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
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8161,926,807 - 1,932,383 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl161,922,131 - 1,932,611 (-)EnsemblGRCr8
mRatBN7.2161,920,062 - 1,925,638 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl161,915,386 - 1,925,887 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx161,922,014 - 1,932,051 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0163,067,710 - 3,077,747 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0161,928,467 - 1,938,505 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0162,357,028 - 2,367,069 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl162,357,028 - 2,367,253 (-)Ensemblrn6Rnor6.0
Rnor_5.0162,332,374 - 2,343,524 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4161,974,440 - 1,984,481 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera161,884,218 - 1,894,257 (-)NCBICelera
RGSC_v3.1161,980,152 - 1,984,665 (-)NCBI
Cytogenetic Map16p16NCBI
JBrowse:




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

Cellular Component
mitochondrial matrix  (IEA,ISO)
mitochondrion  (IBA,ISO)

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   PMID:34800366  


Genomics

Comparative Map Data
Pde12
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8161,926,807 - 1,932,383 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl161,922,131 - 1,932,611 (-)EnsemblGRCr8
mRatBN7.2161,920,062 - 1,925,638 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl161,915,386 - 1,925,887 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx161,922,014 - 1,932,051 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0163,067,710 - 3,077,747 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0161,928,467 - 1,938,505 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0162,357,028 - 2,367,069 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl162,357,028 - 2,367,253 (-)Ensemblrn6Rnor6.0
Rnor_5.0162,332,374 - 2,343,524 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4161,974,440 - 1,984,481 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera161,884,218 - 1,894,257 (-)NCBICelera
RGSC_v3.1161,980,152 - 1,984,665 (-)NCBI
Cytogenetic Map16p16NCBI
PDE12
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38357,556,274 - 57,656,495 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl357,556,274 - 57,656,480 (+)Ensemblhg38GRCh38
GRCh37357,542,001 - 57,642,222 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36357,517,044 - 57,522,720 (+)NCBIBuild 36Build 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 EnsemblGRCm39
GRCm381426,664,117 - 26,669,846 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1426,659,958 - 26,669,883 (-)Ensemblmm10GRCm38
MGSCv371427,483,603 - 27,489,332 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
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 (+)Ensembl
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 (+)EnsemblpanPan2panpan1.1
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 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha2032,812,998 - 32,819,199 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.02033,157,456 - 33,163,631 (-)NCBIROS_Cfam_1.0ROS_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_1.0UU_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 (+)EnsemblSpeTri2.0 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 (+)EnsemblsusScr11Sscrofa11.1
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 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
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_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_004624821306,055 - 311,101 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Pde12
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1132,464,531 - 2,470,730 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Pde12
24 total Variants
miRNA Target Status (No longer updated)

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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1600378Arunc4Aerobic running capacity QTL 40.03exercise endurance trait (VT:0002332)longest distance run on treadmill (CMO:0001406)1638712345387123Rat
1549842Bp248Blood pressure QTL 2480.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1638712345387123Rat
2307172Activ4Activity QTL 43.710.00023locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)16133425095Rat
1354584Despr6Despair related QTL 63.10.0067locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16139568015Rat
2303566Bw90Body weight QTL 902body mass (VT:0001259)body weight (CMO:0000012)16139568015Rat
631524Bp75Blood pressure QTL 750.05arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)161177108157035Rat
2312663Slep9Serum leptin concentration QTL 90.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1683908666195506Rat
2312660Bw95Body weight QTL 950.05inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)1683908666195506Rat
12903955Kidm69Kidney mass QTL 690.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)168392304234212Rat
2312666Insul16Insulin level QTL 160.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1683908666195506Rat
634355Rends4Renal damage susceptibility QTL 40.05kidney blood vessel morphology trait (VT:0000530)organ lesion measurement (CMO:0000677)16126734272Rat
61405Niddm6Non-insulin dependent diabetes mellitus QTL 63.660.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)16126734272Rat
2293343Glom16Glomerulus QTL 167.4kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)1683908652786090Rat
2312669Stl23Serum triglyceride level QTL 230.01blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)1683908666195506Rat
631830Alc7Alcohol consumption QTL 72.9consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16126734272Rat

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

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
16 12 67 164 91 90 59 92 59 6 355 192 11 143 80 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000079625   ⟹   ENSRNOP00000074876
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl161,922,131 - 1,932,383 (-)Ensembl
mRatBN7.2 Ensembl161,915,386 - 1,925,646 (-)Ensembl
Rnor_6.0 Ensembl162,357,028 - 2,367,069 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000083573   ⟹   ENSRNOP00000073047
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl161,926,807 - 1,932,611 (-)Ensembl
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
GenBank Protein Q6AXQ5 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Acc Id: ENSRNOP00000074876   ⟸   ENSRNOT00000079625
Ensembl Acc Id: ENSRNOP00000073047   ⟸   ENSRNOT00000083573
RefSeq Acc Id: NP_001398637   ⟸   NM_001411708
- UniProtKB: Q6AXQ5 (UniProtKB/Swiss-Prot),   A0A8L2R6N5 (UniProtKB/TrEMBL),   A6KMJ7 (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
Ensembl Transcript ENSRNOT00000083573 ENTREZGENE
Gene3D-CATH 3.60.10.10 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7112419 IMAGE-MGC_LOAD
InterPro CCR4/nocturin_mRNA_transcr UniProtKB/Swiss-Prot
  Endo/exonu/phosph_ase_sf UniProtKB/Swiss-Prot
  Endo/exonuclease/phosphatase UniProtKB/Swiss-Prot
  PDE12-like_N UniProtKB/Swiss-Prot
MGC_CLONE MGC:94924 IMAGE-MGC_LOAD
NCBI Gene 306231 ENTREZGENE
PANTHER 2',5'-PHOSPHODIESTERASE 12 UniProtKB/Swiss-Prot
  CARBON CATABOLITE REPRESSOR PROTEIN 4 UniProtKB/Swiss-Prot
Pfam Exo_endo_phos UniProtKB/Swiss-Prot
  PDE12-like_N UniProtKB/Swiss-Prot
PhenoGen Pde12 PhenoGen
RatGTEx ENSRNOG00000059442 RatGTEx
Superfamily-SCOP SSF56219 UniProtKB/Swiss-Prot
UniProt A0A0G2K965_RAT UniProtKB/TrEMBL
  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