Pcnp (PEST proteolytic signal containing nuclear protein) - Rat Genome Database

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Gene: Pcnp (PEST proteolytic signal containing nuclear protein) Rattus norvegicus
Analyze
Symbol: Pcnp
Name: PEST proteolytic signal containing nuclear protein
RGD ID: 1563775
Description: Predicted to be involved in proteasome-mediated ubiquitin-dependent protein catabolic process and protein ubiquitination. Predicted to be located in nuclear body. Predicted to be active in nucleus. Orthologous to human PCNP (PEST proteolytic signal containing nuclear protein); INTERACTS WITH 4,4'-sulfonyldiphenol; bisphenol A; bisphenol F.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: Ab2-416; liver regeneration-related protein LRRG084; LOC288165; PEST proteolytic signal-containing nuclear protein; PEST-containing nuclear protein; similar to PEST-containing nuclear protein
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81158,061,885 - 58,076,436 (+)NCBIGRCr8
mRatBN7.21144,592,766 - 44,607,372 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1144,592,742 - 44,607,348 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1153,369,115 - 53,383,652 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01146,030,729 - 46,045,266 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01145,154,893 - 45,169,429 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01147,055,641 - 47,070,319 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1147,061,354 - 47,068,648 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01150,237,656 - 50,252,209 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41145,572,442 - 45,580,616 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1144,348,073 - 44,356,228 (+)NCBICelera
Cytogenetic Map11q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
nuclear body  (IEA,ISO)
nucleoplasm  (ISO)
nucleus  (IBA,IEA,ISO,ISS)

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:12176013   PMID:14741369  


Genomics

Comparative Map Data
Pcnp
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81158,061,885 - 58,076,436 (+)NCBIGRCr8
mRatBN7.21144,592,766 - 44,607,372 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1144,592,742 - 44,607,348 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1153,369,115 - 53,383,652 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01146,030,729 - 46,045,266 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01145,154,893 - 45,169,429 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01147,055,641 - 47,070,319 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1147,061,354 - 47,068,648 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01150,237,656 - 50,252,209 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41145,572,442 - 45,580,616 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1144,348,073 - 44,356,228 (+)NCBICelera
Cytogenetic Map11q12NCBI
PCNP
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh383101,574,094 - 101,594,465 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl3101,574,180 - 101,594,465 (+)EnsemblGRCh38hg38GRCh38
GRCh373101,292,938 - 101,313,309 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 363102,775,732 - 102,795,971 (+)NCBINCBI36Build 36hg18NCBI36
Celera399,685,397 - 99,705,556 (+)NCBICelera
Cytogenetic Map3q12.3NCBI
HuRef398,661,973 - 98,682,208 (+)NCBIHuRef
CHM1_13101,256,345 - 101,276,587 (+)NCBICHM1_1
T2T-CHM13v2.03104,286,707 - 104,307,080 (+)NCBIT2T-CHM13v2.0
Pcnp
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391655,835,870 - 55,851,590 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1655,827,608 - 55,850,102 (-)EnsemblGRCm39 Ensembl
GRCm381656,015,507 - 56,029,727 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1656,007,245 - 56,029,739 (-)EnsemblGRCm38mm10GRCm38
MGSCv371656,015,621 - 56,029,830 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361655,941,956 - 55,954,632 (-)NCBIMGSCv36mm8
Celera1656,330,376 - 56,345,117 (-)NCBICelera
Cytogenetic Map16C1.1NCBI
cM Map1633.77NCBI
Pcnp
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049554273,142,340 - 3,162,172 (+)NCBIChiLan1.0ChiLan1.0
PCNP
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2299,531,350 - 99,551,609 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1399,536,127 - 99,556,386 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0398,683,411 - 98,703,664 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.13105,362,948 - 105,383,051 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl3105,362,954 - 105,383,051 (+)Ensemblpanpan1.1panPan2
PCNP
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1337,960,097 - 7,978,062 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl337,960,148 - 7,976,618 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha338,114,458 - 8,132,466 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0338,099,133 - 8,117,143 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl338,099,162 - 8,117,646 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1337,986,747 - 8,004,758 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0338,033,322 - 8,051,330 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0338,373,424 - 8,391,453 (+)NCBIUU_Cfam_GSD_1.0
Pcnp
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405602148,902,523 - 148,920,624 (-)NCBIHiC_Itri_2
SpeTri2.0NW_0049366301,800,458 - 1,818,494 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PCNP
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13157,470,050 - 157,491,205 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.113157,468,427 - 157,491,264 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.213166,953,603 - 166,971,766 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PCNP
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12279,272,786 - 79,292,572 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604187,263,911 - 87,283,713 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Pcnp
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462478915,429,793 - 15,448,422 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462478915,429,698 - 15,450,352 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Pcnp
55 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:82
Count of miRNA genes:75
Interacting mature miRNAs:80
Transcripts:ENSRNOT00000039997
Prediction methods:Microtar, 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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1300147Bp187Blood pressure QTL 1873.67arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)11169446234Rat
1558659Tescar1Testicular tumor resistance QTL 13.9testis integrity trait (VT:0010572)percentage of study population developing testis tumors during a period of time (CMO:0001261)11104193166113562Rat
1641927Alcrsp10Alcohol response QTL 10alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)11843667453436674Rat
724554Iddm17Insulin dependent diabetes mellitus QTL 170.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)111897620886241447Rat
10058952Gmadr6Adrenal mass QTL 62.290.0072adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)112295940367959403Rat
8694376Bw156Body weight QTL 1562.250.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)112328045668280456Rat
9590313Scort20Serum corticosterone level QTL 206.510.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)112328045668280456Rat
9589032Epfw10Epididymal fat weight QTL 109.290.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)112328045668280456Rat
8694424Bw162Body weight QTL 1623.80.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)112328045668280456Rat
724563Uae10Urinary albumin excretion QTL 106urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)112767241082846715Rat
1300130Rf20Renal function QTL 204.44kidney glomerulus integrity trait (VT:0010546)kidney glomerulus diameter (CMO:0001166)112952841860324829Rat
1300110Stl7Serum triglyceride level QTL 74.64blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)112952841882566702Rat
2298551Neuinf10Neuroinflammation QTL 103.7nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)113123913478851519Rat
70180BpQTLcluster10Blood pressure QTL cluster 103.19arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)113491804179918041Rat
1300135Rf19Renal function QTL 193.38blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)114094618882566702Rat
2312566Glom20Glomerulus QTL 203.60.001kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)114428575982566702Rat

