Pde10a (phosphodiesterase 10A) - Rat Genome Database

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Gene: Pde10a (phosphodiesterase 10A) Rattus norvegicus
Analyze
Symbol: Pde10a
Name: phosphodiesterase 10A
RGD ID: 68434
Description: Enables cyclic-nucleotide phosphodiesterase activity. Involved in negative regulation of cAMP-mediated signaling and negative regulation of cGMP-mediated signaling. Located in membrane and perikaryon. Orthologous to human PDE10A (phosphodiesterase 10A); PARTICIPATES IN adenine phoshoribosyltransferase deficiency pathway; adenosine monophosphate deaminase deficiency pathway; adenylosuccinate lyase deficiency pathway; INTERACTS WITH 17alpha-ethynylestradiol; 17beta-estradiol; 2,2',4,4'-Tetrabromodiphenyl ether.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A; Pde10a3; testis-specific phosphodiesterase PDE10A2
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
mRatBN7.2151,765,743 - 52,218,086 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl151,770,132 - 52,216,563 (-)Ensembl
Rnor_6.0152,360,296 - 52,544,448 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl152,360,296 - 52,544,450 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0153,617,430 - 53,800,479 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4146,392,900 - 46,589,076 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1146,395,844 - 46,592,020 (-)NCBI
Celera147,539,418 - 47,723,290 (-)NCBICelera
Cytogenetic Map1q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(S)-nicotine  (ISO)
1,2-dichloroethane  (ISO)
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (EXP)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
3',5'-cyclic AMP  (ISO)
3',5'-cyclic GMP  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-(hydroxymethyl)cytosine  (ISO)
acrylamide  (ISO)
aflatoxin B1  (ISO)
aflatoxin B2  (ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
aristolochic acid  (ISO)
arsenite(3-)  (ISO)
atrazine  (EXP)
belinostat  (ISO)
benzo[a]pyrene  (EXP,ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (EXP)
butanal  (ISO)
C60 fullerene  (EXP)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
carbon nanotube  (ISO)
chlorpyrifos  (ISO)
choline  (ISO)
cisplatin  (ISO)
clothianidin  (ISO)
clozapine  (EXP,ISO)
cocaine  (ISO)
Cuprizon  (EXP)
dextran sulfate  (ISO)
diazinon  (EXP)
dipyridamole  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
entinostat  (ISO)
ethanol  (ISO)
flavonoids  (EXP)
folic acid  (ISO)
graphite  (EXP)
haloperidol  (EXP)
L-methionine  (ISO)
mercury dibromide  (ISO)
morphine  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
nickel sulfate  (ISO)
nicotine  (ISO)
p-chloromercuribenzoic acid  (ISO)
panobinostat  (ISO)
paracetamol  (ISO)
pentanal  (ISO)
phencyclidine  (ISO)
phenylmercury acetate  (ISO)
PhIP  (EXP)
rotenone  (EXP)
SB 431542  (ISO)
T-2 toxin  (EXP)
testosterone  (EXP)
testosterone enanthate  (EXP)
titanium dioxide  (ISO)
trichostatin A  (ISO)
valproic acid  (EXP,ISO)
vinclozolin  (EXP)
vorinostat  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

References

Additional References at PubMed
PMID:10359840   PMID:14752115   PMID:18923023   PMID:19056933   PMID:19103603   PMID:21194525   PMID:21494592   PMID:21515371   PMID:21777010   PMID:22142545   PMID:26256420   PMID:27058446  
PMID:30053369  


Genomics

Comparative Map Data
Pde10a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2151,765,743 - 52,218,086 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl151,770,132 - 52,216,563 (-)Ensembl
Rnor_6.0152,360,296 - 52,544,448 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl152,360,296 - 52,544,450 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0153,617,430 - 53,800,479 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4146,392,900 - 46,589,076 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1146,395,844 - 46,592,020 (-)NCBI
Celera147,539,418 - 47,723,290 (-)NCBICelera
Cytogenetic Map1q12NCBI
PDE10A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl6165,327,287 - 165,988,078 (-)EnsemblGRCh38hg38GRCh38
GRCh386165,327,287 - 165,988,115 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh376165,740,778 - 166,076,729 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 366165,664,519 - 165,995,574 (-)NCBINCBI36hg18NCBI36
Build 346165,714,945 - 166,045,996NCBI
Celera6166,478,886 - 166,814,271 (-)NCBI
Cytogenetic Map6q27NCBI
HuRef6163,202,267 - 163,537,621 (-)NCBIHuRef
CHM1_16166,003,719 - 166,338,432 (-)NCBICHM1_1
Pde10a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39178,742,719 - 9,205,480 (+)NCBIGRCm39mm39
