This gene encodes a member of the nucleoporin family that shares 87% sequence identity with rat nucleoporin p58. The protein is localized to the nuclear rim and is a component of the nuclear pore complex (NPC). All molecules entering or leaving the nucleus either diffuse through or are actively transported by the NPC. Alternate transcriptional splice variants, encoding differen... See more...

Aliases for NUP58 Gene

Aliases for NUP58 Gene

  • Nucleoporin 58 2 3 5
  • Nucleoporin-Like Protein 1 3 4
  • Nucleoporin P58/P45 3 4
  • Nucleoporin Like 1 2 3
  • 58 KDa Nucleoporin 3 4
  • Nucleoporin 58kDa 2 3
  • KIAA0410 2 4
  • NUP45 2 3
  • NUPL1 3 4
  • PRO2463 3
  • NUP58 5

External Ids for NUP58 Gene

Previous HGNC Symbols for NUP58 Gene

  • NUPL1

Summaries for NUP58 Gene

Entrez Gene Summary for NUP58 Gene

  • This gene encodes a member of the nucleoporin family that shares 87% sequence identity with rat nucleoporin p58. The protein is localized to the nuclear rim and is a component of the nuclear pore complex (NPC). All molecules entering or leaving the nucleus either diffuse through or are actively transported by the NPC. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Jul 2008]

GeneCards Summary for NUP58 Gene

NUP58 (Nucleoporin 58) is a Protein Coding gene. Among its related pathways are Cell Cycle, Mitotic and Transport of the SLBP independent Mature mRNA.

UniProtKB/Swiss-Prot Summary for NUP58 Gene

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

Gene Wiki entry for NUP58 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for NUP58 Gene

Genomics for NUP58 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for NUP58 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH13J025300 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 259.1 +0.7 748 2.7 BCLAF1 SP1 MYC ZNF600 POLR2A CEBPA CHD4 YY1 CEBPB KLF11 NUP58 ENSG00000260509 lnc-ATP8A2-2 lnc-NUP58-1 CDK8 MTMR6 ATP8A2
GH13J025285 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 7.5 -14.2 -14183 2.6 BCLAF1 ZNF207 MYC ZNF600 POLR2A ZIC2 YY1 REST CTCF ZNF592 MTMR6 hsa-miR-5095-110 lnc-NUP58-4 CENPJ NUP58 MN309626 AMER2
GH13J025316 Enhancer 0.8 Ensembl ENCODE dbSUPER 12.4 +17.5 17491 4 ZNF362 ZNF366 ATF3 FOS ATF2 CEBPB PRDM1 MTMR6 NUP58 ATP8A2 piR-50437-131 HSALNG0095841
GH13J024910 Enhancer 1.2 FANTOM5 Ensembl ENCODE 6.1 -390.0 -389977 1.8 ZNF592 BHLHE40 MNT EP300 FOXA2 CTBP1 ZNF316 USF2 NFE2 FOXM1 NUP58 MTMR6 RNF17 PARP4 PABPC3 CENPJ HSALNG0095810
GH13J025277 Enhancer 0.4 Ensembl dbSUPER 11.8 -24.2 -24166 0.6 HMBOX1 NUP58 ATP8A2 LINC00463 LINC01053 MN309626 MTMR6 AMER2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around NUP58 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for NUP58

Genomic Locations for NUP58 Gene

Latest Assembly
chr13:25,301,084-25,349,800
(GRCh38/hg38)
Size:
48,717 bases
Orientation:
Plus strand

Previous Assembly
chr13:25,875,763-25,916,559
(GRCh37/hg19 by Entrez Gene)
Size:
40,797 bases
Orientation:
Plus strand

chr13:25,875,662-25,923,938
(GRCh37/hg19 by Ensembl)
Size:
48,277 bases
Orientation:
Plus strand

Genomic View for NUP58 Gene

Genes around NUP58 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NUP58 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NUP58 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NUP58 Gene

Proteins for NUP58 Gene

  • Protein details for NUP58 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9BVL2-NUP58_HUMAN
    Recommended name:
    Nucleoporin p58/p45
    Protein Accession:
    Q9BVL2
    Secondary Accessions:
    • A6NI12
    • B4DZJ1
    • O43160
    • Q5JRG2
    • Q5JRG5

    Protein attributes for NUP58 Gene

    Size:
    599 amino acids
    Molecular mass:
    60897 Da
    Quaternary structure:
    • Component of the p62 complex, a complex at least composed of NUP62, NUP54, and NUP58. Interacts with NUTF2. Interacts with SRP1-alpha and Importin p97 proteins when they are together, but not with SRP1-alpha protein alone (By similarity).
    SequenceCaution:
    • Sequence=BAA23706.2; Type=Erroneous initiation; Evidence={ECO:0000305};
    Miscellaneous:
    • In rat, the p62 complex contains two different isoforms of NUP58. Isoform p45 has however not been isolated in human so far.

