Nup188 (nucleoporin 188) - Rat Genome Database

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Gene: Nup188 (nucleoporin 188) Rattus norvegicus
Analyze
Symbol: Nup188
Name: nucleoporin 188
RGD ID: 1306022
Description: Predicted to be a structural constituent of nuclear pore. Predicted to be involved in RNA export from nucleus and protein import into nucleus. Predicted to be located in nuclear envelope. Predicted to be part of nuclear pore inner ring. Human ortholog(s) of this gene implicated in Sandestig-Stefanova syndrome and respiratory failure. Orthologous to human NUP188 (nucleoporin 188); PARTICIPATES IN RNA transport pathway; INTERACTS WITH 2,4-dinitrotoluene; amphetamine; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC100911302; LOC366016; nucleoporin NUP188; nucleoporin NUP188 homolog
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
GRCr8333,957,778 - 34,014,122 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl333,957,791 - 34,014,122 (+)EnsemblGRCr8
mRatBN7.2313,559,917 - 13,616,313 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl313,559,990 - 13,616,307 (+)EnsemblmRatBN7.2
Rnor_6.038,852,271 - 8,908,608 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl38,873,933 - 8,908,438 (+)Ensemblrn6Rnor6.0
Rnor_5.0314,205,251 - 14,261,382 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.439,331,812 - 9,388,204 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera38,326,493 - 8,382,816 (+)NCBICelera
Cytogenetic Map3p12NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. 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.
2. Bi-allelic Loss-of-Function Variants in NUP188 Cause a Recognizable Syndrome Characterized by Neurologic, Ocular, and Cardiac Abnormalities. Muir AM, etal., Am J Hum Genet. 2020 May 7;106(5):623-631. doi: 10.1016/j.ajhg.2020.03.009. Epub 2020 Apr 9.
3. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:19946888   PMID:26878725  


