FlyBase Gene Report: Dmel\Nup98-96

General Information

Symbol

Dmel\Nup98-96

Species

D. melanogaster

Name

Nucleoporin 98-96kD

Annotation Symbol

CG10198

Feature Type

protein_coding_gene

FlyBase ID

FBgn0039120

Gene Model Status

Current

Stock Availability

17 publicly available

Gene Summary

Nucleoporin 98-96kD (Nup98-96) encodes a precursor protein that is cleaved into Nup98 and Nup96 proteins, two integral parts of the nuclear pore. In the male gonad, loss of Nup98-96 function results in premature differentiation of germ line cells at the expense of proliferation. [Date last reviewed: 2019-03-14] (FlyBase Gene Snapshot)

All Summaries

Gene Snapshot
Alliance
Auto summary
Gene Group
UniProtKB
Interactive Fly

Also Known As

Nup98, Nup96, l(3)95BCd, Nucleoporin 98

Key Links

Genomic Location

Cytogenetic map

95B1-95B5

Sequence location

3R:23,774,225..23,781,621 [-]

Recombination map

3-80

RefSeq locus

NT_033777 REGION:23774225..23781621

Sequence

Get Decorated FASTA

Genomic Maps

JBrowse

Other Genome Views

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

Function

Gene Ontology (GO) Annotations (33 terms)

Molecular Function (8 terms)

Terms Based on Experimental Evidence (5 terms)

CV Term

Evidence

References

enables chromatin DNA binding

inferred from mutant phenotype

(Kalverda et al., 2010)

inferred from direct assay

(Ilyin et al., 2017, Pascual-Garcia et al., 2017)

enables promoter-enhancer loop anchoring activity

inferred from mutant phenotype

(Pascual-Garcia et al., 2017)

enables promoter-specific chromatin binding

inferred from direct assay

(Pascual-Garcia et al., 2017, Pascual-Garcia et al., 2014)

enables protein binding

inferred from physical interaction with UniProtKB:Q9W2E7

(Kristó et al., 2017)

inferred from physical interaction with UniProtKB:A1Z8P9

(Pascual-Garcia et al., 2017)

inferred from physical interaction with UniProtKB:P08970

(Pascual-Garcia et al., 2017)

inferred from physical interaction with UniProtKB:P34021

(Pascual-Garcia et al., 2017)

inferred from physical interaction with UniProtKB:Q08605

(Pascual-Garcia et al., 2017)

inferred from physical interaction with UniProtKB:Q24478

(Pascual-Garcia et al., 2017)

inferred from physical interaction with UniProtKB:Q9VS55

(Pascual-Garcia et al., 2017)

inferred from physical interaction with UniProtKB:Q9VKJ3

(Tang and Presgraves, 2009)

inferred from physical interaction with UniProtKB:P20659

(Pascual-Garcia et al., 2014)

inferred from physical interaction with UniProtKB:Q86BS3,UniProtKB:Q9VGA4,UniProtKB:Q9VP57

(Pascual-Garcia et al., 2014)

inferred from physical interaction with UniProtKB:Q9V3J8

(Pascual-Garcia et al., 2014)

enables serine hydrolase activity

inferred from high throughput direct assay

(Kumar et al., 2021)

Terms Based on Predictions or Assertions (3 terms)

CV Term

Evidence

References

enables nuclear localization sequence binding

inferred from biological aspect of ancestor with PANTHER:PTN000574450

(GO Reference Genome Project, 2011-)

enables RNA binding

inferred from biological aspect of ancestor with PANTHER:PTN000574450

(GO Reference Genome Project, 2011-)

enables structural constituent of nuclear pore

inferred from electronic annotation with InterPro:IPR007230

(InterPro Project Members, 2004-)

inferred from biological aspect of ancestor with PANTHER:PTN000574450

(GO Reference Genome Project, 2011-)

inferred from sequence or structural similarity with SGD:S000001551

(Gene Ontology Curators, 2002-)

Biological Process (14 terms)

Terms Based on Experimental Evidence (11 terms)

