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NUP50 nucleoporin 50 [ Homo sapiens (human) ]

Gene ID: 10762, updated on 5-Mar-2024

Summary

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Official Symbol
NUP50provided by HGNC
Official Full Name
nucleoporin 50provided by HGNC
Primary source
HGNC:HGNC:8065
See related
Ensembl:ENSG00000093000 MIM:604646; AllianceGenome:HGNC:8065
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
NPAP60; NPAP60L
Summary
The nuclear pore complex is a massive structure that extends across the nuclear envelope, forming a gateway that regulates the flow of macromolecules between the nucleus and the cytoplasm. Nucleoporins are the main components of the nuclear pore complex in eukaryotic cells. The protein encoded by this gene is a member of the FG-repeat containing nucleoporins that functions as a soluble cofactor in importin-alpha:beta-mediated nuclear protein import. Pseudogenes of this gene are found on chromosomes 5, 6, and 14. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in bone marrow (RPKM 16.3), lymph node (RPKM 14.7) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
22q13.31
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (45163925..45188017)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (45648418..45672453)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (45559806..45583898)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene PHD finger protein 21B Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:45395779-45396638 Neighboring gene uncharacterized LOC101927551 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:45398138-45398996 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:45398997-45399855 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:45404265-45404866 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr22:45427253-45427890 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr22:45427891-45428528 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:45445441-45446014 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:45447813-45448616 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:45448617-45449421 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:45449422-45450225 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr22:45468530-45469729 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:45489639-45490138 Neighboring gene Sharpr-MPRA regulatory region 5228 Neighboring gene NUP50 divergent transcript Neighboring gene Sharpr-MPRA regulatory region 5104 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13872 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:45559735-45560257 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13874 Neighboring gene uncharacterized LOC105373064 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:45586750-45587250 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 22:45598280 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:45606871-45607371 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:45607503-45608052 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:45608053-45608602 Neighboring gene KIAA0930 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:45619103-45619604 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:45619605-45620104 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:45620306-45621300 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:45621301-45622293 Neighboring gene microRNA 1249 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 22:45629066 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19220 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19219 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19218 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 22:45631393 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13875 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13876 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13877 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13878 Neighboring gene HNF1 motif-containing MPRA enhancer 63 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19221 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19222 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19223 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19224 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:45659291-45660126 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13879 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:45665375-45666026 Neighboring gene ribosomal protein S10 pseudogene 31

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. Two isoforms of Npap60 (Nup50) differentially regulate nuclear protein import. Ogawa Y, et al. Mol Biol Cell, 2010 Feb 15. PMID 20016008, Free PMC Article
  2. Nucleocytoplasmic transport: more than the usual suspects. Swaminathan S, et al. Dev Cell, 2002 Sep. PMID 12361592
  3. Mapping and complex expression pattern of the human NPAP60L nucleoporin gene. Trichet V, et al. Cytogenet Cell Genet, 1999. PMID 10449902
  4. The Nup153-Nup50 protein interface and its role in nuclear import. Makise M, et al. J Biol Chem, 2012 Nov 9. PMID 23007389, Free PMC Article
  5. Nucleoporin Nup50 stabilizes closed conformation of armadillo repeat 10 in importin α5. Pumroy RA, et al. J Biol Chem, 2012 Jan 13. PMID 22130666, Free PMC Article

See all (97) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. results further highlight the antagonistic relationship between 53BP1 and BRCA1, and place Nup153 and Nup50 in a molecular pathway that regulates 53BP1 function by counteracting BRCA1-mediated events.
    Title: Nup153 and Nup50 promote recruitment of 53BP1 to DNA repair foci by antagonizing BRCA1-dependent events.
  2. analysis of the Nup153-Nup50 protein interface and its role in nuclear import
    Title: The Nup153-Nup50 protein interface and its role in nuclear import.
  3. Nucleoporin Nup50 stabilizes closed conformation of armadillo repeat 10 in importin alpha5.
    Title: Nucleoporin Nup50 stabilizes closed conformation of armadillo repeat 10 in importin α5.
  4. Results suggest that Npap60L and Npap60S function differently in nuclear protein import.
    Title: Two isoforms of Npap60 (Nup50) differentially regulate nuclear protein import.
  5. 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.
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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Replication interactions

Interaction Pubs
Knockdown of nucleoporin 50kDa (NUP50) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 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

Clone Names

  • MGC39961

Gene Ontology Provided by GOA

Function Evidence Code Pubs
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 import into nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in nuclear envelope IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nuclear membrane IDA
Inferred from Direct Assay
more info
 PubMed 
part_of nuclear pore NAS
Non-traceable Author Statement
more info
 PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
nuclear pore complex protein Nup50
Names
50 kDa nucleoporin
nuclear pore-associated protein 60L
nucleoporin 50kD
nucleoporin 50kDa
nucleoporin Nup50

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_007172.4 → NP_009103.2  nuclear pore complex protein Nup50 isoform b

