Nup62cl (nucleoporin 62 C-terminal like) - Rat Genome Database

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Gene: Nup62cl (nucleoporin 62 C-terminal like) Rattus norvegicus
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Symbol: Nup62cl
Name: nucleoporin 62 C-terminal like
RGD ID: 1564353
Description: Predicted to enable phospholipid binding activity. 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 central transport channel. Orthologous to human NUP62CL (nucleoporin 62 C-terminal like); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; amphetamine; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC300923; RGD1564353; similar to Nucleoporin 62
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
GRCr8X108,457,043 - 108,513,525 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 EnsemblX108,457,043 - 108,512,664 (-)EnsemblGRCr8
mRatBN7.2X103,668,458 - 103,724,957 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX103,668,455 - 103,724,081 (-)EnsemblmRatBN7.2
Rnor_6.0X111,333,274 - 111,390,023 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX111,334,252 - 111,365,849 (-)Ensemblrn6Rnor6.0
Rnor_5.0353,207,455 - 53,264,220 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4X127,752,322 - 127,812,950 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera344,203,467 - 44,259,295 (+)NCBICelera
Cytogenetic MapXq32NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

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. GOA pipeline RGD automated data pipeline
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:15970630  


Genomics

Comparative Map Data
Nup62cl
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X108,457,043 - 108,513,525 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 EnsemblX108,457,043 - 108,512,664 (-)EnsemblGRCr8
mRatBN7.2X103,668,458 - 103,724,957 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX103,668,455 - 103,724,081 (-)EnsemblmRatBN7.2
Rnor_6.0X111,333,274 - 111,390,023 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX111,334,252 - 111,365,849 (-)Ensemblrn6Rnor6.0
Rnor_5.0353,207,455 - 53,264,220 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4X127,752,322 - 127,812,950 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera344,203,467 - 44,259,295 (+)NCBICelera
Cytogenetic MapXq32NCBI
NUP62CL
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X107,123,427 - 107,206,433 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX107,123,427 - 107,206,505 (-)Ensemblhg38GRCh38
GRCh37X106,366,657 - 106,449,663 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X106,253,358 - 106,336,200 (-)NCBIBuild 36Build 36hg18NCBI36
CeleraX106,837,965 - 106,921,027 (-)NCBICelera
Cytogenetic MapXq22.3NCBI
HuRefX95,994,426 - 96,076,159 (-)NCBIHuRef
CHM1_1X106,277,530 - 106,360,560 (-)NCBICHM1_1
T2T-CHM13v2.0X105,559,960 - 105,642,842 (-)NCBIT2T-CHM13v2.0
Nup62cl
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X138,907,551 - 138,963,456 (-)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX138,907,554 - 138,963,461 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm38X140,006,802 - 140,062,707 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX140,006,805 - 140,062,712 (-)Ensemblmm10GRCm38
MGSCv37X136,542,212 - 136,597,107 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36X135,354,037 - 135,408,909 (-)NCBIMGSCv36mm8
CeleraX123,269,854 - 123,324,869 (-)NCBICelera
Cytogenetic MapXF1NCBI
cM MapX61.35NCBI
Nup62cl
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554908,842,889 - 8,860,885 (+)Ensembl
ChiLan1.0NW_0049554908,807,866 - 8,904,153 (+)NCBIChiLan1.0ChiLan1.0
NUP62CL
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2X106,605,716 - 106,722,143 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X106,609,317 - 106,725,744 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X96,222,802 - 96,300,219 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X106,600,838 - 106,676,569 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX106,600,819 - 106,638,256 (-)EnsemblpanPan2panpan1.1
NUP62CL
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X80,708,829 - 80,787,441 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX80,729,667 - 80,784,034 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_TashaX66,827,950 - 66,922,117 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0X82,352,349 - 82,446,668 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 EnsemblX82,373,014 - 82,429,438 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1X79,815,275 - 79,909,439 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X81,526,810 - 81,620,971 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X81,318,837 - 81,412,574 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Nup62cl
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X80,077,312 - 80,154,636 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364997,528,979 - 7,580,656 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049364997,503,475 - 7,579,453 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NUP62CL
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX87,601,042 - 87,630,253 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1X87,578,656 - 87,658,296 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X101,950,958 - 102,030,618 (-)NCBISscrofa10.2Sscrofa10.2susScr3
NUP62CL
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X94,952,017 - 95,033,089 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 EnsemblX94,951,636 - 94,998,052 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366606520,032,182 - 20,116,664 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Nup62cl
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248039,424,628 - 9,487,626 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046248039,391,282 - 9,487,066 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Nup62cl
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1X91,992,116 - 92,074,601 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Nup62cl
273 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:144
Count of miRNA genes:94
Interacting mature miRNAs:124
Transcripts:ENSRNOT00000066497
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
1598872Memor14Memory QTL 144.5exploratory behavior trait (VT:0010471)difference between duration of physical contact or close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X97528096142528096Rat
738025Stresp3Stress response QTL 34.610.0066stress-related behavior trait (VT:0010451)defensive burying - approachX105359969157758123Rat
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X80434318125434318Rat
738029Stresp2Stress response QTL 23.40.0004stress-related behavior trait (VT:0010451)defensive burying - approachX92979612117740458Rat
61431Cia19Collagen induced arthritis QTL 194.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X105468858125434318Rat
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX45182909117740458Rat
2302047Pia34Pristane induced arthritis QTL 345.80.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)1996916163141916163Rat