CV Term

Evidence

References

involved_in cellular response to ecdysone

inferred from direct assay

(Kalverda et al., 2010)

involved_in cellular response to heat

inferred from mutant phenotype

(Capelson et al., 2010)

involved_in heat shock-mediated polytene chromosome puffing

inferred from direct assay

(Kalverda et al., 2010)

involved_in host-mediated suppression of viral transcription

inferred from mutant phenotype

(Panda et al., 2014)

involved_in positive regulation of defense response to virus by host

inferred from mutant phenotype

(Panda et al., 2014)

involved_in positive regulation of transcription by RNA polymerase II

inferred from mutant phenotype

(Panda et al., 2014, Pascual-Garcia et al., 2014, Capelson et al., 2010, Kalverda et al., 2010)

involved_in positive regulation of transcription initiation by RNA polymerase II

inferred from mutant phenotype

(Capelson et al., 2010)

involved_in protein import into nucleus

inferred from mutant phenotype

(Chen and Xu, 2010)

involved_in regulation of nucleocytoplasmic transport

inferred from mutant phenotype

(Wu et al., 2019)

involved_in response to ecdysone

inferred from direct assay

(Pascual-Garcia et al., 2017)

involved_in RNA export from nucleus

inferred from mutant phenotype

(Kristó et al., 2017)

Terms Based on Predictions or Assertions (4 terms)

CV Term

Evidence

References

involved_in nucleocytoplasmic transport

inferred from electronic annotation with InterPro:IPR007230

(InterPro Project Members, 2004-)

involved_in post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery

inferred from biological aspect of ancestor with PANTHER:PTN000574450

(GO Reference Genome Project, 2011-)

involved_in protein import into nucleus

inferred from biological aspect of ancestor with PANTHER:PTN000574450

(GO Reference Genome Project, 2011-)

involved_in telomere tethering at nuclear periphery

inferred from biological aspect of ancestor with PANTHER:PTN000574450

(GO Reference Genome Project, 2011-)

Cellular Component (11 terms)

Terms Based on Experimental Evidence (7 terms)

CV Term

Evidence

References

located_in chromatin

inferred from direct assay

(Pascual-Garcia et al., 2014, Capelson et al., 2010)

inferred from mutant phenotype

(Capelson et al., 2010, Kalverda et al., 2010)

located_in cytoplasm

inferred from direct assay

(Panda et al., 2014)

part_of nuclear pore

inferred from direct assay

(Panda et al., 2014)

inferred from physical interaction with FLYBASE:Rae1; FB:FBgn0034646

(Tian et al., 2011)

located_in nucleus

inferred from direct assay

(Pascual-Garcia et al., 2017, Panda et al., 2014)

inferred from mutant phenotype

(Kalverda et al., 2010)

located_in polytene chromosome band

inferred from direct assay

(Kalverda et al., 2010)

located_in polytene chromosome puff

inferred from direct assay

(Capelson et al., 2010)

inferred from mutant phenotype

(Capelson et al., 2010)

located_in polytene chromosome

inferred from direct assay

(Pascual-Garcia et al., 2014)

Terms Based on Predictions or Assertions (5 terms)

CV Term

Evidence

References

located_in chromosome

inferred from experiment

(Capelson et al., 2010)

located_in nuclear membrane

inferred from experiment

(Panda et al., 2014, Capelson et al., 2010)

part_of nuclear pore central transport channel

inferred from sequence or structural similarity with SGD:S000001551

(Gene Ontology Curators, 2002-)

part_of nuclear pore cytoplasmic filaments

inferred from biological aspect of ancestor with PANTHER:PTN000574450

(GO Reference Genome Project, 2011-)

part_of nuclear pore

inferred from electronic annotation with InterPro:IPR007230, InterPro:IPR037665

(InterPro Project Members, 2004-)

Gene Group (FlyBase)

NUCLEAR PORE COMPLEX

Protein Family (UniProt)

Belongs to the nucleoporin GLFG family. (Q9VCH5)

Protein Signatures (InterPro)

