Pdzrn3 (PDZ domain containing RING finger 3) - Rat Genome Database

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Gene: Pdzrn3 (PDZ domain containing RING finger 3) Rattus norvegicus
Analyze
Symbol: Pdzrn3
Name: PDZ domain containing RING finger 3
RGD ID: 1305250
Description: Predicted to enable ubiquitin protein ligase activity. Predicted to be involved in neuromuscular junction development and protein ubiquitination. Predicted to be located in cytoplasm. Predicted to be active in neuromuscular junction. Orthologous to human PDZRN3 (PDZ domain containing ring finger 3); INTERACTS WITH 1,2-dimethylhydrazine; 1-naphthyl isothiocyanate; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: E3 ubiquitin-protein ligase PDZRN3; LOC312607; PDZ domain-containing RING finger protein 3; RING-type E3 ubiquitin transferase PDZRN3; semaphorin cytoplasmic domain-associated protein 3
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
mRatBN7.24133,770,736 - 133,996,959 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl4133,770,736 - 133,996,959 (-)Ensembl
Rnor_6.04133,717,139 - 133,951,282 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4133,717,139 - 133,951,264 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04198,194,465 - 198,429,457 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44136,044,210 - 136,254,969 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.14136,260,810 - 136,311,636 (-)NCBI
Celera4122,607,053 - 122,831,741 (-)NCBICelera
Cytogenetic Map4q34NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (EXP)
1-naphthyl isothiocyanate  (EXP)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP,ISO)
3,3',4,4',5-pentachlorobiphenyl  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4,4'-diaminodiphenylmethane  (EXP)
6-propyl-2-thiouracil  (EXP)
8-Br-cAMP  (ISO)
acetamide  (EXP)
acrylamide  (EXP)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
amiodarone  (ISO)
andrographolide  (ISO)
arsenite(3-)  (ISO)
atrazine  (ISO)
benzo[a]pyrene  (ISO)
benzo[e]pyrene  (ISO)
beta-naphthoflavone  (ISO)
bisphenol A  (EXP,ISO)
calcitriol  (ISO)
chloroprene  (ISO)
choline  (ISO)
cisplatin  (EXP)
copper atom  (EXP)
copper(0)  (EXP)
dexamethasone  (ISO)
dorsomorphin  (ISO)
flutamide  (EXP)
folic acid  (ISO)
fulvestrant  (ISO)
furan  (EXP)
glafenine  (EXP)
haloperidol  (ISO)
hydrogen peroxide  (ISO)
indometacin  (ISO)
L-methionine  (ISO)
lipopolysaccharide  (ISO)
methapyrilene  (ISO)
methylmercury chloride  (ISO)
N-nitrosodiethylamine  (ISO)
N-nitrosodimethylamine  (EXP)
phenformin  (EXP)
pirinixic acid  (ISO)
potassium dichromate  (ISO)
profenofos  (EXP)
SB 431542  (ISO)
Securinine  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
Soman  (EXP)
temozolomide  (ISO)
testosterone  (ISO)
tetrachloromethane  (EXP)
thioacetamide  (EXP)
titanium dioxide  (ISO)
trichostatin A  (ISO)
triphenyl phosphate  (EXP)
urethane  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:15057822   PMID:15458844   PMID:17576800   PMID:22609016   PMID:28623232  


