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    NUP42 nucleoporin 42 [ Homo sapiens (human) ]

    Gene ID: 11097, updated on 10-Dec-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; nuclear envelope; and nucleoplasm. [provided by Alliance of Genome Resources, Dec 2024]
    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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    See NUP42 in Genome Data Viewer
    Location:
    7p15.3
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (23182048..23201006)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (23318572..23337532)
    RS_2024_09 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. 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
    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. 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
    4. 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
    5. The nucleoporin-like protein NLP1 (hCG1) promotes CRM1-dependent nuclear protein export. Waldmann I, et al. J Cell Sci, 2012 Jan 1. PMID 22250199

    See all (65) 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)

    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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    NEW Try the new Transcript table

    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_2024_08

    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

      UniProtKB/TrEMBL
      B4DT96
      Related
      ENSP00000387330.3, ENST00000410002.7

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

      UniProtKB/TrEMBL
      B4DT96

    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

      UniProtKB/TrEMBL
      B4DT96

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

      UniProtKB/TrEMBL
      B4DT96
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O15504.1 GenPept UniProtKB/Swiss-Prot:O15504

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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