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Aliases for NUP54 Gene

Aliases for NUP54 Gene

  • Nucleoporin 54 2 3 5
  • 54 KDa Nucleoporin 4
  • Nucleoporin 54kDa 2

External Ids for NUP54 Gene

Previous GeneCards Identifiers for NUP54 Gene

  • GC04M076931
  • GC04M077225
  • GC04M077428
  • GC04M077494
  • GC04M077392
  • GC04M077035
  • GC04M072788

Summaries for NUP54 Gene

Entrez Gene Summary for NUP54 Gene

  • The nuclear envelope creates distinct nuclear and cytoplasmic compartments in eukaryotic cells. It consists of two concentric membranes perforated by nuclear pores, large protein complexes that form aqueous channels to regulate the flow of macromolecules between the nucleus and the cytoplasm. These complexes are composed of at least 100 different polypeptide subunits, many of which belong to the nucleoporin family. This gene encodes a member of the phe-gly (FG) repeat-containing nucleoporin subset. Multiple alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jun 2013]

GeneCards Summary for NUP54 Gene

NUP54 (Nucleoporin 54) is a Protein Coding gene. Among its related pathways are Mitotic Prophase and SUMOylation. Gene Ontology (GO) annotations related to this gene include nuclear pore activity.

UniProtKB/Swiss-Prot for NUP54 Gene

  • Component of the nuclear pore complex, a complex required for the trafficking across the nuclear membrane.

Gene Wiki entry for NUP54 Gene

Additional gene information for NUP54 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for NUP54 Gene

Genomics for NUP54 Gene

GeneHancer (GH) Regulatory Elements for NUP54 Gene

Promoters and enhancers for NUP54 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH04I076146 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 618.4 +0.3 344 2.5 FEZF1 DMAP1 IRF4 YY1 ZNF213 E2F8 ZNF416 ZNF143 ZNF548 SP3 NUP54 GC04P076146 THAP6 ART3 RPL7P17 SDAD1
GH04I077072 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE dbSUPER 106.2 -926.2 -926224 5.8 MLX FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF416 ZNF143 CCNI GC04P077075 NUP54 CNOT6L RPL7P17 GC04M077051
GH04I076205 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 39.2 -62.3 -62279 10.3 HDGF PKNOX1 FOXA2 ARNT ARID4B SIN3A DMAP1 ZNF2 IRF4 YY1 FAM47E SCARB2 GC04P076210 NUP54 THAP6 SDAD1 ART3 NAAA G3BP2 STBD1
GH04I076192 Enhancer 1.5 Ensembl ENCODE dbSUPER 37.4 -49.3 -49278 9.7 HDGF PKNOX1 FOXA2 SMAD1 MLX ARID4B FEZF1 YBX1 ZNF2 IRF4 NUP54 SCARB2 RCHY1 THAP6 ART3 NAAA GC04P076210
GH04I075511 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 24.1 +634.7 634694 4.9 HDGF PKNOX1 CLOCK FOXA2 SMAD1 MLX ARNT ZFP64 ARID4B SIN3A THAP6 RCHY1 NUP54
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around NUP54 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the NUP54 gene promoter:

Genomic Locations for NUP54 Gene

Genomic Locations for NUP54 Gene
33,857 bases
Minus strand

Genomic View for NUP54 Gene

Genes around NUP54 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NUP54 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NUP54 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NUP54 Gene

Proteins for NUP54 Gene

  • Protein details for NUP54 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Nucleoporin p54
    Protein Accession:
    Secondary Accessions:
    • B2RCK7
    • B4DT35
    • Q96EA7
    • Q9NVL5
    • Q9P0I1

    Protein attributes for NUP54 Gene

    507 amino acids
    Molecular mass:
    55435 Da
    Quaternary structure:
    • Component of the p62 complex, a complex composed of NUP62, NUP54, and the isoform p58 and isoform p45 of NUP58. Interacts with NUTF2.
    • Sequence=BAA91735.1; Type=Frameshift; Positions=479; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for NUP54 Gene

