Pp2d1 (protein phosphatase 2C-like domain containing 1) - Rat Genome Database

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Gene: Pp2d1 (protein phosphatase 2C-like domain containing 1) Rattus norvegicus
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Symbol: Pp2d1
Name: protein phosphatase 2C-like domain containing 1
RGD ID: 1564811
Description: Predicted to enable protein serine/threonine phosphatase activity. Orthologous to human PP2D1 (protein phosphatase 2C like domain containing 1); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; acetamide; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: hypothetical protein LOC316157; LOC316157; PP2C-like domain-containing protein C3orf48 homolog; RGD1564811; similar to hypothetical protein phosphatase 2C domain containing 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
GRCr896,749,236 - 6,770,235 (-)NCBIGRCr8
mRatBN7.296,512,282 - 6,533,653 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl96,512,657 - 6,533,639 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx97,658,531 - 7,679,530 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0912,816,069 - 12,837,068 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0911,980,423 - 12,001,418 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01472,948,241 - 72,970,335 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1472,948,124 - 72,970,329 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01472,968,262 - 72,989,251 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.491,470,847 - 1,491,827 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Cytogenetic Map9q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

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. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data
Pp2d1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr896,749,236 - 6,770,235 (-)NCBIGRCr8
mRatBN7.296,512,282 - 6,533,653 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl96,512,657 - 6,533,639 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx97,658,531 - 7,679,530 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0912,816,069 - 12,837,068 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0911,980,423 - 12,001,418 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01472,948,241 - 72,970,335 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1472,948,124 - 72,970,329 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01472,968,262 - 72,989,251 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.491,470,847 - 1,491,827 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Cytogenetic Map9q11NCBI
PP2D1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38319,979,961 - 20,012,264 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl319,979,961 - 20,012,267 (-)EnsemblGRCh38hg38GRCh38
GRCh37320,021,453 - 20,053,756 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36320,017,509 - 20,028,730 (-)NCBINCBI36Build 36hg18NCBI36
Celera319,961,983 - 19,994,294 (-)NCBICelera
Cytogenetic Map3p24.3NCBI
HuRef319,961,295 - 19,993,407 (-)NCBIHuRef
CHM1_1319,973,542 - 20,005,850 (-)NCBICHM1_1
T2T-CHM13v2.0319,984,029 - 20,016,332 (-)NCBIT2T-CHM13v2.0
Pp2d1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391753,814,488 - 53,846,479 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1753,814,488 - 53,846,479 (-)EnsemblGRCm39 Ensembl
GRCm381753,507,460 - 53,539,451 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1753,507,460 - 53,539,451 (-)EnsemblGRCm38mm10GRCm38
MGSCv371753,646,785 - 53,678,776 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361752,972,389 - 53,004,380 (-)NCBIMGSCv36mm8
Celera1756,952,974 - 56,985,026 (-)NCBICelera
Cytogenetic Map17CNCBI
cM Map1727.83NCBI
Pp2d1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543012,040,197 - 12,069,254 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495543012,039,391 - 12,070,440 (-)NCBIChiLan1.0ChiLan1.0
PP2D1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2219,950,432 - 19,978,108 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1319,955,199 - 19,982,875 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0319,903,905 - 19,930,536 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1320,233,819 - 20,261,322 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl320,233,831 - 20,261,322 (-)Ensemblpanpan1.1panPan2
PP2D1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12323,285,449 - 23,303,885 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2323,285,452 - 23,305,086 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2323,310,653 - 23,329,094 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02323,772,245 - 23,790,718 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2323,772,269 - 23,791,922 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12323,484,470 - 23,502,924 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02323,549,864 - 23,568,327 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02323,795,983 - 23,814,442 (+)NCBIUU_Cfam_GSD_1.0
Pp2d1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118179,127,574 - 179,153,163 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647312,267,538 - 12,285,582 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493647312,267,353 - 12,291,505 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PP2D1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl136,939,517 - 6,961,810 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1136,939,990 - 6,958,513 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2137,918,804 - 7,940,945 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PP2D1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11564,715,191 - 64,741,586 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604137,735,751 - 37,751,940 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Pp2d1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248215,313,217 - 5,335,169 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248215,312,974 - 5,338,156 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Pp2d1
84 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:33
Count of miRNA genes:32
Interacting mature miRNAs:32
Transcripts:ENSRNOT00000006325
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
10054141Gmadr4Adrenal mass QTL 42.450.0074adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)9114209783Rat
70226Eae4Experimental allergic encephalomyelitis QTL 4nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)9125661317Rat
9589055Scfw5Subcutaneous fat weight QTL 55.550.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)9137999212Rat
7411592Foco8Food consumption QTL 87.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)9137999212Rat
9589158Gluco65Glucose level QTL 656.820.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)9137999212Rat
1300124Cm4Cardiac mass QTL 43.55heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)9140594091Rat
1298088Edpm11Estrogen-dependent pituitary mass QTL 112.5pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)9143718459Rat
1641911Alcrsp13Alcohol response QTL 13response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)9143718459Rat
10054125Srcrt7Stress Responsive Cort QTL 73.330.0011blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)9187073594Rat
1331757Cdexp1CD45RC expression in CD8 T cells QTL 14.3CD8-positive T cell quantity (VT:0008077)blood CD45RC(high) CD8 T cell count to CD45RC(low) CD8 T cell count ratio (CMO:0001990)9102453767509080Rat
1354650Despr5Despair related QTL 54.010.0017locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)9125408446254084Rat
2303559Gluco54Glucose level QTL 542blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)9125408446254084Rat
1578675Bss17Bone structure and strength QTL 173.8femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)9336865213533896Rat
61425Cia15Collagen induced arthritis QTL 154.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)9510982642921101Rat
631211Bw4Body weight QTL45.31retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)9510982650109826Rat