    See identical proteins and their annotated locations for NP_009103.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) represents the longer transcript and encodes the longer isoform (b).
    Source sequence(s)
    AL008718, BC070133, Z82243
    Consensus CDS
    CCDS14062.1
    UniProtKB/Swiss-Prot
    B1AHA4, B2RB15, O75644, Q8N6V5, Q9NPM9, Q9NPR6, Q9P1K5, Q9UKX7
    Related
    ENSP00000345895.3, ENST00000347635.9
    Conserved Domains (2) summary
    cd13170
    Location:350 → 466
    RanBD_NUP50; Nucleoporin 50 Ran-binding domain
    pfam08911
    Location:3 → 64
    NUP50; NUP50 (Nucleoporin 50 kDa)

  2. NM_153645.2 → NP_705931.1  nuclear pore complex protein Nup50 isoform a

    See identical proteins and their annotated locations for NP_705931.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR and coding region compared to variant 2. The resulting isoform (a) is shorter at the N-terminus compared to isoform b.
    Source sequence(s)
    AL008718, BC028125, Z82243
    Consensus CDS
    CCDS14063.1
    UniProtKB/Swiss-Prot
    Q9UKX7
    Related
    ENSP00000379403.2, ENST00000396096.6
    Conserved Domains (2) summary
    cd13170
    Location:322 → 438
    RanBD_NUP50; Nucleoporin 50 Ran-binding domain
    pfam08911
    Location:2 → 39
    NUP50; NUP50 (Nucleoporin 50 kDa)

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_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    45163925..45188017
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024452146.2 → XP_024307914.1  nuclear pore complex protein Nup50 isoform X1

    UniProtKB/Swiss-Prot
    B1AHA4, B2RB15, O75644, Q8N6V5, Q9NPM9, Q9NPR6, Q9P1K5, Q9UKX7
    Conserved Domains (2) summary
    cd13170
    Location:350 → 466
    RanBD_NUP50; Nucleoporin 50 Ran-binding domain
    pfam08911
    Location:3 → 64
    NUP50; NUP50 (Nucleoporin 50 kDa)

  2. XM_011529833.2 → XP_011528135.1  nuclear pore complex protein Nup50 isoform X1

    See identical proteins and their annotated locations for XP_011528135.1

    UniProtKB/Swiss-Prot
    B1AHA4, B2RB15, O75644, Q8N6V5, Q9NPM9, Q9NPR6, Q9P1K5, Q9UKX7
    Conserved Domains (2) summary
    cd13170
    Location:350 → 466
    RanBD_NUP50; Nucleoporin 50 Ran-binding domain
    pfam08911
    Location:3 → 64
    NUP50; NUP50 (Nucleoporin 50 kDa)

  3. XM_006724103.2 → XP_006724166.1  nuclear pore complex protein Nup50 isoform X1

    See identical proteins and their annotated locations for XP_006724166.1

    UniProtKB/Swiss-Prot
    B1AHA4, B2RB15, O75644, Q8N6V5, Q9NPM9, Q9NPR6, Q9P1K5, Q9UKX7
    Conserved Domains (2) summary
    cd13170
    Location:350 → 466
    RanBD_NUP50; Nucleoporin 50 Ran-binding domain
    pfam08911
    Location:3 → 64
    NUP50; NUP50 (Nucleoporin 50 kDa)

  4. XM_047441071.1 → XP_047297027.1  nuclear pore complex protein Nup50 isoform X2

  5. XM_047441072.1 → XP_047297028.1  nuclear pore complex protein Nup50 isoform X2

    Related
    ENSP00000385555.2, ENST00000407019.6

  6. XM_047441073.1 → XP_047297029.1  nuclear pore complex protein Nup50 isoform X3

    UniProtKB/TrEMBL
    B4E2D3, E9PFD1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    45648418..45672453
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054324987.1 → XP_054180962.1  nuclear pore complex protein Nup50 isoform X1

    UniProtKB/Swiss-Prot
    B1AHA4, B2RB15, O75644, Q8N6V5, Q9NPM9, Q9NPR6, Q9P1K5, Q9UKX7

  2. XM_054324988.1 → XP_054180963.1  nuclear pore complex protein Nup50 isoform X1

    UniProtKB/Swiss-Prot
    B1AHA4, B2RB15, O75644, Q8N6V5, Q9NPM9, Q9NPR6, Q9P1K5, Q9UKX7

  3. XM_054324986.1 → XP_054180961.1  nuclear pore complex protein Nup50 isoform X1

    UniProtKB/Swiss-Prot
    B1AHA4, B2RB15, O75644, Q8N6V5, Q9NPM9, Q9NPR6, Q9P1K5, Q9UKX7

  4. XM_054324989.1 → XP_054180964.1  nuclear pore complex protein Nup50 isoform X2

  5. XM_054324990.1 → XP_054180965.1  nuclear pore complex protein Nup50 isoform X2

  6. XM_054324991.1 → XP_054180966.1  nuclear pore complex protein Nup50 isoform X3

    UniProtKB/TrEMBL
    B4E2D3, E9PFD1

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_153684.1: Suppressed sequence

    Description
    NM_153684.1: This RefSeq record was removed by NCBI staff. Contact info@ncbi.nlm.nih.gov for further information.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9UKX7.2 GenPept UniProtKB/Swiss-Prot:Q9UKX7

Gene LinkOut

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