Pml (PML nuclear body scaffold) - Rat Genome Database

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Gene: Pml (PML nuclear body scaffold) Rattus norvegicus
Analyze
Symbol: Pml
Name: PML nuclear body scaffold
RGD ID: 1562602
Description: Predicted to enable several functions, including protein dimerization activity; transition metal ion binding activity; and ubiquitin-like protein transferase activity. Predicted to be involved in several processes, including regulation of cellular protein metabolic process; regulation of nucleobase-containing compound metabolic process; and signal transduction by p53 class mediator. Predicted to act upstream of or within several processes, including apoptotic signaling pathway; positive regulation of macromolecule metabolic process; and protein localization to nucleus. Predicted to be located in chromosome, telomeric region; cytosol; and nucleus. Predicted to be extrinsic component of endoplasmic reticulum membrane. Predicted to be active in PML body and chromatin. Predicted to colocalize with heterochromatin. Human ortholog(s) of this gene implicated in acute promyelocytic leukemia and skin cancer. Orthologous to human PML (PML nuclear body scaffold); PARTICIPATES IN mTOR signaling pathway; transforming growth factor-beta Smad dependent signaling pathway; acute myeloid leukemia pathway; INTERACTS WITH 3,3',5,5'-tetrabromobisphenol A; 6-propyl-2-thiouracil; amphetamine.
Type: protein-coding
RefSeq Status: MODEL
Also known as: LOC315713; promyelocytic leukemia; RGD1562602; similar to promyelocytic leukemia
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
mRatBN7.2858,627,347 - 58,661,927 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl858,628,837 - 58,658,971 (-)Ensembl
Rnor_6.0863,002,515 - 63,034,310 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl863,004,870 - 63,034,226 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0862,778,563 - 62,810,283 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4862,020,438 - 62,051,927 (-)NCBIRGSC3.4rn4RGSC3.4
Celera858,089,954 - 58,121,691 (-)NCBICelera
Cytogenetic Map8q24NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
3,3',5,5'-tetrabromobisphenol A  (EXP)
3-methyladenine  (ISO)
4'-epidoxorubicin  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
5-azacytidine  (ISO)
6-propyl-2-thiouracil  (EXP)
7,9-dihydro-1H-purine-2,6,8(3H)-trione  (ISO)
acrolein  (ISO)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
alpha-pinene  (ISO)
aluminium sulfate (anhydrous)  (ISO)
amphetamine  (EXP)
Antimony trioxide  (ISO)
antimony(0)  (ISO)
aristolochic acid  (ISO)
Aroclor 1254  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
ATP  (ISO)
benzo[a]pyrene  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bleomycin A2  (ISO)
buta-1,3-diene  (ISO)
cadmium dichloride  (ISO)
calciol  (ISO)
carbon nanotube  (ISO)
cisplatin  (ISO)
cobalt dichloride  (ISO)
Cuprizon  (EXP)
cycloheximide  (ISO)
DAPT  (ISO)
deoxynivalenol  (ISO)
diarsenic trioxide  (ISO)
dicrotophos  (ISO)
dimercaprol  (ISO)
dimethylarsinous acid  (ISO)
dioxygen  (ISO)
dipotassium bis[mu-tartrato(4-)]diantimonate(2-) trihydrate  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
elemental selenium  (ISO)
ellagic acid  (ISO)
endosulfan  (EXP)
enzyme inhibitor  (ISO)
erlotinib hydrochloride  (ISO)
ethyl methanesulfonate  (ISO)
fenamidone  (ISO)
fenvalerate  (ISO)
fluoranthene  (ISO)
Ginkgoic acid  (ISO)
hydroxyurea  (ISO)
ibuprofen  (ISO)
ivermectin  (ISO)
leptomycin B  (ISO)
lipopolysaccharide  (ISO)
malathion  (ISO)
methyl methanesulfonate  (ISO)
mitoxantrone  (ISO)
N-(6-acetamidohexyl)acetamide  (ISO)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
N-nitrosodiethylamine  (ISO)
nickel atom  (ISO)
ozone  (ISO)
p-menthan-3-ol  (ISO)
paraquat  (ISO)
pentachlorophenol  (ISO)
phenylmercury acetate  (ISO)
pirinixic acid  (ISO)
propiconazole  (ISO)
puerarin  (ISO)
reactive oxygen species  (ISO)
resiquimod  (ISO)
resveratrol  (ISO)
rofecoxib  (ISO)
SB 431542  (ISO)
selenium atom  (ISO)
silicon dioxide  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sirolimus  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
sulindac  (ISO)
tetrachloromethane  (EXP)
thimerosal  (ISO)
titanium dioxide  (ISO)
Triptolide  (EXP)
triptonide  (ISO)
troglitazone  (ISO)
tungsten  (ISO)
valproic acid  (ISO)
vanadyl sulfate  (ISO)
vitamin E  (ISO)
vorinostat  (ISO)
zebularine  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
activation of cysteine-type endopeptidase activity involved in apoptotic process  (ISO)
apoptotic process  (ISO)
biological_process  (ND)
branching involved in mammary gland duct morphogenesis  (ISO)
cell aging  (ISO)
cell fate commitment  (ISO)
cellular response to interleukin-4  (ISO)
cellular response to leukemia inhibitory factor  (ISO)
cellular senescence  (ISO)
circadian regulation of gene expression  (ISO)
common-partner SMAD protein phosphorylation  (ISO)
DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest  (ISO)
endoplasmic reticulum calcium ion homeostasis  (ISO)
entrainment of circadian clock by photoperiod  (ISO)
extrinsic apoptotic signaling pathway  (ISO)
fibroblast migration  (ISO)
innate immune response  (ISO)
intrinsic apoptotic signaling pathway by p53 class mediator  (ISO)
intrinsic apoptotic signaling pathway in response to DNA damage  (IBA,ISO)
intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator  (ISO)
intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress  (ISO)
intrinsic apoptotic signaling pathway in response to oxidative stress  (ISO)
maintenance of protein location in nucleus  (ISO)
myeloid cell differentiation  (ISO)
negative regulation of angiogenesis  (ISO)
negative regulation of cell growth  (ISO)
negative regulation of cell population proliferation  (ISO)
negative regulation of interleukin-1 beta production  (ISO)
negative regulation of interleukin-1 production  (ISO)
negative regulation of mitotic cell cycle  (ISO)
negative regulation of telomerase activity  (ISO)
negative regulation of telomere maintenance via telomerase  (ISO)
negative regulation of transcription, DNA-templated  (ISO)
negative regulation of translation in response to oxidative stress  (ISO)
negative regulation of ubiquitin-dependent protein catabolic process  (ISO)
PML body organization  (IBA,ISO)
positive regulation of apoptotic process involved in mammary gland involution  (ISO)
positive regulation of apoptotic signaling pathway  (ISO)
positive regulation of defense response to virus by host  (ISO)
positive regulation of extrinsic apoptotic signaling pathway  (ISO)
positive regulation of fibroblast proliferation  (ISO)
positive regulation of histone deacetylation  (ISO)
positive regulation of MHC class I biosynthetic process  (ISO)
positive regulation of protein localization to chromosome, telomeric region  (ISO)
positive regulation of telomere maintenance  (ISO)
positive regulation of transcription by RNA polymerase II  (ISO)
positive regulation of transcription, DNA-templated  (IBA)
proteasome-mediated ubiquitin-dependent protein catabolic process  (ISO)
protein import into nucleus  (ISO)
protein stabilization  (ISO)
protein targeting  (ISO)
protein ubiquitination  (IEA)
protein-containing complex assembly  (ISO)
regulation of calcium ion transport into cytosol  (ISO)
regulation of cell adhesion  (ISO)
regulation of cell cycle  (ISO)
regulation of circadian rhythm  (ISO)
regulation of double-strand break repair  (ISO)
regulation of MHC class I biosynthetic process  (ISO)
regulation of protein phosphorylation  (ISO)
regulation of transcription, DNA-templated  (ISO)
response to cytokine  (ISO)
response to gamma radiation  (ISO)
response to hypoxia  (ISO)
response to UV  (ISO)
retinoic acid receptor signaling pathway  (ISO)
suppression of viral release by host  (ISO)
transforming growth factor beta receptor signaling pathway  (ISO)

Cellular Component

References

References - curated
1. Brown D, etal., Proc Natl Acad Sci U S A. 1997 Mar 18;94(6):2551-6. doi: 10.1073/pnas.94.6.2551.
2. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
3. Kuo HY, etal., Cell Cycle. 2014;13(19):3132-42. doi: 10.4161/15384101.2014.949212.
4. Leavenworth JD, etal., Reprod Sci. 2010 Apr;17(4):339-49. doi: 10.1177/1933719109358455.
5. Lin YC, etal., Cancer Res. 2014 Dec 1;74(23):6935-46. doi: 10.1158/0008-5472.CAN-14-1330. Epub 2014 Oct 7.
6. Mohammed AJ, etal., Iran Biomed J. 2020 Mar;24(2):128-135. Epub 2019 Oct 30.
7. Ohgiya D, etal., Acta Haematol. 2012;128(4):213-22. doi: 10.1159/000339486. Epub 2012 Aug 17.
8. Pipeline to import KEGG annotations from KEGG into RGD
9. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
10. RGD automated data pipeline
11. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
12. RGD automated import pipeline for gene-chemical interactions
13. RGD comprehensive gene curation
14. Straub K, etal., Cancer Med. 2019 Jul;8(8):3793-3802. doi: 10.1002/cam4.2162. Epub 2019 May 29.
15. Virador VM, etal., Mol Carcinog. 2009 Jul;48(7):599-609. doi: 10.1002/mc.20498.
16. Wimmer P, etal., Oncogene. 2010 Oct 7;29(40):5511-22. doi: 10.1038/onc.2010.284. Epub 2010 Jul 19.
17. Yoon GS and Yu E, J Korean Med Sci. 2001 Aug;16(4):433-8. doi: 10.3346/jkms.2001.16.4.433.
18. Zhang X, etal., Cancer Lett. 2015 Sep 28;366(1):112-22. doi: 10.1016/j.canlet.2015.06.014. Epub 2015 Jun 25.
Additional References at PubMed
PMID:7729428   PMID:7935403   PMID:8643677   PMID:9230084   PMID:9294197   PMID:9395203   PMID:9412458   PMID:9448006   PMID:9488655   PMID:9583681   PMID:9798653   PMID:9806545  
PMID:9845074   PMID:9885291   PMID:10684855   PMID:10716735   PMID:10779416   PMID:10910364   PMID:11025664   PMID:11080164   PMID:11259576   PMID:11331580   PMID:12006491   PMID:12402044  
PMID:12529400   PMID:12773567   PMID:12915590   PMID:12917339   PMID:14992722   PMID:15195100   PMID:15252119   PMID:15356634   PMID:15626733   PMID:15833741   PMID:16461359   PMID:16778193  
PMID:16873256   PMID:16873257   PMID:16915281   PMID:17081985   PMID:17081986   PMID:17332504   PMID:18248090   PMID:18298799   PMID:19033381   PMID:19261859   PMID:19416967   PMID:19567472  
PMID:20439489   PMID:21030605   PMID:21639834   PMID:21803845   PMID:22002537   PMID:22082260   PMID:22117195   PMID:22155184   PMID:22274616   PMID:22406621   PMID:22641345   PMID:22869143  
PMID:22904064   PMID:23007646   PMID:23431171   PMID:23555679   PMID:24407287   PMID:26119943   PMID:31505169  


Genomics

Comparative Map Data
Pml
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2858,627,347 - 58,661,927 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl858,628,837 - 58,658,971 (-)Ensembl
Rnor_6.0863,002,515 - 63,034,310 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl863,004,870 - 63,034,226 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0862,778,563 - 62,810,283 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4862,020,438 - 62,051,927 (-)NCBIRGSC3.4rn4RGSC3.4
Celera858,089,954 - 58,121,691 (-)NCBICelera
Cytogenetic Map8q24NCBI
PML
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1573,994,673 - 74,047,827 (+)EnsemblGRCh38hg38GRCh38
GRCh381573,994,716 - 74,047,827 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371574,287,057 - 74,340,168 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361572,074,067 - 72,127,213 (+)NCBINCBI36hg18NCBI36
Build 341572,074,066 - 72,115,787NCBI
Celera1551,164,334 - 51,230,308 (+)NCBI
Cytogenetic Map15q24.1NCBI
HuRef1551,118,849 - 51,172,183 (+)NCBIHuRef
CHM1_11574,404,975 - 74,458,114 (+)NCBICHM1_1
Pml
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39958,124,462 - 58,157,077 (-)NCBIGRCm39mm39
GRCm39 Ensembl958,125,359 - 58,157,069 (-)Ensembl
GRCm38958,217,179 - 58,249,796 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl958,218,076 - 58,249,786 (-)EnsemblGRCm38mm10GRCm38
MGSCv37958,064,986 - 58,097,593 (-)NCBIGRCm37mm9NCBIm37
MGSCv36958,016,679 - 58,047,923 (-)NCBImm8
Celera955,451,359 - 55,484,054 (-)NCBICelera
Cytogenetic Map9BNCBI
cM Map931.63NCBI
Pml
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554503,656,498 - 3,692,406 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554503,654,854 - 3,692,057 (-)NCBIChiLan1.0ChiLan1.0
PML
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11571,658,884 - 71,710,883 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1571,658,884 - 71,710,883 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01552,903,874 - 52,955,151 (+)NCBIMhudiblu_PPA_v0panPan3
PML
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13037,232,337 - 37,278,434 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3037,232,306 - 37,277,741 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3037,167,830 - 37,214,029 (+)NCBI
ROS_Cfam_1.03037,439,424 - 37,485,481 (+)NCBI
UMICH_Zoey_3.13037,391,257 - 37,437,382 (+)NCBI
UNSW_CanFamBas_1.03037,417,163 - 37,463,467 (+)NCBI
UU_Cfam_GSD_1.03037,673,462 - 37,719,075 (+)NCBI
Pml
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024408640115,287,097 - 115,329,964 (+)NCBI
SpeTri2.0NW_00493647133,135,186 - 33,173,218 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PML
