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NUP42 nucleoporin 42 [ Homo sapiens (human) ]

Gene ID: 11097, updated on 3-Apr-2024

Summary

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Official Symbol
NUP42provided by HGNC
Official Full Name
nucleoporin 42provided by HGNC
Primary source
HGNC:HGNC:17010
See related
Ensembl:ENSG00000136243 MIM:619998; AllianceGenome:HGNC:17010
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CG1; NLP1; UIP1; hCG1; NLP-1; NLP_1; NUPL2
Summary
Enables nuclear export signal receptor activity. Involved in protein export from nucleus. Located in cytosol and nucleoplasm. Colocalizes with nuclear envelope. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in testis (RPKM 9.0), lymph node (RPKM 6.4) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
7p15.3
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (23182048..23201006)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (23318572..23337532)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (23221667..23240625)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:23144592-23145578 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:23145579-23146565 Neighboring gene KLHL7 divergent transcript Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:23153733-23154678 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr7:23155468-23156110 Neighboring gene kelch like family member 7 Neighboring gene AK3 pseudogene 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25719 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25720 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:23232880-23233451 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18006 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25721 Neighboring gene uncharacterized LOC101927890 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25722 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25723 Neighboring gene MPRA-validated peak6433 silencer Neighboring gene glycoprotein nmb Neighboring gene ReSE screen-validated silencer GRCh37_chr7:23311287-23311491

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Localization of HIV-1 Vpr to the nuclear envelope: impact on Vpr functions and virus replication in macrophages. Jacquot G, et al. Retrovirology, 2007 Nov 26. PMID 18039376, Free PMC Article
  2. Interaction between the shuttling mRNA export factor Gle1 and the nucleoporin hCG1: a conserved mechanism in the export of Hsp70 mRNA. Kendirgi F, et al. Mol Biol Cell, 2005 Sep. PMID 16000379, Free PMC Article
  3. 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. Van Laer L, et al. Eur J Hum Genet, 1997 Nov-Dec. PMID 9450185
  4. The nucleoporin-like protein NLP1 (hCG1) promotes CRM1-dependent nuclear protein export. Waldmann I, et al. J Cell Sci, 2012 Jan 1. PMID 22250199
  5. Characterization of the molecular determinants of primary HIV-1 Vpr proteins: impact of the Q65R and R77Q substitutions on Vpr functions. Jacquot G, et al. PLoS One, 2009 Oct 19. PMID 19838296, Free PMC Article

See all (60) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. NLP1 functions as an accessory factor in CRM1-dependent nuclear protein export
    Title: The nucleoporin-like protein NLP1 (hCG1) promotes CRM1-dependent nuclear protein export.
  2. Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
    Title: A whole genome association study of mother-to-child transmission of HIV in Malawi.
  3. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
  4. Data show that human nucleoporin CG1 participates in the docking of Vpr at the nuclear envelope, which may contribute to the disruption of the nuclear envelope and to the nuclear import of the viral DNA.
    Title: Docking of HIV-1 Vpr to the nuclear envelope is mediated by the interaction with the nucleoporin hCG1.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Rev rev NLP-1 interacts with CRM-1 (exportin 1), one of the cellular factors that binds to Rev and is required for Rev-mediated nuclear export of HIV-1 mRNA PubMed
rev The central FG repeat-containing region (amino acids 213-380) of NLP-1, also known as hCG1, specifically interacts with the Rev nuclear export signal (amino acids 75-83) PubMed
Vpr vpr HIV-1 (NL43) Vpr K27M mutant demonstrates decreased or absent TNF production from MT4C5 cells suggesting that hCG1-Vpr interaction affects TNF production from HIV-1 infected cells PubMed
vpr HIV-1 Vpr L23F and K27M mutants are specifically altered for their binding to hCG1 PubMed
vpr Nucleoporin CG1 (hCG1; nucleoporin-like protein 1; NLP-1) interacts with HIV-1 Vpr to mediate the docking of Vpr at the nuclear envelope which may contribute to the disruption of the nuclear envelope and to the nuclear import of viral DNA by Vpr PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA binding HDA PubMed 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables nuclear export signal receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables nuclear export signal receptor activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in mRNA transport IEA
Inferred from Electronic Annotation
more info
  