GRCm39 Ensembl178,744,204 - 9,205,480 (+)Ensembl
GRCm38178,525,187 - 8,986,648 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl178,525,372 - 8,986,648 (+)EnsemblGRCm38mm10GRCm38
MGSCv37178,994,610 - 9,179,513 (+)NCBIGRCm37mm9NCBIm37
MGSCv36178,639,919 - 8,824,822 (+)NCBImm8
Celera178,848,994 - 9,030,858 (+)NCBICelera
Cytogenetic Map17A1NCBI
Pde10a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543916,114,530 - 16,365,146 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495543916,114,530 - 16,370,648 (+)NCBIChiLan1.0ChiLan1.0
PDE10A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.16168,259,978 - 168,596,401 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl6168,265,707 - 168,645,231 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v06163,274,252 - 163,612,749 (-)NCBIMhudiblu_PPA_v0panPan3
PDE10A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1153,457,781 - 54,049,735 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl153,462,979 - 53,801,966 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha154,243,884 - 54,542,326 (-)NCBI
ROS_Cfam_1.0153,634,410 - 54,231,358 (-)NCBI
UMICH_Zoey_3.1153,531,754 - 53,830,179 (-)NCBI
UNSW_CanFamBas_1.0153,379,457 - 53,678,753 (-)NCBI
UU_Cfam_GSD_1.0154,012,303 - 54,310,827 (-)NCBI
Pde10a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404946148,143,922 - 148,659,124 (-)NCBI
SpeTri2.0NW_00493648915,401,248 - 15,671,594 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PDE10A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13,120,223 - 3,392,651 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.113,120,418 - 3,394,236 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.214,618,673 - 4,742,489 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PDE10A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11393,012,027 - 93,684,349 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1393,020,696 - 93,344,369 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604064,833,189 - 65,491,475 (-)NCBIVero_WHO_p1.0
Pde10a
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462478513,208,518 - 13,885,261 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
D17Mit247  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2151,776,532 - 51,776,645 (+)MAPPERmRatBN7.2
Rnor_6.0152,366,636 - 52,366,748NCBIRnor6.0
Rnor_5.0153,623,770 - 53,623,882UniSTSRnor5.0
RGSC_v3.4146,399,301 - 46,399,413UniSTSRGSC3.4
Celera147,545,819 - 47,545,931UniSTS
Cytogenetic Map1q11UniSTS
BE121313  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2151,943,640 - 51,943,799 (+)MAPPERmRatBN7.2
Rnor_6.0152,534,475 - 52,534,633NCBIRnor6.0
Rnor_5.0153,790,506 - 53,790,664UniSTSRnor5.0
RGSC_v3.4146,579,103 - 46,579,261UniSTSRGSC3.4
Celera147,713,317 - 47,713,475UniSTS
RH 3.4 Map1607.2UniSTS
Cytogenetic Map1q11UniSTS
BE097292  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2151,964,411 - 51,964,566 (+)MAPPERmRatBN7.2
Rnor_6.0152,554,878 - 52,555,032NCBIRnor6.0
Rnor_5.0153,810,943 - 53,811,097UniSTSRnor5.0
RGSC_v3.4146,600,046 - 46,600,200UniSTSRGSC3.4
Celera147,733,835 - 47,733,989UniSTS
RH 3.4 Map1606.7UniSTS
Cytogenetic Map1q11UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
738020Pia8Pristane induced arthritis QTL 84.7joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1165833076Rat
1554320Bmd1Bone mineral density QTL 112.20.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)150910886060548Rat
631688Hcas2Hepatocarcinoma susceptibility QTL 230.0001liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)15925874115540829Rat
631508Sald1Serum aldosterone level QTL 13.7blood aldosterone amount (VT:0005346)serum aldosterone level (CMO:0000487)1985600154856001Rat
2302038Pia31Pristane induced arthritis QTL 315.50.001blood autoantibody amount (VT:0003725)serum immunoglobulin M-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002111)11099206555992065Rat
1300167Hrtrt2Heart rate QTL 24.35heart pumping trait (VT:2000009)heart rate (CMO:0000002)11148131275088344Rat
2313062Bmd73Bone mineral density QTL 733.90.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)11148131282174945Rat
2313065Bss67Bone structure and strength QTL 673.10.0001tibia area (VT:1000281)tibia total energy absorbed before break (CMO:0001736)11148131282174945Rat
2313069Bss68Bone structure and strength QTL 682.90.0001tibia size trait (VT:0100001)tibia total energy absorbed before break (CMO:0001736)11148131282174945Rat
2313075Bss66Bone structure and strength QTL 663.40.0001tibia length (VT:0004357)tibia length (CMO:0000450)11148131282174945Rat