Markers in Region
RH129271  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.296,514,848 - 6,514,998 (+)MAPPERmRatBN7.2
Rnor_6.01472,951,547 - 72,951,696NCBIRnor6.0
Rnor_5.01472,970,463 - 72,970,612UniSTSRnor5.0
RGSC_v3.491,489,486 - 1,489,635UniSTSRGSC3.4
Cytogenetic Map9q11UniSTS
RH132760  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.296,529,512 - 6,529,695 (+)MAPPERmRatBN7.2
Rnor_6.01472,966,211 - 72,966,393NCBIRnor6.0
Rnor_5.01472,985,127 - 72,985,309UniSTSRnor5.0
RGSC_v3.491,474,789 - 1,474,971UniSTSRGSC3.4
Cytogenetic Map9q11UniSTS
AU048967  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.296,532,996 - 6,533,142 (+)MAPPERmRatBN7.2
Rnor_6.01472,969,695 - 72,969,838NCBIRnor6.0
Rnor_5.01472,988,611 - 72,988,754UniSTSRnor5.0
RGSC_v3.491,471,344 - 1,471,487UniSTSRGSC3.4
Cytogenetic Map9q11UniSTS


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 2 2 2 8 10
Low 3 11 25 11 17 11 8 10 9 11 8 1 8
Below cutoff 1 3 4

Sequence


RefSeq Acc Id: ENSRNOT00000006325   ⟹   ENSRNOP00000006325
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl96,512,657 - 6,533,639 (-)Ensembl
Rnor_6.0 Ensembl1472,948,124 - 72,970,329 (-)Ensembl
RefSeq Acc Id: NM_001134567   ⟹   NP_001128039
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr896,749,236 - 6,770,216 (-)NCBI
mRatBN7.296,512,657 - 6,533,639 (-)NCBI
Rnor_6.01472,949,355 - 72,970,335 (-)NCBI
Rnor_5.01472,968,262 - 72,989,251 (-)NCBI
RGSC_v3.491,470,847 - 1,491,827 (+)RGD
Sequence:
RefSeq Acc Id: XM_017599267   ⟹   XP_017454756
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr896,749,396 - 6,769,905 (-)NCBI
mRatBN7.296,512,282 - 6,533,311 (-)NCBI
Rnor_6.01472,948,241 - 72,970,058 (-)NCBI
Sequence:
RefSeq Acc Id: XR_010054589
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr896,750,309 - 6,770,235 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001128039 (Get FASTA)   NCBI Sequence Viewer  
  XP_017454756 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL82850 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000006325
  ENSRNOP00000006325.7
RefSeq Acc Id: NP_001128039   ⟸   NM_001134567
- UniProtKB: D3ZZT7 (UniProtKB/TrEMBL),   A6KUI3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017454756   ⟸   XM_017599267
- Peptide Label: isoform X1
- UniProtKB: D3ZZT7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000006325   ⟸   ENSRNOT00000006325
Protein Domains
PPM-type phosphatase

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZZT7-F1-model_v2 AlphaFold D3ZZT7 1-579 view protein structure

Transcriptome

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

Promoters
RGD ID:13699359
Promoter ID:EPDNEW_R9884
Type:initiation region
Name:Pp2d1_1
Description:protein phosphatase 2C-like domain containing 1
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_6.01472,970,308 - 72,970,368EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1564811 AgrOrtholog
BioCyc Gene G2FUF-28396 BioCyc
Ensembl Genes ENSRNOG00000004719 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000006325 ENTREZGENE
  ENSRNOT00000006325.7 UniProtKB/TrEMBL
Gene3D-CATH 3.60.40.10 UniProtKB/TrEMBL
InterPro PP2C UniProtKB/TrEMBL
  PP2C-related UniProtKB/TrEMBL
  PPM-type_dom_sf UniProtKB/TrEMBL
KEGG Report rno:316157 UniProtKB/TrEMBL
NCBI Gene 316157 ENTREZGENE
PANTHER PP2C UniProtKB/TrEMBL
  PROTEIN PHOSPHATASE 2C-LIKE DOMAIN-CONTAINING PROTEIN 1 UniProtKB/TrEMBL
Pfam PP2C UniProtKB/TrEMBL
PhenoGen Pp2d1 PhenoGen
PROSITE PPM_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000004719 RatGTEx
SMART PP2Cc UniProtKB/TrEMBL
Superfamily-SCOP PP2C-related UniProtKB/TrEMBL
UniProt A6KUI3 ENTREZGENE, UniProtKB/TrEMBL
  D3ZZT7 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2011-08-01 Pp2d1  protein phosphatase 2C-like domain containing 1  RGD1564811  similar to hypothetical protein phosphatase 2C domain containing protein  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1564811  similar to hypothetical protein phosphatase 2C domain containing protein   RGD1564811_predicted  similar to hypothetical protein phosphatase 2C domain containing protein (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-07 RGD1564811_predicted  similar to hypothetical protein phosphatase 2C domain containing protein (predicted)  LOC316157  similar to hypothetical protein phosphatase 2C domain containing protein  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC316157  similar to hypothetical protein phosphatase 2C domain containing protein      Symbol and Name status set to provisional 70820 PROVISIONAL