Ppp1r42 (protein phosphatase 1, regulatory subunit 42) - Rat Genome Database

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Gene: Ppp1r42 (protein phosphatase 1, regulatory subunit 42) Rattus norvegicus
Analyze
Symbol: Ppp1r42
Name: protein phosphatase 1, regulatory subunit 42
RGD ID: 1585679
Description: Predicted to enable actin binding activity; dynein complex binding activity; and tubulin binding activity. Predicted to be located in centrosome and manchette. Orthologous to human PPP1R42 (protein phosphatase 1 regulatory subunit 42); INTERACTS WITH bisphenol A; flutamide; furan.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: hypothetical protein LOC683514; LOC683514; uncharacterized protein LOC683514
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
GRCr8514,009,972 - 14,057,330 (+)NCBIGRCr8
mRatBN7.259,227,109 - 9,274,461 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl59,227,204 - 9,274,453 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx511,379,422 - 11,430,891 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0513,006,578 - 13,060,838 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0512,714,074 - 12,765,558 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.058,911,356 - 8,956,313 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl58,916,633 - 8,956,119 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0513,718,715 - 13,763,672 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.458,773,373 - 8,818,333 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera58,740,514 - 8,787,374 (+)NCBICelera
Cytogenetic Map5q11NCBI
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

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. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:18237440   PMID:19886865   PMID:21738792  


Genomics

Comparative Map Data
Ppp1r42
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8514,009,972 - 14,057,330 (+)NCBIGRCr8
mRatBN7.259,227,109 - 9,274,461 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl59,227,204 - 9,274,453 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx511,379,422 - 11,430,891 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0513,006,578 - 13,060,838 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0512,714,074 - 12,765,558 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.058,911,356 - 8,956,313 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl58,916,633 - 8,956,119 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0513,718,715 - 13,763,672 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.458,773,373 - 8,818,333 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera58,740,514 - 8,787,374 (+)NCBICelera
Cytogenetic Map5q11NCBI
PPP1R42
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38866,964,103 - 67,028,554 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl866,964,099 - 67,056,604 (-)EnsemblGRCh38hg38GRCh38
GRCh37867,876,338 - 67,940,789 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36868,062,920 - 68,103,340 (-)NCBINCBI36Build 36hg18NCBI36
Celera863,893,786 - 63,934,229 (-)NCBICelera
Cytogenetic Map8q13.1NCBI
HuRef863,393,125 - 63,433,545 (-)NCBIHuRef
CHM1_1867,955,410 - 67,995,835 (-)NCBICHM1_1
T2T-CHM13v2.0867,390,584 - 67,455,035 (-)NCBIT2T-CHM13v2.0
Ppp1r42
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39110,038,847 - 10,083,766 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl110,038,849 - 10,079,361 (-)EnsemblGRCm39 Ensembl
GRCm3819,968,622 - 10,013,541 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl19,968,624 - 10,009,136 (-)EnsemblGRCm38mm10GRCm38
MGSCv3719,958,705 - 9,999,211 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3619,953,838 - 9,994,344 (-)NCBIMGSCv36mm8
Celera19,942,800 - 9,983,315 (-)NCBICelera
Cytogenetic Map1A2NCBI
cM Map12.25NCBI
Ppp1r42
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495544412,259,941 - 12,308,911 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495544412,255,381 - 12,294,605 (+)NCBIChiLan1.0ChiLan1.0
PPP1R42
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2782,701,653 - 82,769,756 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1858,343,914 - 58,412,017 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0863,507,439 - 63,572,137 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1865,193,802 - 65,233,450 (-)NCBIpanpan1.1PanPan1.1panPan2
PPP1R42
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12916,507,235 - 16,549,210 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2916,492,392 - 16,549,320 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2916,799,958 - 16,865,364 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02916,588,125 - 16,630,441 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2916,580,978 - 16,630,181 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12916,620,104 - 16,661,985 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02916,696,676 - 16,762,177 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02916,953,032 - 17,018,688 (-)NCBIUU_Cfam_GSD_1.0
Ppp1r42
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440530367,672,550 - 67,722,170 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364967,063,304 - 7,106,130 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364967,063,335 - 7,112,890 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PPP1R42
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl467,772,806 - 67,816,230 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1467,771,755 - 67,816,392 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2473,833,186 - 73,875,554 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PPP1R42
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1862,823,763 - 62,891,976 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366603978,624,276 - 78,679,408 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ppp1r42
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474424,336,145 - 24,379,811 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474424,331,557 - 24,371,988 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Ppp1r42
465 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:29
Count of miRNA genes:24
Interacting mature miRNAs:29
Transcripts:ENSRNOT00000066395
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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1331756Rf34Renal function QTL 344.16275kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5190450412Rat
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51131345958Rat
1331771Rf35Renal function QTL 354.36965kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)572947086724018Rat
2312562Pur18Proteinuria QTL 182.60.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)5213896532656739Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
8662454Vetf3Vascular elastic tissue fragility QTL 327.4artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)5228222669540447Rat
2313085Bss59Bone structure and strength QTL 592.90.0001long bone metaphysis morphology trait (VT:0000133)tibia midshaft total cross-sectional area (CMO:0001715)5384401826141981Rat
1300117Hrtrt8Heart rate QTL 83.49heart pumping trait (VT:2000009)heart rate (CMO:0000002)5384401847869213Rat
61462Niddm10Non-insulin dependent diabetes mellitus QTL 103.90.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)5511215947171491Rat
631827Alc4Alcohol consumption QTL 43.5consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)5818750118616199Rat
2293666Bmd38Bone mineral density QTL 384.4femur size trait (VT:1000369)femoral neck cortical cross-sectional area (CMO:0001702)5894822853948228Rat