Summaries

Gene Snapshot

Gene Group (FlyBase)

NUCLEAR PORE COMPLEX -: The Nuclear Pore Complex (NPC) is a large protein complex embedded in the nuclear membrane that facilitates nucleocytoplasmic traffic. The NPC is composed of approximately 30 different proteins: the nucleoporins. The NPC displays 8-fold symmetry and each nucleoporin is present in multiple copies. From the central ring that forms the pore, filaments protrude into the cytoplasm (cytoplasmic filaments) and the nucleoplasm (nuclear basket). Many nucleoporins contain FG repeats which are thought to act as a diffusion barrier and docking sight for transport receptors (karyopherins). Export and import is controlled by the interaction of the karyopherins with localization and export sequences. (Adapted from FBrf0220062 and PMID:21495847).

Protein Function (UniProtKB)

Part of the nuclear pore complex (NPC) (PubMed:25197089). Required for MAD import as part of the Nup107-160 complex and required for nuclear export of Moe probably via its association with Rae1 (PubMed:20547758, PubMed:28554770). Plays a role in nuclear mRNA export (PubMed:28554770). Promotes cell antiviral response by up-regulating FoxK-dependent antiviral gene transcription (PubMed:25197089, PubMed:25852164). In germline stem cells, involved in their maintenance and division together with the TGF-Beta and EGFR signaling pathways (PubMed:21949861). In larval lymph glands, has a role in the maintenance of hematopoiesis by regulating Pvr expression (PubMed:25201876).

(UniProt, Q9VCH5)

Summary (Interactive Fly)

transcriptional regulator - viral-induced primary response gene - lymph gland hematopoietic development

Interactive Fly

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\Nup98-96 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

Protein 3D structure (Predicted by AlphaFold) (AlphaFold entry Q9VCH5)

If you don't see a structure in the viewer, 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.

Experimentally Determined Structures

Crossreferences

Comments on Gene Model

The larger Nup98-RA transcript encodes a single, large precursor polyprotein that, in other eukaryotes, and thus presumably in flies, autoproteolytically cleaves itself between residues Phe1028 and Ser1029, yielding separate Nup98 and Nup96 proteins (FBrf0159638).

Gene model reviewed during 5.41

Gene model reviewed during 5.47

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

Nup98-96-RA

FBtr0084460

NM_142930

6624

1960

Nup98-96-RC

FBtr0304567

NM_001260337

3987

1179

Nup98-96-RD

FBtr0334894

NM_001275956

6412

1960

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

UniProt

RefSeq ID

GenBank

Nup98-96-PA

FBpp0083851

210.1

1960

6.50

FBpp0293109

121.6

1179

6.47

FBpp0306915

210.1

1960

6.50

Q9VCH5

NP_001262885

AGB96265

Polypeptides with Identical Sequences

The group(s) of polypeptides indicated below share identical sequence to each other.

1960 aa isoforms: Nup98-96-PA, Nup98-96-PD

Additional Polypeptide Data and Comments

Reported size (kDa)

Comments

External Data

Subunit Structure (UniProtKB)

Part of the nuclear pore complex (NPC) (PubMed:25310983). Interacts with Rae1 (PubMed:21874015, PubMed:28554770). Nuclear pore complex protein Nup98: Interacts with pzg and Chro (PubMed:25310983). Interacts with MBD-R2; the interaction allows Nup98 recruitment to chromatin (PubMed:25310983). Interacts with Trx (PubMed:25310983). Interacts with Wds (PubMed:25310983). Interacts with Mgtor and Cp190 (PubMed:28366641). Upon ecdysone stimulation, interacts with EcR, CTCF, su(Hw) and Trl (PubMed:28366641).

(UniProt, Q9VCH5)

Post Translational Modification

Isoform A and isoform C are autoproteolytically cleaved to yield Nup98 and Nup96 or Nup98 only, respectively.

(UniProt, Q9VCH5)

Domain

Contains FG repeats. FG repeats are interaction sites for karyopherins (importins, exportins) and form probably an affinity gradient, guiding the transport proteins unidirectionally with their cargo through the NPC. FG repeat regions are highly flexible and lack ordered secondary structure. The overall conservation of FG repeats regarding exact sequence, spacing, and repeat unit length is limited.

