NUP50 nucleoporin 50 [Homo sapiens (human)] - Gene

Summary

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: mouse all
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Genomic context

Location:: 22q13.31

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	22	NC_000022.11 (45163925..45188017)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	22	NC_060946.1 (45648418..45672453)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	22	NC_000022.10 (45559806..45583898)

Chromosome 22 - NC_000022.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
Results suggest that Npap60L and Npap60S function differently in nuclear protein import.
Title: Two isoforms of Npap60 (Nup50) differentially regulate nuclear protein import.
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)

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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D8S2279 (e-PCR)
- UniSTS:473907

D12S2114 (e-PCR)
- UniSTS:23136

AL008660 (e-PCR)
- UniSTS:39047

PMC166143P11 (e-PCR)
- UniSTS:271561

RH26205 (e-PCR)
- UniSTS:87774

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 neural tube formation	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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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)

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)
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_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000022.11 Reference GRCh38.p14 Primary Assembly

Range

45163925..45188017

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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)
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)
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)
XM_047441071.1 → XP_047297027.1 nuclear pore complex protein Nup50 isoform X2
XM_047441072.1 → XP_047297028.1 nuclear pore complex protein Nup50 isoform X2

Related

ENSP00000385555.2, ENST00000407019.6
XM_047441073.1 → XP_047297029.1 nuclear pore complex protein Nup50 isoform X3

UniProtKB/TrEMBL

B4E2D3, E9PFD1

Alternate T2T-CHM13v2.0

Genomic

NC_060946.1 Alternate T2T-CHM13v2.0

Range

45648418..45672453

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/Swiss-Prot

B1AHA4, B2RB15, O75644, Q8N6V5, Q9NPM9, Q9NPR6, Q9P1K5, Q9UKX7
XM_054324988.1 → XP_054180963.1 nuclear pore complex protein Nup50 isoform X1

UniProtKB/Swiss-Prot

B1AHA4, B2RB15, O75644, Q8N6V5, Q9NPM9, Q9NPR6, Q9P1K5, Q9UKX7
XM_054324986.1 → XP_054180961.1 nuclear pore complex protein Nup50 isoform X1

UniProtKB/Swiss-Prot

B1AHA4, B2RB15, O75644, Q8N6V5, Q9NPM9, Q9NPR6, Q9P1K5, Q9UKX7
XM_054324989.1 → XP_054180964.1 nuclear pore complex protein Nup50 isoform X2
XM_054324990.1 → XP_054180965.1 nuclear pore complex protein Nup50 isoform X2
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

NM_153684.1: Suppressed sequence

Description

NM_153684.1: This RefSeq record was removed by NCBI staff. Contact [email protected] for further information.