Aliases for NUP42 Gene

Aliases for NUP42 Gene

  • Nucleoporin 42 2 3 5
  • Nucleoporin-Like Protein 2 3 4
  • Nucleoporin-Like Protein 1 2 3
  • Nucleoporin Like 2 2 3
  • Nucleoporin NUP42 3 4
  • Nucleoporin HCG1 3 4
  • NUP42 Homolog 3 4
  • NUPL2 3 4
  • NLP-1 3 4
  • CG1 3 4
  • Nucleoporin-42 4
  • H_RG271G13.9 3
  • NLP_1 3
  • HCG1 3

External Ids for NUP42 Gene

Previous HGNC Symbols for NUP42 Gene

  • NUPL2

Summaries for NUP42 Gene

GeneCards Summary for NUP42 Gene

NUP42 (Nucleoporin 42) is a Protein Coding gene. Diseases associated with NUP42 include Lethal Congenital Contracture Syndrome 1 and Neonatal Respiratory Failure. Among its related pathways are Metabolism of proteins and HIV Life Cycle. An important paralog of this gene is LENG9.

UniProtKB/Swiss-Prot Summary for NUP42 Gene

  • Required for the export of mRNAs containing poly(A) tails from the nucleus into the cytoplasm.
  • (Microbial infection) In case of infection by HIV-1, it may participate in the docking of viral Vpr at the nuclear envelope.

Gene Wiki entry for NUP42 Gene

Additional gene information for NUP42 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for NUP42 Gene

Genomics for NUP42 Gene

GeneHancer (GH) Regulatory Elements for NUP42 Gene

Promoters and enhancers for NUP42 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 NUP42 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for NUP42

Genomic Locations for NUP42 Gene

Genomic Locations for NUP42 Gene
chr7:23,181,827-23,201,011
(GRCh38/hg38)
Size:
19,185 bases
Orientation:
Plus strand
chr7:23,221,446-23,240,630
(GRCh37/hg19)
Size:
19,185 bases
Orientation:
Plus strand

Genomic View for NUP42 Gene

Genes around NUP42 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NUP42 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NUP42 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NUP42 Gene

Proteins for NUP42 Gene

  • Protein details for NUP42 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O15504-NUP42_HUMAN
    Recommended name:
    Nucleoporin NUP42
    Protein Accession:
    O15504
    Secondary Accessions:
    • A4D143
    • B4DP42
    • Q49AE7
    • Q9BS49

    Protein attributes for NUP42 Gene

    Size:
    423 amino acids
    Molecular mass:
    44872 Da
    Quaternary structure:
    • Probable component of the nuclear pore complex (NPC). Interacts with nuclear export protein NXF1 (PubMed:10228171). Interacts with GLE1. Able to form a heterotrimer with NUP155 and GLE1 in vitro (PubMed:16000379). Interacts with XPO1 (PubMed:10358091).
    • (Microbial infection) Interacts with the HIV-1 virus proteins Rev and Vpr. The interaction with HIV-1 Rev, a protein that mediates nuclear export of unspliced viral RNAs, suggests that its function may be bypassed by the HIV-1 virus.

    Three dimensional structures from OCA and Proteopedia for NUP42 Gene

    Alternative splice isoforms for NUP42 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for NUP42 Gene

Post-translational modifications for NUP42 Gene

No data available for DME Specific Peptides for NUP42 Gene

Domains & Families for NUP42 Gene

Gene Families for NUP42 Gene

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

Protein Domains for NUP42 Gene

Blocks:
  • Zn-finger, C-x8-C-x5-C-x3-H type
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for NUP42 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ57429, highly similar to Nucleoporin-like 2 (B4DT96_HUMAN)
  • Nucleoporin hCG1 (NUPL2_HUMAN)
  • Nucleoporin like 2 (Q3B7J4_HUMAN)

Graphical View of Domain Structure for InterPro Entry

O15504

UniProtKB/Swiss-Prot:

NUP42_HUMAN :
  • The 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.
Domain:
  • The 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.
genes like me logo Genes that share domains with NUP42: view

Function for NUP42 Gene

Molecular function for NUP42 Gene

UniProtKB/Swiss-Prot Function:
Required for the export of mRNAs containing poly(A) tails from the nucleus into the cytoplasm.
UniProtKB/Swiss-Prot Function:
(Microbial infection) In case of infection by HIV-1, it may participate in the docking of viral Vpr at the nuclear envelope.

Phenotypes From GWAS Catalog for NUP42 Gene

Gene Ontology (GO) - Molecular Function for NUP42 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding HDA 22681889
GO:0005049 nuclear export signal receptor activity IDA 10358091
GO:0005515 protein binding IPI 10358091
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with NUP42: view
genes like me logo Genes that share phenotypes with NUP42: view

Animal Model Products

CRISPR Products

miRNA for NUP42 Gene

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for NUP42

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for NUP42 Gene

Localization for NUP42 Gene

Subcellular locations from UniProtKB/Swiss-Prot for NUP42 Gene

Nucleus, nuclear pore complex. Nucleus membrane; Peripheral membrane protein; Cytoplasmic side. Note=Excluded from the nucleolus. {ECO:0000269 PubMed:10358091}.

