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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 HIV Life Cycle and Transport of the SLBP independent Mature mRNA. GO annotations related to this gene include nucleocytoplasmic transporter 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

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

Genomics for NUP54 Gene

Regulatory Elements for NUP54 Gene

Enhancers for NUP54 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH04G076089 1.6 FANTOM5 Ensembl ENCODE 38.7 +58.2 58184 2.1 PKNOX1 ATF1 ARNT BRCA1 TCF12 ZNF766 GATA2 FOS ZNF592 MEF2D NUP54 CXCL10 CXCL9 SDAD1 ART3 NAAA CXCL11 GC04P076101
GH04G076192 1.6 Ensembl ENCODE dbSUPER 28.8 -49.3 -49279 9.7 HDGF PKNOX1 MLX ARID4B FEZF1 YBX1 ZNF2 YY1 ZNF766 ZNF302 NUP54 SCARB2 ART3 NAAA GC04P076210
GH04G076146 1.2 ENCODE 29.5 +0.3 344 2.5 CREB3L1 AGO1 FEZF1 DMAP1 YY1 ZNF416 ZNF143 ZNF548 SP3 TBX21 NUP54 ART3 THAP6 SDAD1 GC04P076146
GH04G076154 1.2 dbSUPER 27.7 -7.7 -7670 2.4 CREB3L1 MLX DMAP1 FEZF1 YY1 SLC30A9 ZNF143 ZNF416 ZNF263 SP3 RPL7P17 NUP54 THAP6 SCARB2 CDKL2 FAM47E RNU6-1000P NAAA GC04P076210
GH04G076179 1 ENCODE dbSUPER 26.6 -31.5 -31508 0.1 CTCF FOXA2 RB1 WRNIP1 EBF1 RAD21 CHAMP1 YY1 FOSL1 ZNF121 NUP54 FAM47E SCARB2 CCDC158 STBD1 RNU6-1000P GC04P076210
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around NUP54 on UCSC Golden Path with GeneCards custom track

Promoters for NUP54 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000169451 315 2401 CREB3L1 AGO1 FEZF1 DMAP1 YY1 ZNF416 ZNF143 ZNF548 SP3 TBX21

Genomic Location for NUP54 Gene

Chromosome:
4
Start:
76,114,659 bp from pter
End:
76,148,515 bp from pter
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; Positions=479; 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

No data available for DME Specific Peptides for NUP54 Gene

Domains & Families for NUP54 Gene

Gene Families for NUP54 Gene

Protein Domains for NUP54 Gene

Suggested Antigen Peptide Sequences for NUP54 Gene

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.

Gene Ontology (GO) - Molecular Function for NUP54 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005487 nucleocytoplasmic transporter 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

Clone 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

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
mitochondrion 1

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
.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

Pathways by source for NUP54 Gene

Gene Ontology (GO) - Biological Process for NUP54 Gene

GO ID Qualified GO term Evidence PubMed IDs
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 --
GO:0006810 transport IEA --
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

Clone 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: - -
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
ECgene alternative splicing isoforms for
NUP54

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:

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

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 35 34
  • 99.71 (n)
OneToOne
cow
(Bos Taurus)
Mammalia NUP54 35 34
  • 93.25 (n)
OneToMany
-- 35
  • 92 (a)
OneToMany
oppossum
(Monodelphis domestica)
Mammalia NUP54 35
  • 92 (a)
OneToOne
dog
(Canis familiaris)
Mammalia NUP54 35 34
  • 91.29 (n)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia NUP54 35
  • 91 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Nup54 34
  • 88.16 (n)
mouse
(Mus musculus)
Mammalia Nup54 16 35 34
  • 87.87 (n)
chicken
(Gallus gallus)
Aves NUP54 35 34
  • 80.02 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia NUP54 35
  • 86 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia nup54 34
  • 75.29 (n)
Str.1826 34
African clawed frog
(Xenopus laevis)
Amphibia MGC68541 34
zebrafish
(Danio rerio)
Actinopterygii nup54 34
  • 62.09 (n)
NUP54 35
  • 46 (a)
OneToOne
wufp63g06 34
fruit fly
(Drosophila melanogaster)
Insecta Nup54 34 35
  • 49.06 (n)
CG8831 36
  • 39 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP006031 34
  • 48.26 (n)
worm
(Caenorhabditis elegans)
Secernentea npp-1 35
  • 21 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 47 (a)
OneToMany
-- 35
  • 42 (a)
OneToMany
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

ENSEMBL:
Gene Tree for NUP54 (if available)
TreeFam:
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 Sequence Context AA Info Type
rs1000001655 -- 76,130,565(+) TAAGA(C/T)AAAAC intron-variant
rs1000011117 -- 76,116,993(+) TACAT(G/T)TATGC intron-variant
rs1000040826 -- 76,143,021(+) GTAAC(C/G)CCTAA intron-variant
rs1000108170 -- 76,137,303(+) CTAAT(A/G)ATGTT intron-variant
rs1000381167 -- 76,125,447(+) TGGGC(A/C)AAATG intron-variant

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)

Relevant External Links for NUP54 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
NUP54

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

Disorders for NUP54 Gene

Relevant External Links for NUP54

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
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. (Nat. Genet. 2004) 3 4 64
  2. Gene expression profiling in the human hypothalamus-pituitary-adrenal axis and full-length cDNA cloning. (PMID: 10931946) Hu R.-M. … Chen J.-L. (Proc. Natl. Acad. Sci. U.S.A. 2000) 3 4 64
  3. Molecular and functional characterization of the p62 complex, an assembly of nuclear pore complex glycoproteins. (PMID: 8707840) Hu T. … Gerace L. (J. Cell Biol. 1996) 2 3 64
  4. Systematic Protein-Protein Interaction Analysis Reveals Intersubcomplex Contacts in the Nuclear Pore Complex. (PMID: 27194810) Apelt L. … Stelzl U. (Mol. Cell Proteomics 2016) 3 64
  5. Interactions of the Antiviral Factor Interferon Gamma-Inducible Protein 16 (IFI16) Mediate Immune Signaling and Herpes Simplex Virus-1 Immunosuppression. (PMID: 25693804) Diner B.A. … Cristea I.M. (Mol. Cell Proteomics 2015) 3 64

Products for NUP54 Gene

Sources for NUP54 Gene

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