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

Gene ID: 4928, updated on 6-Sep-2020

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
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

Genomic context

See NUP98 in Genome Data Viewer
Location:
11p15.4
Exon count:
34
Annotation release Status Assembly Chr Location
109.20200815 current GRCh38.p13 (GCF_000001405.39) 11 NC_000011.10 (3675010..3797554, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (3696240..3819022, complement)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene ADP-ribosyltransferase 1 Neighboring gene cholinergic receptor nicotinic alpha 10 subunit Neighboring gene RNA, U6 small nuclear 1143, pseudogene Neighboring gene nucleoporin 98kDa recombination region Neighboring gene RNA, U7 small nuclear 50 pseudogene Neighboring gene post-GPI attachment to proteins 2 Neighboring gene ras homolog family member G

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Genome-wide association study of a heart failure related metabolomic profile among African Americans in the Atherosclerosis Risk in Communities (ARIC) study.
GeneReviews: Not available

HIV-1 interactions

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

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
mRNA binding IMP
Inferred from Mutant Phenotype
more info
PubMed 
nuclear localization sequence binding IEA
Inferred from Electronic Annotation
more info
 
promoter-specific chromatin binding IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
serine-type peptidase activity IEA
Inferred from Electronic Annotation
more info
 
structural constituent of nuclear pore IMP
Inferred from Mutant Phenotype
more info
PubMed 
structural constituent of nuclear pore NAS
Non-traceable Author Statement
more info
PubMed 
transcription coactivator activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
transporter activity TAS
Traceable Author Statement
more info
PubMed 
Process Evidence Code Pubs
intracellular transport of virus TAS
Traceable Author Statement
more info
 
mRNA export from nucleus TAS
Traceable Author Statement
more info
 
nuclear pore complex assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
nuclear pore organization NAS
Non-traceable Author Statement
more info
PubMed 
nucleocytoplasmic transport TAS
Traceable Author Statement
more info
PubMed 
positive regulation of mRNA splicing, via spliceosome IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of nucleic acid-templated transcription IEA
Inferred from Electronic Annotation
more info
 
protein import into nucleus IEA
Inferred from Electronic Annotation
more info
 
protein sumoylation TAS
Traceable Author Statement
more info
 
proteolysis IEA
Inferred from Electronic Annotation
more info
 
regulation of cellular response to heat TAS
Traceable Author Statement
more info
 
regulation of gene silencing by miRNA TAS
Traceable Author Statement
more info
 
regulation of glycolytic process TAS
Traceable Author Statement
more info
 
tRNA export from nucleus TAS
Traceable Author Statement
more info
 
viral process TAS
Traceable Author Statement
more info
 
viral transcription TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
cytosol TAS
Traceable Author Statement
more info
 
host cell IEA
Inferred from Electronic Annotation
more info
 
intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
 
colocalizes_with kinetochore IDA
Inferred from Direct Assay
more info
PubMed 
nuclear body IDA
Inferred from Direct Assay
more info
PubMed 
nuclear envelope IDA
Inferred from Direct Assay
more info
PubMed 
nuclear envelope TAS
Traceable Author Statement
more info
 
nuclear inclusion body IDA
Inferred from Direct Assay
more info
PubMed 
nuclear membrane IDA
Inferred from Direct Assay
more info
PubMed 
nuclear periphery IDA
Inferred from Direct Assay
more info
PubMed 
nuclear pore IDA
Inferred from Direct Assay
more info
PubMed 
nuclear pore NAS
Non-traceable Author Statement
more info
PubMed 
nuclear pore nuclear basket IDA
Inferred from Direct Assay
more info
PubMed 
nuclear pore outer ring IDA
Inferred from Direct Assay
more info
PubMed 
nuclear pore outer ring NAS
Non-traceable Author Statement
more info
PubMed 
nucleoplasm IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm TAS
Traceable Author Statement
more info
 
ribonucleoprotein complex IMP
Inferred from Mutant Phenotype
more info
PubMed 

General protein information

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)

