Human Gene NUP98 (ENST00000324932.12_9) from GENCODE V45lift37
Description: Homo sapiens nucleoporin 98 and 96 precursor (NUP98), transcript variant 1, mRNA. (from RefSeq NM_016320) RefSeq Summary (NM_016320): 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]. Gencode Transcript: ENST00000324932.12_9 Gencode Gene: ENSG00000110713.18_16 Transcript (Including UTRs) Position: hg19 chr11:3,696,249-3,818,784 Size: 122,536 Total Exon Count: 33 Strand: - Coding Region Position: hg19 chr11:3,697,389-3,803,347 Size: 105,959 Coding Exon Count: 32
ID:NUP98_HUMAN DESCRIPTION: RecName: Full=Nuclear pore complex protein Nup98-Nup96 ; EC=3.4.21.- ; Contains: RecName: Full=Nuclear pore complex protein Nup98; AltName: Full=98 kDa nucleoporin; AltName: Full=Nucleoporin Nup98; Short=Nup98; Contains: RecName: Full=Nuclear pore complex protein Nup96; AltName: Full=96 kDa nucleoporin; AltName: Full=Nucleoporin Nup96; Short=Nup96; Flags: Precursor; FUNCTION: Plays a role in the nuclear pore complex (NPC) assembly and/or maintenance. NUP98 and NUP96 are involved in the bidirectional transport across the NPC (PubMed:33097660). May anchor NUP153 and TPR to the NPC. In cooperation with DHX9, plays a role in transcription and alternative splicing activation of a subset of genes (PubMed:28221134). Involved in the localization of DHX9 in discrete intranuclear foci (GLFG-body) (PubMed:28221134). FUNCTION: (Microbial infection) Interacts with HIV-1 capsid protein P24 and nucleocapsid protein P7 and may thereby promote the integration of the virus in the host nucleus (in vitro) (PubMed:23523133). Binding affinity to HIV-1 CA-NC complexes bearing the capsid change Asn-74-Asp is reduced (in vitro) (PubMed:23523133). SUBUNIT: Part of the nuclear pore complex (NPC) (PubMed:15229283, PubMed:18287282). Interacts directly with NUP96 (PubMed:12191480). Part of the Nup160 subcomplex in the nuclear pore which is composed of NUP160, NUP133, NUP107 and NUP96; this complex plays a role in RNA export and in tethering NUP98 and NUP153 to the nucleus (PubMed:11684705). Interacts with RAE1 (PubMed:10209021, PubMed:20498086). Does not interact with TPR (PubMed:11684705). Interacts with NUP88 (PubMed:30543681). Interacts directly with NUP88 and NUP214, subunits of the cytoplasmic filaments of the NPC (By similarity). Interacts (via N-terminus) with DHX9 (via DRBM, OB-fold and RGG domains); this interaction occurs in a RNA-dependent manner and stimulates DHX9-mediated ATPase activity (PubMed:28221134). SUBUNIT: (Microbial infection) Interacts with HIV-1 capsid protein P24 and nucleocapsid protein P7 (in vitro); the interaction may promote the integration of the virus in the host nucleus (in vitro). SUBUNIT: (Microbial infection) Interacts with vesicular stomatitis virus protein M (PubMed:11106761). SUBUNIT: (Microbial infection) Interacts with SARS coronavirus-2/SARS- CoV-2 ORF6 protein; the interaction blocks STAT1 nuclear translocation, antagonizes interferon signaling and blocks mRNA nuclear export (ex vivo). SUBUNIT: (Microbial infection) Interacts with SARS coronavirus/SARS-CoV ORF6 protein. INTERACTION: P52948; P78406: RAE1; NbExp=11; IntAct=EBI-295727, EBI-724495; P52948; P0DTC6: 6; Xeno; NbExp=11; IntAct=EBI-295727, EBI-25475897; P52948; P59634: 6; Xeno; NbExp=6; IntAct=EBI-295727, EBI-25489038; SUBCELLULAR LOCATION: Nucleus membrane eripheral membrane protein; Nucleoplasmic side Nucleus, nuclear pore complex cleus, nucleoplasm Note=Localized to the nucleoplasmic side of the nuclear pore complex (NPC), at or near the nucleoplasmic basket (PubMed:11839768). Dissociates from the dissasembled NPC structure early during prophase of mitosis (PubMed:12802065). Colocalized with NUP153 and TPR to the nuclear basket of NPC (PubMed:11839768). Colocalized with DHX9 in diffuse and discrete intranuclear foci (GLFG-body) (PubMed:11839768, PubMed:28221134). SUBCELLULAR LOCATION: Nucleus membrane Note=(Microbial infection) Remains localized to the nuclear membrane after poliovirus (PV) infection. DOMAIN: Contains G-L-F-G repeats. The FG repeat domains in Nup98 have a direct role in the transport. PTM: Isoform 1 to isoform 4 are autoproteolytically cleaved to yield Nup98 and Nup96 or Nup98 only, respectively (PubMed:10087256, PubMed:20407419, PubMed:12191480, PubMed:18287282). Cleaved Nup98 is necessary for the targeting of Nup98 to the nuclear pore and the interaction with Nup96 (PubMed:20407419, PubMed:12191480). PTM: Proteolytically degraded after poliovirus (PV) infection; degradation is partial and NCP- and TPR-binding domains withstand degradation. DISEASE: Note=Chromosomal aberrations involving NUP98 have been found in acute myeloid leukemia. Translocation t(7;11)(p15;p15) with HOXA9 (PubMed:8563753). The chimera includes NUP98 intrinsic disordered regions which contribute to aberrant liquid-liquid phase separation puncta of the chimera in the nucleus. This phase-separation enhances the chimera genomic targeting and induces organization of aberrant three-dimensional chromatin structures leading to tumorous transformation (PubMed:34163069). Translocation t(11;17)(p15;p13) with PHF23 (PubMed:17287853). DISEASE: Note=A chromosomal aberration involving NUP98 has been found in M0 type acute myeloid leukemia. Translocation t(4;11)(q23;p15) with RAP1GDS1. DISEASE: Note=A chromosomal aberration involving NUP98 has been found in T-cell acute lymphocytic leukemia. Translocation t(4;11)(q23;p15) with RAP1GDS1. DISEASE: Note=A chromosomal aberration involving NUP98 has been found in M5 type acute myeloid leukemia. Translocation t(11;12)(p15;p13) with KDM5A. DISEASE: Note=Chromosomal aberrations involving NUP98 have been found in childhood acute myeloid leukemia. Translocation t(5;11)(q35;p15.5) with NSD1. Translocation t(8;11)(p11.2;p15) with WHSC1L1. DISEASE: Note=Chromosomal aberrations involving NUP98 have been found in M7 type childhood acute myeloid leukemia. Translocation t(11;12)(p15;p13) with KDM5A. DISEASE: Note=A chromosomal aberration involving NUP98 is found in a form of therapy-related myelodysplastic syndrome. Translocation t(11;20)(p15;q11) with TOP1. DISEASE: Note=A chromosomal aberration involving NUP98 is found in a form of T-cell acute lymphoblastic leukemia (T-ALL). Translocation t(3;11)(q12.2;p15.4) with LNP1. DISEASE: Note=A chromosomal aberration involving NUP98 is associated with pediatric acute myeloid leukemia (AML) with intermediate characteristics between M2-M3 French-American-British (FAB) subtypes. Translocation t(9;11)(p22;p15) with PSIP1/LEDGF. The chimeric transcript is an in-frame fusion of NUP98 exon 8 to PSIP1/LEDGF exon 4. DISEASE: Note=A chromosomal aberration involving NUP98 has been identified in acute leukemias. Translocation t(6;11)(q24.1;p15.5) with CCDC28A. The chimeric transcript is an in-frame fusion of NUP98 exon 13 to CCDC28A exon 2. Ectopic expression of NUP98-CCDC28A in mouse promotes the proliferative capacity and self-renewal potential of hematopoietic progenitors and rapidly induced fatal myeloproliferative neoplasms and defects in the differentiation of the erythro- megakaryocytic lineage. SIMILARITY: Belongs to the nucleoporin GLFG family. SEQUENCE CAUTION: Sequence=AAD22395.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Sequence of unknown origin in the C-terminal part.; Evidence=; Sequence=AAD22396.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Sequence of unknown origin in the C-terminal part.; Evidence=; Sequence=AAF19342.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence=; Sequence=AAF19342.1; Type=Frameshift; Evidence=; WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="https://atlasgeneticsoncology.org/gene/98/NUP";
The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.
ModBase Predicted Comparative 3D Structure on P52948
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Gene Ontology (GO) Annotations with Structured Vocabulary
Biological Process: GO:0000973 posttranscriptional tethering of RNA polymerase II gene DNA at nuclear periphery GO:0006110 regulation of glycolytic process GO:0006405 RNA export from nucleus GO:0006406 mRNA export from nucleus GO:0006409 tRNA export from nucleus GO:0006508 proteolysis GO:0006606 protein import into nucleus GO:0006913 nucleocytoplasmic transport GO:0006999 nuclear pore organization GO:0015031 protein transport GO:0016032 viral process GO:0016925 protein sumoylation GO:0019083 viral transcription GO:0034398 telomere tethering at nuclear periphery GO:0048026 positive regulation of mRNA splicing, via spliceosome GO:0051028 mRNA transport GO:0051292 nuclear pore complex assembly GO:0060964 regulation of gene silencing by miRNA GO:0075733 intracellular transport of virus GO:1900034 regulation of cellular response to heat GO:1903508 positive regulation of nucleic acid-templated transcription
Sequence and Links to Tools and Databases 
Common Gene Haplotype Alleles 
