NUP153 nucleoporin 153 [Homo sapiens (human)] - Gene

Summary

Official Symbol: NUP153provided by HGNC
Official Full Name: nucleoporin 153provided by HGNC
Primary source: HGNC:HGNC:8062
See related: Ensembl:ENSG00000124789 MIM:603948; AllianceGenome:HGNC:8062
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: N153; HNUP153
Summary: Nuclear pore complexes regulate the transport of macromolecules between the nucleus and cytoplasm. They are composed of at least 100 different polypeptide subunits, many of which belong to the nucleoporin family. Nucleoporins are glycoproteins found in nuclear pores and contain characteristic pentapeptide XFXFG repeats as well as O-linked N-acetylglucosamine residues oriented towards the cytoplasm. The protein encoded by this gene has three distinct domains: a N-terminal region containing a pore targeting and an RNA-binding domain domain, a central region containing multiple zinc finger motifs, and a C-terminal region containing multiple XFXFG repeats. Alternative splicing results in multiple transcript variants of this gene. [provided by RefSeq, May 2013]
Expression: Ubiquitous expression in testis (RPKM 19.5), bone marrow (RPKM 18.1) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 6p22.3

Exon count:: 23

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	6	NC_000006.12 (17615037..17706925, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	6	NC_060930.1 (17487223..17579176, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	6	NC_000006.11 (17615268..17707156, complement)

Chromosome 6 - NC_000006.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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?

Nucleoporin 153 deficiency in adult neural stem cells defines a pathological protein-network signature and defective neurogenesis in a mouse model of AD.
Title: Nucleoporin 153 deficiency in adult neural stem cells defines a pathological protein-network signature and defective neurogenesis in a mouse model of AD.
Human RTEL1 Interacts with KPNB1 (Importin beta) and NUP153 and Connects Nuclear Import to Nuclear Envelope Stability in S-Phase.
Title: Human RTEL1 Interacts with KPNB1 (Importin β) and NUP153 and Connects Nuclear Import to Nuclear Envelope Stability in S-Phase.
NUP153 promotes HCC cells proliferation via c-Myc-mediated downregulation of P15[INK4b].
Title: NUP153 promotes HCC cells proliferation via c-Myc-mediated downregulation of P15(INK4b).
Defining the HIV Capsid Binding Site of Nucleoporin 153.
Title: Defining the HIV Capsid Binding Site of Nucleoporin 153.
Viral protein X unlocks the nuclear pore complex through a human Nup153-dependent pathway to promote nuclear translocation of the lentiviral genome.
Title: Viral protein X unlocks the nuclear pore complex through a human Nup153-dependent pathway to promote nuclear translocation of the lentiviral genome.
Seh1 is not required for the association of the Nup107 complex with mitotic chromosomes, but it is essential for the association of both the GATOR2 complex and nucleoporin Nup153 with mitotic chromosomes.
Title: Seh1 targets GATOR2 and Nup153 to mitotic chromosomes.
Nup153 effectively assembled Nup98, Nup62 and Pom121 of the nuclear pore complex at the end of the mitosis.
Title: Roles of Nup133, Nup153 and membrane fenestrations in assembly of the nuclear pore complex at the end of mitosis.
Nup153 is essential for the HIV-1 nuclear import in nondividing cells, and CPSF6 is important for HIV-1 integration.
Title: Nup153 Unlocks the Nuclear Pore Complex for HIV-1 Nuclear Translocation in Nondividing Cells.
Despite the requirement of all three nucleoporins for accurate NHEJ, only Nup153 is needed for proper nuclear import of 53BP1 and SENP1-dependent sumoylation of 53BP1. Our data support the role of Nup153 as an important regulator of 53BP1 activity and efficient NHEJ.
Title: Localisation of Nup153 and SENP1 to nuclear pore complexes is required for 53BP1-mediated DNA double-strand break repair.
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.

