NUP98 nucleoporin 98 and 96 precursor [Homo sapiens (human)] - Gene

Summary

Official Symbol: NUP98provided by HGNC
Official Full Name: nucleoporin 98 and 96 precursorprovided by HGNC
Primary source: HGNC:HGNC:8068
See related: Ensembl:ENSG00000110713 MIM:601021; AllianceGenome:HGNC:8068
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: ADIR2; NUP96; NUP196; Nup98-96
Summary: Nuclear pore complexes (NPCs) regulate the transport of macromolecules between the nucleus and cytoplasm, and are composed of many polypeptide subunits, many of which belong to the nucleoporin family. This gene belongs to the nucleoporin gene family and encodes a 186 kDa precursor protein that undergoes autoproteolytic cleavage to generate a 98 kDa nucleoporin and 96 kDa nucleoporin. The 98 kDa nucleoporin contains a Gly-Leu-Phe-Gly (GLGF) repeat domain and participates in many cellular processes, including nuclear import, nuclear export, mitotic progression, and regulation of gene expression. The 96 kDa nucleoporin is a scaffold component of the NPC. Proteolytic cleavage is important for targeting of the proteins to the NPC. Translocations between this gene and many other partner genes have been observed in different leukemias. Rearrangements typically result in chimeras with the N-terminal GLGF domain of this gene to the C-terminus of the partner gene. Alternative splicing results in multiple transcript variants encoding different isoforms, at least two of which are proteolytically processed. Some variants lack the region that encodes the 96 kDa nucleoporin. [provided by RefSeq, Feb 2016]
Expression: Broad expression in testis (RPKM 38.3), bone marrow (RPKM 17.8) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 11p15.4

Exon count:: 34

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	11	NC_000011.10 (3675010..3797554, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	11	NC_060935.1 (3740382..3862891, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	11	NC_000011.9 (3696240..3818784, complement)

Chromosome 11 - NC_000011.10 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?

Allogeneic hematopoietic stem cell transplantation for adult acute myeloid leukemia patients with nucleoporin 98 (NUP98) gene rearrangements: a real-world study in China.
Title: Allogeneic hematopoietic stem cell transplantation for adult acute myeloid leukemia patients with nucleoporin 98 (NUP98) gene rearrangements: a real-world study in China.
NUP98::Nsd1 and FLT3-ITD collaborate to generate acute myeloid leukemia.
Title: NUP98::Nsd1 and FLT3-ITD collaborate to generate acute myeloid leukemia.
Molecular interactions of FG nucleoporin repeats at high resolution.
Title: Molecular interactions of FG nucleoporin repeats at high resolution.
Adult acute myeloid leukemia patients with NUP98 rearrangement have frequent cryptic translocations and unfavorable outcome.
Title: Adult acute myeloid leukemia patients with NUP98 rearrangement have frequent cryptic translocations and unfavorable outcome.
Knockdown of FLT4, Nup98, and Nup205 Cellular Genes Effectively Suppresses the Reproduction of Influenza Virus Strain A/WSN/1933 (H1N1) In vitro.
Title: Knockdown of FLT4, Nup98, and Nup205 Cellular Genes Effectively Suppresses the Reproduction of Influenza Virus Strain A/WSN/1933 (H1N1) In vitro.
Distinct pathologic feature of myeloid neoplasm with t(v;11p15); NUP98 rearrangement.
Title: Distinct pathologic feature of myeloid neoplasm with t(v;11p15); NUP98 rearrangement.
Phase separation drives aberrant chromatin looping and cancer development.
Title: Phase separation drives aberrant chromatin looping and cancer development.
The Retinoblastoma Tumor Suppressor Is Required for the NUP98-HOXA9-Induced Aberrant Nuclear Envelope Phenotype.
Title: The Retinoblastoma Tumor Suppressor Is Required for the NUP98-HOXA9-Induced Aberrant Nuclear Envelope Phenotype.
Mutant Idh2 Cooperates with a NUP98-HOXD13 Fusion to Induce Early Immature Thymocyte Precursor ALL.
Title: Mutant Idh2 Cooperates with a NUP98-HOXD13 Fusion to Induce Early Immature Thymocyte Precursor ALL.
[Clinical Characteristics and Prognosis of Adult Acute Myeloid Leukemia with NUP98 Gene Rearrangement].
Title: [Clinical Characteristics and Prognosis of Adult Acute Myeloid Leukemia with NUP98 Gene Rearrangement].