Markers in Region
RH138989  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21144,603,624 - 44,603,769 (+)MAPPERmRatBN7.2
Rnor_6.01147,066,572 - 47,066,716NCBIRnor6.0
Rnor_5.01150,248,462 - 50,248,606UniSTSRnor5.0
RGSC_v3.41145,578,529 - 45,578,673UniSTSRGSC3.4
Celera1144,354,141 - 44,354,285UniSTS
RH 3.4 Map11321.0UniSTS
Cytogenetic Map11q12UniSTS
RH135010  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21144,605,942 - 44,606,162 (+)MAPPERmRatBN7.2
Rnor_6.01147,068,890 - 47,069,109NCBIRnor6.0
Rnor_5.01150,250,780 - 50,250,999UniSTSRnor5.0
RGSC_v3.41145,580,847 - 45,581,066UniSTSRGSC3.4
Celera1144,356,459 - 44,356,678UniSTS
Cytogenetic Map11q12UniSTS
RH137327  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21144,607,025 - 44,607,239 (+)MAPPERmRatBN7.2
Rnor_6.01147,069,973 - 47,070,186NCBIRnor6.0
Rnor_5.01150,251,863 - 50,252,076UniSTSRnor5.0
RGSC_v3.41145,581,930 - 45,582,143UniSTSRGSC3.4
Celera1144,357,542 - 44,357,755UniSTS
RH 3.4 Map11331.3UniSTS
Cytogenetic Map11q12UniSTS
RH138089  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21144,596,480 - 44,596,648 (+)MAPPERmRatBN7.2
Rnor_6.01147,059,434 - 47,059,601NCBIRnor6.0
Rnor_5.01150,241,324 - 50,241,491UniSTSRnor5.0
RGSC_v3.41145,571,391 - 45,571,558UniSTSRGSC3.4
Celera1144,347,022 - 44,347,189UniSTS
RH 3.4 Map11324.5UniSTS
Cytogenetic Map11q12UniSTS