Submit: New GeneRIF Correction See all GeneRIFs (43)

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

EBI GWAS Catalog

Description
Many sequence variants affecting diversity of adult human height. EBI GWAS Catalog EBI GWAS CatalogPubMed
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. EBI GWAS Catalog EBI GWAS CatalogPubMed

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
HIV-1 replication requires amino acids 896-1475 in NUP153; deletion of the c-terminal domain of NUP153 amino acid stretch disrupts viral infectivity	PubMed
HIV-1 replication requires NUP153 for import into the nucleus as shown through shRNA treatment	PubMed
Knockdown of CPSF6, TNPO3, or NUP153 through siRNA leads to decreased CA and proviral DNA nuclear entry	PubMed
Depletion of nucleoporin 153kDa (NUP153) by shRNA inhibits HIV-1 infection in human Jurkat lymphocytes	PubMed
HIV-1 requires NUP153 and TPR for infectivity as shown by shRNA knockdown experiments utilizing HeLa-derived P4-CCR5 cells and jurkat T cells	PubMed
shRNA knockdown of NUP153 renders cells less permissive to HIV-1 WT; HIV-1 is enhanced by NUP153	PubMed
Knockdown of nucleoporin 153kDa (NUP153) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells	PubMed
Knockdown of nucleoporin 153kDa (NUP153) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1	PubMed

Protein interactions

Protein	Gene	Interaction	Pubs
Rev	rev	antibodies to nup153 can block the nuclear export of Rev as well as Rev-dependent RNA export	PubMed
	rev	nup153 is involved in Rev-mediated nuclear export of HIV-1 mRNA through an interaction with eukaryotic initiation factor 5A (eIF-5A) which binds to Rev	PubMed
Tat	tat	Interaction of HIV-1 Tat with Nup153 in T-cells is identified by a proteomic strategy based on affinity chromatography	PubMed
Vpr	vpr	HIV-1 Vpr co-immunoprecipitates in vitro-translated human Nup153	PubMed
capsid	gag	HIV-1 CA binds NUP153; HIV-1 CA mutations S41A, Q67H, V165I and V172I in combination abrogate this interaction	PubMed
	gag	HIV-1 CA interacts with NUP153, which is required for replication	PubMed
	gag	Full-length NUP153 binids to the CA hexamer with lower affinity compared with the CPSF6 peptide	PubMed
	gag	Amino-acid residues 1199-1475 in the C-terminal phenylalanine-glycine motifs of NUP153 are involved in the binding to HIV-1 CA. Mutation of CA Asn74 to Ala diminishes the binding, while mutation to Asp enhances the binding	PubMed
	gag	Nucleoporins NUP153 and NUP98 bind in vitro assembled HIV-1 CA-NC complexes, suggesting that both nucleoporins bind the HIV-1 core during the early stages of infection	PubMed
	gag	HIV-1 CA mutant N74D and depletion of NUP153 and LEDGF/p75 significantly reduce HIV-1 DNA integration into gene-rich regions of chromosomes and gene bodies	PubMed
integrase	gag-pol	Depletion of the nuclear pore complex component NUP153 by RNAi blocks HIV-1 nuclear import and integration efficiency as assayed by the appearance of circular viral DNAs, suggesting HIV-1 IN interacts with NUP153 in cells	PubMed
	gag-pol	NUP153 dependency during HIV-1 infection is dependent on HIV-1 integrase (IN)	PubMed
	gag-pol	NTF2 is enriched at the nuclear envelope and interacts with NUP153, When added in excess to the import assay, NUP153C inhibited the nuclear import of IN.	PubMed
	gag-pol	HIV-1 IN binds directly to nucleoporin NUP153 in cells. The binding involves the C-terminal FxFG-rich region of NUP153	PubMed
nucleocapsid	gag	Nucleoporins NUP153 and NUP98 bind in vitro assembled HIV-1 CA-NC complexes, suggesting that both nucleoporins bind the HIV-1 core during the early stages of infection	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

D6S1356 (e-PCR)
- UniSTS:153607

D9S2018 (e-PCR)
- UniSTS:78930

RH66430 (e-PCR)
- UniSTS:40823

RH80550 (e-PCR)
- UniSTS:88703

RH68534 (e-PCR)
- UniSTS:72835

WI-19208 (e-PCR)
- UniSTS:16267

G17061 (e-PCR)
- UniSTS:75754

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables molecular condensate scaffold activity	IDA Inferred from Direct Assay more info	PubMed
enables nuclear localization sequence binding	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein-membrane adaptor activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables structural constituent of nuclear pore	IBA Inferred from Biological aspect of Ancestor more info
enables structural constituent of nuclear pore	IDA Inferred from Direct Assay more info	PubMed
enables structural constituent of nuclear pore	IMP Inferred from Mutant Phenotype more info	PubMed