2313077Bss69Bone structure and strength QTL 693.50.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)11148131282174945Rat
2313092Bmd72Bone mineral density QTL 722.50.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)11148131282174945Rat
2313097Bss70Bone structure and strength QTL 703.50.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)11148131282174945Rat
1578756Iddm22Insulin dependent diabetes mellitus QTL 222.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)11183518156835181Rat
634353Rends2Renal damage susceptibility QTL 20.05kidney blood vessel morphology trait (VT:0000530)organ lesion measurement (CMO:0000677)11933357156983283Rat
724520Bp145Blood pressure QTL 1452.10.0024arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)12078482865784828Rat
1357400Bw62Body weight QTL624.05inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)12234064767340647Rat
631495Bp96Blood pressure QTL 964.52arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)122340647102268831Rat
1331785Rf27Renal function QTL 274.643urine sodium amount (VT:0006274)urine sodium level (CMO:0000129)12887978078430678Rat
1358359Sradr1Stress Responsive Adrenal Weight QTL 14.74adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)130882023123479925Rat
70225Bp58Blood pressure QTL 583.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)132356093162846471Rat
1300172Bp172Blood pressure QTL 1723.56arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)13273727390665040Rat
10059597Bp377Blood pressure QTL 3773.420.025arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)132737458199368955Rat
1354599Bw29Body weight QTL 293.460.001body mass (VT:0001259)body weight (CMO:0000012)13344984878449848Rat
1354643Foco2Food consumption QTL 27.170.0001eating behavior trait (VT:0001431)food intake rate (CMO:0000427)13344984878449848Rat
8552900Pigfal1Plasma insulin-like growth factor 1 level QTL 17.4blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)13483685879836858Rat
8552948Pigfal11Plasma insulin-like growth factor 1 level QTL 114.7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)13483685879836858Rat
9589820Insglur3Insulin/glucose ratio QTL 310.750.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)13483685879836858Rat
1331732Srn4Serum renin concentration QTL 44.467renin activity (VT:0005581)plasma renin activity level (CMO:0000116)13523959878430678Rat
1331792Rf29Renal function QTL 294.589urine potassium amount (VT:0010539)urine potassium level (CMO:0000128)13523959878430678Rat
2313051Bss57Bone structure and strength QTL 573.70.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)143284731118944897Rat
2313059Bss55Bone structure and strength QTL 553.20.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)143284731118944897Rat
2313072Bss53Bone structure and strength QTL 534.30.0001tibia length (VT:0004357)tibia length (CMO:0000450)143284731118944897Rat
2313078Bss54Bone structure and strength QTL 543.50.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)143284731118944897Rat
2313094Bss58Bone structure and strength QTL 583.70.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)143284731118944897Rat
2313098Bmd70Bone mineral density QTL 703.60.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)143284731118944897Rat
2313099Bss56Bone structure and strength QTL 562.40.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)143284731118944897Rat
2302059Pia36Pristane induced arthritis QTL 363.80.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)14333300288333002Rat
1331778Rf28Renal function QTL 284.66urine potassium amount (VT:0010539)urine potassium excretion rate (CMO:0000761)14580314078430678Rat
2313402Anxrr24Anxiety related response QTL 24aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)148963584144267916Rat
4889962Bss94Bone structure and strength QTL 943.8tibia area (VT:1000281)tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)14936146582174945Rat
1578649Bmd8Bone mineral density QTL 84.9femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)14939317294393172Rat
1578654Bss10Bone structure and strength QTL 104femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)149393172159356837Rat
634314Niddm44Non-insulin dependent diabetes mellitus QTL 44blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)149393289199050459Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:182
Count of miRNA genes:91
Interacting mature miRNAs:110
Transcripts:ENSRNOT00000043474, ENSRNOT00000067142
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.