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl759,405,048 - 59,450,150 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1759,405,044 - 59,450,155 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2764,023,286 - 64,071,578 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PML
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1269,441,998 - 9,494,949 (-)NCBIChlSab1.1chlSab2
ChlSab1.1269,441,998 - 9,494,949 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl269,451,112 - 9,494,931 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666048132,120,299 - 132,175,245 (+)NCBIVero_WHO_p1.0
Pml
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624781464,858 - 498,146 (-)NCBIHetGla_female_1.0hetGla2


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1581557Eae16Experimental allergic encephalomyelitis QTL 163.8nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)88462195110921472Rat
631650Stl6Serum triglyceride level QTL 640.0019blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)810378157112202585Rat
1558646Swd5Spike wave discharge measurement QTL 53.450.00036brain electrophysiology trait (VT:0010557)brain spike-and-wave discharge frequency (CMO:0001742)81490675159906751Rat
61373Mcs4Mammary carcinoma susceptibility QTL 41.1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)81629044461290444Rat
631271Lecl1Lens clarity QTL 10.001lens clarity trait (VT:0001304)age of onset/diagnosis of cataract (CMO:0001584)81898416884531599Rat
731182Uae24Urinary albumin excretion QTL 246.4urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)81933115293965294Rat
631842Inf1Infertility severity QTL 14.10.001seminal gland mass (VT:0010524)seminal vesicle wet weight (CMO:0001603)82266233067662330Rat
2303564Gluco43Glucose level QTL 433blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)82613018771130187Rat
2303572Insul13Insulin level QTL 132blood insulin amount (VT:0001560)blood insulin level (CMO:0000349)82613018771130187Rat
1358892Kidm26Kidney mass QTL 263.69kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)82720571599103503Rat
1358896Bp262Blood pressure QTL 2622.89arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)82720571599103503Rat
1358907Cm40Cardiac mass QTL 401.89heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)82720571599103503Rat
1300146Rf17Renal function QTL 172.9renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)82824291273242912Rat
8662823Vetf5Vascular elastic tissue fragility QTL 51.9artery integrity trait (VT:0010639)patent ductus arteriosus score (CMO:0002566)82824291299525068Rat
724514Uae15Urinary albumin excretion QTL 152.9urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)82950266570386295Rat
1549908Neudeg1Neurodegradation QTL 15.50nervous system integrity trait (VT:0010566)logarithm of the ratio of the lesioned side motor neuron count to contralateral side motor neuron count (CMO:0001986)83018886794457446Rat
61353Bp35Blood pressure QTL 350.001arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)83084815461290444Rat
61353Bp35Blood pressure QTL 350.001arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)83084815461290444Rat
61353Bp35Blood pressure QTL 350.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)83084815461290444Rat
61353Bp35Blood pressure QTL 350.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)83084815461290444Rat
11556286Cm81Cardiac mass QTL 810.01heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)83084815461290444Rat
1359033Bp273Blood pressure QTL 273arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)83084815461290444Rat
2313046Bss78Bone structure and strength QTL 783.50.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)83084815482460899Rat
2313057Bss76Bone structure and strength QTL 7630.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)83084815482460899Rat
2313067Bss77Bone structure and strength QTL 773.10.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)83084815482460899Rat
2313088Bss75Bone structure and strength QTL 753.10.0001body length (VT:0001256)body length, nose to rump (CMO:0000079)83084815482460899Rat
1578755Pur5Proteinuria QTL 53.30.0001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)830848154101699754Rat
1578765Klgr1Kidney lesion grade QTL 13.30.0001kidney morphology trait (VT:0002135)organ lesion measurement (CMO:0000677)830848154101699754Rat
1578769Uae31Urinary albumin excretion QTL 313.30.001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)830848154101699754Rat
2316950Scl66Serum cholesterol level QTL 664.1blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)830848259105647037Rat
1298065Scl16Serum cholesterol level QTL 163.8blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)83085640475856404Rat
1582222Epfw2Epididymal fat weight QTL 23.20.0005epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)83173772976737729Rat
61358Bp39Blood pressure QTL 392arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)83555193880551938Rat
61464Niddm11Non-insulin dependent diabetes mellitus QTL 113.10.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)83558203280582032Rat
1331838Niddm61Non-insulin dependent diabetes mellitus QTL 613.530.0004blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)83646953599083736Rat