Markers in Region
AI179798  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X103,668,657 - 103,668,809 (+)MAPPERmRatBN7.2
Rnor_6.0X111,333,477 - 111,333,628NCBIRnor6.0
Rnor_5.0353,263,866 - 53,264,017UniSTSRnor5.0
RGSC_v3.4X127,752,525 - 127,752,676UniSTSRGSC3.4
Celera344,258,941 - 44,259,092UniSTS
RH 3.4 Map71122.91UniSTS
Cytogenetic MapXq35UniSTS
AU049450  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X103,719,292 - 103,719,485 (+)MAPPERmRatBN7.2
Rnor_6.0X111,384,962 - 111,385,154NCBIRnor6.0
Rnor_5.0353,212,340 - 53,212,532UniSTSRnor5.0
RGSC_v3.4X127,808,138 - 127,808,330UniSTSRGSC3.4
Celera344,208,851 - 44,209,043UniSTS
Cytogenetic MapXq35UniSTS


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
14 2 40 127 72 73 47 65 47 2 236 125 5 110 48 87 26 7 7

Sequence


Ensembl Acc Id: ENSRNOT00000088979   ⟹   ENSRNOP00000075626
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 EnsemblX108,457,043 - 108,512,664 (-)Ensembl
mRatBN7.2 EnsemblX103,668,455 - 103,724,081 (-)Ensembl
Rnor_6.0 EnsemblX111,334,252 - 111,365,849 (-)Ensembl
RefSeq Acc Id: NM_001427605   ⟹   NP_001414534
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X108,457,883 - 108,512,665 (-)NCBI
RefSeq Acc Id: XM_006234254   ⟹   XP_006234316
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X108,457,043 - 108,512,880 (-)NCBI
mRatBN7.2X103,669,293 - 103,724,191 (-)NCBI
Rnor_6.0X111,333,274 - 111,389,404 (-)NCBI
Rnor_5.0353,207,455 - 53,264,220 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006234255   ⟹   XP_006234317
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X108,457,043 - 108,513,525 (-)NCBI
mRatBN7.2X103,669,293 - 103,724,957 (-)NCBI
Rnor_6.0X111,333,274 - 111,390,023 (-)NCBI
Rnor_5.0353,207,455 - 53,264,220 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039100269   ⟹   XP_038956197
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X108,457,043 - 108,511,533 (-)NCBI
mRatBN7.2X103,669,293 - 103,722,940 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001414534 (Get FASTA)   NCBI Sequence Viewer  
  XP_006234316 (Get FASTA)   NCBI Sequence Viewer  
  XP_006234317 (Get FASTA)   NCBI Sequence Viewer  
  XP_038956197 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI60918 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000075626
  ENSRNOP00000075626.1
RefSeq Acc Id: XP_006234317   ⟸   XM_006234255
- Peptide Label: isoform X1
- UniProtKB: A0A0G2KB27 (UniProtKB/TrEMBL),   A6HLS3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006234316   ⟸   XM_006234254
- Peptide Label: isoform X1
- UniProtKB: A0A0G2KB27 (UniProtKB/TrEMBL),   A6HLS3 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000075626   ⟸   ENSRNOT00000088979
RefSeq Acc Id: XP_038956197   ⟸   XM_039100269
- Peptide Label: isoform X1
- UniProtKB: A0A0G2KB27 (UniProtKB/TrEMBL),   A6HLS3 (UniProtKB/TrEMBL)
RefSeq Acc Id: NP_001414534   ⟸   NM_001427605
- UniProtKB: A0A0G2KB27 (UniProtKB/TrEMBL),   A6HLS3 (UniProtKB/TrEMBL)
Protein Domains
Nucleoporin NSP1-like C-terminal

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A0G2KB27-F1-model_v2 AlphaFold A0A0G2KB27 1-273 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:1564353 AgrOrtholog
BioCyc Gene G2FUF-1548 BioCyc
Ensembl Genes ENSRNOG00000057753 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000088979 ENTREZGENE
  ENSRNOT00000088979.3 UniProtKB/TrEMBL
Gene3D-CATH 1.20.5.170 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7458042 IMAGE-MGC_LOAD
InterPro NSP1/NUP62 UniProtKB/TrEMBL
  Nucleoporin_NSP1_C UniProtKB/TrEMBL
KEGG Report rno:300923 UniProtKB/TrEMBL
MGC_CLONE MGC:188661 IMAGE-MGC_LOAD
NCBI Gene 300923 ENTREZGENE
PANTHER NUCLEOPORIN 62 C-TERMINAL-LIKE UniProtKB/TrEMBL
  PTHR12084 UniProtKB/TrEMBL
Pfam Nsp1_C UniProtKB/TrEMBL
PhenoGen Nup62cl PhenoGen
RatGTEx ENSRNOG00000057753 RatGTEx
UniProt A0A0G2KB27 ENTREZGENE, UniProtKB/TrEMBL
  A6HLS3 ENTREZGENE, UniProtKB/TrEMBL
  B1H298_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-06 Nup62cl  nucleoporin 62 C-terminal like  RGD1564353_predicted  similar to Nucleoporin 62 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1564353_predicted  similar to Nucleoporin 62 (predicted)  LOC300923  similar to Nucleoporin 62  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC300923  similar to Nucleoporin 62      Symbol and Name status set to provisional 70820 PROVISIONAL