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 5 64 8
Low 2 38 16 7 17 7 8 10 10 35 33 9 8
Below cutoff 1 5 32 30 2 30 1 2

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001388509 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001388510 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001388511 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_022236 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039089147 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039089154 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039089156 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039089160 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039089171 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039089177 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039089181 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039089184 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039089188 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039089191 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005491608 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AB027155 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB027156 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY462091 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY462092 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY462093 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY462094 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY462095 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH474059 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ212600 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000017 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000043474   ⟹   ENSRNOP00000042134
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl151,770,132 - 51,953,616 (-)Ensembl
Rnor_6.0 Ensembl152,360,296 - 52,544,450 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000067142   ⟹   ENSRNOP00000060834
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl151,770,850 - 52,216,563 (-)Ensembl
Rnor_6.0 Ensembl152,361,038 - 52,495,582 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000098030   ⟹   ENSRNOP00000081805
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl151,770,132 - 51,953,616 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000102087   ⟹   ENSRNOP00000086612
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl151,770,132 - 51,904,854 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000106865   ⟹   ENSRNOP00000086886
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl151,770,132 - 51,830,095 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000111002   ⟹   ENSRNOP00000092661
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl151,770,132 - 52,216,563 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000111873   ⟹   ENSRNOP00000091632
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl151,770,138 - 52,216,563 (-)Ensembl
RefSeq Acc Id: NM_001388509   ⟹   NP_001375438
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2151,770,138 - 52,218,086 (-)NCBI
RefSeq Acc Id: NM_001388510   ⟹   NP_001375439
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2151,770,138 - 52,218,086 (-)NCBI
RefSeq Acc Id: NM_001388511   ⟹   NP_001375440
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2151,770,138 - 52,218,086 (-)NCBI
RefSeq Acc Id: NM_022236   ⟹   NP_071572
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2151,770,138 - 51,953,614 (-)NCBI
Rnor_6.0152,360,296 - 52,544,448 (-)NCBI
Rnor_5.0153,617,430 - 53,800,479 (-)NCBI
RGSC_v3.4146,392,900 - 46,589,076 (-)RGD
Celera147,539,418 - 47,723,290 (-)RGD
Sequence:
RefSeq Acc Id: XM_039089147   ⟹   XP_038945075
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2151,770,107 - 51,999,679 (-)NCBI
RefSeq Acc Id: XM_039089154   ⟹   XP_038945082
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2151,770,107 - 51,999,690 (-)NCBI
RefSeq Acc Id: XM_039089156   ⟹   XP_038945084
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2151,765,743 - 51,954,190 (-)NCBI
RefSeq Acc Id: XM_039089160   ⟹   XP_038945088
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2151,770,107 - 52,216,507 (-)NCBI
RefSeq Acc Id: XM_039089171   ⟹   XP_038945099
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2151,770,107 - 52,216,507 (-)NCBI
RefSeq Acc Id: XM_039089177   ⟹   XP_038945105
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2151,770,107 - 51,904,826 (-)NCBI
RefSeq Acc Id: XM_039089181   ⟹   XP_038945109
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2151,770,107 - 51,904,826 (-)NCBI
RefSeq Acc Id: XM_039089184   ⟹   XP_038945112
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2151,770,107 - 51,906,531 (-)NCBI
RefSeq Acc Id: XM_039089188   ⟹   XP_038945116
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2151,770,107 - 51,868,011 (-)NCBI
RefSeq Acc Id: XM_039089191   ⟹   XP_038945119
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2151,770,107 - 51,825,465 (-)NCBI
RefSeq Acc Id: XR_005491608
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2151,800,923 - 51,999,679 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001375438 (Get FASTA)   NCBI Sequence Viewer  
  NP_001375439 (Get FASTA)   NCBI Sequence Viewer  
  NP_001375440 (Get FASTA)   NCBI Sequence Viewer  
  NP_071572 (Get FASTA)   NCBI Sequence Viewer  
  XP_038945075 (Get FASTA)   NCBI Sequence Viewer  
  XP_038945082 (Get FASTA)   NCBI Sequence Viewer  
  XP_038945084 (Get FASTA)   NCBI Sequence Viewer  
  XP_038945088 (Get FASTA)   NCBI Sequence Viewer  
  XP_038945099 (Get FASTA)   NCBI Sequence Viewer  
  XP_038945105 (Get FASTA)   NCBI Sequence Viewer  
  XP_038945109 (Get FASTA)   NCBI Sequence Viewer  
  XP_038945112 (Get FASTA)   NCBI Sequence Viewer  
  XP_038945116 (Get FASTA)   NCBI Sequence Viewer  
  XP_038945119 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAS21243 (Get FASTA)   NCBI Sequence Viewer  
  AAS21244 (Get FASTA)   NCBI Sequence Viewer  
  AAS21245 (Get FASTA)   NCBI Sequence Viewer  
  AAS21246 (Get FASTA)   NCBI Sequence Viewer  
  AAS21247 (Get FASTA)   NCBI Sequence Viewer  
  BAA88996 (Get FASTA)   NCBI Sequence Viewer  
  BAA88997 (Get FASTA)   NCBI Sequence Viewer  
  EDL83102 (Get FASTA)   NCBI Sequence Viewer  
  EDL83103 (Get FASTA)   NCBI Sequence Viewer  
  EDL83104 (Get FASTA)   NCBI Sequence Viewer  
  EDL83105 (Get FASTA)   NCBI Sequence Viewer  
  EDL83106 (Get FASTA)   NCBI Sequence Viewer  
  Q9QYJ6 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_071572   ⟸   NM_022236
- Peptide Label: isoform 1
- UniProtKB: Q9QYJ6 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000042134   ⟸   ENSRNOT00000043474
RefSeq Acc Id: ENSRNOP00000060834   ⟸   ENSRNOT00000067142
RefSeq Acc Id: XP_038945084   ⟸   XM_039089156
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038945099   ⟸   XM_039089171