737824Hcar10Hepatocarcinoma resistance QTL 102.9liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)84071306682925667Rat
1358906Bp253Blood pressure QTL 25340.0004arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)84071306693965294Rat
1554321Bmd3Bone mineral density QTL 37.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)840952565123900184Rat
1331769Rf39Renal function QTL 393.871urine output (VT:0003620)timed urine volume (CMO:0000260)84186687675097878Rat
1298079Activ2Activity QTL 29.50.000001voluntary movement trait (VT:0003491)rearing measurement (CMO:0001515)84186687686866876Rat
631216Stl9Serum triglyceride level QTL 94.710.0001blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)84186701070386132Rat
70161Bp62Blood pressure QTL 622.90.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)84269268490165460Rat
12879882Am8Aortic mass QTL 80.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)84329616998968765Rat
12879878Bw183Body weight QTL 1830.001body mass (VT:0001259)body weight (CMO:0000012)84329616998968765Rat
12879879Cm99Cardiac mass QTL 990.001heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)84329616998968765Rat
12879880Cm100Cardiac mass QTL 1000.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)84329616998968765Rat
12879881Cm101Cardiac mass QTL 1010.001heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)84329616998968765Rat
12879883Kidm65Kidney mass QTL 650.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)84329616998968765Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)846531639119088624Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)846531639119088624Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)846531639119088624Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)846531639119088624Rat
1331837Bw23Body weight QTL 234.190.00007body mass (VT:0001259)body weight (CMO:0000012)84653172299083736Rat
2303570Gluco48Glucose level QTL 482blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)84980583194805831Rat
2313086Bss60Bone structure and strength QTL 604.10.0001tibia length (VT:0004357)tibia length (CMO:0000450)85009524982460899Rat
4889938Bss89Bone structure and strength QTL 893.8tibia size trait (VT:0100001)tibia cortical bone volume (CMO:0001725)85009524982460899Rat
5684973Bss100Bone structure and strength QTL 1004.7tibia area (VT:1000281)tibia area measurement (CMO:0001382)85009524982460899Rat
1358912Bw51Body weight QTL 512.95body mass (VT:0001259)body weight (CMO:0000012)851351728107062046Rat
10402857Bp380Blood pressure QTL 3800.95arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)85396876598968765Rat
2301402Bp316Blood pressure QTL 3160.005arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)85396876598968765Rat
2293697Bmd39Bone mineral density QTL 39femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)85404374498968765Rat
1582243Bw66Body weight QTL 663.40.0048body mass (VT:0001259)body weight (CMO:0000012)85423764485365202Rat
1582254Kidm31Kidney mass QTL 313kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)85423764485365202Rat
631664Hcar3Hepatocarcinoma resistance QTL 32.90.0005liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)85423764499103503Rat
1300177Cm2Cardiac mass QTL 23.65heart mass (VT:0007028)heart weight (CMO:0000017)854259986100382532Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:220
Count of miRNA genes:91
Interacting mature miRNAs:93
Transcripts:ENSRNOT00000043434, ENSRNOT00000071610
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 2 20 35 19 19 19 14 31 34 11
Low 1 23 22 22 22 8 11 60 4 7 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000043434   ⟹   ENSRNOP00000042091
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl858,628,837 - 58,658,971 (-)Ensembl
Rnor_6.0 Ensembl863,004,870 - 63,034,226 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000096130   ⟹   ENSRNOP00000091871
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl858,628,837 - 58,657,836 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000110939   ⟹   ENSRNOP00000094203
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl858,628,837 - 58,658,971 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000115525   ⟹   ENSRNOP00000090583
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl858,628,837 - 58,658,971 (-)Ensembl
RefSeq Acc Id: XM_039082399   ⟹   XP_038938327
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2858,627,347 - 58,661,927 (-)NCBI
RefSeq Acc Id: XM_039082400   ⟹   XP_038938328
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2858,627,347 - 58,659,060 (-)NCBI
RefSeq Acc Id: XM_039082401   ⟹   XP_038938329
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2858,630,535 - 58,659,048 (-)NCBI
Protein Sequences
Protein RefSeqs XP_038938327 (Get FASTA)   NCBI Sequence Viewer  
  XP_038938328 (Get FASTA)   NCBI Sequence Viewer  
  XP_038938329 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL95670 (Get FASTA)   NCBI Sequence Viewer  
  EDL95671 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: ENSRNOP00000042091   ⟸   ENSRNOT00000043434
RefSeq Acc Id: XP_038938327   ⟸   XM_039082399
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038938328   ⟸   XM_039082400