Submit: New GeneRIF Correction See all GeneRIFs (111)

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
Genome-wide association study of a heart failure related metabolomic profile among African Americans in the Atherosclerosis Risk in Communities (ARIC) study. 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
Knockdown of nucleoporin 98kDa (NUP98) by shRNA library screening inhibits HIV-1 replication in cultured Jurkat T-cells	PubMed
Knockdown of nucleoporin 98kDa (NUP98) 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	nup98 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
	rev	the FG repeat region of nup98 interacts directly with the nuclear export sequence of HIV-1 Rev, suggesting a physiological role for nup98 in modulating Rev-dependent RNA export during HIV infection	PubMed
	rev	Rev can recruit nup98 to the nucleolus	PubMed
	rev	the FG-containing repeat domain of Nup98 can inhibit Rev-mediated expression of viral proteins	PubMed
Tat	tat	Interaction of HIV-1 Tat with Nup98 in T-cells is identified by a proteomic strategy based on affinity chromatography	PubMed
capsid	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
integrase	gag-pol	Nucleoporin 98kD protein (NUP98) is involved in nuclear import for HIV-1 integration by IN	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

RH18062 (e-PCR)
- UniSTS:73995

D11S1883 (e-PCR)
- UniSTS:2574

D11S3624 (e-PCR)
- UniSTS:152861

SHGC-150849 (e-PCR)
- UniSTS:173611

G29170 (e-PCR)
- UniSTS:344

D11S1254 (e-PCR)
- UniSTS:148346

RH81020 (e-PCR)
- UniSTS:88212

G59577 (e-PCR)
- UniSTS:136881

SHGC-106541 (e-PCR)
- UniSTS:169929

G30118 (e-PCR)
- UniSTS:11212

RH48599 (e-PCR)
- UniSTS:46823

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables mRNA binding	IMP Inferred from Mutant Phenotype more info	PubMed
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 promoter-specific chromatin binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables serine-type peptidase activity	IEA Inferred from Electronic Annotation more info
enables structural constituent of nuclear pore	IBA Inferred from Biological aspect of Ancestor more info
enables structural constituent of nuclear pore	IMP Inferred from Mutant Phenotype more info	PubMed
enables structural constituent of nuclear pore	NAS Non-traceable Author Statement more info	PubMed
enables transcription coactivator activity	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 mRNA transport	IEA Inferred from Electronic Annotation more info
involved_in nuclear pore complex assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in nuclear pore organization	NAS Non-traceable Author Statement more info	PubMed
involved_in nucleocytoplasmic transport	TAS Traceable Author Statement more info	PubMed
involved_in positive regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of mRNA splicing, via spliceosome	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery	IBA Inferred from Biological aspect of Ancestor more info
involved_in protein import into nucleus	IBA Inferred from Biological aspect of Ancestor more info
involved_in proteolysis	IEA Inferred from Electronic Annotation more info
involved_in telomere tethering at nuclear periphery	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in cytosol	TAS Traceable Author Statement more info
colocalizes_with kinetochore	IDA Inferred from Direct Assay more info	PubMed
located_in nuclear body	IDA Inferred from Direct Assay more info	PubMed
located_in nuclear envelope	IDA Inferred from Direct Assay more info	PubMed
located_in nuclear envelope	TAS Traceable Author Statement more info
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	IDA Inferred from Direct Assay more info	PubMed
part_of nuclear pore	NAS Non-traceable Author Statement more info	PubMed
part_of nuclear pore cytoplasmic filaments	IBA Inferred from Biological aspect of Ancestor more info
part_of nuclear pore nuclear basket	IDA Inferred from Direct Assay more info	PubMed
part_of nuclear pore outer ring	IDA Inferred from Direct Assay more info	PubMed
part_of nuclear pore outer ring	NAS Non-traceable Author Statement more info	PubMed
located_in nucleoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	TAS Traceable Author Statement more info
part_of ribonucleoprotein complex	IMP Inferred from Mutant Phenotype more info	PubMed

General protein information

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Preferred Names: nuclear pore complex protein Nup98-Nup96; nuclear pore complex protein Nup98

Names: GLFG-repeat containing nucleoporin; NUP98/PHF23 fusion 2 protein; Nup98-Nup96; nucleoporin 96; nucleoporin 98kD; nucleoporin 98kDa

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_001365125.2 → NP_001352054.1 nuclear pore complex protein Nup98-Nup96 isoform 5

Status: REVIEWED

Description

Transcript Variant: This variant (5) contains an alternate in-frame exon in the 3' coding region, compared to variant 1. The encoded isoform (5) has the same N- and C-termini, but is longer than isoform 1. This isoform (5) may undergo proteolytic processing similar to that of isoform 1.