(UniProt, Q9VCH5)

Crossreferences

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

Linkouts

Sequences Consistent with the Gene Model

Nucleotide / Polypeptide Records

UniProt

Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\Nup98-96 using the Feature Mapper tool.

External Data

Crossreferences

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

Linkouts

Expression Data

Testis-specificity index

The testis specificity index was calculated from modENCODE tissue expression data by Vedelek et al., 2018 to indicate the degree of testis enrichment compared to other tissues. Scores range from -2.52 (underrepresented) to 5.2 (very high testis bias).

0.46

Transcript Expression

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

immunolocalization

Stage

Tissue/Position (including subcellular localization)

Reference

adult stage | male & spermatogenesis

cyst progenitor cell

(Chen et al., 2013)

male germline stem cell

(Chen et al., 2013)

mass spectroscopy

Stage

Tissue/Position (including subcellular localization)

Reference

adult stage

adult head

• membrane

(Aradska et al., 2015)

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Evidence

References

located_in chromatin

inferred from direct assay

(Pascual-Garcia et al., 2014, Capelson et al., 2010)

inferred from mutant phenotype

(Capelson et al., 2010, Kalverda et al., 2010)

located_in cytoplasm

inferred from direct assay

(Panda et al., 2014)

part_of nuclear pore

inferred from direct assay

(Panda et al., 2014)

inferred from physical interaction with FLYBASE:Rae1; FB:FBgn0034646

(Tian et al., 2011)

located_in nucleus

inferred from direct assay

(Pascual-Garcia et al., 2017, Panda et al., 2014)

inferred from mutant phenotype

(Kalverda et al., 2010)

located_in polytene chromosome band

inferred from direct assay

(Kalverda et al., 2010)

located_in polytene chromosome puff

inferred from direct assay

(Capelson et al., 2010)

inferred from mutant phenotype

(Capelson et al., 2010)

located_in polytene chromosome

inferred from direct assay

(Pascual-Garcia et al., 2014)

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\Nup98-96 in JBrowse

RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region

View exonic expression by developmental stage for Dmel\Nup98-96

View exonic expression by tissue for Dmel\Nup98-96

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

42816/tissue=All

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

FBgn0039120

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0039120

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

FBgn0039120

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

CG10198

Flygut - An atlas of the Drosophila adult midgut

FBgn0039120

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 11 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 11 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of Nup98-96

Transgenic constructs containing regulatory region of Nup98-96

Aberrations (Deficiencies and Duplications) ( 15 )

Inferred from experimentation ( 15 )

Gene not disrupted in

Df(3R)CA2

(Erickson et al., 1997)

Df(3R)CA

(Presgraves et al., 2003, Keller et al., 1998)

Df(3R)nau-4A

(Presgraves et al., 2003, Keller et al., 1998)

Df(3R)nau-11a4

(Presgraves et al., 2003, Keller et al., 1998)

Inferred from location ( 7 )

Variants

Variant Molecular Consequences

Alleles Representing Disease-Implicated Variants

Phenotypes

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

Lethality

Allele

lethal, with Scer\GAL4^pnr-MD237

Nup98-96^GD6897

lethal | recessive

Nup98-96³³⁹

lethal - all die during P-stage, with Scer\GAL4^Mef2.PR

Nup98-96^GD6897

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

Nup98-96^GD6897

viable, with Scer\GAL4^tin.CΔ4

Nup98-96^GD6897

Other Phenotypes

Allele

abnormal neuroanatomy | third instar larval stage, with Hsim\VP16^AD.nrv2, Scer\GAL4^{DBD.wrapper.932i}

short lived | heat sensitive, with Scer\GAL4^tin.CΔ4

Nup98-96^GD6897

Phenotype manifest in

Allele

embryonic/larval cell body glial cell | third instar larval stage, with Hsim\VP16^AD.nrv2, Scer\GAL4^{DBD.wrapper.932i}

embryonic/larval lymph gland, with Scer\GAL4^HCH.Hand, Scer\GAL4^Hml.Δ

Nup98-96^NIG.10198R

embryonic/larval lymph gland, with Scer\GAL4^Hml.Δ

Nup98-96^NIG.10198R

female fusome

Nup98-96²²⁸⁸

female fusome (with Df(3R)mbc-R1)

Nup98-96²²⁸⁸

female germline cell | adult stage (with Df(3R)mbc-R1)

Nup98-96²²⁸⁸

male fusome | adult stage (with Df(3R)mbc-R1)

Nup98-96²²⁸⁸

male fusome | third instar larval stage (with Df(3R)mbc-R1)

Nup98-96²²⁸⁸

male germline cell, with Scer\GAL4^{VP16.nanos.UTR}

Nup98-96^GD6897

male germline cell | adult stage (with Df(3R)mbc-R1)

Nup98-96²²⁸⁸

male germline stem cell | third instar larval stage (with Df(3R)mbc-R1)

Nup98-96²²⁸⁸

nurse cell spectrosome

Nup98-96²²⁸⁸

nurse cell spectrosome (with Df(3R)mbc-R1)

Nup98-96²²⁸⁸

primary gonial cell | third instar larval stage (with Df(3R)mbc-R1)

Nup98-96²²⁸⁸

spermatogonium | third instar larval stage (with Df(3R)mbc-R1)

Nup98-96²²⁸⁸

Orthologs

Downloads

Download All DIOPT Orthologs

Human Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Homo sapiens (Human) (4)

Hsap\NUP98

14 of 14

Yes

Hsap\NCOA5

1 of 14

Hsap\NUP54

1 of 14

Hsap\NUP58

1 of 14

Model Organism Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Rattus norvegicus (Norway rat) (5)

Rnor\Nup98

14 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

Mus musculus (laboratory mouse) (4)

Mmus\Nup98

13 of 14

Yes

Mmus\Ncoa5

1 of 14

Mmus\Nup54

1 of 14

Mmus\Nupl1

1 of 14

Xenopus tropicalis (Western clawed frog) (5)

Xtro\nup98

8 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

Danio rerio (Zebrafish) (4)

Drer\nup98

14 of 14

Yes

Drer\nup54

1 of 14

Drer\nup58

1 of 14

Drer\si:ch211-216l23.2

1 of 14

Caenorhabditis elegans (Nematode, roundworm) (7)

Cele\npp-10

12 of 14

Yes

2 of 14

2 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Yes

Anopheles gambiae (African malaria mosquito) (6)

Agam\AgaP_AGAP002351

12 of 12

Yes

Agam\AgaP_AGAP008772

2 of 12

Agam\AgaP_AGAP006031

1 of 12

Agam\AgaP_AGAP006897

1 of 12

Yes

Agam\AgaP_AGAP007689

1 of 12

Agam\AgaP_AGAP010978

1 of 12

Arabidopsis thaliana (thale-cress) (5)

Atha\AT1G10390

10 of 13

Yes

Atha\AT1G59660

10 of 13

Yes

Atha\SAR3

9 of 13

Yes

Atha\AT1G63540

1 of 13

Yes

Atha\NUP1

1 of 13

Yes

Saccharomyces cerevisiae (Brewer's yeast) (6)

Scer\NUP145

11 of 13

Yes

Scer\NUP100

6 of 13

Yes

Scer\NUP116

6 of 13

Yes

Scer\NUP49

2 of 13

Scer\NUP42

1 of 13

Yes

Scer\NUP57

1 of 13

Schizosaccharomyces pombe (Fission yeast) (4)

Spom\nup189

11 of 12

Yes

Spom\nup45

2 of 12

Spom\amo1

1 of 12

Spom\nup44

1 of 12

Escherichia coli (enterobacterium) (0)

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:Nup98-96. Refer to their site for version information.

Paralogs

Downloads

Download All DIOPT Paralogs

Paralogs (via DIOPT v9.1)

Gene Symbol

Score

Source

Alignment

Drosophila melanogaster (Fruit fly) (7)

Nup58

2 of 13

dpy

1 of 13

fon

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Human Disease Associations

FlyBase Human Disease Model Reports

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 )

Allele

Disease

Interaction

References

Nup98-96^KK100388

ameliorates amyotrophic lateral sclerosis

modeled by Zzzz\GGGGCC^58.UAS.EGFP

(Freibaum et al., 2015)

ameliorates frontotemporal dementia

modeled by Zzzz\GGGGCC^58.UAS.EGFP

(Freibaum et al., 2015)

ameliorates amyotrophic lateral sclerosis type 6

modeled by Hsap\FUS^UAS.Tag:HA

(Lin et al., 2021)

modeled by Hsap\FUS^{R518K.UAS.Tag:HA}

(Lin et al., 2021)

modeled by Hsap\FUS^{R521C.UAS.Tag:HA}

(Lin et al., 2021)

Nup98-96^GD6897

ameliorates amyotrophic lateral sclerosis

modeled by Zzzz\GGGGCC^58.UAS.EGFP

(Freibaum et al., 2015)

ameliorates frontotemporal dementia

modeled by Zzzz\GGGGCC^58.UAS.EGFP

(Freibaum et al., 2015)

Disease Associations of Human Orthologs (via DIOPT v9.1 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?

NUP98; nucleoporin 98 and 96 precursor

14 of 14

NUCLEOPORIN, 98-KD; NUP98

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

Interaction Browsers

View in FlyBase Interactions Browser View in MIST tool (external link)

Please see the Physical Interaction reports below for full details

protein-protein

Physical Interaction

Assay

References

Nup98-96 - CTCF

anti bait coimmunoprecipitation, western blot

(Pascual-Garcia et al., 2017)

Nup98-96 - Chro

anti bait coimmunoprecipitation, western blot

(Pascual-Garcia et al., 2014)

Nup98-96 - Cp190

anti bait coimmunoprecipitation, western blot

(Pascual-Garcia et al., 2017)

Nup98-96 - EcR

anti bait coimmunoprecipitation, western blot

(Pascual-Garcia et al., 2017)

Nup98-96 - Lkb1

anti tag coimmunoprecipitation, Identification by mass spectrometry

(Vinayagam et al., 2016)

Nup98-96 - MBD-R2

anti bait coimmunoprecipitation, western blot

(Pascual-Garcia et al., 2014)

Nup98-96 - Mgtor

anti bait coimmunoprecipitation, western blot

(Pascual-Garcia et al., 2017)

Nup98-96 - Pdk1

anti tag coimmunoprecipitation, Identification by mass spectrometry

(Vinayagam et al., 2016)

Nup98-96 - Pten

anti tag coimmunoprecipitation, Identification by mass spectrometry

(Vinayagam et al., 2016)

Nup98-96 - Rae1

tandem affinity purification, Identification by mass spectrometry, anti tag coimmunoprecipitation, western blot

(Kristó et al., 2017, Tian et al., 2011)

Nup98-96 - Trl

anti bait coimmunoprecipitation, western blot

(Pascual-Garcia et al., 2017)

Nup98-96 - br

anti bait coimmunoprecipitation, western blot

(Pascual-Garcia et al., 2014)

Nup98-96 - cnn

anti bait coimmunoprecipitation, peptide massfingerprinting

(Habermann et al., 2012)

Nup98-96 - mof

anti tag coimmunoprecipitation, Identification by mass spectrometry

(Mendjan et al., 2006)

Nup98-96 - su(Hw)

anti bait coimmunoprecipitation, western blot

(Pascual-Garcia et al., 2017)

Nup98-96 - trx

anti bait coimmunoprecipitation, western blot

(Pascual-Garcia et al., 2014)

Nup98-96 - wds

anti bait coimmunoprecipitation, western blot

(Pascual-Garcia et al., 2014)

Summary of Genetic Interactions

Interaction Browsers

View in FlyBase Interactions Browser View in MIST tool (external link)

Please look at the allele data for full details of the genetic interactions

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

Nup98-96

suppressible

bip1

(Mondal et al., 2014)

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

External Data

Subunit Structure (UniProtKB)

(UniProt, Q9VCH5 )

Linkouts

BioGRID - A database of protein and genetic interactions.

67753

DroID - A comprehensive database of gene and protein interactions.

FBgn0039120

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

42816

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyBase

External Links

External Data

Linkouts

KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.

Nucleocytoplasmic transport

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

Class of Gene

nuclear_gene

protein_coding_gene

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

3-80

Cytogenetic map

95B1-95B5

Sequence location

3R:23,774,225..23,781,621 [-]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

95B1-95B5

Limits computationally determined from genome sequence between P{PZ}l(3)04684⁰⁴⁶⁸⁴ and P{PZ}Atg6⁰⁰⁰⁹⁶

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

3-80

(FlyBase, 2016)

3-82.0

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (17)

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

Bloomington

92790

w¹¹¹⁸; P{UAS-Nup96.myc}2

92791

w¹¹¹⁸; P{UAS-Nup98.myc}3

92789

w¹¹¹⁸; P{UAS-lacI-Nup98-myc}8

28562

y¹ v¹; P{TRiP.HM05048}attP2

96272

y¹ w^*; P{TKO-UAS.GS05924}attP40/CyO

107965

10198R-1

10198R-3

v109279

v31198

w¹¹¹⁸; P{GD6897}v31198

v31199

w¹¹¹⁸; P{GD6897}v31199

v318656

PBac{fTRG00763.sfGFP-TVPTBF}VK00002

More stocks available...

Genomic Clones (23)

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

cDNA Clones (64)

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 JBrowse 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.

FBgn0039120

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0039120

Antibody Information

Laboratory Generated Antibodies

polyclonal

(Parrott et al., 2011)

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

S2 cells treated with dsRNA directed against Nup98 show decreased uptake of S.aureus by phagocytosis compared to control cells.

(Stuart et al., 2007)

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

(Stroschein-Stevenson et al., 2006)

Identified as a potential component of the hh signalling pathway in a genome-wide RNAi screen. dsRNA made from templates generated with primers directed affects the extent of expression of a hh signaling reporter construct in Clone 8 cells.

(Nybakken et al., 2005)

This gene is alternatively transcribed, giving rise to a minor 3.5kb Nup98 transcript and a major 7.3kb Nup98-Nup96 transcript. Which may autoproteolytically cleaves itself yielding separate Nup98 and Nup96 proteins.

(Presgraves et al., 2003)

Nup98 causes epistatic inviability in hybrids between D.melanogaster and D.simulans.

(Presgraves et al., 2003)

Relationship to Other Genes

Source for database merge of

Source for merge of: l(3)95BCd Nup98

(Presgraves et al., 2003)

Source for merge of: CG10198 CG10201

(FlyBase, 1996-)

Additional comments

FlyBase Curator comment: Correspondence with author Lan Xu revealed that 'nup145' = CG10198.

(Chen and Xu, 2010)

Source for merge of CG10198 CG10201 was a shared cDNA ( date:010720 ).

(FlyBase, 1996-)

Nomenclature History

Source for database identify of

Nomenclature comments

Etymology

Synonyms and Secondary IDs (25)

Reported As

Symbol Synonym

CG10198

(Kumar et al., 2021, Hosono et al., 2015, Müller et al., 2010, Keleman et al., 2009.8.5, Perkins et al., 2009, Sabri et al., 2007, Stuart et al., 2007, Nybakken et al., 2005, Giot et al., 2003, Presgraves et al., 2003)

CG10201

NUP98

(Morin-Poulard et al., 2021, Chen et al., 2013, Stenberg and Larsson, 2011)

NUP98-NUP96

(Raices and D'Angelo, 2012)

Nup

(Mensch et al., 2013)

Nup 96

(Clark and Aquadro, 2010)

Nup 98

(Clark and Aquadro, 2010)

Nup-98

(Kallappagoudar et al., 2010)

Nup96

(McQuarrie et al., 2023, Sawamura, 2012, Nei and Nozawa, 2011, Capelson et al., 2010, Presgraves, 2010, Barbash, 2007, Presgraves and Stephan, 2007, Pennisi, 2006, Albert and Schluter, 2005, Orr, 2005, Orr et al., 2004, Presgraves et al., 2003, Swanson, 2003)

Nup96-98

(Neumann et al., 2010)

Nup98

(Dubey et al., 2026, Sachweh et al., 2025, Doronin et al., 2024, Goins et al., 2024, Danilov et al., 2023, McQuarrie et al., 2023, Benoit et al., 2022, Pascual-Garcia et al., 2022, Lin et al., 2021, Llorens-Giralt et al., 2021, Mehta et al., 2020, Swevers et al., 2018, Panda et al., 2015, Schmidt and Görlich, 2015, Ashwal-Fluss et al., 2014, Mondal et al., 2014, Pascual-Garcia et al., 2014, Habermann et al., 2012, Japanese National Institute of Genetics, 2012.5.21, Ranz et al., 2012, Finan et al., 2011, Friedman et al., 2011, Tian et al., 2011, Capelson et al., 2010, Kalverda and Fornerod, 2010, Kalverda et al., 2010, Müller et al., 2010, Doheny et al., 2008, Baeg et al., 2007, Barbash, 2007, Presgraves and Stephan, 2007, Stuart et al., 2007, Mendjan et al., 2006, Stroschein-Stevenson et al., 2006, Nybakken et al., 2005, Loop et al., 2004)

Nup98-96

(Hanson et al., 2025, Klimkowski Arango and Morgante, 2025, Shindo et al., 2025, Ding et al., 2022, Layalle et al., 2021, Vorobyeva and Mazina, 2019, Wu et al., 2019, Chou et al., 2018, Gene Disruption Project members, 2018-, Hirai et al., 2018, Pascual-Garcia et al., 2017, Transgenic RNAi Project members, 2017-, Sarov et al., 2016, Freibaum et al., 2015, Katsani et al., 2014, Sawamura et al., 2014)

Nup98-Nup96

(Presgraves et al., 2003)

Nup98/96

(Sarkar et al., 2006)

l(3)95BCd

(Bloomington Drosophila Stock Center, 1999.6.28, Keller et al., 1998, Erickson et al., 1997)

nup145

(Chen and Xu, 2010)

nup96

(Klumpe et al., 2025)

nup98

(Munafò et al., 2021)

nup98-96

(Munafò et al., 2021, Hampoelz et al., 2019, Parrott et al., 2011)

Name Synonyms

Nucleoporin 96

(Presgraves, 2010)

Nucleoporin 98

(Ranz et al., 2012)

Nucleoporin 98-96

Nucleoporin 98-96kD

Nup98

nucleoporin 98-96

(Coutinho-Budd et al., 2017)

nucleoporin98-96

(Parrott et al., 2011)

Secondary FlyBase IDs

FBgn0021781
FBgn0039119

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 125 )

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.

42816

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.

Q9VCH5

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

Q9VCH5

UniProt/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information

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.

Q9VCH5

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

42816/tissue=All

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

FBgn0039120

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

FBgn0039120

FlyMine - An integrated database for Drosophila genomics

FBgn0039120

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

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

dme:Dmel_CG10198

MARRVEL_MODEL - MARRVEL (model organism gene)

42816

Linkouts

BioGRID - A database of protein and genetic interactions.

67753

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

FBgn0039120

DroID - A comprehensive database of gene and protein interactions.

FBgn0039120

DRSC - Results frm RNAi screens

FBgn0039120

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

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0039120

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0039120

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

CG10198

Flygut - An atlas of the Drosophila adult midgut

FBgn0039120

FlyMet - A comprehensive tissue-specific metabolomics resource for Drosophila.

FBgn0039120

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

TC013629

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

Interactive Fly

KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.

Nucleocytoplasmic transport

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

42816

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

References (134)

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

0.46

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