    Alternative splice isoforms for NUP54 Gene


neXtProt entry for NUP54 Gene

Post-translational modifications for NUP54 Gene

No data available for DME Specific Peptides for NUP54 Gene

Domains & Families for NUP54 Gene

Gene Families for NUP54 Gene

Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins
  • Transporters

Protein Domains for NUP54 Gene

Suggested Antigen Peptide Sequences for NUP54 Gene

Graphical View of Domain Structure for InterPro Entry



  • Contains FG repeats.
  • Belongs to the NUP54 family.
  • Contains FG repeats.
  • Belongs to the NUP54 family.
genes like me logo Genes that share domains with NUP54: view

Function for NUP54 Gene

Molecular function for NUP54 Gene

UniProtKB/Swiss-Prot Function:
Component of the nuclear pore complex, a complex required for the trafficking across the nuclear membrane.

Phenotypes From GWAS Catalog for NUP54 Gene

Gene Ontology (GO) - Molecular Function for NUP54 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005487 nuclear pore activity IBA --
GO:0005515 protein binding IPI 16189514
GO:0017056 structural constituent of nuclear pore IBA --
genes like me logo Genes that share ontologies with NUP54: view
genes like me logo Genes that share phenotypes with NUP54: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for NUP54 Gene

Localization for NUP54 Gene

Subcellular locations from UniProtKB/Swiss-Prot for NUP54 Gene

Nucleus, nuclear pore complex. Nucleus membrane; Peripheral membrane protein; Cytoplasmic side. Nucleus membrane; Peripheral membrane protein; Nucleoplasmic side. Note=Biased towards cytoplasmic side. Central region of the nuclear pore complex, within the transporter. {ECO:0000250 UniProtKB:P70582}.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for NUP54 gene
Compartment Confidence
nucleus 5
cytosol 2
mitochondrion 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for NUP54 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005635 nuclear envelope TAS --
GO:0005643 nuclear pore IEA --
GO:0016020 membrane IEA --
GO:0031965 nuclear membrane IEA --
genes like me logo Genes that share ontologies with NUP54: view

Pathways & Interactions for NUP54 Gene

SuperPathways for NUP54 Gene

SuperPathway Contained pathways
1 Transport of the SLBP independent Mature mRNA
2 HIV Life Cycle
3 Cell Cycle, Mitotic
4 Mitotic Prophase
5 Influenza Viral RNA Transcription and Replication
genes like me logo Genes that share pathways with NUP54: view

Pathways by source for NUP54 Gene

Gene Ontology (GO) - Biological Process for NUP54 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006110 regulation of glycolytic process TAS --
GO:0006406 mRNA export from nucleus TAS --
GO:0006409 tRNA export from nucleus TAS --
GO:0006605 protein targeting IEA --
GO:0006607 NLS-bearing protein import into nucleus IBA --
genes like me logo Genes that share ontologies with NUP54: view

No data available for SIGNOR curated interactions for NUP54 Gene

Drugs & Compounds for NUP54 Gene

No Compound Related Data Available

Transcripts for NUP54 Gene

Unigene Clusters for NUP54 Gene

Nucleoporin 54kDa:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for NUP54 Gene

ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3a · 3b ^ 4 ^ 5a · 5b ^ 6a · 6b · 6c ^ 7a · 7b ^ 8a · 8b ^ 9 ^ 10a · 10b · 10c ^ 11 ^ 12a · 12b ^ 13a · 13b ^
SP1: - - - - -
SP2: - - - - - -
SP3: - - - - - -
SP4: - - - - - - - -
SP5: - -
SP6: - - - - -
SP7: - - - - - - - - - - - - - - - - - -
SP8: - - - - - - -
SP9: - -
SP10: - - - - -
SP11: -
SP12: - - -
SP13: - -
SP15: - - - - - - - -

ExUns: 14a · 14b · 14c · 14d

Relevant External Links for NUP54 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for NUP54 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for NUP54 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for NUP54 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (15.5) and Placenta (6.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for NUP54 Gene

Protein tissue co-expression partners for NUP54 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of NUP54 Gene:


SOURCE GeneReport for Unigene cluster for NUP54 Gene:


Evidence on tissue expression from TISSUES for NUP54 Gene

  • Nervous system(4.6)
genes like me logo Genes that share expression patterns with NUP54: view

Primer Products

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for NUP54 Gene

Orthologs for NUP54 Gene

This gene was present in the common ancestor of animals.

