Human Gene NUP50 (ENST00000347635.9) from GENCODE V44
  Description: Homo sapiens nucleoporin 50 (NUP50), transcript variant 2, mRNA. (from RefSeq NM_007172)
RefSeq Summary (NM_007172): The nuclear pore complex is a massive structure that extends across the nuclear envelope, forming a gateway that regulates the flow of macromolecules between the nucleus and the cytoplasm. Nucleoporins are the main components of the nuclear pore complex in eukaryotic cells. The protein encoded by this gene is a member of the FG-repeat containing nucleoporins that functions as a soluble cofactor in importin-alpha:beta-mediated nuclear protein import. Pseudogenes of this gene are found on chromosomes 5, 6, and 14. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008].
Gencode Transcript: ENST00000347635.9
Gencode Gene: ENSG00000093000.19
Transcript (Including UTRs)
   Position: hg38 chr22:45,163,925-45,188,017 Size: 24,093 Total Exon Count: 8 Strand: +
Coding Region
   Position: hg38 chr22:45,168,178-45,184,655 Size: 16,478 Coding Exon Count: 7 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr22:45,163,925-45,188,017)mRNA (may differ from genome)Protein (468 aa)
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-  Comments and Description Text from UniProtKB
  ID: NUP50_HUMAN
DESCRIPTION: RecName: Full=Nuclear pore complex protein Nup50; AltName: Full=50 kDa nucleoporin; AltName: Full=Nuclear pore-associated protein 60 kDa-like; AltName: Full=Nucleoporin Nup50;
FUNCTION: Component of the nuclear pore complex that has a direct role in nuclear protein import. Actively displaces NLSs from importin-alpha, and facilitates disassembly of the importin- alpha:beta-cargo complex and importin recycling. Interacts with multiple transport receptor proteins including CDKN1B. This interaction is required for correct intracellular transport and degradation of CDKN1B.
SUBUNIT: Interacts with Importin alpha-2, Importin beta, Importin beta-2, NUP153, Ran binding protein 7, CDKN1B and itself (By similarity).
SUBCELLULAR LOCATION: Nucleus, nuclear pore complex. Nucleus membrane; Peripheral membrane protein; Nucleoplasmic side (By similarity). Note=Localizes to the nucleoplasmic fibrils of the nuclear pore complex (By similarity).
TISSUE SPECIFICITY: Ubiquitous. Highest levels in testis, peripheral blood leukocytes and fetal liver.
DOMAIN: Contains FG repeats.
SIMILARITY: Contains 1 RanBD1 domain.

-  Primer design for this transcript
 

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-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 20.01 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 335.91 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -168.20382-0.440 Picture PostScript Text
3' UTR -871.403362-0.259 Picture PostScript Text

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.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR015007 - NUP2/50/61
IPR011993 - PH_like_dom
IPR000156 - Ran_bind_dom

Pfam Domains:
PF08911 - NUP50 (Nucleoporin 50 kDa)
PF00638 - RanBP1 domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2EC1 - NMR MuPIT 3TJ3 - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q9UKX7
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-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologGenome BrowserNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD Ensembl  
Protein SequenceProtein Sequence Protein Sequence  
AlignmentAlignment Alignment  

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0008536 Ran GTPase binding

Biological Process:
GO:0006406 mRNA export from nucleus
GO:0006606 protein import into nucleus
GO:0015031 protein transport
GO:0016032 viral process
GO:0046907 intracellular transport
GO:0051028 mRNA transport

Cellular Component:
GO:0005634 nucleus
GO:0005643 nuclear pore
GO:0005654 nucleoplasm
GO:0016020 membrane
GO:0031965 nuclear membrane
GO:0043231 intracellular membrane-bounded organelle