Source sequence(s)

AC060812, AC090587

UniProtKB/TrEMBL

A0A8V8TQF7

Conserved Domains (4) summary

pfam04096
Location:723 → 862

Nucleoporin2; Nucleoporin autopeptidase

pfam12110
Location:1348 → 1637

Nup96; Nuclear protein 96

pfam13634
Location:40 → 149

Nucleoporin_FG; Nucleoporin FG repeat region

cl25496
Location:243 → 666

Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
NM_001365126.2 → NP_001352055.1 nuclear pore complex protein Nup98-Nup96 isoform 6 precursor

Status: REVIEWED

Description

Transcript Variant: This variant (6) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. The encoded isoform (6) has the same N- and C-termini, but is longer than isoform 1. This isoform (6) may undergo proteolytic processing similar to that of isoform 1.

Source sequence(s)

AC060812, AC090587

Consensus CDS

CCDS91412.1

UniProtKB/Swiss-Prot

P52948, Q8IUT2, Q8WYB0, Q96E54, Q9H3Q4, Q9NT02, Q9UF57, Q9UHX0, Q9Y6J4, Q9Y6J5

UniProtKB/TrEMBL

A0A8V8TQF7

Related

ENSP00000352091.5, ENST00000359171.8

Conserved Domains (4) summary

pfam04096
Location:740 → 879

Nucleoporin2; Nucleoporin autopeptidase

pfam12110
Location:1334 → 1623

Nup96; Nuclear protein 96

pfam13634
Location:40 → 149

Nucleoporin_FG; Nucleoporin FG repeat region

cl27636
Location:208 → 480

PPE; PPE family
NM_001365127.2 → NP_001352056.1 nuclear pore complex protein Nup98-Nup96 isoform 7 precursor

Status: REVIEWED

Description

Transcript Variant: This variant (7) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. The encoded isoform (7) has the same N- and C-termini, but is shorter than isoform 1. This isoform (7) may undergo proteolytic processing similar to that of isoform 1.

Source sequence(s)

AC060812, AC090587

Consensus CDS

CCDS91414.1

UniProtKB/TrEMBL

A0A8V8TQF7, H0YEN4

Related

ENSP00000436226.2, ENST00000527104.6

Conserved Domains (4) summary

pfam04096
Location:715 → 854

Nucleoporin2; Nucleoporin autopeptidase

pfam12110
Location:1309 → 1598

Nup96; Nuclear protein 96

pfam13634
Location:40 → 149

Nucleoporin_FG; Nucleoporin FG repeat region

cl25496
Location:243 → 658

Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
NM_001365128.2 → NP_001352057.1 nuclear pore complex protein Nup98-Nup96 isoform 8 precursor

Status: REVIEWED

Description

Transcript Variant: This variant (8) uses two alternate in-frame splice sites in the 5' coding region, compared to variant 1. The encoded isoform (8) has the same N- and C-termini, but is shorter than isoform 1. This isoform (8) may undergo proteolytic processing similar to that of isoform 1.

Source sequence(s)

AC060812, AC090587

Consensus CDS

CCDS91415.1

UniProtKB/TrEMBL

A0A8V8TQF7, A0A8V8TR21

Related

ENSP00000515088.1, ENST00000700598.1

Conserved Domains (4) summary

pfam04096
Location:706 → 845

Nucleoporin2; Nucleoporin autopeptidase

pfam12110
Location:1300 → 1589

Nup96; Nuclear protein 96

pfam13634
Location:40 → 149

Nucleoporin_FG; Nucleoporin FG repeat region

cl25496
Location:229 → 649

Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
NM_001365129.2 → NP_001352058.1 nuclear pore complex protein Nup98-Nup96 isoform 9

Status: REVIEWED

Description

Transcript Variant: This variant (9) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1. The encoded isoform (9) has the same N- and C-termini, but is shorter than isoform 1. This isoform (9) may undergo proteolytic processing similar to that of isoform 1.

