Human Gene NUP54 (uc003hjs.3) Description and Page Index
  Description: Homo sapiens nucleoporin 54kDa (NUP54), mRNA.
RefSeq Summary (NM_017426): The nuclear envelope creates distinct nuclear and cytoplasmic compartments in eukaryotic cells. It consists of two concentric membranes perforated by nuclear pores, large protein complexes that form aqueous channels to regulate the flow of macromolecules between the nucleus and the cytoplasm. These complexes are composed of at least 100 different polypeptide subunits, many of which belong to the nucleoporin family. This gene encodes a member of the phe-gly (FG) repeat-containing nucleoporin subset. Multiple alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jun 2013].
Transcript (Including UTRs)
   Position: hg19 chr4:77,035,817-77,069,655 Size: 33,839 Total Exon Count: 12 Strand: -
Coding Region
   Position: hg19 chr4:77,036,519-77,069,527 Size: 33,009 Coding Exon Count: 12 

Page IndexSequence and LinksUniProtKB CommentsCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr4:77,035,817-77,069,655)mRNA (may differ from genome)Protein (507 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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neXtProtOMIMPubMedReactomeStanford SOURCETreefam

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Nucleoporin p54; AltName: Full=54 kDa nucleoporin;
FUNCTION: Component of the nuclear pore complex, a complex required for the trafficking across the nuclear membrane (By similarity).
SUBUNIT: Component of the p62 complex, a complex composed of NUP62, NUP54, and the isoform p58 and isoform p45 of NUPL1 (By similarity).
SUBCELLULAR LOCATION: Nucleus, nuclear pore complex (By similarity). Nucleus membrane; Peripheral membrane protein; Cytoplasmic side (By similarity). Nucleus membrane; Peripheral membrane protein; Nucleoplasmic side (By similarity). Note=Biased towards cytoplasmic side. Central region of the nuclear pore complex, within the transporter (By similarity).
DOMAIN: Contains FG repeats.
PTM: O-glycosylated (By similarity).
SIMILARITY: Belongs to the NUP54 family.
SEQUENCE CAUTION: Sequence=BAA91735.1; Type=Frameshift; Positions=479;

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

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 15.34 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 460.45 RPKM

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

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -53.10128-0.415 Picture PostScript Text
3' UTR -153.80702-0.219 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
IPR024864 - Nucleoporin_Nup54
IPR025712 - Nup54_alpha-helical_dom

Pfam Domains:
PF13874 - Nucleoporin complex subunit 54

ModBase Predicted Comparative 3D Structure on Q7Z3B4
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 BrowserNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 Protein SequenceProtein Sequence   

-  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:0006605 protein targeting
GO:0006607 NLS-bearing protein import into nucleus
GO:0006913 nucleocytoplasmic transport
GO:0006999 nuclear pore organization
GO:0015031 protein transport
GO:0016032 viral process
GO:0036228 protein targeting to nuclear inner membrane
GO:0042306 regulation of protein import into nucleus
GO:0051028 mRNA transport
GO:0051260 protein homooligomerization
GO:0051290 protein heterotetramerization
GO:0051291 protein heterooligomerization
GO:0070208 protein heterotrimerization

Cellular Component:
GO:0005634 nucleus
GO:0005635 nuclear envelope
GO:0005643 nuclear pore
GO:0016020 membrane
GO:0031965 nuclear membrane
GO:0032991 macromolecular complex
GO:0044613 nuclear pore central transport channel