Genomics

Comparative Map Data
Nup188
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8333,957,778 - 34,014,122 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl333,957,791 - 34,014,122 (+)EnsemblGRCr8
mRatBN7.2313,559,917 - 13,616,313 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl313,559,990 - 13,616,307 (+)EnsemblmRatBN7.2
Rnor_6.038,852,271 - 8,908,608 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl38,873,933 - 8,908,438 (+)Ensemblrn6Rnor6.0
Rnor_5.0314,205,251 - 14,261,382 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.439,331,812 - 9,388,204 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera38,326,493 - 8,382,816 (+)NCBICelera
Cytogenetic Map3p12NCBI
NUP188
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh389128,947,699 - 129,007,096 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl9128,947,683 - 129,007,835 (+)Ensemblhg38GRCh38
GRCh379131,709,978 - 131,769,375 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 369130,749,798 - 130,809,195 (+)NCBIBuild 36Build 36hg18NCBI36
Build 349128,789,563 - 128,848,928NCBI
Celera9102,361,838 - 102,421,686 (+)NCBICelera
Cytogenetic Map9q34.11NCBI
HuRef9101,317,691 - 101,376,696 (+)NCBIHuRef
CHM1_19131,861,021 - 131,920,403 (+)NCBICHM1_1
T2T-CHM13v2.09141,151,108 - 141,210,530 (+)NCBIT2T-CHM13v2.0
Nup188
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39230,176,419 - 30,234,278 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl230,176,409 - 30,234,278 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm38230,286,407 - 30,344,266 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl230,286,397 - 30,344,266 (+)Ensemblmm10GRCm38
MGSCv37230,141,953 - 30,199,782 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36230,108,442 - 30,166,271 (+)NCBIMGSCv36mm8
Celera229,991,190 - 30,049,297 (+)NCBICelera
Cytogenetic Map2BNCBI
cM Map221.49NCBI
Nup188
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555701,312,998 - 1,369,513 (+)Ensembl
ChiLan1.0NW_0049555701,312,998 - 1,369,513 (+)NCBIChiLan1.0ChiLan1.0
NUP188
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21110,346,228 - 10,404,809 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1910,348,576 - 10,407,139 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v09100,069,656 - 100,130,521 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.19128,733,749 - 128,791,252 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl9128,733,780 - 128,791,252 (+)EnsemblpanPan2panpan1.1
NUP188
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1954,657,520 - 54,712,900 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl954,657,682 - 54,712,827 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha953,853,072 - 53,908,426 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0955,578,563 - 55,633,941 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl955,578,567 - 55,633,921 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1954,340,129 - 54,395,076 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0954,652,331 - 54,707,442 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0954,745,638 - 54,800,996 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Nup188
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947196,639,939 - 196,694,386 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493648716,408,518 - 16,462,923 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_00493648716,408,523 - 16,462,916 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NUP188
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1269,259,519 - 269,312,862 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.11269,259,496 - 269,312,872 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21303,275,625 - 303,328,996 (+)NCBISscrofa10.2Sscrofa10.2susScr3
NUP188
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1129,150,603 - 9,213,512 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl129,151,005 - 9,208,452 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_023666096299,833 - 407,072 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Nup188
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247606,111,621 - 6,118,084 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla_female_1.0 EnsemblNW_0046247606,061,130 - 6,106,853 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046247606,061,130 - 6,120,597 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Nup188
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v155,287,533 - 5,344,279 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Nup188
589 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:83
Count of miRNA genes:67
Interacting mature miRNAs:79
Transcripts:ENSRNOT00000030996
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
1558647Cm46Cardiac mass QTL 465.40.0000055heart mass (VT:0007028)heart wet weight (CMO:0000069)32267715050766390Rat
1358357Srcrtb1Stress Responsive Cort Basal QTL 16.360.002blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)32905627547904329Rat
6893355Bw101Body weight QTL 1010.40.38body mass (VT:0001259)body weight (CMO:0000012)3576639050766390Rat
10450811Scl73Serum cholesterol level QTL 734.70.001blood LDL cholesterol amount (VT:0000181)blood low density lipoprotein cholesterol level (CMO:0000053)3290432947904329Rat
2292615Ept17Estrogen-induced pituitary tumorigenesis QTL 176.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)3655634751556347Rat
10450808Scl72Serum cholesterol level QTL 724.40.001blood LDL cholesterol amount (VT:0000181)blood low density lipoprotein cholesterol level (CMO:0000053)3290432947904329Rat
10450806Scl71Serum cholesterol level QTL 715.80.001blood LDL cholesterol amount (VT:0000181)blood low density lipoprotein cholesterol level (CMO:0000053)3290432947904329Rat
1558654Bw56Body weight QTL 564.50.0000171body mass (VT:0001259)body weight (CMO:0000012)3576639050766390Rat
10401810Kidm53Kidney mass QTL 53kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)32862533967641995Rat
1298526Arunc3Aerobic running capacity QTL 32.2exercise endurance trait (VT:0002332)longest distance run on treadmill (CMO:0001406)3612543751125437Rat
8693641Alc30Alcohol consumption QTL 3020.739drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)33083238444921701Rat
631545Bp85Blood pressure QTL 853.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3136721849Rat
1358885Bp251Blood pressure QTL 2513.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)31141509147Rat
631679Cm10Cardiac mass QTL 107.340.0001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)3655634751556347Rat
1558657Cm43Cardiac mass QTL 436.63e-08heart mass (VT:0007028)heart wet weight (CMO:0000069)32267715050766390Rat
631568Bp92Blood pressure QTL 922.20.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)31527234860272348Rat
6893363Bw105Body weight QTL 1052.60.0036body mass (VT:0001259)body weight (CMO:0000012)3576639050766390Rat
70203Gcr2Gastric cancer resistance QTL 22.6stomach morphology trait (VT:0000470)stomach tumor susceptibility score (CMO:0002043)32905627547904329Rat
1358888Bp264Blood pressure QTL 2644.43arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)35675975141509147Rat
1358185Ept6Estrogen-induced pituitary tumorigenesis QTL 66.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)3655634751556347Rat

Markers in Region
RH129640  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2313,616,073 - 13,616,256 (+)MAPPERmRatBN7.2
Rnor_6.038,908,369 - 8,908,551NCBIRnor6.0
Rnor_5.0314,261,143 - 14,261,325UniSTSRnor5.0
RGSC_v3.439,387,965 - 9,388,147UniSTSRGSC3.4
Celera38,382,577 - 8,382,759UniSTS
RH 3.4 Map351.31UniSTS
Cytogenetic Map3p12UniSTS
RH134009  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2313,616,943 - 13,617,144 (+)MAPPERmRatBN7.2
Rnor_6.038,909,239 - 8,909,439NCBIRnor6.0
Rnor_5.0314,262,013 - 14,262,213UniSTSRnor5.0
RGSC_v3.439,388,835 - 9,389,035UniSTSRGSC3.4
Celera38,383,447 - 8,383,647UniSTS
Cytogenetic Map3p12UniSTS
MARC_17455-17456:1028295191:1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2313,590,331 - 13,591,009 (+)MAPPERmRatBN7.2
Rnor_6.038,882,657 - 8,883,334NCBIRnor6.0
Rnor_5.0314,235,607 - 14,236,284UniSTSRnor5.0
RGSC_v3.439,362,143 - 9,362,820UniSTSRGSC3.4
Celera38,356,878 - 8,357,555UniSTS
Cytogenetic Map3p12UniSTS