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038945088   ⟸   XM_039089160
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038945082   ⟸   XM_039089154
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038945075   ⟸   XM_039089147
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038945112   ⟸   XM_039089184
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038945105   ⟸   XM_039089177
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038945109   ⟸   XM_039089181
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038945116   ⟸   XM_039089188
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038945119   ⟸   XM_039089191
- Peptide Label: isoform X6
RefSeq Acc Id: NP_001375440   ⟸   NM_001388511
- Peptide Label: isoform 3
RefSeq Acc Id: NP_001375438   ⟸   NM_001388509
- Peptide Label: isoform 2
RefSeq Acc Id: NP_001375439   ⟸   NM_001388510
- Peptide Label: isoform 2
RefSeq Acc Id: ENSRNOP00000086886   ⟸   ENSRNOT00000106865
RefSeq Acc Id: ENSRNOP00000092661   ⟸   ENSRNOT00000111002
RefSeq Acc Id: ENSRNOP00000086612   ⟸   ENSRNOT00000102087
RefSeq Acc Id: ENSRNOP00000081805   ⟸   ENSRNOT00000098030
RefSeq Acc Id: ENSRNOP00000091632   ⟸   ENSRNOT00000111873
Protein Domains
PDEase

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
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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)
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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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
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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)
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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-Lx/CubMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
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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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
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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)
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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)
DA/OlaHsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
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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)
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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
F344/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
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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)
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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)
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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)
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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
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
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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/FarMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
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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
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
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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 (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
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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)
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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
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
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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/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
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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/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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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)
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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)
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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/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
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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)
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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 (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
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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)
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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/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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:68434 AgrOrtholog
Ensembl Genes ENSRNOG00000011310 Ensembl, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000042134 UniProtKB/Swiss-Prot
  ENSRNOP00000060834 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000043474 UniProtKB/Swiss-Prot
  ENSRNOT00000067142 UniProtKB/TrEMBL
Gene3D-CATH 1.10.1300.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.30.450.40 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro GAF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  GAF-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HD/PDEase_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDEase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDEase_catalytic_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDEase_catalytic_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDEase_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:63885 UniProtKB/Swiss-Prot
NCBI Gene 63885 ENTREZGENE
Pfam GAF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDEase_I UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Pde10a PhenoGen
PRINTS PDIESTERASE1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE PDEASE_I_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDEASE_I_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART GAF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HDc UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC206846
UniProt F1LX13_RAT UniProtKB/TrEMBL
  PDE10_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q6S9E6 UniProtKB/Swiss-Prot
  Q6S9E7 UniProtKB/Swiss-Prot
  Q6S9E8 UniProtKB/Swiss-Prot
  Q6S9E9 UniProtKB/Swiss-Prot
  Q9QYJ5 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Pde10a  phosphodiesterase 10A      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference