FB2026_01 , released March 12, 2026
FB2026_01 , released March 12, 2026
Gene: Dmel\Nup93-1
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General Information
Symbol
Dmel\Nup93-1
Species
D. melanogaster
Name
Nucleoporin 93kD-1
Annotation Symbol
CG11092
Feature Type
protein_coding_gene
FlyBase ID
FBgn0027537
Gene Model Status
Current
Stock Availability
9 publicly available
Gene Summary
Nucleoporin 93kD-1 (Nup93-1) encodes a protein that directly interacts with the product of Nup154. However, the product of Nup93-1 is not necessary for the Nup154-dependent organization of the inner nuclear membrane proteins at the nuclear envelope. [Date last reviewed: 2019-03-14] (FlyBase Gene Snapshot)
All Summaries
Also Known As

Nup93, BcDNA:LD21129

Key Links
Genomic Location
Cytogenetic map
12C6-12C6
Sequence location
Recombination map
1-46
RefSeq locus
NC_004354 REGION:13822826..13825910
Sequence
Get Decorated FASTA
Genomic Maps
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
NCBI
UCSC
Ensembl
PopFly
Function
Gene Ontology (GO) Annotations (16 terms)
Molecular Function (4 terms)
Terms Based on Experimental Evidence (3 terms)
CV Term
Evidence
References
enables chromatin binding
inferred from direct assay
(Gozalo et al., 2020)
enables chromatin DNA binding
inferred from direct assay
(Pascual-Garcia et al., 2017)
enables protein binding
inferred from physical interaction with UniProtKB:P26017,UniProtKB:P42124
(Gozalo et al., 2020)
inferred from physical interaction with FLYBASE:Nup154; FB:FBgn0021761
(Busayavalasa et al., 2012)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
enables structural constituent of nuclear pore
inferred from sequence or structural similarity with SGD:S000001898
(Gene Ontology Curators, 2002-)
inferred from electronic annotation with InterPro:IPR007231
(InterPro Project Members, 2004-)
inferred from biological aspect of ancestor with PANTHER:PTN000131983
(GO Reference Genome Project, 2011-)
Biological Process (9 terms)
Terms Based on Experimental Evidence (7 terms)
CV Term
Evidence
References
involved_in chromosome attachment to the nuclear envelope
inferred from mutant phenotype
(Breuer and Ohkura, 2015)
involved_in negative regulation of gene expression, epigenetic
inferred from mutant phenotype
(Gozalo et al., 2020)
involved_in oocyte karyosome formation
inferred from mutant phenotype
(Breuer and Ohkura, 2015)
involved_in protein import into nucleus
inferred from mutant phenotype
(Chen and Xu, 2010)
involved_in protein localization to nuclear inner membrane
inferred from mutant phenotype
(Busayavalasa et al., 2012)
involved_in regulation of nucleus size
inferred from mutant phenotype
(Breuer and Ohkura, 2015)
NOT involved_in NLS-bearing protein import into nucleus
inferred from mutant phenotype
(Chen and Xu, 2010)
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
involved_in nuclear pore organization
inferred from sequence or structural similarity with SGD:S000001898
(Gene Ontology Curators, 2002-)
involved_in poly(A)+ mRNA export from nucleus
inferred from biological aspect of ancestor with PANTHER:PTN000131983
(GO Reference Genome Project, 2011-)
involved_in protein import into nucleus
inferred from biological aspect of ancestor with PANTHER:PTN000131983
(GO Reference Genome Project, 2011-)
Cellular Component (3 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
located_in nuclear periphery
inferred from direct assay
(Gozalo et al., 2020)
part_of nuclear pore
inferred from direct assay
(Gozalo et al., 2020)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
part_of nuclear pore nuclear basket
inferred from sequence or structural similarity with SGD:S000001898
(Gene Ontology Curators, 2002-)
part_of nuclear pore
inferred from biological aspect of ancestor with PANTHER:PTN000131983
(GO Reference Genome Project, 2011-)
inferred from electronic annotation with InterPro:IPR007231
(InterPro Project Members, 2004-)
Gene Group (FlyBase)
Protein Family (UniProt)
Belongs to the nucleoporin interacting component (NIC) family. (Q9XZ06)
Protein Signatures (InterPro)
Summaries
Gene Snapshot
Nucleoporin 93kD-1 (Nup93-1) encodes a protein that directly interacts with the product of Nup154. However, the product of Nup93-1 is not necessary for the Nup154-dependent organization of the inner nuclear membrane proteins at the nuclear envelope. [Date last reviewed: 2019-03-14]
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)
Required for nuclear pore complex assembly, maintenance and function (PubMed:20547758, PubMed:22718353). Required for nuclear import of phosphorylated Mad via importin msk (PubMed:20547758). Has no role in classical nuclear localization signal (cNLS)-dependent nuclear import via importin-beta (PubMed:20547758). Mediates the association between the nuclear pore complex and a subclass of silenced regions bound by Polycomb group (PcG) proteins, enables long-range interactions between Polycomb loci and contributes to repression of polycomb targets (PubMed:31784359). Together with Nup62 and Nup154, contributes to karyosome morphology and chromatin organization including attachment to the nuclear envelope in oocytes and nurse cells (PubMed:26341556).
(UniProt, Q9XZ06)
Summary (Interactive Fly)

nuclear pore complex - scaffold nucleoporin considered important for the overall integrity of the nuclear pore complex - functions in supporting Smad nuclear import - a core component of the inner ring sub-complex - associates primarily with Polycomb-silenced regions - Nup93 recruits Nup62 to suppress chromatin tethering by Nup155

Gene Model and Products
Number of Transcripts
1
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\Nup93-1 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 Q9XZ06)

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

Gene model reviewed during 5.50

Gene model reviewed during 5.45

RNA-Seq data support multiple isoforms with extended 3' UTRs of differing length, some of which appear to be stage and/or tissue specific.

Gene model reviewed during 5.55

Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
Nup93-1-RA
FBtr0073828
NM_132701
2786
823
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
Nup93-1-PA
FBpp0073659
93.9
823
6.20
Q9XZ06
NP_572929
AAF48327
Polypeptides with Identical Sequences

There is only one protein coding transcript and one polypeptide associated with this gene

Additional Polypeptide Data and Comments
Reported size (kDa)
Comments
External Data
Subunit Structure (UniProtKB)

Part of the nuclear pore complex (NPC) (By similarity). Interacts with msk (via C-terminus); this association might be facilitated by Nup75 (PubMed:20547758). Interacts with Mad (preferentially when phosphorylated) (PubMed:20547758). Interacts with Nup154 (via N-terminus) (PubMed:22718353). Interacts with the Polycomb group (PcG) proteins Pc and E(z) (PubMed:31784359).

(UniProt, Q9XZ06)
Crossreferences
InterPro - A database of protein families, domains and functional sites
Linkouts
Sequences Consistent with the Gene Model
Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\Nup93-1 using the Feature Mapper tool.

External Data
Crossreferences
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).

-0.08

Transcript Expression
Polypeptide Expression
mass spectroscopy
Stage
Tissue/Position (including subcellular localization)
Reference
adult stage
adult head
(Aradska et al., 2015)
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
located_in nuclear periphery
inferred from direct assay
(Gozalo et al., 2020)
part_of nuclear pore
inferred from direct assay
(Gozalo et al., 2020)
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\Nup93-1 in JBrowse
RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region
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
BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
Flygut - An atlas of the Drosophila adult midgut
Images
FlyBase Wiki
Image Based Resources
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 3 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 8 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Nup93-1
Transgenic constructs containing regulatory region of Nup93-1
Aberrations (Deficiencies and Duplications) ( 0 )
Inferred from experimentation ( 0 )
Inferred from location ( 10 )
Variants
Variant Molecular Consequences
Alleles Representing Disease-Implicated Variants
Phenotypes
Orthologs
Downloads
Download All DIOPT Orthologs
Human Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
Domainoid
eggNOG
Hieranoid
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Complementation?
Transgene?
Homo sapiens (Human) (1)
Hsap\NUP93
13 of 14
Yes
No
Model Organism Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
Domainoid
eggNOG
Hieranoid
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Complementation?
Transgene?
Rattus norvegicus (Norway rat) (1)
Rnor\Nup93
13 of 14
Yes
No
Mus musculus (laboratory mouse) (1)
Mmus\Nup93
11 of 14
Yes
No
Xenopus tropicalis (Western clawed frog) (2)
Xtro\nup93
10 of 13
Yes
No
Xtro\atp10a
1 of 13
No
No
Danio rerio (Zebrafish) (1)
Drer\nup93
13 of 14
Yes
No
Caenorhabditis elegans (Nematode, roundworm) (1)
Cele\npp-13
11 of 14
Yes
No
Anopheles gambiae (African malaria mosquito) (1)
Agam\AgaP_AGAP003459
8 of 12
Yes
No
Arabidopsis thaliana (thale-cress) (2)
Atha\AT2G41620
11 of 13
Yes
No
Atha\AT3G57350
11 of 13
Yes
No
Saccharomyces cerevisiae (Brewer's yeast) (1)
Scer\NIC96
12 of 13
Yes
No
Schizosaccharomyces pombe (Fission yeast) (2)
Spom\nup97
11 of 12
Yes
No
Spom\npp106
10 of 12
No
No
Escherichia coli (enterobacterium) (0)
Other Organism Orthologs (via OrthoDB)
Data provided directly from OrthoDB:Nup93-1. Refer to their site for version information.
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v9.1)
Gene Symbol
Score
Source
Compara
Domainoid
eggNOG
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Drosophila melanogaster (Fruit fly) (1)
Nup93-2
12 of 13
Human Disease Associations
FlyBase Human Disease Model Reports
Disease Ontology (DO) Annotations
Models Based on Experimental Evidence ( 1 )
Allele
Disease
Evidence
References
Nup93-1HMS00898
model of  nephrotic syndrome type 12
CEC
(Bierzynska et al., 2022)
Potential Models Based on Orthology ( 1 )
Human Ortholog
Disease
Evidence
References
NUP93; nucleoporin 93
model of  nephrotic syndrome type 12
IEA
(FlyBase, 2019-)
Modifiers Based on Experimental Evidence ( 1 )
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?
NUP93; nucleoporin 93
13 of 14
614351
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
Summary of Genetic Interactions
Interaction Browsers
Starting gene(s)
Interaction type
Interacting gene(s)
Reference
Starting gene(s)
Interaction type
Interacting gene(s)
Reference
External Data
Subunit Structure (UniProtKB)
Part of the nuclear pore complex (NPC) (By similarity). Interacts with msk (via C-terminus); this association might be facilitated by Nup75 (PubMed:20547758). Interacts with Mad (preferentially when phosphorylated) (PubMed:20547758). Interacts with Nup154 (via N-terminus) (PubMed:22718353). Interacts with the Polycomb group (PcG) proteins Pc and E(z) (PubMed:31784359).
(UniProt, Q9XZ06 )
Linkouts
BioGRID - A database of protein and genetic interactions.
DroID - A comprehensive database of gene and protein interactions.
MIST (protein-protein) - An integrated Molecular Interaction Database
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.
Class of Gene
Genomic Location and Detailed Mapping Data
Chromosome (arm)
X
Recombination map
1-46
Cytogenetic map
12C6-12C6
Sequence location
FlyBase Computed Cytological Location
Cytogenetic map
Evidence for location
12C6-12C6
Limits computationally determined from genome sequence between P{EP}CG33174EP1101 and P{EP}EP1595EP1595
Experimentally Determined Cytological Location
Cytogenetic map
Notes
References
Experimentally Determined Recombination Data
Location

