Human Gene NUP93 (uc002eka.3) Description and Page Index
  Description: Homo sapiens nucleoporin 93kDa (NUP93), transcript variant 1, mRNA.
RefSeq Summary (NM_014669): 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. This gene encodes a nucleoporin protein that localizes both to the basket of the pore and to the nuclear entry of the central gated channel of the pore. The encoded protein is a target of caspase cysteine proteases that play a central role in programmed cell death by apoptosis. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2016].
Transcript (Including UTRs)
   Position: hg19 chr16:56,764,017-56,878,861 Size: 114,845 Total Exon Count: 22 Strand: +
Coding Region
   Position: hg19 chr16:56,782,160-56,878,521 Size: 96,362 Coding Exon Count: 21 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr16:56,764,017-56,878,861)mRNA (may differ from genome)Protein (819 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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UniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: NUP93_HUMAN
DESCRIPTION: RecName: Full=Nuclear pore complex protein Nup93; AltName: Full=93 kDa nucleoporin; AltName: Full=Nucleoporin Nup93;
FUNCTION: Part of the nucleoporin complex; required for correct nuclear pore assembly.
SUBUNIT: Component of the p62 complex, a complex composed of NUP62 and NUP54. Forms a complex with NUP53, NUP155, NUP205 and lamin B; the interaction with NUP53 is direct.
SUBCELLULAR LOCATION: Nucleus, nuclear pore complex. Nucleus membrane; Peripheral membrane protein (By similarity). Note=Localizes at the nuclear basket and at or near the nuclear entry to the gated channel of the pore.
SIMILARITY: Belongs to the nucleoporin interacting component (NIC) family.
SEQUENCE CAUTION: Sequence=BAA07680.2; Type=Erroneous initiation; Note=Translation N-terminally shortened;

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): NUP93
CDC HuGE Published Literature: NUP93
Positive Disease Associations: Body Mass Index , Body Weight , HDL cholesterol
Related Studies:
  1. Body Mass Index
    Caroline S Fox et al. BMC medical genetics 2007, Genome-wide association to body mass index and waist circumference: the Framingham Heart Study 100K project., BMC medical genetics. [PubMed 17903300]
    Adiposity traits are associated with SNPs on the Affymetrix 100K SNP GeneChip. Replication of these initial findings is necessary. These data will serve as a resource for replication as more genes become identified with BMI and WC.
  2. Body Weight
    Caroline S Fox et al. BMC medical genetics 2007, Genome-wide association to body mass index and waist circumference: the Framingham Heart Study 100K project., BMC medical genetics. [PubMed 17903300]
    Adiposity traits are associated with SNPs on the Affymetrix 100K SNP GeneChip. Replication of these initial findings is necessary. These data will serve as a resource for replication as more genes become identified with BMI and WC.
  3. HDL cholesterol
    Ridker ,et al. 2009, Polymorphism in the CETP Gene Region, HDL Cholesterol, and Risk of Future Myocardial Infarction: Genomewide Analysis Among 18 245 Initially Healthy Women From the Women's Genome Health Study, Circulation. Cardiovascular genetics 2009 2- 1 : 26-33. [PubMed 20031564]
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: NUP93
Diseases sorted by gene-association score: nephrotic syndrome, type 12* (1300), glomerulosclerosis, focal segmental, 1* (247), familial idiopathic steroid-resistant nephrotic syndrome with diffuse mesangial sclerosis* (175), nephrotic syndrome (12)
* = Manually curated disease association

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

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 19.34 RPKM in Testis
Total median expression: 310.19 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 -53.50121-0.442 Picture PostScript Text
3' UTR -69.32340-0.204 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
IPR007231 - Nucleoporin_int_Nup93/Nic96

Pfam Domains:
PF04097 - Nup93/Nic96

ModBase Predicted Comparative 3D Structure on Q8N1F7
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  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
No orthologGenome BrowserGenome BrowserGenome BrowserNo orthologGenome Browser
Gene DetailsGene Details Gene Details Gene Details
Gene SorterGene Sorter Gene Sorter Gene Sorter
 RGDEnsemblFlyBase SGD
 Protein SequenceProtein SequenceProtein Sequence Protein Sequence
 AlignmentAlignmentAlignment Alignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0017056 structural constituent of nuclear pore

Biological Process:
GO:0006406 mRNA export from nucleus
GO:0006998 nuclear envelope organization
GO:0015031 protein transport
GO:0016032 viral process
GO:0016973 poly(A)+ mRNA export from nucleus
GO:0051028 mRNA transport
GO:0051292 nuclear pore complex assembly
GO:0060391 positive regulation of SMAD protein import into nucleus
GO:0060395 SMAD protein signal transduction
GO:0072001 renal system development
GO:0072015 glomerular visceral epithelial cell development
GO:0090521 glomerular visceral epithelial cell migration
GO:1903206 negative regulation of hydrogen peroxide-induced cell death

Cellular Component:
GO:0005634 nucleus
GO:0005635 nuclear envelope
GO:0005643 nuclear pore
GO:0016020 membrane
GO:0031965 nuclear membrane
GO:0034399 nuclear periphery


-  Descriptions from all associated GenBank mRNAs
  D42085 - Homo sapiens KIAA0095 mRNA.
AF086282 - Homo sapiens full length insert cDNA clone ZD46B07.
BC034346 - Homo sapiens nucleoporin 93kDa, mRNA (cDNA clone MGC:21106 IMAGE:4750923), complete cds.
AK292262 - Homo sapiens cDNA FLJ78686 complete cds, highly similar to Homo sapiens nucleoporin 93kDa (NUP93), mRNA.
AB385278 - Synthetic construct DNA, clone: pF1KA0095, Homo sapiens NUP93 gene for nucleoporin 93kDa, complete cds, without stop codon, in Flexi system.
AK056637 - Homo sapiens cDNA FLJ32075 fis, clone OCBBF1000146, highly similar to Nuclear pore complex protein Nup93.
AK294176 - Homo sapiens cDNA FLJ58756 complete cds, highly similar to Nuclear pore complex protein Nup93.
AK123594 - Homo sapiens cDNA FLJ41600 fis, clone CTONG2026920.
JD456712 - Sequence 437736 from Patent EP1572962.
AK125165 - Homo sapiens cDNA FLJ43175 fis, clone FCBBF3008311.

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

Protein Q8N1F7 (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: B3KPQ8, KIAA0095, NM_014669, NP_001229725, NUP93_HUMAN, Q14705, Q8N1F7
UCSC ID: uc002eka.3
RefSeq Accession: NM_014669
Protein: Q8N1F7 (aka NUP93_HUMAN or NU93_HUMAN)
CCDS: CCDS10769.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_014669.4
exon count: 22CDS single in 3' UTR: no RNA size: 2922
ORF size: 2460CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 4939.00frame shift in genome: no % Coverage: 99.97
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.