-  Descriptions from all associated GenBank mRNAs
  AL137650 - Homo sapiens mRNA; cDNA DKFZp434L1613 (from clone DKFZp434L1613); partial cds.
AF157322 - Homo sapiens nucleoporin p54 protein (NUP54) mRNA, complete cds.
BX538002 - Homo sapiens mRNA; cDNA DKFZp686B1269 (from clone DKFZp686B1269); complete cds.
AK001517 - Homo sapiens cDNA FLJ10655 fis, clone NT2RP2005933, weakly similar to NUCLEOPORIN NUP57.
BC012559 - Homo sapiens nucleoporin 54kDa, mRNA (cDNA clone IMAGE:3931652).
LF205332 - JP 2014500723-A/12835: Polycomb-Associated Non-Coding RNAs.
LF319431 - JP 2014500723-A/126934: Polycomb-Associated Non-Coding RNAs.
JD087387 - Sequence 68411 from Patent EP1572962.
BC034226 - Homo sapiens cDNA clone IMAGE:5265492, containing frame-shift errors.
LF319432 - JP 2014500723-A/126935: Polycomb-Associated Non-Coding RNAs.
JD307813 - Sequence 288837 from Patent EP1572962.
AK223352 - Homo sapiens mRNA for nucleoporin 54kDa variant, clone: TST08373.
LF319433 - JP 2014500723-A/126936: Polycomb-Associated Non-Coding RNAs.
JD553632 - Sequence 534656 from Patent EP1572962.
LF319434 - JP 2014500723-A/126937: Polycomb-Associated Non-Coding RNAs.
AK307571 - Homo sapiens cDNA, FLJ97519.
JD338390 - Sequence 319414 from Patent EP1572962.
JD260035 - Sequence 241059 from Patent EP1572962.
AK300036 - Homo sapiens cDNA FLJ52746 complete cds, highly similar to Nucleoporin p54.
JD438997 - Sequence 420021 from Patent EP1572962.
AK299442 - Homo sapiens cDNA FLJ60840 complete cds, highly similar to Nucleoporin p54.
JD168322 - Sequence 149346 from Patent EP1572962.
AK222752 - Homo sapiens mRNA for nucleoporin 54kDa variant, clone: DMC05352.
AK315160 - Homo sapiens cDNA, FLJ96134, Homo sapiens nucleoporin 54kDa (NUP54), mRNA.
BC156685 - Synthetic construct Homo sapiens clone IMAGE:100062168, MGC:190190 nucleoporin 54kDa (NUP54) mRNA, encodes complete protein.
AB527805 - Synthetic construct DNA, clone: pF1KB5929, Homo sapiens NUP54 gene for nucleoporin 54kDa, without stop codon, in Flexi system.
LF319435 - JP 2014500723-A/126938: Polycomb-Associated Non-Coding RNAs.
DQ895978 - Synthetic construct Homo sapiens clone IMAGE:100010438; FLH189189.01L; RZPDo839C0764D nucleoporin 54kDa (NUP54) gene, encodes complete protein.
EU176395 - Synthetic construct Homo sapiens clone IMAGE:100006481; FLH189196.01X; RZPDo839A03252D nucleoporin 54kDa (NUP54) gene, encodes complete protein.
KJ902628 - Synthetic construct Homo sapiens clone ccsbBroadEn_12022 NUP54 gene, encodes complete protein.
LF319436 - JP 2014500723-A/126939: Polycomb-Associated Non-Coding RNAs.
LF319437 - JP 2014500723-A/126940: Polycomb-Associated Non-Coding RNAs.
JD174428 - Sequence 155452 from Patent EP1572962.
JD328516 - Sequence 309540 from Patent EP1572962.
MA440909 - JP 2018138019-A/12835: Polycomb-Associated Non-Coding RNAs.
MA555008 - JP 2018138019-A/126934: Polycomb-Associated Non-Coding RNAs.
MA555009 - JP 2018138019-A/126935: Polycomb-Associated Non-Coding RNAs.
MA555010 - JP 2018138019-A/126936: Polycomb-Associated Non-Coding RNAs.
MA555011 - JP 2018138019-A/126937: Polycomb-Associated Non-Coding RNAs.
MA555012 - JP 2018138019-A/126938: Polycomb-Associated Non-Coding RNAs.
MA555013 - JP 2018138019-A/126939: Polycomb-Associated Non-Coding RNAs.
MA555014 - JP 2018138019-A/126940: Polycomb-Associated Non-Coding RNAs.

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

Protein Q7Z3B4 (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: B2RCK7, NM_017426, NP_059122, NUP54_HUMAN, Q7Z3B4, Q96EA7, Q9NVL5, Q9P0I1
UCSC ID: uc003hjs.3
RefSeq Accession: NM_017426
Protein: Q7Z3B4 (aka NUP54_HUMAN or NU54_HUMAN)
CCDS: CCDS3576.1

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: NM_017426.2
exon count: 12CDS single in 3' UTR: no RNA size: 2358
ORF size: 1524CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3248.00frame shift in genome: no % Coverage: 99.83
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.