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038938329   ⟸   XM_039082401
- Peptide Label: isoform X2
RefSeq Acc Id: ENSRNOP00000094203   ⟸   ENSRNOT00000110939
RefSeq Acc Id: ENSRNOP00000091871   ⟸   ENSRNOT00000096130
RefSeq Acc Id: ENSRNOP00000090583   ⟸   ENSRNOT00000115525
Protein Domains
B box-type   RING-type

Transcriptome

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

Promoters
RGD ID:13696030
Promoter ID:EPDNEW_R6552
Type:initiation region
Name:Pml_1
Description:promyelocytic leukemia
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_6.0863,034,178 - 63,034,238EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (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
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-Lx/CubMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (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
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 (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
BXH2/CubMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
DA/OlaHsd (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: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (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
F344/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
F344/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
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
F344/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
FXLE16/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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/FarMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
HXB10/IpcvMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (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
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
LEXF10A/StmMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LH/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
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
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)
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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
M520/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
M520/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
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)
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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
MNS/Gib (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
MR/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
MR/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
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)
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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
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)
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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/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)
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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
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)
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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/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)
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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/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)
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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
WKY/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
WKY/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
WKY/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
WKY/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
WKY/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
WN/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
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:1562602 AgrOrtholog
Ensembl Genes ENSRNOG00000008400 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000042091 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000043434 UniProtKB/TrEMBL
Gene3D-CATH 3.30.40.10 UniProtKB/TrEMBL
InterPro DUF3583 UniProtKB/TrEMBL
  Znf_B-box UniProtKB/TrEMBL
  Znf_RING UniProtKB/TrEMBL
  Znf_RING/FYVE/PHD UniProtKB/TrEMBL
  Znf_RING_CS UniProtKB/TrEMBL
NCBI Gene 315713 ENTREZGENE
Pfam DUF3583 UniProtKB/TrEMBL
  zf-B_box UniProtKB/TrEMBL
PhenoGen Pml PhenoGen
PROSITE ZF_BBOX UniProtKB/TrEMBL
  ZF_RING_1 UniProtKB/TrEMBL
  ZF_RING_2 UniProtKB/TrEMBL
SMART BBOX UniProtKB/TrEMBL
  RING UniProtKB/TrEMBL
UniProt F1M589_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2020-05-22 Pml  PML nuclear body scaffold  Pml  promyelocytic leukemia  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-29 Pml  promyelocytic leukemia  RGD1562602_predicted  similar to promyelocytic leukemia (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1562602_predicted  similar to promyelocytic leukemia (predicted)  LOC315713  similar to promyelocytic leukemia  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC315713  similar to promyelocytic leukemia      Symbol and Name status set to provisional 70820 PROVISIONAL