involved_in nucleocytoplasmic transport NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in protein export from nucleus IGI
Inferred from Genetic Interaction
more info
 PubMed 
Component Evidence Code Pubs
located_in cytosol IDA
Inferred from Direct Assay
more info
  
located_in cytosol TAS
Traceable Author Statement
more info
  
colocalizes_with nuclear envelope IBA
Inferred from Biological aspect of Ancestor
more info
  
colocalizes_with nuclear envelope IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nuclear envelope IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nuclear membrane IEA
Inferred from Electronic Annotation
more info
  
part_of nuclear pore NAS
Non-traceable Author Statement
more info
 PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
nucleoporin NUP42
Names
H_RG271G13.9
NUP42 homolog
nucleoporin hCG1
nucleoporin like 2
nucleoporin-like protein 1
nucleoporin-like protein 2

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001370443.1 → NP_001357372.1  nucleoporin NUP42 isoform 1

    Status: VALIDATED

    Source sequence(s)
    AC005082
    UniProtKB/TrEMBL
    C9JYA1
    Related
    ENSP00000401475.1, ENST00000413919.1
    Conserved Domains (2) summary
    pfam15967
    Location:238 → 340
    Nucleoporin_FG2; Nucleoporin FG repeated region
    pfam18345
    Location:4 → 22
    zf_CCCH_4; Zinc finger domain

  2. NM_001370444.1 → NP_001357373.1  nucleoporin NUP42 isoform 3

    Status: VALIDATED

    Source sequence(s)
    AC005082
    UniProtKB/TrEMBL
    Q3B7J4
    Conserved Domains (2) summary
    pfam15967
    Location:210 → 312
    Nucleoporin_FG2; Nucleoporin FG repeated region
    pfam18345
    Location:4 → 22
    zf_CCCH_4; Zinc finger domain

  3. NM_001370445.1 → NP_001357374.1  nucleoporin NUP42 isoform 4

    Status: VALIDATED

    Source sequence(s)
    AC005082
    Conserved Domains (1) summary
    pfam15967
    Location:90 → 192
    Nucleoporin_FG2; Nucleoporin FG repeated region

  4. NM_001370446.1 → NP_001357375.1  nucleoporin NUP42 isoform 5

    Status: VALIDATED

    Source sequence(s)
    AC005082

  5. NM_007342.3 → NP_031368.1  nucleoporin NUP42 isoform 2

    See identical proteins and their annotated locations for NP_031368.1

    Status: VALIDATED

    Source sequence(s)
    AI352214, U97198
    Consensus CDS
    CCDS5379.1
    UniProtKB/Swiss-Prot
    A4D143, B4DP42, O15504, Q49AE7, Q9BS49
    UniProtKB/TrEMBL
    Q3B7J4
    Related
    ENSP00000258742.5, ENST00000258742.10
    Conserved Domains (2) summary
    pfam15967
    Location:213 → 315
    Nucleoporin_FG2; Nucleoporin FG repeated region
    pfam18345
    Location:4 → 22
    zf_CCCH_4; Zinc finger domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    23182048..23201006
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047419833.1 → XP_047275789.1  nucleoporin NUP42 isoform X2

    Related
    ENSP00000387330.3, ENST00000410002.7

  2. XM_047419832.1 → XP_047275788.1  nucleoporin NUP42 isoform X1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    23318572..23337532
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054357165.1 → XP_054213140.1  nucleoporin NUP42 isoform X2

  2. XM_054357164.1 → XP_054213139.1  nucleoporin NUP42 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O15504.1 GenPept UniProtKB/Swiss-Prot:O15504

Gene LinkOut

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