Genomics

Comparative Map Data
Pdzrn3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.24133,770,736 - 133,996,959 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl4133,770,736 - 133,996,959 (-)Ensembl
Rnor_6.04133,717,139 - 133,951,282 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4133,717,139 - 133,951,264 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04198,194,465 - 198,429,457 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44136,044,210 - 136,254,969 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.14136,260,810 - 136,311,636 (-)NCBI
Celera4122,607,053 - 122,831,741 (-)NCBICelera
Cytogenetic Map4q34NCBI
PDZRN3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38373,382,431 - 73,624,941 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl373,382,431 - 73,624,941 (-)EnsemblGRCh38hg38GRCh38
GRCh37373,431,582 - 73,674,092 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36373,514,342 - 73,756,762 (-)NCBINCBI36hg18NCBI36
Celera373,365,735 - 73,608,750 (-)NCBI
Cytogenetic Map3p13NCBI
HuRef373,434,331 - 73,676,506 (-)NCBIHuRef
CHM1_1373,385,013 - 73,627,407 (-)NCBICHM1_1
Pdzrn3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm396101,126,568 - 101,354,858 (-)NCBIGRCm39mm39
GRCm39 Ensembl6101,126,570 - 101,354,858 (-)Ensembl
GRCm386101,149,607 - 101,377,897 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl6101,149,609 - 101,377,897 (-)EnsemblGRCm38mm10GRCm38
MGSCv376101,099,601 - 101,327,891 (-)NCBIGRCm37mm9NCBIm37
MGSCv366101,115,712 - 101,343,995 (-)NCBImm8
Celera6103,016,258 - 103,244,142 (-)NCBICelera
Cytogenetic Map6D3NCBI
Pdzrn3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542114,648,524 - 14,877,822 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495542114,648,436 - 14,878,759 (+)NCBIChiLan1.0ChiLan1.0
PDZRN3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1375,245,623 - 75,488,415 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl375,246,558 - 75,488,499 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0373,322,613 - 73,565,929 (-)NCBIMhudiblu_PPA_v0panPan3
PDZRN3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12018,621,960 - 18,859,620 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2018,622,069 - 18,859,550 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2018,594,042 - 18,830,979 (+)NCBI
ROS_Cfam_1.02018,656,854 - 18,893,815 (+)NCBI
ROS_Cfam_1.0 Ensembl2018,656,915 - 18,893,825 (+)Ensembl
UMICH_Zoey_3.12018,344,911 - 18,581,831 (+)NCBI
UNSW_CanFamBas_1.02018,685,052 - 18,922,922 (+)NCBI
UU_Cfam_GSD_1.02018,750,258 - 18,987,822 (+)NCBI
Pdzrn3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244049424,218,675 - 4,420,201 (-)NCBI
SpeTri2.0NW_0049366034,218,675 - 4,423,450 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PDZRN3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1354,659,589 - 54,904,900 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11354,659,657 - 54,904,742 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21360,422,724 - 60,650,319 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PDZRN3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12234,325,208 - 34,567,748 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl2234,326,144 - 34,567,633 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666041132,201,578 - 132,443,428 (+)NCBIVero_WHO_p1.0
Pdzrn3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247737,901,560 - 8,144,455 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
D4Rat58  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24133,821,995 - 133,822,342 (+)MAPPERmRatBN7.2
Rnor_6.04133,776,133 - 133,776,479NCBIRnor6.0
Rnor_5.04198,254,543 - 198,254,889UniSTSRnor5.0
RGSC_v3.44136,095,832 - 136,096,179RGDRGSC3.4
RGSC_v3.44136,095,833 - 136,096,179UniSTSRGSC3.4
RGSC_v3.14136,340,671 - 136,341,022RGD
Celera4122,658,291 - 122,658,637UniSTS
SHRSP x BN Map460.61RGD
SHRSP x BN Map460.61UniSTS
Cytogenetic Map4q34UniSTS
RH128427  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_5.04198,194,524 - 198,194,708NCBIRnor5.0
RGSC_v3.44136,044,276 - 136,044,459UniSTSRGSC3.4
Celera4122,607,113 - 122,607,296UniSTS
RH 3.4 Map4809.0UniSTS
Cytogenetic Map4q34UniSTS
RH129369  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24133,884,426 - 133,884,636 (+)MAPPERmRatBN7.2
Rnor_6.04133,838,559 - 133,838,768NCBIRnor6.0
Rnor_5.04198,316,969 - 198,317,178UniSTSRnor5.0
RGSC_v3.44136,158,259 - 136,158,468UniSTSRGSC3.4
Celera4122,720,663 - 122,720,872UniSTS
RH 3.4 Map4808.9UniSTS
Cytogenetic Map4q34UniSTS
BF395872  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24133,893,687 - 133,893,880 (+)MAPPERmRatBN7.2
Rnor_6.04133,847,819 - 133,848,011NCBIRnor6.0
Rnor_5.04198,326,229 - 198,326,421UniSTSRnor5.0
RGSC_v3.44136,167,519 - 136,167,711UniSTSRGSC3.4
Celera4122,729,914 - 122,730,106UniSTS
RH 3.4 Map4810.32UniSTS
Cytogenetic Map4q34UniSTS
RH141666  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24133,837,561 - 133,837,742 (+)MAPPERmRatBN7.2
Rnor_6.04133,791,699 - 133,791,879NCBIRnor6.0
Rnor_5.04198,270,109 - 198,270,289UniSTSRnor5.0
RGSC_v3.44136,111,399 - 136,111,579UniSTSRGSC3.4
Celera4122,673,857 - 122,674,037UniSTS
RH 3.4 Map4808.0UniSTS
Cytogenetic Map4q34UniSTS
AI008935  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24133,919,855 - 133,920,036 (+)MAPPERmRatBN7.2
Rnor_6.04133,873,953 - 133,874,133NCBIRnor6.0
Rnor_5.04198,352,042 - 198,352,222UniSTSRnor5.0
RGSC_v3.44136,178,084 - 136,178,264UniSTSRGSC3.4
Celera4122,755,027 - 122,755,207UniSTS
RH 3.4 Map4810.32UniSTS
Cytogenetic Map4q34UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2293840Kiddil9Kidney dilation QTL 92.9kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)4120926564148090731Rat
61434Cia3Collagen induced arthritis QTL 34.8joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4103194656148194656Rat
70177Xhs1X-ray hypersensitivity QTL 125.1intestine integrity trait (VT:0010554)post-insult time to onset of moribundity (CMO:0001896)482798864152731274Rat
70200Alc18Alcohol consumption QTL 189.2drinking behavior trait (VT:0001422)ethanol intake volume to total fluid intake volume ratio (CMO:0001591)456647873149491524Rat
70201Gcr1Gastric cancer resistance QTL 12.7stomach morphology trait (VT:0000470)stomach tumor susceptibility score (CMO:0002043)4120260281147278687Rat
1578655Bmd11Bone mineral density QTL 1111femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)490850165135850165Rat
2303168Bp330Blood pressure QTL 3304.250.017arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)45214602146446691Rat
2302049Pia32Pristane induced arthritis QTL 325.10.001blood autoantibody amount (VT:0003725)serum immunoglobulin G-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002112)4105789505150789505Rat
61451Ciaa4CIA Autoantibody QTL 43.1blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)4126395976167139601Rat
724535Cm18Cardiac mass QTL 182.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)4118856416163856416Rat
724558Plsm2Polydactyly-luxate syndrome (PLS) morphotypes QTL 20.0003hindlimb integrity trait (VT:0010563)hind foot phalanges count (CMO:0001949)4132422778177422778Rat
731165Uae21Urinary albumin excretion QTL 212.40.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)4106649412151649412Rat
1331759Hrtrt13Heart rate QTL 133.54628heart pumping trait (VT:2000009)heart rate (CMO:0000002)4110275411168266883Rat
737821Hcar9Hepatocarcinoma resistance QTL 93.7liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)4109866907167139601Rat
1298082Stresp4Stress response QTL 4blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)450119848146803430Rat
631674Iddm14Insulin dependent diabetes mellitus QTL 14blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)464528739157573521Rat
631683Bp116Blood pressure QTL 1160.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4124303370169303370Rat
631689Scl4Serum cholesterol level QTL 41.90.008blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)495174120140174120Rat
737978Pia23Pristane induced arthritis QTL 235.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4131730738167139601Rat
1331802Srn5Serum renin concentration QTL 53.045renin activity (VT:0005581)plasma renin activity level (CMO:0000116)4119428175157578333Rat
1582232Gluco25Glucose level QTL 253.60.0023blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)485253748148090731Rat
738009Sach4Saccharine consumption QTL 44.90.000016consumption behavior trait (VT:0002069)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)459948935154902892Rat
738016Alc16Alcohol consumption QTL 163.60.00015consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)459948935154902892Rat
738031Alc14Alcohol consumption QTL 147.60.00003consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)459948935154902892Rat
631511Pia7Pristane induced arthritis QTL 74.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4131730738167139601Rat
634335Anxrr16Anxiety related response QTL 167.22locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)493308457167139447Rat