    Three dimensional structures from OCA and Proteopedia for NUP58 Gene

    Alternative splice isoforms for NUP58 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for NUP58 Gene

Post-translational modifications for NUP58 Gene

No data available for DME Specific Peptides for NUP58 Gene

Domains & Families for NUP58 Gene

Gene Families for NUP58 Gene

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

Protein Domains for NUP58 Gene

Suggested Antigen Peptide Sequences for NUP58 Gene

GenScript: Design optimal peptide antigens:
  • Nucleoporin-like protein 1 (NUPL1_HUMAN)
  • Nucleoporin like 1 (Q5JRG1_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9BVL2

UniProtKB/Swiss-Prot:

NUP58_HUMAN :
  • 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.
  • Belongs to the NUP58 family.
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.
Family:
  • Belongs to the NUP58 family.
genes like me logo Genes that share domains with NUP58: view

Function for NUP58 Gene

Molecular function for NUP58 Gene

UniProtKB/Swiss-Prot Function:
Component of the nuclear pore complex, a complex required for the trafficking across the nuclear membrane.
GENATLAS Biochemistry:
nucleoporin,component of multiple RNA export pathway

Gene Ontology (GO) - Molecular Function for NUP58 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 17500595
GO:0008139 nuclear localization sequence binding IEA,IBA 21873635
GO:0017056 structural constituent of nuclear pore IEA,IBA 21873635
GO:0042802 identical protein binding IEA --
GO:0044877 protein-containing complex binding IEA --
genes like me logo Genes that share ontologies with NUP58: view
genes like me logo Genes that share phenotypes with NUP58: view

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for NUP58

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for NUP58 Gene

Localization for NUP58 Gene

Subcellular locations from UniProtKB/Swiss-Prot for NUP58 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:P70581}.

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 NUP58 gene
Compartment Confidence
nucleus 5
mitochondrion 3
cytosol 3
plasma membrane 2
extracellular 1
cytoskeleton 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for NUP58 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005635 nuclear envelope TAS --
GO:0005643 nuclear pore IEA,IBA 21873635
GO:0016020 membrane IEA --
GO:0031965 nuclear membrane IEA --
genes like me logo Genes that share ontologies with NUP58: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for NUP58 Gene

Pathways & Interactions for NUP58 Gene

PathCards logo

SuperPathways for NUP58 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 NUP58: view

Gene Ontology (GO) - Biological Process for NUP58 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:0006913 nucleocytoplasmic transport IEA --
GO:0015031 protein transport IEA --
genes like me logo Genes that share ontologies with NUP58: view

No data available for SIGNOR curated interactions for NUP58 Gene

Drugs & Compounds for NUP58 Gene

No Compound Related Data Available

Transcripts for NUP58 Gene

mRNA/cDNA for NUP58 Gene

3 REFSEQ mRNAs :
11 NCBI additional mRNA sequence :
14 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 NUP58

Alternative Splicing Database (ASD) splice patterns (SP) for NUP58 Gene

No ASD Table

Relevant External Links for NUP58 Gene

GeneLoc Exon Structure for
NUP58

Expression for NUP58 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for NUP58

Evidence on tissue expression from TISSUES for NUP58 Gene

  • Nervous system(4.8)
  • Liver(4.3)
genes like me logo Genes that share expression patterns with NUP58: view

Primer products for research

No data available for mRNA expression in normal human tissues , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for NUP58 Gene

Orthologs for NUP58 Gene

This gene was present in the common ancestor of animals.

Orthologs for NUP58 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia NUPL1 29 30
  • 99.72 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia NUPL1 29 30
  • 93.75 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Nupl1 29 16 30
  • 90.06 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Nupl1 29
  • 89.91 (n)
Cow
(Bos Taurus)
Mammalia NUPL1 29 30
  • 89.14 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia NUPL1 30
  • 89 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia NUPL1 30
  • 87 (a)
OneToOne
Chicken
(Gallus gallus)
Aves NUPL1 29 30
  • 83.19 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia NUPL1 30
  • 85 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia nupl1 29
  • 71.37 (n)
Str.19038 29
Zebrafish
(Danio rerio)
Actinopterygii nupl1 29 30
  • 64.51 (n)
OneToOne
Dr.4435 29
Fruit Fly
(Drosophila melanogaster)
Insecta Nup58 30
  • 24 (a)
OneToOne
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.1035 30
  • 39 (a)
OneToOne
Species where no ortholog for NUP58 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • 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)
  • Worm (Caenorhabditis elegans)

Evolution for NUP58 Gene

ENSEMBL:
Gene Tree for NUP58 (if available)
TreeFam:
Gene Tree for NUP58 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for NUP58: view image
Alliance of Genome Resources:
Additional Orthologs for NUP58

Paralogs for NUP58 Gene

Pseudogenes.org Pseudogenes for NUP58 Gene

genes like me logo Genes that share paralogs with NUP58: view

No data available for Paralogs for NUP58 Gene

Variants for NUP58 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for NUP58 Gene

SNP ID Clinical significance and condition Chr 13 pos Variation AA Info Type
rs12430715 Benign: not provided 25,327,027(+) C/G
NM_014089.4(NUP58):c.1143C>G (p.Thr381=)
SYNONYMOUS
rs11556093 -- p.Ala34Thr
rs12871608 -- p.Ser166Pro

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for NUP58 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 NUP58 Gene

Variant ID Type Subtype PubMed ID
esv2747161 CNV deletion 23290073
esv3582237 CNV gain 25503493
nsv435952 OTHER inversion 17901297
nsv561352 CNV loss 21841781
nsv974065 CNV duplication 23825009

Variation tolerance for NUP58 Gene

Residual Variation Intolerance Score: 69.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.56; 82.47% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for NUP58 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
NUP58
Leiden Open Variation Database (LOVD)
NUP58

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NUP58 Gene

Disorders for NUP58 Gene

Additional Disease Information for NUP58

No disorders were found for NUP58 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for NUP58 Gene

Publications for NUP58 Gene

  1. Prediction of the coding sequences of unidentified human genes. VIII. 78 new cDNA clones from brain which code for large proteins in vitro. (PMID: 9455477) Ishikawa K … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 1997) 2 3 4
  2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  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 NUP58 Gene

Sources for NUP58 Gene