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

    Gene ID: 4928, updated on 9-Dec-2024

    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
    NEW
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    Try the new Transcript table

    Genomic context

    See NUP98 in Genome Data Viewer
    Location:
    11p15.4
    Exon count:
    34
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (3675010..3797554, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (3740382..3862891, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (3696240..3818784, 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 small nucleolar RNA U13 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:3717665-3717885 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:3723311-3723810 Neighboring gene RNA, U6 small nuclear 1143, pseudogene Neighboring gene nucleoporin 98kDa recombination region Neighboring gene MPRA-validated peak1178 silencer Neighboring gene MPRA-validated peak1179 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:3811721-3812640 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:3812641-3813558 Neighboring gene RNA, U7 small nuclear 50 pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3082 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3083 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3084 Neighboring gene uncharacterized LOC124902618 Neighboring gene post-GPI attachment to proteins 2 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:3841189-3841380 Neighboring gene uncharacterized LOC124902619 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

    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

    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

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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

    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)

    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_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
      UniProtKB/TrEMBL
      A0A8V8TQF7
      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
      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: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
      Consensus CDS
      CCDS91414.1
      UniProtKB/TrEMBL
      A0A8V8TQF7, H0YEN4
      Related
      ENSP00000436226.2, ENST00000527104.6
      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
      Consensus CDS
      CCDS91415.1
      UniProtKB/TrEMBL
      A0A8V8TQF7, A0A8V8TR21
      Related
      ENSP00000515088.1, ENST00000700598.1
      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
      Consensus CDS
      CCDS91413.1
      UniProtKB/TrEMBL
      A0A8V8TQF7, H0YCR0
      Related
      ENSP00000432142.2, ENST00000529379.2
      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/TrEMBL
      A8KA17
      Related
      ENSP00000380202.4, ENST00000397007.10
      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/TrEMBL
      A0A8V8TQF7
      Related
      ENSP00000316032.7, ENST00000324932.12
      Conserved Domains (4) summary
      pfam05109
      Location:243666
      Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
      pfam04096
      Location:721863
      Nucleoporin2; Nucleoporin autopeptidase
      pfam12110
      Location:13151606
      Nup96; Nuclear protein 96
      pfam13634
      Location:40149
      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/TrEMBL
      A0A8V8TQG5
      Related
      ENSP00000380199.4, ENST00000397004.9
      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/TrEMBL
      A0A8V8TQF7
      Related
      ENSP00000347404.3, ENST00000355260.8
      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
      ENST00000700601.1
    2. NR_157590.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC060812, AC090587
      Related
      ENST00000529063.2
    3. NR_157591.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC060812, AC090587
      Related
      ENST00000700602.1

    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

    1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

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

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      3740382..3862891 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)