Nup54 (nucleoporin 54) - Rat Genome Database

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Gene: Nup54 (nucleoporin 54) Rattus norvegicus
Analyze
Symbol: Nup54
Name: nucleoporin 54
RGD ID: 619926
Description: Enables identical protein binding activity. A structural constituent of nuclear pore. Involved in nucleocytoplasmic transport; protein targeting; and regulation of protein import into nucleus. Located in nuclear envelope. Part of nuclear pore. Human ortholog(s) of this gene implicated in dystonia 37, early-onset with striatal lesions. Orthologous to human NUP54 (nucleoporin 54); PARTICIPATES IN mRNA nuclear export pathway; RNA transport pathway; INTERACTS WITH (+)-schisandrin B; 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: 54 kDa nucleoporin; nuclear pore complex protein Nup54; nucleoporin Nup54; nucleoporin p54
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81415,901,936 - 15,920,335 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1415,901,991 - 15,920,334 (+)EnsemblGRCr8
mRatBN7.21415,617,630 - 15,636,029 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1415,617,679 - 15,636,028 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1415,625,954 - 15,644,122 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01416,944,808 - 16,962,972 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01415,640,226 - 15,658,388 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01417,123,434 - 17,141,832 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1417,123,360 - 17,141,767 (+)Ensemblrn6Rnor6.0
Rnor_5.01417,039,514 - 17,057,924 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41417,178,761 - 17,197,062 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1415,012,204 - 15,030,485 (+)NCBICelera
RGSC_v3.11417,178,760 - 17,197,061 (+)NCBI
Cytogenetic Map14p22NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Gradient of increasing affinity of importin beta for nucleoporins along the pathway of nuclear import. Ben-Efraim I and Gerace L, J Cell Biol. 2001 Jan 22;152(2):411-7.
2. Regulation of mRNA trafficking by nuclear pore complexes. Bonnet A and Palancade B, Genes (Basel). 2014 Sep 2;5(3):767-91. doi: 10.3390/genes5030767.
3. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
4. Structural analysis of the p62 complex, an assembly of O-linked glycoproteins that localizes near the central gated channel of the nuclear pore complex. Guan T, etal., Mol Biol Cell. 1995 Nov;6(11):1591-603.
5. Molecular and functional characterization of the p62 complex, an assembly of nuclear pore complex glycoproteins. Hu T, etal., J Cell Biol 1996 Aug;134(3):589-601.
6. Allosteric Regulation in Gating the Central Channel of the Nuclear Pore Complex. Koh J and Blobel G, Cell. 2015 Jun 4;161(6):1361-73. doi: 10.1016/j.cell.2015.05.013.
7. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
8. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
9. GOA pipeline RGD automated data pipeline
10. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
11. Molecular architecture of the transport channel of the nuclear pore complex. Solmaz SR, etal., Cell. 2011 Oct 28;147(3):590-602. doi: 10.1016/j.cell.2011.09.034.
12. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
13. The stoichiometry of the nucleoporin 62 subcomplex of the nuclear pore in solution. Ulrich A, etal., Mol Biol Cell. 2014 May;25(9):1484-92. doi: 10.1091/mbc.E13-12-0745. Epub 2014 Feb 26.
Additional References at PubMed
PMID:15489334   PMID:26025361  