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 43 57 41 19 41 8 11 74 35 41 11 8
Low
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000039997   ⟹   ENSRNOP00000039022
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1144,598,441 - 44,605,712 (+)Ensembl
Rnor_6.0 Ensembl1147,061,354 - 47,068,648 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000103996   ⟹   ENSRNOP00000079800
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1144,592,742 - 44,607,348 (+)Ensembl
RefSeq Acc Id: NM_001395615   ⟹   NP_001382544
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81158,061,885 - 58,076,436 (+)NCBI
mRatBN7.21144,592,819 - 44,607,372 (+)NCBI
RefSeq Acc Id: NM_001395616   ⟹   NP_001382545
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81158,061,885 - 58,076,436 (+)NCBI
mRatBN7.21144,592,819 - 44,607,372 (+)NCBI
RefSeq Acc Id: NM_001395617   ⟹   NP_001382546
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81158,061,885 - 58,076,436 (+)NCBI
mRatBN7.21144,592,819 - 44,607,372 (+)NCBI
RefSeq Acc Id: XM_063270407   ⟹   XP_063126477
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81158,067,507 - 58,076,435 (+)NCBI
RefSeq Acc Id: XM_063270408   ⟹   XP_063126478
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81158,067,507 - 58,076,435 (+)NCBI
Reference Protein Sequences
RefSeq Acc Id: ENSRNOP00000039022   ⟸   ENSRNOT00000039997
RefSeq Acc Id: ENSRNOP00000079800   ⟸   ENSRNOT00000103996
RefSeq Acc Id: NP_001382544   ⟸   NM_001395615
- Peptide Label: isoform 1
- UniProtKB: Q7TP40 (UniProtKB/Swiss-Prot),   A6IQQ1 (UniProtKB/TrEMBL)
RefSeq Acc Id: NP_001382545   ⟸   NM_001395616
- Peptide Label: isoform 2
- UniProtKB: Q7TP40 (UniProtKB/Swiss-Prot),   A0A8I5ZNV8 (UniProtKB/TrEMBL)
RefSeq Acc Id: NP_001382546   ⟸   NM_001395617
- Peptide Label: isoform 3
- UniProtKB: A6IQQ2 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063126477   ⟸   XM_063270407
- Peptide Label: isoform X1
RefSeq Acc Id: XP_063126478   ⟸   XM_063270408
- Peptide Label: isoform X2

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q7TP40-F1-model_v2 AlphaFold Q7TP40 1-189 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:1563775 AgrOrtholog
BioCyc Gene G2FUF-21512 BioCyc
Ensembl Genes ENSRNOG00000028411 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ENSRNOG00055013770 UniProtKB/Swiss-Prot
  ENSRNOG00060013069 UniProtKB/Swiss-Prot
  ENSRNOG00065002281 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000039997 UniProtKB/TrEMBL
  ENSRNOT00000039997.5 UniProtKB/Swiss-Prot
  ENSRNOT00000103996 ENTREZGENE
  ENSRNOT00000103996.1 UniProtKB/TrEMBL
  ENSRNOT00055023680 UniProtKB/Swiss-Prot
  ENSRNOT00060022284 UniProtKB/Swiss-Prot
  ENSRNOT00065003004 UniProtKB/Swiss-Prot
InterPro PCNP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:288165 UniProtKB/Swiss-Prot
NCBI Gene 288165 ENTREZGENE
PANTHER PEST PROTEOLYTIC SIGNAL-CONTAINING NUCLEAR PROTEIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR16523 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam PCNP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Pcnp PhenoGen
RatGTEx ENSRNOG00000028411 RatGTEx
  ENSRNOG00055013770 RatGTEx
  ENSRNOG00060013069 RatGTEx
  ENSRNOG00065002281 RatGTEx
UniProt A0A0H2UHW4_RAT UniProtKB/TrEMBL
  A0A8I5ZNV8 ENTREZGENE, UniProtKB/TrEMBL
  A6IQQ1 ENTREZGENE, UniProtKB/TrEMBL
  A6IQQ2 ENTREZGENE, UniProtKB/TrEMBL
  PCNP_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-04 Pcnp  PEST proteolytic signal containing nuclear protein  LOC288165  similar to PEST-containing nuclear protein  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-02-09 LOC288165  similar to PEST-containing nuclear protein      Symbol and Name status set to provisional 70820 PROVISIONAL