Process	Evidence Code	Pubs
involved_in RNA export from nucleus	IBA Inferred from Biological aspect of Ancestor more info
involved_in amyloid fibril formation	IPI Inferred from Physical Interaction more info	PubMed
involved_in mRNA transport	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of RNA export from nucleus	IDA Inferred from Direct Assay more info	PubMed
involved_in nuclear pore complex assembly	IMP Inferred from Mutant Phenotype more info	PubMed
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
involved_in symbiont entry into host cell	IEA Inferred from Electronic Annotation more info
involved_in viral penetration into host nucleus	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in cytosol	IDA Inferred from Direct Assay more info
located_in host cell	IEA Inferred from Electronic Annotation more info
located_in membrane	IMP Inferred from Mutant Phenotype more info	PubMed
located_in nuclear envelope	IDA Inferred from Direct Assay more info	PubMed
located_in nuclear inclusion body	IDA Inferred from Direct Assay more info	PubMed
located_in nuclear membrane	IDA Inferred from Direct Assay more info	PubMed
located_in nuclear periphery	IDA Inferred from Direct Assay more info	PubMed
part_of nuclear pore	IBA Inferred from Biological aspect of Ancestor more info
part_of nuclear pore	IDA Inferred from Direct Assay more info	PubMed
part_of nuclear pore	NAS Non-traceable Author Statement more info	PubMed
part_of nuclear pore nuclear basket	IDA Inferred from Direct Assay more info	PubMed
located_in nucleolus	IDA Inferred from Direct Assay more info
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 Nup153

Names: 153 kDa nucleoporin; nuclear pore complex protein hnup153; nucleoporin 153kD; nucleoporin 153kDa; nucleoporin Nup153

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_001278209.2 → NP_001265138.1 nuclear pore complex protein Nup153 isoform 1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).

Source sequence(s)

AB210024, AI948895, AK295644, AL138724, AL597150, BC052965

Consensus CDS

CCDS64359.1

Related

ENSP00000444029.1, ENST00000537253.5

Conserved Domains (4) summary

sd00025
Location:693 → 712

zf-RanBP2; RanBP2-type Zn finger [structural motif]

pfam00641
Location:754 → 782

zf-RanBP; Zn-finger in Ran binding protein and others

pfam08604
Location:113 → 660

Nup153; Nucleoporin Nup153-like

pfam10599
Location:1417 → 1506

Nup_retrotrp_bd; Retro-transposon transporting motif
NM_001278210.2 → NP_001265139.1 nuclear pore complex protein Nup153 isoform 3

See identical proteins and their annotated locations for NP_001265139.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) lacks two alternate in-frame exons in the 5' coding region compared to variant 1. It encodes isoform 3 which is shorter than isoform 1.

Source sequence(s)

AB210024, AI948895, AL138724, AL597150, DA856239

Consensus CDS

CCDS75407.1

Related

ENSP00000478627.1, ENST00000613258.4

Conserved Domains (5) summary

sd00025
Location:620 → 639

zf-RanBP2; RanBP2-type Zn finger [structural motif]

pfam10599
Location:1344 → 1433

Nup_retrotrp_bd; Retro-transposon transporting motif

pfam00641
Location:681 → 709

zf-RanBP; Zn-finger in Ran binding protein and others

pfam08604
Location:113 → 588

Nup153; Nucleoporin Nup153-like

pfam15967
Location:1223 → 1399

Nucleoporin_FG2; Nucleoporin FG repeated region
NM_005124.4 → NP_005115.2 nuclear pore complex protein Nup153 isoform 2

See identical proteins and their annotated locations for NP_005115.2

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' coding region compared to variant 1. It encodes isoform 2 which is shorter than isoform 1.

Source sequence(s)

AB210024, AI948895, AL138724, AL597150, BC052965

Consensus CDS

CCDS4541.1

UniProtKB/Swiss-Prot

B4DIK2, E7EPX5, F6QR24, P49790, Q4LE47, Q5T9I7, Q7Z743

Related

ENSP00000262077.3, ENST00000262077.3

Conserved Domains (5) summary

sd00025
Location:662 → 681

zf-RanBP2; RanBP2-type Zn finger [structural motif]

pfam10599
Location:1386 → 1475

Nup_retrotrp_bd; Retro-transposon transporting motif

pfam00641
Location:723 → 751

zf-RanBP; Zn-finger in Ran binding protein and others

pfam08604
Location:113 → 621

Nup153; Nucleoporin Nup153-like

pfam15967
Location:1265 → 1441

Nucleoporin_FG2; Nucleoporin FG repeated region