBgn0053554

Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.

Nipped-A_1

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0053554

FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data

FBgn0053554

Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns

Flygut - An atlas of the Drosophila adult midgut

FBgn0053554

GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents

35483

iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)

TC033331

InterPro - A database of protein families, domains and functional sites

KEGG Genes - Molecular building blocks of life in the genomic space.

Dmel_CG33554

MARRVEL_MODEL - MARRVEL (model organism gene)

35483

modMine - A data warehouse for the modENCODE project

FBgn0053554

SignaLink - A signaling pathway resource with multi-layered regulatory networks.

Q8I8U7

Linkouts

BioGRID - A database of protein and genetic interactions.

61398

DroID - A comprehensive database of gene and protein interactions.

FBgn0053554

DRSC - Results frm RNAi screens

FBgn0053554

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0053554

FlyMine - An integrated database for Drosophila genomics

FBgn0053554

Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution

Interactive Fly

MIST (genetic) - An integrated Molecular Interaction Database

Nipped-A

MIST (protein-protein) - An integrated Molecular Interaction Database

Nipped-A

Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.

Synonyms and Secondary IDs (25)

Reported As

Symbol Synonym

41Ah

(Dimitri et al., 2005, Cenci et al., 2003, Dimitri et al., 2003)

CG10549

CG2905

(Christis and Munro, 2012, Hughes et al., 2008, Miranda-Saavedra and Barton, 2007, Dimitri et al., 2005, Bartolome and Maside, 2004, Kusch et al., 2004, Myster et al., 2004, Song et al., 2004, Corradini et al., 2003)

CG33554

(Çiçek et al., 2016, Stegeman et al., 2016, Hosono et al., 2015, Mohan et al., 2014, Cammarato et al., 2011, Glatter et al., 2011, Ni et al., 2011.7.19, Ni et al., 2008, Panhuis and Swanson, 2006, FlyBase Genome Annotators, 2005)

DmTrrap

(Elías-Villalobos et al., 2019)

GroupV

(Ganetzky, 1977, Hilliker, 1976)

Nip-A

(Somma et al., 2008)

NipA

(Gause et al., 2006)

Nipped A

(Palomera-Sanchez et al., 2010)

Nipped-A

(Baker et al., 2021, Cornelio-Parra et al., 2021, Helmlinger et al., 2021, Srikanta and Cermakian, 2021, Torres-Zelada and Weake, 2021, Vidaurre and Chen, 2021, Yang et al., 2021, Mahesh et al., 2020, Bailetti et al., 2019, Elías-Villalobos et al., 2019, Saha and Mishra, 2019, Tiwari et al., 2019, Lee et al., 2018, McCarthy et al., 2018, Rust et al., 2018, Branco et al., 2017, Rossi et al., 2017, Tauc et al., 2017, Gene Disruption Project members, 2016-, Lefebvre et al., 2016, Sanchez et al., 2016, Stegeman et al., 2016, Gene Disruption Project members, 2015-, Zang et al., 2015, Ashwal-Fluss et al., 2014, Sopko et al., 2014, Westholm et al., 2014, Kwon et al., 2013, Neumüller et al., 2013, Vaque et al., 2013, Di Stefano et al., 2011, Neumüller et al., 2011, Rees et al., 2011, Roy et al., 2011, Coulthard et al., 2010, Mourikis et al., 2010, Wasbrough et al., 2010, Zhang et al., 2010, Sackton et al., 2009, Yasuhara and Wakimoto, 2008, Yin et al., 2008, Zhou et al., 2008, Rossi et al., 2007, Roy et al., 2007)

Nipped^A

(Yedvobnick et al., 2001)

TRA1

(Kwon et al., 2013, Bouazoune and Brehm, 2006)

TRRAP

(Popova et al., 2018, Kurshakova et al., 2009, Lebedeva et al., 2007, Ullah et al., 2007, Gause et al., 2006, Stadeli, 2006, Lebedeva, 2005, Lebedeva et al., 2005)

Tra-1

(Greil et al., 2003)

Tra1

(Stegeman et al., 2016, Mohan et al., 2014, Spedale et al., 2012, Weake et al., 2011, Clapier and Cairns, 2009, Rodriguez-Navarro, 2009, Weake et al., 2009, Yatsu et al., 2008, Latouche et al., 2007, Gause et al., 2006, Guelman et al., 2006, Marr et al., 2006, Stroschein-Stevenson et al., 2006)

dTRRAP

(Sanchez et al., 2016, Mohan et al., 2010, Kurshakova et al., 2007)

dTra1

(Spedale et al., 2012, Latouche et al., 2007, Raisner and Madhani, 2006, Jin, 2005, Kusch et al., 2004, Kusch et al., 2004, Kusch et al., 2003)

dmTRRAP

(Lebedeva, 2005, Lebedeva et al., 2005)

l(2)41Ah

(Corradini et al., 2003, Dimitri et al., 2003, Rollins et al., 1999)

l(2)C123

l(2)EMS34-12

(Eberl et al., 1993)

tra1

(Zhang et al., 2010, Echard et al., 2004)

Name Synonyms

Nipped

(Rollins et al., 1997)

Nipped-A

(Cammarato et al., 2011, Mohan et al., 2010, Gambetta and Müller, 2009.8.18, Bakal et al., 2008, Sathyanarayanan et al., 2008, Yasuhara and Wakimoto, 2008, Roy et al., 2007, Gause et al., 2006)

NippedA

(Somma et al., 2008)

lethal(2)41Ah

Secondary FlyBase IDs

FBan0002905
FBtr0086095
FBan0033554
FBgn0002067
FBgn0002172
FBgn0004661
FBgn0020393
FBgn0033013
FBgn0039989

Datasets (8)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (8)

Result

Result Type

Title

scRNAseq_2020_Cattenoz_NI_seq_clustering

cell clustering analysis

Clustering analysis of hemocytes from non-infested third instar larvae

scRNAseq_2020_Cattenoz_WI_seq_clustering

cell clustering analysis

Clustering analysis of hemocytes from wasp-infested third instar larvae

scRNAseq_2020_Cho_NI72LG_seq_clustering

cell clustering analysis

Clustering analysis of lymph gland cells from non-infested larvae at 72 h after egg-laying

scRNAseq_2020_Cho_NI96LG_seq_clustering

cell clustering analysis

Clustering analysis of lymph gland cells from non-infested larvae at 96 h after egg-laying

scRNAseq_2020_Cho_NI120LG_seq_clustering

cell clustering analysis

Clustering analysis of lymph gland cells from non-infested larvae at 120 h after egg-laying

scRNAseq_2020_Cho_WI96LG_seq_clustering

cell clustering analysis

Clustering analysis of lymph gland cells from wasp-infested larvae at 96 h after egg-laying

scRNAseq_2020_Cho_NI96HL_seq_clustering

cell clustering analysis

Clustering analysis of circulating hemocytes from non-infested larvae at 96 h after egg-laying

scRNAseq_2020_Cho_NI120HL_seq_clustering

cell clustering analysis

Clustering analysis of circulating hemocytes from non-infested larvae at 120 h after egg-laying

References (167)

The following external sites may use different assemblies or annotations than FlyBase.

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