Nup43 (nucleoporin 43) - Rat Genome Database

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Gene: Nup43 (nucleoporin 43) Rattus norvegicus
Analyze
Symbol: Nup43
Name: nucleoporin 43
RGD ID: 1596513
Description: Predicted to be located in cytosol; kinetochore; and nucleus. Predicted to be part of nuclear pore outer ring. Orthologous to human NUP43 (nucleoporin 43); PARTICIPATES IN mRNA nuclear export pathway; RNA transport pathway; INTERACTS WITH (+)-schisandrin B; 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC683983; MGC187947; nucleoporin Nup43; similar to Nucleoporin Nup43
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr813,964,814 - 3,978,277 (+)NCBIGRCr8
mRatBN7.212,144,427 - 2,157,887 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl12,148,043 - 2,158,186 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx11,797,864 - 1,807,689 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.017,798,264 - 7,808,085 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.012,079,965 - 2,089,786 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.011,771,468 - 1,781,554 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl11,771,710 - 1,782,091 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.013,468,454 - 3,478,304 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera1696,096 - 705,929 (+)NCBICelera
Cytogenetic Map1p13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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. 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.
2. 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.
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
5. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:12477932   PMID:15146057   PMID:17360435  


Genomics

Comparative Map Data
Nup43
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr813,964,814 - 3,978,277 (+)NCBIGRCr8
mRatBN7.212,144,427 - 2,157,887 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl12,148,043 - 2,158,186 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx11,797,864 - 1,807,689 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.017,798,264 - 7,808,085 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.012,079,965 - 2,089,786 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.011,771,468 - 1,781,554 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl11,771,710 - 1,782,091 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.013,468,454 - 3,478,304 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera1696,096 - 705,929 (+)NCBICelera
Cytogenetic Map1p13NCBI
NUP43
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh386149,724,315 - 149,749,358 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl6149,724,315 - 149,749,665 (-)EnsemblGRCh38hg38GRCh38
GRCh376150,045,451 - 150,067,665 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 366150,087,150 - 150,109,381 (-)NCBINCBI36Build 36hg18NCBI36
Celera6150,780,717 - 150,802,949 (-)NCBICelera
Cytogenetic Map6q25.1NCBI
HuRef6147,611,223 - 147,633,455 (-)NCBIHuRef
CHM1_16150,310,097 - 150,332,327 (-)NCBICHM1_1
T2T-CHM13v2.06150,924,084 - 150,946,307 (-)NCBIT2T-CHM13v2.0
Nup43
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39107,543,268 - 7,554,650 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl107,543,267 - 7,554,645 (+)EnsemblGRCm39 Ensembl
GRCm38107,667,504 - 7,678,886 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl107,667,503 - 7,678,881 (+)EnsemblGRCm38mm10GRCm38
MGSCv37107,387,302 - 7,398,684 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36107,357,706 - 7,369,068 (+)NCBIMGSCv36mm8
Celera107,545,069 - 7,556,444 (+)NCBICelera
Cytogenetic Map10A1NCBI
cM Map102.28NCBI
Nup43
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543911,534,512 - 11,553,598 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495543911,534,519 - 11,548,977 (+)NCBIChiLan1.0ChiLan1.0
NUP43
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v25169,746,055 - 169,768,601 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan16167,639,605 - 167,662,142 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v06147,539,588 - 147,562,124 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.16152,245,700 - 152,267,747 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl6152,245,700 - 152,267,747 (-)Ensemblpanpan1.1panPan2
NUP43
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1140,481,447 - 40,491,903 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl140,482,518 - 40,491,844 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha141,320,836 - 41,331,293 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0140,663,454 - 40,673,912 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl140,663,534 - 40,673,897 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1140,539,283 - 40,549,732 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0140,405,591 - 40,415,676 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0140,745,691 - 40,756,151 (-)NCBIUU_Cfam_GSD_1.0
Nup43
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404946135,403,264 - 135,422,941 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364892,655,215 - 2,674,942 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364892,657,657 - 2,674,942 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NUP43
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl116,249,546 - 16,267,624 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1116,249,493 - 16,267,636 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2118,575,742 - 18,591,609 (+)NCBISscrofa10.2Sscrofa10.2susScr3
NUP43
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11321,869,727 - 21,889,198 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1321,870,539 - 21,888,811 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666040197,902,591 - 197,921,451 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Nup43
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247858,329,131 - 8,345,345 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247858,329,172 - 8,343,934 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Nup43
64 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:10
Count of miRNA genes:10
Interacting mature miRNAs:10
Transcripts:ENSRNOT00000073528
Prediction methods:Miranda, Rnahybrid
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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354647Despr8Despair related QTL 80.0000341locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)1124744506Rat
2298546Neuinf4Neuroinflammation QTL 45.1nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)1128736750Rat
2313053Bss51Bone structure and strength QTL 513.80.0001tibia length (VT:0004357)tibia length (CMO:0000450)1132356093Rat
2313070Bss52Bone structure and strength QTL 524.40.0001body length (VT:0001256)body length (CMO:0000013)1132356093Rat
2313090Bmd69Bone mineral density QTL 694.40.0001tibia mineral mass (VT:1000283)compact volumetric bone mineral density (CMO:0001730)1132356093Rat
738020Pia8Pristane induced arthritis QTL 84.7joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1165833076Rat
1578650Bmd6Bone mineral density QTL 612.2femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)150910843284926Rat
1578651Bmd7Bone mineral density QTL 714.2femur mineral mass (VT:0010011)compact volumetric bone mineral density (CMO:0001730)150910843284926Rat
1578669Bss9Bone structure and strength QTL 96.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)150910843284926Rat
1554320Bmd1Bone mineral density QTL 112.20.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)150910886060548Rat