634347Hcar8Hepatocarcinoma resistance QTL 85.8liver integrity trait (VT:0010547)liver tumorous lesion area to total liver area ratio (CMO:0001075)4123143783168143783Rat
1576305Emca6Estrogen-induced mammary cancer QTL 65.8mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)444463720155883716Rat
1576316Ept5Estrogen-induced pituitary tumorigenesis QTL 53.8pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)483428419177635233Rat
1300116Hrtrt5Heart rate QTL 53.76heart pumping trait (VT:2000009)heart rate (CMO:0000002)4116179486151161268Rat
1358352Srcrt3Stress Responsive Cort QTL 32.29blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)438465774146803430Rat
1354612Foco1Food consumption QTL 18.87eating behavior trait (VT:0001431)food intake rate (CMO:0000427)444463908148090542Rat
1354660Salc1Saline consumption QTL 111.26drinking behavior trait (VT:0001422)saline drink intake rate (CMO:0001627)444463908148090542Rat
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)411320076180699135Rat
1358202Gluco11Glucose level QTL 112.40.02adipocyte glucose uptake trait (VT:0004185)absolute change in adipocyte glucose uptake (CMO:0000873)485379421167139601Rat
2312567Glom19Glomerulus QTL 191.90.006kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)445456990146803430Rat
1549827Scl46Serum cholesterol level QTL 463.5blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)4132396220177396220Rat
1549832Bss3Bone structure and strength QTL 311femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)4109827074154827074Rat
61406Scwia1Streptococcal cell wall induced arthritis QTL 12.3joint integrity trait (VT:0010548)experimental arthritis severity measurement (CMO:0001459)4106805662151805662Rat
61422Cia13Collagen induced arthritis QTL 134.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4132642577167139601Rat
6478760Anxrr45Anxiety related response QTL 450.06717locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4110870972155870972Rat
6478763Anxrr46Anxiety related response QTL 460.07428locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4110870972155870972Rat
6478778Anxrr51Anxiety related response QTL 510.25384locomotor behavior trait (VT:0001392)measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)4124778595169778595Rat
7411558Bw133Body weight QTL 13313.840.001body mass (VT:0001259)body weight gain (CMO:0000420)4125590636170590636Rat
7207480Bss105Bone structure and strength QTL 1058.1femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)4109827074154827074Rat
12798519Anxrr54Anxiety related response QTL 542.540.05locomotor behavior trait (VT:0001392)distance moved per unit of time into, out of or within a discrete space in an experimental apparatus (CMO:0001493)4114627026159627026Rat
12798527Anxrr58Anxiety related response QTL 584.110.05locomotor behavior trait (VT:0001392)distance moved per unit of time into, out of or within a discrete space in an experimental apparatus (CMO:0001493)4119463257147278687Rat
12798523Anxrr56Anxiety related response QTL 562.830.05locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)485253748150276390Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:50
Count of miRNA genes:45
Interacting mature miRNAs:50
Transcripts:ENSRNOT00000039201
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 3 34 12 4 4 8 11 69 24 30 9 8
Low 9 45 37 19 37 5 11 11 2
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000090506   ⟹   ENSRNOP00000073080
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4133,770,736 - 133,996,959 (-)Ensembl
Rnor_6.0 Ensembl4133,717,139 - 133,951,264 (-)Ensembl
RefSeq Acc Id: NM_001271251   ⟹   NP_001258180
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24133,770,736 - 133,996,959 (-)NCBI
Rnor_6.04133,717,139 - 133,951,264 (-)NCBI
Rnor_5.04198,194,465 - 198,429,457 (-)NCBI
Celera4122,607,053 - 122,831,741 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017592642   ⟹   XP_017448131
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24133,770,736 - 133,818,888 (-)NCBI
Rnor_6.04133,717,470 - 133,775,301 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001258180 (Get FASTA)   NCBI Sequence Viewer  
  XP_017448131 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL91453 (Get FASTA)   NCBI Sequence Viewer  
  P68907 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001258180   ⟸   NM_001271251
- Sequence:
RefSeq Acc Id: XP_017448131   ⟸   XM_017592642
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000073080   ⟸   ENSRNOT00000090506
Protein Domains
PDZ   RING-type   TRAF-type