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 7
Low 7 2 2 51 23 27 11
Below cutoff 2 43 37 27 17 27 5 6 23 12 7 5

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000066395   ⟹   ENSRNOP00000061242
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl59,227,204 - 9,274,453 (+)Ensembl
Rnor_6.0 Ensembl58,916,633 - 8,956,119 (+)Ensembl
RefSeq Acc Id: NM_001127569   ⟹   NP_001121041
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8514,010,022 - 14,057,330 (+)NCBI
mRatBN7.259,227,149 - 9,274,461 (+)NCBI
Rnor_6.058,911,356 - 8,956,313 (+)NCBI
Rnor_5.0513,718,715 - 13,763,672 (+)NCBI
RGSC_v3.458,773,373 - 8,818,333 (+)RGD
Celera58,740,514 - 8,787,374 (+)RGD
Sequence:
RefSeq Acc Id: XM_039110784   ⟹   XP_038966712
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8514,018,587 - 14,057,330 (+)NCBI
mRatBN7.259,235,715 - 9,274,455 (+)NCBI
RefSeq Acc Id: XM_063288419   ⟹   XP_063144489
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8514,009,972 - 14,049,523 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001121041 (Get FASTA)   NCBI Sequence Viewer  
  XP_038966712 (Get FASTA)   NCBI Sequence Viewer  
  XP_063144489 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI61888 (Get FASTA)   NCBI Sequence Viewer  
  EDM11551 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000061242
  ENSRNOP00000061242.2
Reference Protein Sequences
RefSeq Acc Id: NP_001121041   ⟸   NM_001127569
- UniProtKB: B1WBU1 (UniProtKB/TrEMBL),   E9PTW7 (UniProtKB/TrEMBL),   A0A9K3Y8A7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000061242   ⟸   ENSRNOT00000066395
RefSeq Acc Id: XP_038966712   ⟸   XM_039110784
- Peptide Label: isoform X2
RefSeq Acc Id: XP_063144489   ⟸   XM_063288419
- Peptide Label: isoform X1

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:1585679 AgrOrtholog
BioCyc Gene G2FUF-42208 BioCyc
Ensembl Genes ENSRNOG00000006804 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000066395 ENTREZGENE
  ENSRNOT00000066395.3 UniProtKB/TrEMBL
Gene3D-CATH 3.80.10.10 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7134408 IMAGE-MGC_LOAD
InterPro L_dom-like UniProtKB/TrEMBL
  Leu-rich_rpt UniProtKB/TrEMBL
  Leu-rich_rpt_2_copies UniProtKB/TrEMBL
KEGG Report rno:683514 UniProtKB/TrEMBL
MGC_CLONE MGC:187463 IMAGE-MGC_LOAD
NCBI Gene 683514 ENTREZGENE
PANTHER LEUCINE-RICH REPEAT AND IQ DOMAIN-CONTAINING PROTEIN 1-RELATED UniProtKB/TrEMBL
  PROTEIN PHOSPHATASE 1 REGULATORY SUBUNIT 42 UniProtKB/TrEMBL
Pfam LRR_4 UniProtKB/TrEMBL
  LRR_9 UniProtKB/TrEMBL
PhenoGen Ppp1r42 PhenoGen
PROSITE LRR UniProtKB/TrEMBL
RatGTEx ENSRNOG00000006804 RatGTEx
SMART LRR_SD22 UniProtKB/TrEMBL
Superfamily-SCOP L domain-like UniProtKB/TrEMBL
UniProt A0A9K3Y8A7 ENTREZGENE, UniProtKB/TrEMBL
  B1WBU1 ENTREZGENE, UniProtKB/TrEMBL
  E9PTW7 ENTREZGENE
UniProt Secondary E9PTW7 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-09-26 Ppp1r42  protein phosphatase 1, regulatory subunit 42  LOC683514  hypothetical protein LOC683514  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-19 LOC683514  hypothetical protein LOC683514      Symbol and Name status set to provisional 70820 PROVISIONAL