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 NUP42 gene
Compartment Confidence
nucleus 5
cytosol 5
plasma membrane 1
extracellular 1
cytoskeleton 1
mitochondrion 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for NUP42 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA 10358091
GO:0005635 colocalizes_with nuclear envelope IDA 22250199
GO:0005643 nuclear pore IEA --
GO:0005654 nucleoplasm IDA --
GO:0005829 cytosol IDA,TAS --
genes like me logo Genes that share ontologies with NUP42: view

Pathways & Interactions for NUP42 Gene

PathCards logo

SuperPathways for NUP42 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 NUP42: view

Pathways by source for NUP42 Gene

Gene Ontology (GO) - Biological Process for NUP42 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:0006611 protein export from nucleus IGI 22250199
GO:0015031 protein transport IEA --
genes like me logo Genes that share ontologies with NUP42: view

No data available for SIGNOR curated interactions for NUP42 Gene

Drugs & Compounds for NUP42 Gene

No Compound Related Data Available

Transcripts for NUP42 Gene

mRNA/cDNA for NUP42 Gene

5 REFSEQ mRNAs :
11 NCBI additional mRNA sequence :
12 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for NUP42

Alternative Splicing Database (ASD) splice patterns (SP) for NUP42 Gene

No ASD Table

Relevant External Links for NUP42 Gene

GeneLoc Exon Structure for
NUP42

Expression for NUP42 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for NUP42

SOURCE GeneReport for Unigene cluster for NUP42 Gene:

Hs.408241

mRNA Expression by UniProt/SwissProt for NUP42 Gene:

O15504-NUP42_HUMAN
Tissue specificity: Ubiquitously expressed.

Evidence on tissue expression from TISSUES for NUP42 Gene

  • Nervous system(3.1)

No data available for mRNA expression in normal human tissues , mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for NUP42 Gene

Orthologs for NUP42 Gene

This gene was present in the common ancestor of chordates.

Orthologs for NUP42 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia NUPL2 31 30
  • 99.76 (n)
OneToOne
dog
(Canis familiaris)
Mammalia NUPL2 31 30
  • 87.35 (n)
OneToOne
cow
(Bos Taurus)
Mammalia NUPL2 31 30
  • 85.95 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Nupl2 17 31 30
  • 78.49 (n)
rat
(Rattus norvegicus)
Mammalia Nupl2 30
  • 77.97 (n)
oppossum
(Monodelphis domestica)
Mammalia NUPL2 31
  • 58 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia NUPL2 31
  • 57 (a)
OneToOne
chicken
(Gallus gallus)
Aves LOC100857529 30
  • 65.43 (n)
NUPL2 31
  • 47 (a)
OneToMany
-- 31
  • 33 (a)
OneToMany
-- 31
  • 32 (a)
OneToMany
-- 31
  • 31 (a)
OneToMany
-- 31
  • 27 (a)
OneToMany
lizard
(Anolis carolinensis)
Reptilia NUPL2 31
  • 44 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia nupl2 30
  • 55.18 (n)
zebrafish
(Danio rerio)
Actinopterygii nupl2 31 30
  • 49.37 (n)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 25 (a)
OneToOne
Species where no ortholog for NUP42 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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)
  • fruit fly (Drosophila melanogaster)
  • 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)
  • worm (Caenorhabditis elegans)

Evolution for NUP42 Gene

ENSEMBL:
Gene Tree for NUP42 (if available)
TreeFam:
Gene Tree for NUP42 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for NUP42: view image

Paralogs for NUP42 Gene

Paralogs for NUP42 Gene

Pseudogenes.org Pseudogenes for NUP42 Gene

genes like me logo Genes that share paralogs with NUP42: view

Variants for NUP42 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for NUP42 Gene

SNP ID Clinical significance and condition Chr 07 pos Variation AA Info Type
rs13243961 - p.Asp391Asn
rs34902971 - p.Lys392Asn

Additional dbSNP identifiers (rs#s) for NUP42 Gene

Structural Variations from Database of Genomic Variants (DGV) for NUP42 Gene

Variant ID Type Subtype PubMed ID
esv2734129 CNV deletion 23290073
nsv1027363 CNV gain 25217958
nsv473535 CNV novel sequence insertion 20440878
nsv526131 CNV loss 19592680
nsv7393 OTHER inversion 18451855

Variation tolerance for NUP42 Gene

Residual Variation Intolerance Score: 78.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.39; 77.06% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for NUP42 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
NUP42

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NUP42 Gene

Disorders for NUP42 Gene

MalaCards: The human disease database

(3) MalaCards diseases for NUP42 Gene - From: DISEASES

Disorder Aliases PubMed IDs
lethal congenital contracture syndrome 1
  • lccs1
neonatal respiratory failure
  • respiratory failure of newborn
amyotrophic lateral sclerosis 1
  • als1
- elite association - COSMIC cancer census association via MalaCards
Search NUP42 in MalaCards View complete list of genes associated with diseases
genes like me logo Genes that share disorders with NUP42: view

No data available for UniProtKB/Swiss-Prot , Genatlas and External Links for NUP42 Gene

Publications for NUP42 Gene

  1. Interaction between the shuttling mRNA export factor Gle1 and the nucleoporin hCG1: a conserved mechanism in the export of Hsp70 mRNA. (PMID: 16000379) Kendirgi F … Wente SR (Molecular biology of the cell 2005) 3 4 23 54
  2. Docking of HIV-1 Vpr to the nuclear envelope is mediated by the interaction with the nucleoporin hCG1. (PMID: 12228227) Le Rouzic E … Benichou S (The Journal of biological chemistry 2002) 3 4 23 54
  3. A new nucleoporin-like protein interacts with both HIV-1 Rev nuclear export signal and CRM-1. (PMID: 10358091) Farjot G … Mikaélian I (The Journal of biological chemistry 1999) 2 3 4 54
  4. Refined mapping of a gene for autosomal dominant progressive sensorineural hearing loss (DFNA5) to a 2-cM region, and exclusion of a candidate gene that is expressed in the cochlea. (PMID: 9450185) Van Laer L … Willems P (European journal of human genetics : EJHG 1997) 2 3 4 54
  5. 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 54

Products for NUP42 Gene

Sources for NUP42 Gene