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_001365125.2NP_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
    Conserved Domains (4) summary
    pfam04096
    Location:723862
    Nucleoporin2; Nucleoporin autopeptidase
    pfam12110
    Location:13481637
    Nup96; Nuclear protein 96
    pfam13634
    Location:40149
    Nucleoporin_FG; Nucleoporin FG repeat region
    cl25496
    Location:243666
    Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
  2. NM_001365126.2NP_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
    Related
    ENSP00000352091.5, ENST00000359171.8
    Conserved Domains (4) summary
    pfam04096
    Location:740879
    Nucleoporin2; Nucleoporin autopeptidase
    pfam12110
    Location:13341623
    Nup96; Nuclear protein 96
    pfam13634
    Location:40149
    Nucleoporin_FG; Nucleoporin FG repeat region
    cl27636
    Location:208480
    PPE; PPE family
  3. NM_001365127.2NP_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
    Conserved Domains (4) summary
    pfam04096
    Location:715854
    Nucleoporin2; Nucleoporin autopeptidase
    pfam12110
    Location:13091598
    Nup96; Nuclear protein 96
    pfam13634
    Location:40149
    Nucleoporin_FG; Nucleoporin FG repeat region
    cl25496
    Location:243658
    Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
  4. NM_001365128.2NP_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
    Conserved Domains (4) summary
    pfam04096
    Location:706845
    Nucleoporin2; Nucleoporin autopeptidase
    pfam12110
    Location:13001589
    Nup96; Nuclear protein 96
    pfam13634
    Location:40149
    Nucleoporin_FG; Nucleoporin FG repeat region
    cl25496
    Location:229649
    Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
  5. NM_001365129.2NP_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
    Conserved Domains (3) summary
    pfam04096
    Location:676815
    Nucleoporin2; Nucleoporin autopeptidase
    pfam12110
    Location:12701559
    Nup96; Nuclear protein 96
    pfam13634
    Location:40149
    Nucleoporin_FG; Nucleoporin FG repeat region
  6. NM_005387.7NP_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/Swiss-Prot
    P52948
    Related
    ENSP00000380202.4, ENST00000397007.8
    Conserved Domains (2) summary
    COG5651
    Location:208480
    COG5651; PPE-repeat protein [Function unknown]
    pfam04096
    Location:740880
    Nucleoporin2; Nucleoporin autopeptidase
  7. NM_016320.5NP_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/Swiss-Prot
    P52948
    Related
    ENSP00000316032.7, ENST00000324932.12
    Conserved Domains (3) summary
    pfam04096
    Location:723863
    Nucleoporin2; Nucleoporin autopeptidase
    pfam12110
    Location:13171608
    Nup96; Nuclear protein 96
    pfam13634
    Location:25149
    Nucleoporin_FG; Nucleoporin FG repeat region
  8. NM_139131.5NP_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/Swiss-Prot
    P52948
    Related
    ENSP00000380199.4, ENST00000397004.8
    Conserved Domains (1) summary
    pfam04096
    Location:723863
    Nucleoporin2; Nucleoporin autopeptidase
  9. NM_139132.4NP_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/Swiss-Prot
    P52948
    Related
    ENSP00000347404.3, ENST00000355260.7
    Conserved Domains (3) summary
    pfam04096
    Location:723863
    Nucleoporin2; Nucleoporin autopeptidase
    pfam12110
    Location:13171534
    Nup96; Nuclear protein 96
    pfam13634
    Location:25149
    Nucleoporin_FG; Nucleoporin FG repeat region

RNA

  1. NR_157589.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC060812, AC090587
    Related
    ENST00000650171.1
  2. NR_157590.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC060812, AC090587
  3. NR_157591.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC060812, AC090587

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20200815

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p13 Primary Assembly

    Range
    3675010..3797554 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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