-  Descriptions from all associated GenBank mRNAs
  AK314454 - Homo sapiens cDNA, FLJ95255, Homo sapiens nucleoporin 50kDa (NUP50), transcript variant 2, mRNA.
BC070133 - Homo sapiens nucleoporin 50kDa, mRNA (cDNA clone MGC:88113 IMAGE:6463796), complete cds.
AK304223 - Homo sapiens cDNA FLJ54237 complete cds, highly similar to Nucleoporin 50 kDa.
JD395091 - Sequence 376115 from Patent EP1572962.
BC016055 - Homo sapiens nucleoporin 50kDa, mRNA (cDNA clone MGC:23022 IMAGE:4856954), complete cds.
AF107840 - Homo sapiens nuclear pore-associated protein (NPAP60L) mRNA, complete cds.
AL389950 - Homo sapiens mRNA full length insert cDNA clone EUROIMAGE 1841188.
AL389949 - Homo sapiens mRNA full length insert cDNA clone EUROIMAGE 139505.
BC028125 - Homo sapiens nucleoporin 50kDa, mRNA (cDNA clone MGC:39961 IMAGE:5166132), complete cds.
CR456533 - Homo sapiens NUP50 full length open reading frame (ORF) cDNA clone (cDNA clone C22ORF:pGEM.NUP50).
AF116624 - Homo sapiens PRO1146 mRNA, complete cds.
CU687046 - Synthetic construct Homo sapiens gateway clone IMAGE:100023120 5' read NUP50 mRNA.
AB463151 - Synthetic construct DNA, clone: pF1KB8459, Homo sapiens NUP50 gene for nucleoporin, without stop codon, in Flexi system.
CU013421 - Homo sapiens NUP50, mRNA (cDNA clone IMAGE:100000390), complete cds, without stop codon, in Gateway system.
GQ129293 - Synthetic construct Homo sapiens clone HAIB:100068471; DKFZo004C0134 nucleoporin 50kDa protein (NUP50) gene, partial cds.
CU013133 - Homo sapiens NUP50, mRNA (cDNA clone IMAGE:100000486), complete cds, with stop codon, in Gateway system.
EU832782 - Synthetic construct Homo sapiens clone HAIB:100067811; DKFZo008C0133 nucleoporin 50kDa protein (NUP50) gene, encodes complete protein.
JD053200 - Sequence 34224 from Patent EP1572962.
CU677565 - Synthetic construct Homo sapiens gateway clone IMAGE:100023073 5' read NUP50 mRNA.
KJ898281 - Synthetic construct Homo sapiens clone ccsbBroadEn_07675 NUP50 gene, encodes complete protein.
JD275997 - Sequence 257021 from Patent EP1572962.
AK095860 - Homo sapiens cDNA FLJ38541 fis, clone HCHON2001523, highly similar to Homo sapiens nuclear pore-associated protein (NPAP60L) mRNA.
JD478686 - Sequence 459710 from Patent EP1572962.
JD148501 - Sequence 129525 from Patent EP1572962.
JD184910 - Sequence 165934 from Patent EP1572962.
JD548505 - Sequence 529529 from Patent EP1572962.
JD137965 - Sequence 118989 from Patent EP1572962.
JD062173 - Sequence 43197 from Patent EP1572962.
AL389951 - Homo sapiens mRNA full length insert cDNA clone EUROIMAGE 2004669.
JD312767 - Sequence 293791 from Patent EP1572962.
JD289479 - Sequence 270503 from Patent EP1572962.
AF267865 - Homo sapiens DC41 mRNA, complete cds.
BC039468 - Homo sapiens nucleoporin 50kDa, mRNA (cDNA clone IMAGE:3889720).
JD022055 - Sequence 3079 from Patent EP1572962.
BC020260 - Homo sapiens nucleoporin 50kDa, mRNA (cDNA clone IMAGE:4873861), with apparent retained intron.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9UKX7 (Reactome details) participates in the following event(s):

