Pde12 (phosphodiesterase 12) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Pde12 (phosphodiesterase 12) Rattus norvegicus
Analyze
Symbol: Pde12
Name: phosphodiesterase 12
RGD ID: 1310975
Description: Predicted to have 3'-5'-exoribonuclease activity. Predicted to be involved in several processes, including RNA metabolic process; cellular response to cytokine stimulus; and regulation of mitochondrial mRNA stability. Predicted to localize to mitochondrial matrix. Orthologous to human PDE12 (phosphodiesterase 12); INTERACTS WITH (+)-schisandrin B; 6-propyl-2-thiouracil; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also 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: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2161,915,386 - 1,925,427 (-)NCBI
Rnor_6.0 Ensembl162,357,028 - 2,367,253 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0162,357,028 - 2,367,069 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0162,332,374 - 2,343,524 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4161,974,440 - 1,984,481 (-)NCBIRGSC3.4rn4RGSC3.4
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

References

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
mRatBN7.2161,915,386 - 1,925,427 (-)NCBI
Rnor_6.0 Ensembl162,357,028 - 2,367,253 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0162,357,028 - 2,367,069 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0162,332,374 - 2,343,524 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4161,974,440 - 1,984,481 (-)NCBIRGSC3.4rn4RGSC3.4
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
GRCh38.p13 Ensembl357,556,274 - 57,566,848 (+)EnsemblGRCh38hg38GRCh38
GRCh38357,556,274 - 57,656,495 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37357,542,001 - 57,642,222 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36357,517,044 - 57,522,720 (+)NCBINCBI36hg18NCBI36
Celera357,555,770 - 57,561,606 (+)NCBI
Cytogenetic Map3p14.3NCBI
HuRef357,639,405 - 57,645,202 (+)NCBIHuRef
CHM1_1357,492,074 - 57,592,295 (+)NCBICHM1_1
Pde12
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391426,385,272 - 26,391,001 (-)NCBIGRCm39mm39
GRCm39 Ensembl1426,381,113 - 26,391,038 (-)Ensembl
GRCm381426,664,117 - 26,669,846 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1426,659,958 - 26,669,883 (-)EnsemblGRCm38mm10GRCm38
MGSCv371427,483,603 - 27,489,332 (-)NCBIGRCm37mm9NCBIm37
MGSCv361425,497,301 - 25,503,030 (-)NCBImm8
Celera1422,906,785 - 22,912,518 (-)NCBICelera
Cytogenetic Map14A3NCBI
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
PanPan1.1358,695,951 - 58,703,257 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl358,696,083 - 58,699,719 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0357,489,602 - 57,502,240 (+)NCBIMhudiblu_PPA_v0panPan3
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 (-)NCBI
ROS_Cfam_1.02033,157,456 - 33,163,631 (-)NCBI
UMICH_Zoey_3.12032,613,238 - 32,619,411 (-)NCBI
UNSW_CanFamBas_1.02032,971,314 - 32,977,518 (-)NCBI
UU_Cfam_GSD_1.02033,142,175 - 33,148,378 (-)NCBI
Pde12
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118174,755,477 - 174,759,271 (+)NCBI
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 - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12218,863,676 - 18,869,778 (+)NCBI
ChlSab1.1 Ensembl2218,863,696 - 18,867,736 (+)Ensembl
Pde12
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624821306,055 - 311,101 (+)NCBI

Position Markers
RH127924  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2161,920,095 - 1,920,301 (+)MAPPER
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


QTLs in Region (Rnor_6.0)
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)1613525217Rat
1357403Slep4Serum leptin concentration QTL 43.91blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)16110660736Rat
1600369Hcas8Hepatocarcinoma susceptibility QTL 8liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)16124228366Rat
631830Alc7Alcohol consumption QTL 72.9consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16127556253Rat
634355Rends4Renal damage susceptibility QTL 40.05kidney blood vessel morphology trait (VT:0000530)organ lesion measurement (CMO:0000677)16127556253Rat
1582235Insul8Insulin level QTL 83.30.0063blood insulin amount (VT:0001560)calculated serum insulin level (CMO:0000359)16127556253Rat
9590151Scort8Serum corticosterone level QTL 88.450.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)16131816439Rat
2302380Slep6Serum leptin concentration QTL 63.36blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)16133160624Rat
2307172Activ4Activity QTL 43.710.00023locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)16134465490Rat
1354584Despr6Despair related QTL 63.10.0067locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16141240937Rat
2303566Bw90Body weight QTL 902body mass (VT:0001259)body weight (CMO:0000012)16141240937Rat
631561Hcuc2Hepatic copper content QTL 22.8hepatic copper amount (VT:0003065)liver total copper weight (CMO:0001507)16141240957Rat
6903319Bw114Body weight QTL 1142.70.0037body mass (VT:0001259)body weight (CMO:0000012)1624459345244593Rat
1549842Bp248Blood pressure QTL 2480.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1610900543439762Rat
1600378Arunc4Aerobic running capacity QTL 40.03exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)16109005486162972Rat
7411664Foco30Food consumption QTL 30110.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)16134074146340741Rat
2293343Glom16Glomerulus QTL 167.4kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)16155018749247447Rat
2312660Bw95Body weight QTL 950.05inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)16155018763210301Rat
2312663Slep9Serum leptin concentration QTL 90.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)16155018763210301Rat
2312666Insul16Insulin level QTL 160.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)16155018763210301Rat
2312669Stl23Serum triglyceride level QTL 230.01blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)16155018763210301Rat
2301404Bp321Blood pressure QTL 3210.05arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1615503303439525Rat
12903278Am16Aortic mass QTL 160.019aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)1615503303439525Rat
12903279Cm115Cardiac mass QTL 1150.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)1615503303439525Rat
12903281Cm116Cardiac mass QTL 1160.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)1615503303439525Rat
12903952Cm117Cardiac mass QTL 1170.001heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)1615503303439525Rat
12903954Bw186Body weight QTL 1860.011body mass (VT:0001259)body weight (CMO:0000012)1615503303439525Rat
12903955Kidm69Kidney mass QTL 690.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)1615503305013802Rat
1354625Despr7Despair related QTL 73.160.016locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16172829746728297Rat

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.


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
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl162,357,028 - 2,367,069 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000083573   ⟹   ENSRNOP00000073047
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl162,362,741 - 2,367,253 (-)Ensembl
RefSeq Acc Id: NM_001013998   ⟹   NP_001014020
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2161,915,386 - 1,925,427 (-)NCBI
Rnor_6.0162,357,028 - 2,367,069 (-)NCBI
Rnor_5.0162,332,374 - 2,343,524 (-)NCBI
RGSC_v3.4161,974,440 - 1,984,481 (-)RGD
Celera161,884,218 - 1,894,257 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001014020 (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  
  Q6AXQ5 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001014020   ⟸   NM_001013998
- UniProtKB: Q6TUH0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000074876   ⟸   ENSRNOT00000079625
RefSeq Acc Id: ENSRNOP00000073047   ⟸   ENSRNOT00000083573
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

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1310975 AgrOrtholog
Ensembl Genes ENSRNOG00000059442 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000073047 UniProtKB/Swiss-Prot
  ENSRNOP00000074876 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000079625 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000083573 UniProtKB/Swiss-Prot
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
KEGG Report rno:306231 UniProtKB/TrEMBL
MGC_CLONE MGC:94924 IMAGE-MGC_LOAD
NCBI Gene 306231 ENTREZGENE
Pfam Exo_endo_phos UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Pde12 PhenoGen
Superfamily-SCOP SSF56219 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt PDE12_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  Q6TUH0 ENTREZGENE, 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