Pde12 (phosphodiesterase 12) - Rat Genome Database

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Gene: Pde12 (phosphodiesterase 12) Rattus norvegicus
Analyze
Symbol: Pde12
Name: phosphodiesterase 12
RGD ID: 1310975
Description: Predicted to enable poly(A)-specific ribonuclease activity. Predicted to be involved in several processes, including cellular response to interferon-alpha; innate immune response; and mRNA catabolic process. Predicted to be located in mitochondrial matrix. Predicted to be active in mitochondrion. Orthologous to human PDE12 (phosphodiesterase 12); INTERACTS WITH (+)-schisandrin B; 6-propyl-2-thiouracil; amitrole.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: 2',5'-phosphodiesterase 12; 2'-PDE; 2-PDE; LOC306231; LRRGT00074; mitochondrial deadenylase; RGD1310975; similar to CG31759-PA
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
GRCr8161,926,807 - 1,932,383 (-)NCBIGRCr8
mRatBN7.2161,920,062 - 1,925,638 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl161,915,386 - 1,925,887 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx161,922,014 - 1,932,051 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0163,067,710 - 3,077,747 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0161,928,467 - 1,938,505 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0162,357,028 - 2,367,069 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl162,357,028 - 2,367,253 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0162,332,374 - 2,343,524 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4161,974,440 - 1,984,481 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1161,980,152 - 1,984,665 (-)NCBI
Celera161,884,218 - 1,894,257 (-)NCBICelera
Cytogenetic Map16p16NCBI
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
mitochondrial matrix  (IEA,ISO)
mitochondrion  (IBA,IEA)

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. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
3. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
Additional References at PubMed
PMID:15231837   PMID:18614015   PMID:21245038   PMID:21666256   PMID:22285541   PMID:22871113  