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 67 162 91 90 59 92 59 6 356 192 11 141 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000030996   ⟹   ENSRNOP00000032298
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl333,957,806 - 34,014,119 (+)Ensembl
mRatBN7.2 Ensembl313,559,990 - 13,616,307 (+)Ensembl
Rnor_6.0 Ensembl38,873,933 - 8,908,438 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000099170   ⟹   ENSRNOP00000084918
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl333,962,391 - 34,014,122 (+)Ensembl
mRatBN7.2 Ensembl313,559,990 - 13,616,304 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000102741   ⟹   ENSRNOP00000077884
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl333,957,791 - 33,975,407 (+)Ensembl
mRatBN7.2 Ensembl313,559,990 - 13,577,592 (+)Ensembl
RefSeq Acc Id: NM_001427655   ⟹   NP_001414584
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8333,957,812 - 34,014,122 (+)NCBI
RefSeq Acc Id: XM_006233905   ⟹   XP_006233967
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8333,957,778 - 34,014,120 (+)NCBI
mRatBN7.2313,559,917 - 13,616,313 (+)NCBI
Rnor_6.038,852,271 - 8,908,608 (+)NCBI
Rnor_5.0314,205,251 - 14,261,382 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006233906   ⟹   XP_006233968
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8333,962,427 - 34,014,120 (+)NCBI
mRatBN7.2313,564,593 - 13,616,313 (+)NCBI
Rnor_6.038,856,428 - 8,908,608 (+)NCBI
Rnor_5.0314,205,251 - 14,261,382 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039106780   ⟹   XP_038962708
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8333,957,778 - 34,008,021 (+)NCBI
mRatBN7.2313,559,917 - 13,610,198 (+)NCBI
RefSeq Acc Id: XP_006233967   ⟸   XM_006233905
- Peptide Label: isoform X1
- UniProtKB: F1LRC6 (UniProtKB/TrEMBL),   A6JTX0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006233968   ⟸   XM_006233906
- Peptide Label: isoform X2
- UniProtKB: A6JTX0 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000032298   ⟸   ENSRNOT00000030996
RefSeq Acc Id: XP_038962708   ⟸   XM_039106780
- Peptide Label: isoform X3
Ensembl Acc Id: ENSRNOP00000077884   ⟸   ENSRNOT00000102741
Ensembl Acc Id: ENSRNOP00000084918   ⟸   ENSRNOT00000099170
RefSeq Acc Id: NP_001414584   ⟸   NM_001427655
- UniProtKB: A6JTX0 (UniProtKB/TrEMBL)
Protein Domains
Nucleoporin Nup188 N-terminal   Nucleoporin Nup188 N-terminal subdomain III

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1LRC6-F1-model_v2 AlphaFold F1LRC6 1-1541 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1306022 AgrOrtholog
BioCyc Gene G2FUF-50221 BioCyc
Ensembl Genes ENSRNOG00000025185 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000030996 ENTREZGENE
  ENSRNOT00000030996.8 UniProtKB/TrEMBL
  ENSRNOT00000099170 ENTREZGENE
  ENSRNOT00000099170.2 UniProtKB/TrEMBL
  ENSRNOT00000102741.2 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7303973 IMAGE-MGC_LOAD
InterPro ARM-type_fold UniProtKB/TrEMBL
  Nucleoporin_Nup188 UniProtKB/TrEMBL
  Nup188 UniProtKB/TrEMBL
  Nup188_N-subdom_III UniProtKB/TrEMBL
KEGG Report rno:366016 UniProtKB/TrEMBL
MGC_CLONE MGC:106006 IMAGE-MGC_LOAD
NCBI Gene 366016 ENTREZGENE
PANTHER NUCLEOPORIN NUP188 UniProtKB/TrEMBL
  PTHR31431 UniProtKB/TrEMBL
Pfam Nup188 UniProtKB/TrEMBL
  Nup188_N-subdom_III UniProtKB/TrEMBL
  Nup188_SH3-like UniProtKB/TrEMBL
PhenoGen Nup188 PhenoGen
RatGTEx ENSRNOG00000025185 RatGTEx
Superfamily-SCOP SSF48371 UniProtKB/TrEMBL
UniProt A0A8I5Y6G4_RAT UniProtKB/TrEMBL
  A0A8I6GC98_RAT UniProtKB/TrEMBL
  A6JTX0 ENTREZGENE, UniProtKB/TrEMBL
  F1LRC6 ENTREZGENE, UniProtKB/TrEMBL
  Q5RJY5_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Nup188  nucleoporin 188  LOC100911302  nucleoporin NUP188 homolog  Data merged from RGD:6494074 737654 PROVISIONAL
2012-07-05 LOC100911302  nucleoporin NUP188 homolog      Symbol and Name status set to provisional 70820 PROVISIONAL
2005-12-06 Nup188  nucleoporin 188  Nup188_predicted  nucleoporin 188 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Nup188_predicted  nucleoporin 188 (predicted)      Symbol and Name status set to approved 70820 APPROVED