Markers in Region
RH139199  
Rat AssemblyChrPosition (strand)SourceJBrowse
RH 3.4 Map111.7UniSTS
RH131252  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.212,157,625 - 2,157,823 (+)MAPPERmRatBN7.2
Rnor_6.011,781,293 - 1,781,490NCBIRnor6.0
Rnor_5.013,478,043 - 3,478,240UniSTSRnor5.0
Celera1705,668 - 705,865UniSTS


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 29 34 18 19 18 1 1 60 25 39 11 1
Low 14 23 23 23 7 10 14 10 2 7
Below cutoff

Sequence


RefSeq Acc Id: ENSRNOT00000073528   ⟹   ENSRNOP00000066318
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl12,148,054 - 2,157,887 (+)Ensembl
Rnor_6.0 Ensembl11,771,721 - 1,781,554 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000080138   ⟹   ENSRNOP00000071201
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl12,148,043 - 2,158,186 (+)Ensembl
Rnor_6.0 Ensembl11,771,710 - 1,782,091 (+)Ensembl
RefSeq Acc Id: NM_001128191   ⟹   NP_001121663
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr813,968,466 - 3,978,277 (+)NCBI
mRatBN7.212,148,076 - 2,157,887 (+)NCBI
Rnor_6.011,771,721 - 1,781,554 (+)NCBI
Rnor_5.013,468,454 - 3,478,304 (+)NCBI
Celera1696,096 - 705,929 (+)RGD
Sequence:
RefSeq Acc Id: NM_001401290   ⟹   NP_001388219
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr813,968,466 - 3,978,270 (+)NCBI
mRatBN7.212,148,076 - 2,157,880 (+)NCBI
RefSeq Acc Id: XM_039090803   ⟹   XP_038946731
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr813,964,814 - 3,978,270 (+)NCBI
mRatBN7.212,144,427 - 2,157,880 (+)NCBI
RefSeq Acc Id: NP_001121663   ⟸   NM_001128191
- Peptide Label: isoform 2
- UniProtKB: M0R9Y3 (UniProtKB/TrEMBL),   A6JP15 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000071201   ⟸   ENSRNOT00000080138
RefSeq Acc Id: ENSRNOP00000066318   ⟸   ENSRNOT00000073528
RefSeq Acc Id: XP_038946731   ⟸   XM_039090803
- Peptide Label: isoform X1
RefSeq Acc Id: NP_001388219   ⟸   NM_001401290
- Peptide Label: isoform 1
- UniProtKB: B0BNB5 (UniProtKB/TrEMBL)

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-B0BNB5-F1-model_v2 AlphaFold B0BNB5 1-378 view protein structure

Transcriptome

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

Promoters
RGD ID:13689479
Promoter ID:EPDNEW_R3
Type:initiation region
Name:Nup43_1
Description:nucleoporin 43
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_6.011,771,743 - 1,771,803EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1596513 AgrOrtholog
BioCyc Gene G2FUF-62452 BioCyc
Ensembl Genes ENSRNOG00000049505 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000073528 ENTREZGENE
  ENSRNOT00000073528.3 UniProtKB/TrEMBL
  ENSRNOT00000080138 ENTREZGENE
  ENSRNOT00000080138.2 UniProtKB/TrEMBL
Gene3D-CATH 2.130.10.10 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:9103164 IMAGE-MGC_LOAD
InterPro WD40/YVTN_repeat-like_dom_sf UniProtKB/TrEMBL
  WD40_repeat UniProtKB/TrEMBL
  WD40_repeat_CS UniProtKB/TrEMBL
  WD40_repeat_dom_sf UniProtKB/TrEMBL
KEGG Report rno:683983 UniProtKB/TrEMBL
MGC_CLONE MGC:187947 IMAGE-MGC_LOAD
NCBI Gene 683983 ENTREZGENE
PANTHER NUCLEOPORIN NUP43 UniProtKB/TrEMBL
  NUCLEOPORIN NUP43 UniProtKB/TrEMBL
Pfam WD40 UniProtKB/TrEMBL
PhenoGen Nup43 PhenoGen
PROSITE WD_REPEATS_1 UniProtKB/TrEMBL
  WD_REPEATS_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000049505 RatGTEx
SMART WD40 UniProtKB/TrEMBL
Superfamily-SCOP WD40_like UniProtKB/TrEMBL
UniProt A6JP15 ENTREZGENE, UniProtKB/TrEMBL
  B0BNB5 ENTREZGENE, UniProtKB/TrEMBL
  M0R9Y3 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2010-12-09 Nup43  nucleoporin 43  LOC683983  similar to Nucleoporin Nup43  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 LOC683983  similar to Nucleoporin Nup43      Symbol and Name status set to provisional 70820 PROVISIONAL