R-HSA-75096 Docking of the TAP:EJC Complex with the NPC
R-HSA-165043 Rev multimer-bound HIV mRNA:Crm1:Ran:GTP complex associates with the NPC
R-HSA-180622 Vpr binds nucleoporins
R-HSA-180710 Rev:importin beta:B23 recruited to the nuclear pore
R-HSA-2990882 CDK1 phosphorylates NUP98
R-HSA-75098 mRNP complex dissociates from cytosolic face of NPC
R-HSA-165047 Translocation of nuclear RNA transport complex to cytoplasm
R-HSA-180732 Translocation of Rev:importin-beta:B23 to the nucleus
R-HSA-2990880 NEK6/NEK7 phosphorylates NUP98
R-HSA-170796 NPC transports GCK1:GKRP from cytosol to nucleoplasm
R-HSA-5578744 Importin-8 imports AGO2:miRNA into the nucleus
R-HSA-6783483 tRNA:XPOT:RAN:GTP translocates from the nucleus to the cytosol
R-HSA-3000348 RANBP2 SUMOylates SP100 with SUMO2
R-HSA-3000399 RANBP2 SUMOylates SP100 with SUMO1
R-HSA-3000411 RANBP2 SUMOylates PML with SUMO2
R-HSA-4570493 RANBP2 (NUP358) SUMOylates HNRNPC with SUMO1
R-HSA-4615872 RANBP2 SUMOylates HDAC4 with SUMO1
R-HSA-4615987 RANBP2 SUMOylates HDAC4 with SUMO2,3
R-HSA-5228508 RANBP2 SUMOylates PML with SUMO1
R-HSA-5228525 RANBP2 SUMOylates TOP2A with SUMO1
R-HSA-192627 Viral mRNA Export
R-HSA-192925 Export of Spliced Viral mRNA
R-HSA-5252041 NPC transports Hikeshi:HSP70s:ATP from cytosol to nucleoplasm
R-HSA-159236 Transport of Mature mRNA derived from an Intron-Containing Transcript
R-HSA-165054 Rev-mediated nuclear export of HIV RNA
R-HSA-180910 Vpr-mediated nuclear import of PICs
R-HSA-180746 Nuclear import of Rev protein
R-HSA-3301854 Nuclear Pore Complex (NPC) Disassembly
R-HSA-72202 Transport of Mature Transcript to Cytoplasm
R-HSA-162599 Late Phase of HIV Life Cycle
R-HSA-177243 Interactions of Rev with host cellular proteins
R-HSA-176033 Interactions of Vpr with host cellular proteins
R-HSA-2980766 Nuclear Envelope Breakdown
R-HSA-170822 Regulation of Glucokinase by Glucokinase Regulatory Protein
R-HSA-168276 NS1 Mediated Effects on Host Pathways
R-HSA-1169408 ISG15 antiviral mechanism
R-HSA-5578749 Transcriptional regulation by small RNAs
R-HSA-6784531 tRNA processing in the nucleus
R-HSA-3108214 SUMOylation of DNA damage response and repair proteins
R-HSA-4570464 SUMOylation of RNA binding proteins
R-HSA-4551638 SUMOylation of chromatin organization proteins
R-HSA-4615885 SUMOylation of DNA replication proteins
R-HSA-168325 Viral Messenger RNA Synthesis
R-HSA-3371453 Regulation of HSF1-mediated heat shock response
R-HSA-72203 Processing of Capped Intron-Containing Pre-mRNA
R-HSA-162587 HIV Life Cycle
R-HSA-162909 Host Interactions of HIV factors
R-HSA-68875 Mitotic Prophase
R-HSA-70171 Glycolysis
R-HSA-168253 Host Interactions with Influenza Factors
R-HSA-1169410 Antiviral mechanism by IFN-stimulated genes
R-HSA-211000 Gene Silencing by RNA
R-HSA-72306 tRNA processing
R-HSA-3108232 SUMO E3 ligases SUMOylate target proteins
R-HSA-168273 Influenza Viral RNA Transcription and Replication
R-HSA-3371556 Cellular response to heat stress
R-HSA-8953854 Metabolism of RNA
R-HSA-162906 HIV Infection
R-HSA-68886 M Phase
R-HSA-70326 Glucose metabolism
R-HSA-168254 Influenza Infection
R-HSA-913531 Interferon Signaling
R-HSA-74160 Gene expression (Transcription)
R-HSA-2990846 SUMOylation
R-HSA-168255 Influenza Life Cycle
R-HSA-2262752 Cellular responses to stress
R-HSA-5663205 Infectious disease
R-HSA-69278 Cell Cycle (Mitotic)
R-HSA-71387 Metabolism of carbohydrates
R-HSA-1280215 Cytokine Signaling in Immune system
R-HSA-597592 Post-translational protein modification
R-HSA-8953897 Cellular responses to external stimuli
R-HSA-1643685 Disease
R-HSA-1640170 Cell Cycle
R-HSA-1430728 Metabolism
R-HSA-168256 Immune System
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: B1AHA4, B2RB15, ENST00000347635.1, ENST00000347635.2, ENST00000347635.3, ENST00000347635.4, ENST00000347635.5, ENST00000347635.6, ENST00000347635.7, ENST00000347635.8, NM_007172, NPAP60L, NUP50_HUMAN, O75644, PRO1146, Q8N6V5, Q9NPM9, Q9NPR6, Q9P1K5, Q9UKX7, uc003bfr.1, uc003bfr.2, uc003bfr.3, uc003bfr.4, uc003bfr.5
UCSC ID: ENST00000347635.9
RefSeq Accession: NM_007172
Protein: Q9UKX7 (aka NUP50_HUMAN or NU50_HUMAN)
CCDS: CCDS14062.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.