Genomics

Comparative Map Data
Pde12
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8161,926,807 - 1,932,383 (-)NCBIGRCr8
mRatBN7.2161,920,062 - 1,925,638 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl161,915,386 - 1,925,887 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx161,922,014 - 1,932,051 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0163,067,710 - 3,077,747 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0161,928,467 - 1,938,505 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0162,357,028 - 2,367,069 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl162,357,028 - 2,367,253 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0162,332,374 - 2,343,524 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4161,974,440 - 1,984,481 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1161,980,152 - 1,984,665 (-)NCBI
Celera161,884,218 - 1,894,257 (-)NCBICelera
Cytogenetic Map16p16NCBI
PDE12
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38357,556,274 - 57,656,495 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl357,556,274 - 57,566,848 (+)EnsemblGRCh38hg38GRCh38
GRCh37357,542,001 - 57,642,222 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36357,517,044 - 57,522,720 (+)NCBINCBI36Build 36hg18NCBI36
Celera357,555,770 - 57,561,606 (+)NCBICelera
Cytogenetic Map3p14.3NCBI
HuRef357,639,405 - 57,645,202 (+)NCBIHuRef
CHM1_1357,492,081 - 57,497,868 (+)NCBICHM1_1
T2T-CHM13v2.0357,596,636 - 57,696,867 (+)NCBIT2T-CHM13v2.0
Pde12
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391426,381,113 - 26,390,823 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1426,381,113 - 26,391,038 (-)EnsemblGRCm39 Ensembl
GRCm381426,664,117 - 26,669,846 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1426,659,958 - 26,669,883 (-)EnsemblGRCm38mm10GRCm38
MGSCv371427,483,603 - 27,489,332 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361425,497,301 - 25,503,030 (-)NCBIMGSCv36mm8
Celera1422,906,785 - 22,912,518 (-)NCBICelera
Cytogenetic Map14A3NCBI
cM Map1416.09NCBI
Pde12
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554307,272,765 - 7,277,726 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554307,272,911 - 7,277,726 (+)NCBIChiLan1.0ChiLan1.0
PDE12
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2257,524,569 - 57,538,387 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1357,529,167 - 57,544,328 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0357,489,602 - 57,502,240 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1358,695,951 - 58,703,257 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl358,696,083 - 58,699,719 (+)Ensemblpanpan1.1panPan2
PDE12
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12032,884,819 - 32,890,995 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2032,886,972 - 32,890,890 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2032,812,998 - 32,819,199 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02033,157,456 - 33,163,631 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2033,157,477 - 33,163,624 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12032,613,238 - 32,619,411 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02032,971,314 - 32,977,518 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02033,142,175 - 33,148,378 (-)NCBIUU_Cfam_GSD_1.0
Pde12
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118174,755,477 - 174,759,271 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364737,893,893 - 7,898,938 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364737,894,026 - 7,897,844 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PDE12
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1339,395,541 - 39,402,650 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11339,395,517 - 39,402,653 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21343,327,075 - 43,330,812 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PDE12
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12218,863,676 - 18,869,778 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2218,863,696 - 18,867,736 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666041148,001,044 - 148,008,656 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Pde12
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624821305,864 - 313,881 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624821306,055 - 311,101 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Pde12
13 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:255
Count of miRNA genes:170
Interacting mature miRNAs:185
Transcripts:ENSRNOT00000017800, ENSRNOT00000051486
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
2325838Bp347Blood pressure QTL 3470.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1613080679Rat
1357403Slep4Serum leptin concentration QTL 43.91blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1619639137Rat
1600369Hcas8Hepatocarcinoma susceptibility QTL 8liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)16122477621Rat
631830Alc7Alcohol consumption QTL 72.9consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16126727669Rat
634355Rends4Renal damage susceptibility QTL 40.05kidney blood vessel morphology trait (VT:0000530)organ lesion measurement (CMO:0000677)16126727669Rat
1582235Insul8Insulin level QTL 83.30.0063blood insulin amount (VT:0001560)calculated serum insulin level (CMO:0000359)16126727669Rat
9590151Scort8Serum corticosterone level QTL 88.450.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)16130836262Rat
2302380Slep6Serum leptin concentration QTL 63.36blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)16132139025Rat
2307172Activ4Activity QTL 43.710.00023locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)16133418960Rat
1354584Despr6Despair related QTL 63.10.0067locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16139533930Rat
2303566Bw90Body weight QTL 902body mass (VT:0001259)body weight (CMO:0000012)16139533930Rat
631561Hcuc2Hepatic copper content QTL 22.8liver copper amount (VT:0003065)liver total copper weight (CMO:0001507)16139533949Rat
6903319Bw114Body weight QTL 1142.70.0037body mass (VT:0001259)body weight (CMO:0000012)16143534949Rat
7411664Foco30Food consumption QTL 30110.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)16144588133Rat
1354625Despr7Despair related QTL 73.160.016locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16144977551Rat
1549842Bp248Blood pressure QTL 2480.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)163802452995463Rat
1600378Arunc4Aerobic running capacity QTL 40.03exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)1638024580345693Rat
2293343Glom16Glomerulus QTL 167.4kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)1683223646053497Rat
2312660Bw95Body weight QTL 950.05inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)1683223659492508Rat
2312663Slep9Serum leptin concentration QTL 90.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1683223659492508Rat
2312666Insul16Insulin level QTL 160.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1683223659492508Rat
2312669Stl23Serum triglyceride level QTL 230.01blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)1683223659492508Rat
12903278Am16Aortic mass QTL 160.019aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)168323802995225Rat
12903279Cm115Cardiac mass QTL 1150.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)168323802995225Rat
12903281Cm116Cardiac mass QTL 1160.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)168323802995225Rat
12903952Cm117Cardiac mass QTL 1170.001heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)168323802995225Rat
12903954Bw186Body weight QTL 1860.011body mass (VT:0001259)body weight (CMO:0000012)168323802995225Rat
2301404Bp321Blood pressure QTL 3210.05arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)168323802995225Rat
12903955Kidm69Kidney mass QTL 690.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)168323804227609Rat