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P68907-F1-model_v2 AlphaFold P68907 1-1062 view protein structure

Transcriptome

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


Strain Variation

Strain Sequence Variants (MRatBN7.2)
ACI/EurMcwi (2019)
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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/N (2020)
Visual CSV TAB Printer
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-Lx/CubMcwi (2019)
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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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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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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
BUF/N (2020)
Visual CSV TAB Printer
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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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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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
DA/OlaHsd (2019)
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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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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)
Visual CSV TAB Printer
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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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/Stm (2019)
Visual CSV TAB Printer
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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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
FXLE16/Stm (2020)
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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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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
GK/FarMcwi (2019)
Visual CSV TAB Printer
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
HXB10/IpcvMcwi (2019)
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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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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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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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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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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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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
LEW/Crl (2019)
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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
LEXF10A/StmMcwi (2020)
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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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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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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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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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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/MavRrrcAek (2020)
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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/MavRrrcAek (2020)
Visual CSV TAB Printer
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/MavRrrcAek (2020)
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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
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/NRrrcMcwi (2019)
Visual CSV TAB Printer
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
MR/N (2020)
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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
MWF/Hsd (2019)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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
SHR/OlalpcvMcwi (2019)
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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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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
SR/JrHsd (2020)
Visual CSV TAB Printer
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
SS/JrHsdMcwi (2019)
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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
WAG/RijCrl (2020)
Visual CSV TAB Printer
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/N (2020)
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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/NCrl (2019)
Visual CSV TAB Printer
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
WN/N (2020)
Visual CSV TAB Printer
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
Damaging Variants


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
4 133744843 133744844 T C snv ACI/EurMcwi (MCW), COP/CrCrl (MCW & UW), GH/OmrMcwi (MCW), ACI/N (MCW), PVG/Seac (2019), ACI/EurMcwi (2019), ACI/N (2020), DA/OlaHsd (2019), ACI/EurMcwi (RGD)


Assembly: mRatBN7.2

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
4 133790809 133790810 T C snv ACI/N (2020), ACI/EurMcwi (2019), PVG/Seac (2019), DA/OlaHsd (2019)
4 133996265 133996266 T A snv BXH2/CubMcwi (2020)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1305250 AgrOrtholog
BioCyc Gene G2FUF-43521 BioCyc
Ensembl Genes ENSRNOG00000057556 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000073080 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000090506 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 2.30.42.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.30.40.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro PDZ UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDZ_6 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDZ_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_RING UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_RING/FYVE/PHD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_RING_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_TRAF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 312607 ENTREZGENE
Pfam PDZ UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDZ_6 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Pdzrn3 PhenoGen
PROSITE PDZ UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZF_RING_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZF_RING_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZF_TRAF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART PDZ UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RING UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF50156 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2K4K7_RAT UniProtKB/TrEMBL
  P68907 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Pdzrn3  PDZ domain containing RING finger 3   Pdzrn3_predicted  PDZ domain containing RING finger 3 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Pdzrn3_predicted  PDZ domain containing RING finger 3 (predicted)      Symbol and Name status set to approved 70820 APPROVED