Source sequence(s)

AC060812, AC090587

Consensus CDS

CCDS91413.1

UniProtKB/TrEMBL

A0A8V8TQF7, H0YCR0

Related

ENSP00000432142.2, ENST00000529379.2

Conserved Domains (3) summary

pfam04096
Location:676 → 815

Nucleoporin2; Nucleoporin autopeptidase

pfam12110
Location:1270 → 1559

Nup96; Nuclear protein 96

pfam13634
Location:40 → 149

Nucleoporin_FG; Nucleoporin FG repeat region
NM_005387.7 → NP_005378.4 nuclear pore complex protein Nup98 isoform 3 precursor

See identical proteins and their annotated locations for NP_005378.4

Status: REVIEWED

Description

Transcript Variant: This variant (3) uses an alternate in-frame splice site in the 5' coding region, lacks multiple exons, and its 3' terminal exon extends past a splice site that is used in variant 1. This results in a novel 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (2) has an additional internal segment and a shorter and distinct C-terminus, compared to isoform 1. This isoform (3) may undergo proteolytic processing similar to that of isoform 2.

Source sequence(s)

AB040538, AC090587, AI436199, DB084013

Consensus CDS

CCDS41605.1

UniProtKB/TrEMBL

A8KA17

Related

ENSP00000380202.4, ENST00000397007.10

Conserved Domains (2) summary

COG5651
Location:208 → 480

COG5651; PPE-repeat protein [Function unknown]

pfam04096
Location:740 → 880

Nucleoporin2; Nucleoporin autopeptidase
NM_016320.5 → NP_057404.2 nuclear pore complex protein Nup98-Nup96 isoform 1 precursor

See identical proteins and their annotated locations for NP_057404.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes isoform 1.

Source sequence(s)

AF071076, AF231130, BC012906, DB084013

Consensus CDS

CCDS7746.1

UniProtKB/TrEMBL

A0A8V8TQF7

Related

ENSP00000316032.7, ENST00000324932.12

Conserved Domains (4) summary

pfam05109
Location:243 → 666

Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)

pfam04096
Location:721 → 863

Nucleoporin2; Nucleoporin autopeptidase

pfam12110
Location:1315 → 1606

Nup96; Nuclear protein 96

pfam13634
Location:40 → 149

Nucleoporin_FG; Nucleoporin FG repeat region
NM_139131.5 → NP_624357.1 nuclear pore complex protein Nup98 isoform 2 precursor

See identical proteins and their annotated locations for NP_624357.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks multiple exons and its 3' terminal exon extends past a splice site that is used in variant 1. This results in a novel 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (2) is shorter and has a distinct C-terminus, compared to isoform 1.

Source sequence(s)

AC090587, AI436199, BC041136, DB084013, U41815

Consensus CDS

CCDS41606.1

UniProtKB/TrEMBL

A0A8V8TQG5

Related

ENSP00000380199.4, ENST00000397004.9

Conserved Domains (1) summary

pfam04096
Location:723 → 863

Nucleoporin2; Nucleoporin autopeptidase
NM_139132.4 → NP_624358.2 nuclear pore complex protein Nup98-Nup96 isoform 4

See identical proteins and their annotated locations for NP_624358.2

Status: REVIEWED

Description

Transcript Variant: This variant (4) lacks an alternate in-frame exon in the 3' coding region, compared to variant 1. The encoded isoform (4) has the same N- and C-termini, but is shorter than isoform 1. This isoform (4) may undergo proteolytic processing similar to that of isoform 1.

Source sequence(s)

AF071077, AF116074, AF231130, DB084013

Consensus CDS

CCDS31347.1

UniProtKB/TrEMBL

A0A8V8TQF7

Related

ENSP00000347404.3, ENST00000355260.8

Conserved Domains (3) summary

pfam04096
Location:723 → 863

Nucleoporin2; Nucleoporin autopeptidase

pfam12110
Location:1317 → 1534

Nup96; Nuclear protein 96

pfam13634
Location:25 → 149

Nucleoporin_FG; Nucleoporin FG repeat region