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 w... See more...

Aliases for NUP54 Gene

Aliases for NUP54 Gene

  • Nucleoporin 54 2 3 5
  • 54 KDa Nucleoporin 3 4
  • Nucleoporin 54kDa 2 3
  • Nucleoporin P54 3 4
  • Nucleoporin 54kD 3
  • NUP54 5

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. Diseases associated with NUP54 include Branchiootorenal Syndrome 1 and Achalasia-Addisonianism-Alacrima Syndrome. Among its related pathways are Cell Cycle, Mitotic and Transport of the SLBP independent Mature mRNA.

UniProtKB/Swiss-Prot Summary 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

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for NUP54 Gene

Genomics for NUP54 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for NUP54 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around NUP54 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for NUP54

Top Transcription factor binding sites by QIAGEN in the NUP54 gene promoter:
  • E2F
  • E2F-1
  • E2F-2
  • E2F-3a
  • E2F-4
  • E2F-5
  • Ik-3
  • POU3F2
  • POU3F2 (N-Oct-5a)
  • POU3F2 (N-Oct-5b)

Genomic Locations for NUP54 Gene

Latest Assembly
chr4:76,114,659-76,148,444
(GRCh38/hg38)
Size:
33,786 bases
Orientation:
Minus strand

Previous Assembly
chr4:77,035,817-77,069,550
(GRCh37/hg19 by Entrez Gene)
Size:
33,734 bases
Orientation:
Minus strand

chr4:77,035,812-77,069,668
(GRCh37/hg19 by Ensembl)
Size:
33,857 bases
Orientation:
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:
    Q7Z3B4-NUP54_HUMAN
    Recommended name:
    Nucleoporin p54
    Protein Accession:
    Q7Z3B4
    Secondary Accessions:
    • B2RCK7
    • B4DT35
    • Q96EA7
    • Q9NVL5
    • Q9P0I1

    Protein attributes for NUP54 Gene

    Size:
    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.
    SequenceCaution:
    • Sequence=BAA91735.1; Type=Frameshift; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for NUP54 Gene

    Alternative splice isoforms for NUP54 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for NUP54 Gene

Post-translational modifications for NUP54 Gene

Antibodies for research

  • Abcam antibodies for NUP54
  • Boster Bio Antibodies for NUP54

No data available for DME Specific Peptides for NUP54 Gene

Domains & Families for NUP54 Gene

Gene Families for NUP54 Gene

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

Protein Domains for NUP54 Gene

Suggested Antigen Peptide Sequences for NUP54 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ52746, highly similar to Nucleoporin p54 (B4DT35_HUMAN)
  • 54 kDa nucleoporin (NUP54_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q7Z3B4

UniProtKB/Swiss-Prot:

NUP54_HUMAN :
  • Contains FG repeats.
  • Belongs to the NUP54 family.
Domain:
  • Contains FG repeats.
Family:
  • 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:0005515 protein binding IPI 16189514
GO:0017056 structural constituent of nuclear pore IBA 21873635
GO:0042802 identical protein binding IEA --
GO:0044877 protein-containing complex binding IEA --
genes like me logo Genes that share ontologies with NUP54: view
genes like me logo Genes that share phenotypes with NUP54: view

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for NUP54

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

COMPARTMENTS
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
plasma membrane 1
extracellular 1
cytoskeleton 1
mitochondrion 1
endoplasmic reticulum 1
golgi apparatus 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

PathCards logo

SuperPathways for NUP54 Gene

SuperPathway Contained pathways
1 Transport of the SLBP independent Mature mRNA
2 HIV Life Cycle
.45
3 Cell Cycle, Mitotic
.60
4 Mitotic Prophase
5 Influenza Viral RNA Transcription and Replication
genes like me logo Genes that share pathways with NUP54: view

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 21873635
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

mRNA/cDNA for NUP54 Gene

2 REFSEQ mRNAs :
16 NCBI additional mRNA sequence :
18 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for NUP54

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: - -
SP14:
SP15: - - - - - - - -
SP16:

ExUns: 14a · 14b · 14c · 14d
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:
SP13:
SP14:
SP15:
SP16:

Relevant External Links for NUP54 Gene

GeneLoc Exon Structure for
NUP54

Expression for NUP54 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and 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, MaxQB, and MOPED for NUP54 Gene



Protein tissue co-expression partners for NUP54 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for NUP54

SOURCE GeneReport for Unigene cluster for NUP54 Gene:

Hs.430435

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 for research

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
Chimpanzee
(Pan troglodytes)
Mammalia NUP54 29 30
  • 99.71 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia NUP54 29 30
  • 93.25 (n)
OneToMany
-- 30
  • 92 (a)
OneToMany
Oppossum
(Monodelphis domestica)
Mammalia NUP54 30
  • 92 (a)
OneToOne
Dog
(Canis familiaris)
Mammalia NUP54 29 30
  • 91.29 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia NUP54 30
  • 91 (a)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Nup54 29
  • 88.16 (n)
Mouse
(Mus musculus)
Mammalia Nup54 29 16 30
  • 87.87 (n)
OneToOne
Chicken
(Gallus gallus)
Aves NUP54 29 30
  • 80.02 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia NUP54 30
  • 86 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia nup54 29
  • 75.29 (n)
Str.1826 29
African clawed frog
(Xenopus laevis)
Amphibia MGC68541 29
Zebrafish
(Danio rerio)
Actinopterygii nup54 29
  • 62.09 (n)
NUP54 30
  • 46 (a)
OneToOne
wufp63g06 29
Fruit Fly
(Drosophila melanogaster)
Insecta Nup54 29 30
  • 49.06 (n)
OneToOne
CG8831 31
  • 39 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP006031 29
  • 48.26 (n)
Worm
(Caenorhabditis elegans)
Secernentea npp-1 30
  • 21 (a)
OneToOne
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 30
  • 47 (a)
OneToMany
-- 30
  • 42 (a)
OneToMany
Species where no ortholog for NUP54 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (Ciona intestinalis)
  • 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

ENSEMBL:
Gene Tree for NUP54 (if available)
TreeFam:
Gene Tree for NUP54 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for NUP54: view image
Alliance of Genome Resources:
Additional Orthologs for NUP54

Paralogs for NUP54 Gene

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

  • NUP54_HUMAN
  • B4DT35_HUMAN
  • D6RAH0_HUMAN
  • D6RB65_HUMAN
  • D6RBF7_HUMAN
  • D6RFI8_HUMAN
  • E7EUM5_HUMAN
genes like me logo Genes that share paralogs with NUP54: view

No data available for Paralogs for NUP54 Gene

Variants for NUP54 Gene

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for NUP54 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

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

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

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
NUP54
Leiden Open Variation Database (LOVD)
NUP54

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for NUP54 Gene

Disorders for NUP54 Gene

MalaCards: The human disease database

(2) MalaCards diseases for NUP54 Gene - From: COP

- elite association - COSMIC cancer census association via MalaCards
Search NUP54 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for NUP54

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

No data available for 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
  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
  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
  4. Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms. (PMID: 33060197) Gordon DE … Krogan NJ (Science (New York, N.Y.) 2020) 3
  5. A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. (PMID: 32353859) Gordon DE … Krogan NJ (Nature 2020) 3

Products for NUP54 Gene

Sources for NUP54 Gene