Markers in Region
RH127924  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2161,920,095 - 1,920,301 (+)MAPPERmRatBN7.2
Rnor_6.0162,361,738 - 2,361,943NCBIRnor6.0
Rnor_5.0162,337,084 - 2,337,289UniSTSRnor5.0
RGSC_v3.4161,979,150 - 1,979,355UniSTSRGSC3.4
Celera161,888,928 - 1,889,133UniSTS
RH 3.4 Map1616.3UniSTS
Cytogenetic Map16p16UniSTS


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 1 4 23 8 16 8 14 22 16 8
Low 2 39 34 33 3 33 8 11 60 13 25 3 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000079625   ⟹   ENSRNOP00000074876
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl161,915,386 - 1,925,646 (-)Ensembl
Rnor_6.0 Ensembl162,357,028 - 2,367,069 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000083573   ⟹   ENSRNOP00000073047
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl161,921,107 - 1,925,887 (-)Ensembl
Rnor_6.0 Ensembl162,362,741 - 2,367,253 (-)Ensembl
RefSeq Acc Id: NM_001411708   ⟹   NP_001398637
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8161,926,807 - 1,932,383 (-)NCBI
mRatBN7.2161,920,062 - 1,925,638 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001398637 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH79396 (Get FASTA)   NCBI Sequence Viewer  
  AAQ91030 (Get FASTA)   NCBI Sequence Viewer  
  EDL75071 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000073047
  ENSRNOP00000073047.2
  ENSRNOP00000074876.1
GenBank Protein Q6AXQ5 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: ENSRNOP00000074876   ⟸   ENSRNOT00000079625
RefSeq Acc Id: ENSRNOP00000073047   ⟸   ENSRNOT00000083573
RefSeq Acc Id: NP_001398637   ⟸   NM_001411708
- UniProtKB: Q6AXQ5 (UniProtKB/Swiss-Prot),   A6KMJ7 (UniProtKB/TrEMBL),   A0A8L2R6N5 (UniProtKB/TrEMBL)
Protein Domains
2',5'-phosphodiesterase 12-like N-terminal   Endonuclease/exonuclease/phosphatase

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q6AXQ5-F1-model_v2 AlphaFold Q6AXQ5 1-608 view protein structure

Transcriptome

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

Promoters
RGD ID:13699900
Promoter ID:EPDNEW_R10420
Type:multiple initiation site
Name:Pde12_1
Description:phosphodiesterase 12
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_6.0162,367,264 - 2,367,324EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1310975 AgrOrtholog
BioCyc Gene G2FUF-12251 BioCyc
Ensembl Genes ENSRNOG00000059442 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000079625.2 UniProtKB/TrEMBL
  ENSRNOT00000083573 ENTREZGENE
  ENSRNOT00000083573.2 UniProtKB/TrEMBL
Gene3D-CATH 3.60.10.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7112419 IMAGE-MGC_LOAD
InterPro Endo/exonu/phosph_ase_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Endo/exonuclease/phosphatase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDE12-like_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:306231 UniProtKB/TrEMBL
MGC_CLONE MGC:94924 IMAGE-MGC_LOAD
NCBI Gene 306231 ENTREZGENE
PANTHER 2',5'-PHOSPHODIESTERASE 12 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CARBON CATABOLITE REPRESSOR PROTEIN 4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Exo_endo_phos UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDE12-like_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Pde12 PhenoGen
RatGTEx ENSRNOG00000059442 RatGTEx
Superfamily-SCOP SSF56219 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8L2R6N5 ENTREZGENE, UniProtKB/TrEMBL
  A6KMJ7 ENTREZGENE, UniProtKB/TrEMBL
  PDE12_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  Q6TUH0_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-05-19 Pde12  phosphodiesterase 12  RGD1310975  similar to CG31759-PA  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 RGD1310975  similar to CG31759-PA  RGD1310975_predicted  similar to CG31759-PA (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-20 RGD1310975_predicted  similar to CG31759-PA (predicted)  LOC306231_predicted  similar to CG31759-PA (predicted)  Symbol and Name status set to approved 1331353 APPROVED