Genomics

Comparative Map Data
Nup54
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81415,901,936 - 15,920,335 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1415,901,991 - 15,920,334 (+)EnsemblGRCr8
mRatBN7.21415,617,630 - 15,636,029 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1415,617,679 - 15,636,028 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1415,625,954 - 15,644,122 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01416,944,808 - 16,962,972 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01415,640,226 - 15,658,388 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01417,123,434 - 17,141,832 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1417,123,360 - 17,141,767 (+)Ensemblrn6Rnor6.0
Rnor_5.01417,039,514 - 17,057,924 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41417,178,761 - 17,197,062 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1415,012,204 - 15,030,485 (+)NCBICelera
RGSC_v3.11417,178,760 - 17,197,061 (+)NCBI
Cytogenetic Map14p22NCBI
NUP54
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38476,114,664 - 76,148,397 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl476,107,562 - 76,148,509 (-)Ensemblhg38GRCh38
GRCh37477,035,817 - 77,069,550 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36477,254,841 - 77,288,679 (-)NCBIBuild 36Build 36hg18NCBI36
Build 34477,392,996 - 77,426,834NCBI
Celera474,336,017 - 74,369,792 (-)NCBICelera
Cytogenetic Map4q21.1NCBI
HuRef472,788,244 - 72,821,694 (-)NCBIHuRef
CHM1_1477,012,297 - 77,046,159 (-)NCBICHM1_1
T2T-CHM13v2.0479,455,330 - 79,489,069 (-)NCBIT2T-CHM13v2.0
Nup54
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39592,563,399 - 92,583,117 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl592,563,399 - 92,583,078 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm38592,415,540 - 92,435,259 (-)NCBIGRCm38GRCm38mm10GRCm38
Cytogenetic Map5E2NCBI
cM Map546.75NCBI
Nup54
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955433853,654 - 879,861 (-)Ensembl
ChiLan1.0NW_004955433853,921 - 879,861 (-)NCBIChiLan1.0ChiLan1.0
NUP54
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2353,924,149 - 53,958,784 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1454,113,869 - 54,150,174 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0448,057,553 - 48,091,471 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1453,896,058 - 53,929,596 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl453,896,058 - 53,929,596 (+)EnsemblpanPan2panpan1.1
NUP54
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.132751,568 - 782,342 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl32751,982 - 782,314 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha3241,100,154 - 41,131,148 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.032777,963 - 808,974 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl32777,883 - 808,921 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.132776,011 - 807,023 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.032730,301 - 761,292 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03239,408,219 - 39,439,234 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Nup54
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440528511,345,313 - 11,377,591 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936676133,782 - 161,938 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_004936676130,877 - 161,914 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NUP54
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl871,792,155 - 71,833,157 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1871,792,153 - 71,833,180 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2875,992,615 - 76,028,904 (-)NCBISscrofa10.2Sscrofa10.2susScr3
NUP54
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1724,616,645 - 24,649,595 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl724,613,767 - 24,650,359 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_0236660372,964,814 - 2,997,872 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Nup54
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475714,800,780 - 14,840,115 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Nup54
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1115,267,705 - 5,285,647 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Nup54
115 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:64
Count of miRNA genes:48
Interacting mature miRNAs:62
Transcripts:ENSRNOT00000003070
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1300114Srn2Serum renin concentration QTL 23.27blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)14395787821572472Rat
2293089Iddm31Insulin dependent diabetes mellitus QTL 314.7blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)14395787818558812Rat
7411573Bw139Body weight QTL 1394.70.001body mass (VT:0001259)body weight gain (CMO:0000420)14140068101Rat
9589814Gluco67Glucose level QTL 674.540.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)14140068101Rat
731183Pia20Pristane induced arthritis QTL 203.55joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)14939329839411170Rat
631212Bw5Body weight QTL55.43retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)141133490630674469Rat
2302277Gluco38Glucose level QTL 385.8blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141133471628389666Rat
1331740Bw26Body weight QTL 263.028body mass (VT:0001259)body weight (CMO:0000012)14395787831121464Rat
71117Niddm17Non-insulin dependent diabetes mellitus QTL 172.35blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)14117877928Rat
1358296Ael3Aortic elastin QTL 33.70.00051aorta elastin amount (VT:0003905)aortic elastin14862139853621398Rat
70195Mcs8Mammary carcinoma susceptibility QTL 84.28mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)14395787824886169Rat
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1411334716100078267Rat
634352Apr6Acute phase response QTL 63.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)14141415516Rat
70204Niddm20Non-insulin dependent diabetes mellitus QTL 205.10.000008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)14131893212Rat
2302045Pia39Pristane induced arthritis QTL 394.90.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G2a level (CMO:0002116)14862139853621398Rat
1300140Srn3Serum renin concentration QTL 33.19blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)141513759431238250Rat

Markers in Region
D14Ulb1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21415,629,029 - 15,629,335 (+)MAPPERmRatBN7.2
Rnor_6.01417,134,835 - 17,135,138NCBIRnor6.0
Rnor_5.01417,050,927 - 17,051,230UniSTSRnor5.0
RGSC_v3.41417,190,065 - 17,190,368UniSTSRGSC3.4
Celera1415,023,508 - 15,023,811UniSTS
Cytogenetic Map14p22UniSTS
RH142315  
Rat AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map14p22UniSTS
AI060908  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21415,631,785 - 15,633,459 (+)MAPPERmRatBN7.2
Rnor_6.01417,137,589 - 17,139,262NCBIRnor6.0
Rnor_5.01417,053,681 - 17,055,354UniSTSRnor5.0
RGSC_v3.41417,192,819 - 17,194,492UniSTSRGSC3.4
Celera1415,026,262 - 15,027,935UniSTS
Cytogenetic Map14p22UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 165 91 90 59 92 59 6 356 192 11 144 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000003070   ⟹   ENSRNOP00000003070
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1415,901,991 - 15,920,334 (+)Ensembl
mRatBN7.2 Ensembl1415,617,679 - 15,636,026 (+)Ensembl
Rnor_6.0 Ensembl1417,123,360 - 17,141,767 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000118729   ⟹   ENSRNOP00000081526
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1415,902,100 - 15,920,334 (+)Ensembl
mRatBN7.2 Ensembl1415,617,792 - 15,636,028 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000155411   ⟹   ENSRNOP00000106209
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1415,902,047 - 15,920,334 (+)Ensembl
RefSeq Acc Id: NM_017361   ⟹   NP_059057
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81415,902,034 - 15,920,335 (+)NCBI
mRatBN7.21415,617,726 - 15,636,029 (+)NCBI
Rnor_6.01417,123,531 - 17,141,832 (+)NCBI
Rnor_5.01417,039,514 - 17,057,924 (+)NCBI
RGSC_v3.41417,178,761 - 17,197,062 (+)RGD
Celera1415,012,204 - 15,030,485 (+)RGD
Sequence:
RefSeq Acc Id: XM_017599341   ⟹   XP_017454830
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81415,901,936 - 15,920,335 (+)NCBI
mRatBN7.21415,617,630 - 15,636,029 (+)NCBI
Rnor_6.01417,123,434 - 17,141,832 (+)NCBI
Sequence:
RefSeq Acc Id: NP_059057   ⟸   NM_017361
- UniProtKB: P70582 (UniProtKB/Swiss-Prot),   A6KK71 (UniProtKB/TrEMBL),   A0A8I5ZV73 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017454830   ⟸   XM_017599341
- Peptide Label: isoform X1
- Sequence:
Ensembl Acc Id: ENSRNOP00000003070   ⟸   ENSRNOT00000003070
Ensembl Acc Id: ENSRNOP00000081526   ⟸   ENSRNOT00000118729
Ensembl Acc Id: ENSRNOP00000106209   ⟸   ENSRNOT00000155411
Protein Domains
Nucleoporin Nup54 alpha-helical   Nup54 C-terminal interacting

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P70582-F1-model_v2 AlphaFold P70582 1-510 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13699209
Promoter ID:EPDNEW_R9734
Type:initiation region
Name:Nup54_1
Description:nucleoporin 54
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01417,123,572 - 17,123,632EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:619926 AgrOrtholog
BioCyc Gene G2FUF-16266 BioCyc
Ensembl Genes ENSRNOG00000002247 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000003070 ENTREZGENE
  ENSRNOT00000003070.6 UniProtKB/Swiss-Prot
  ENSRNOT00000155411 ENTREZGENE
Gene3D-CATH 1.20.5.170 UniProtKB/Swiss-Prot
  Single helix bin UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7134682 IMAGE-MGC_LOAD
InterPro Nup54/Nup57/Nup44 UniProtKB/Swiss-Prot
  Nup54_alpha-helical_dom UniProtKB/Swiss-Prot
  Nup54_C UniProtKB/Swiss-Prot
KEGG Report rno:53372 UniProtKB/Swiss-Prot
MGC_CLONE MGC:93519 IMAGE-MGC_LOAD
NCBI Gene 53372 ENTREZGENE
PANTHER NUCLEOPORIN P54 UniProtKB/Swiss-Prot
  PTHR13000 UniProtKB/Swiss-Prot
Pfam Nup54 UniProtKB/Swiss-Prot
  Nup54_C UniProtKB/Swiss-Prot
PhenoGen Nup54 PhenoGen
RatGTEx ENSRNOG00000002247 RatGTEx
UniProt A0A8I5ZV73 ENTREZGENE, UniProtKB/TrEMBL
  A0ABK0LVV9_RAT UniProtKB/TrEMBL
  A6KK71 ENTREZGENE, UniProtKB/TrEMBL
  NUP54_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-01-20 Nup54  nucleoporin 54    nucleoporin p54  Name updated 1299863 APPROVED
2002-08-07 Nup54  nucleoporin p54      Symbol and Name status set to provisional 70820 PROVISIONAL