Orthologs for NUP54 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia NUP54 33 34
  • 99.71 (n)
(Bos Taurus)
Mammalia NUP54 33 34
  • 93.25 (n)
-- 34
  • 92 (a)
(Monodelphis domestica)
Mammalia NUP54 34
  • 92 (a)
(Canis familiaris)
Mammalia NUP54 34 33
  • 91.29 (n)
(Ornithorhynchus anatinus)
Mammalia NUP54 34
  • 91 (a)
(Rattus norvegicus)
Mammalia Nup54 33
  • 88.16 (n)
(Mus musculus)
Mammalia Nup54 16 34 33
  • 87.87 (n)
(Gallus gallus)
Aves NUP54 33 34
  • 80.02 (n)
(Anolis carolinensis)
Reptilia NUP54 34
  • 86 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia nup54 33
  • 75.29 (n)
Str.1826 33
African clawed frog
(Xenopus laevis)
Amphibia MGC68541 33
(Danio rerio)
Actinopterygii nup54 33
  • 62.09 (n)
NUP54 34
  • 46 (a)
wufp63g06 33
fruit fly
(Drosophila melanogaster)
Insecta Nup54 33 34
  • 49.06 (n)
CG8831 35
  • 39 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP006031 33
  • 48.26 (n)
(Caenorhabditis elegans)
Secernentea npp-1 34
  • 21 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 47 (a)
-- 34
  • 42 (a)
Species where no ortholog for NUP54 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for NUP54 Gene

Gene Tree for NUP54 (if available)
Gene Tree for NUP54 (if available)

Paralogs for NUP54 Gene

(1) SIMAP similar genes for NUP54 Gene using alignment to 7 proteins:

genes like me logo Genes that share paralogs with NUP54: view

No data available for Paralogs for NUP54 Gene

Variants for NUP54 Gene

Sequence variations from dbSNP and Humsavar for NUP54 Gene

SNP ID Clin Chr 04 pos Variation AA Info Type
rs1000001655 -- 76,130,565(-) T/C intron_variant
rs1000011117 -- 76,116,993(-) T/G intron_variant
rs1000040826 -- 76,143,021(-) C/G intron_variant
rs1000108170 -- 76,137,303(-) G/A intron_variant
rs1000381167 -- 76,125,447(-) A/C intron_variant

Structural Variations from Database of Genomic Variants (DGV) for NUP54 Gene

Variant ID Type Subtype PubMed ID
nsv7363 OTHER inversion 18451855
nsv470047 CNV gain 18288195
nsv461558 CNV gain 19166990
nsv1139274 CNV deletion 24896259
nsv1009047 CNV loss 25217958
nsv1000178 CNV gain 25217958
esv275315 CNV gain+loss 21479260
dgv9136n54 CNV gain 21841781

Variation tolerance for NUP54 Gene

Residual Variation Intolerance Score: 35.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 9.81; 89.55% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for NUP54 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NUP54 Gene

Disorders for NUP54 Gene

Additional Disease Information for NUP54

No disorders were found for NUP54 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for NUP54 Gene

Publications for NUP54 Gene

  1. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  2. Gene expression profiling in the human hypothalamus-pituitary-adrenal axis and full-length cDNA cloning. (PMID: 10931946) Hu RM … Chen JL (Proceedings of the National Academy of Sciences of the United States of America 2000) 3 4 58
  3. Molecular and functional characterization of the p62 complex, an assembly of nuclear pore complex glycoproteins. (PMID: 8707840) Hu T … Gerace L (The Journal of cell biology 1996) 2 3 58
  4. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58
  5. An inter-species protein-protein interaction network across vast evolutionary distance. (PMID: 27107014) Zhong Q … Vidal M (Molecular systems biology 2016) 3 58

Products for NUP54 Gene

Sources for NUP54 Gene

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