1-46

(FlyBase, 2016)

1-44.2

(Comeron et al., 2012)
Left of (cM)
Right of (cM)
Notes
Stocks and Reagents
Stocks (9)
Genomic Clones (15)
 

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

cDNA Clones (109)
 

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.

    cDNA Clones, End Sequenced (ESTs)
    BDGP DGC clones
    Other clones
    RNAi and Array Information
    Linkouts
    DRSC - Results frm RNAi screens
    Antibody Information
    Laboratory Generated Antibodies
     

    polyclonal

    (Pascual-Garcia et al., 2017)
    Commercially Available Antibodies
     
    Cell Line Information
    Publicly Available Cell Lines
     
      Other Stable Cell Lines
       
        Other Comments
        Relationship to Other Genes
        Source for database merge of
        Additional comments

        FlyBase Curator comment: Correspondence with author Lan Xu revealed that 'nup93' = CG11092.

        (Chen and Xu, 2010)

        FlyBase curator comment: There appears to be 2 'Nup93' orthologs in D. melanogaster: CG7262 and CG11092.

        (Chen and Xu, 2010)
        Nomenclature History
        Source for database identify of

        Source for identity of: Nup93-1 CG11092

        (FlyBase, 2009-)
        Nomenclature comments

        There appears to be 2 'Nup93' orthologs in D. melanogaster: CG11092 (see FBrf0211334) and CG7262 (see FBrf0212515). BLAST analysis using human NUP93 as a query confirms this. For this reason, CG11092 is being named 'Nup93-1', and CG7262 is being named 'Nup93-2'.

        (FlyBase, 2009-)
        Etymology
        Synonyms and Secondary IDs (7)
        Datasets (0)
        Study focus (0)
        Experimental Role
        Project
        Project Type
        Title
        Study result (0)
        Result
        Result Type
        Title
        External Crossreferences and Linkouts ( 33 )
        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/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.
        UniProt/Swiss-Prot - Manually annotated and reviewed 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.
        BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
        DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
        EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
        FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
        FlyMine - An integrated database for Drosophila genomics
        InterPro - A database of protein families, domains and functional sites
        KEGG Genes - Molecular building blocks of life in the genomic space.
        MARRVEL_MODEL - MARRVEL (model organism gene)
        Linkouts
        BioGRID - A database of protein and genetic interactions.
        Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
        DroID - A comprehensive database of gene and protein interactions.
        DRSC - Results frm RNAi screens
        FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
        FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
        Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
        Flygut - An atlas of the Drosophila adult midgut
        iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
        Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution
        KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.
        MIST (protein-protein) - An integrated Molecular Interaction Database
        References (62)