Dsp (desmoplakin) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Dsp (desmoplakin) Rattus norvegicus
Analyze
Symbol: Dsp
Name: desmoplakin
RGD ID: 1305794
Description: Predicted to enable protein kinase C binding activity; scaffold protein binding activity; and structural molecule activity. Involved in wound healing. Located in desmosome and fascia adherens. Human ortholog(s) of this gene implicated in Carvajal syndrome; arrhythmogenic right ventricular cardiomyopathy; arrhythmogenic right ventricular dysplasia 8; and dilated cardiomyopathy. Orthologous to human DSP (desmoplakin); PARTICIPATES IN arrhythmogenic right ventricular cardiomyopathy pathway; INTERACTS WITH 17alpha-ethynylestradiol; 2,4-dinitrotoluene; 2,6-dinitrotoluene.
Type: protein-coding
RefSeq Status: MODEL
Also known as: LOC306871
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
mRatBN7.21726,623,602 - 26,671,692 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1726,623,588 - 26,671,800 (-)Ensembl
Rnor_6.01727,286,811 - 27,334,453 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1727,286,796 - 27,334,379 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01729,201,872 - 29,249,490 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41732,848,313 - 32,896,044 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11732,851,800 - 32,898,885 (-)NCBI
Celera1726,257,726 - 26,305,766 (-)NCBICelera
Cytogenetic Map17p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
arrhythmogenic right ventricular cardiomyopathy  (ISO)
arrhythmogenic right ventricular dysplasia 1  (ISO)
arrhythmogenic right ventricular dysplasia 8  (ISO)
arrhythmogenic right ventricular dysplasia 9  (ISO)
Brugada syndrome  (ISO)
cardiac arrest  (ISO)
Cardiac Arrhythmias  (ISO)
cardiomyopathy  (ISO)
Carvajal syndrome  (ISO)
catecholaminergic polymorphic ventricular tachycardia 1  (ISO)
chronic obstructive pulmonary disease  (ISO)
Developmental Disabilities  (ISO)
dilated cardiomyopathy  (ISO)
dilated cardiomyopathy 1A  (ISO)
dilated cardiomyopathy 1B  (ISO)
dilated cardiomyopathy 1H  (ISO)
dilated cardiomyopathy 1S  (ISO)
Dilated Cardiomyopathy with Left Ventricular Noncompaction  (ISO)
Dilated Cardiomyopathy with Woolly Hair, Keratoderma, and Tooth Agenesis  (ISO)
Ectodermal Dysplasia-Skin Fragility Syndrome  (ISO)
Epidermolysis Bullosa, Lethal Acantholytic  (ISO)
familial hypertrophic cardiomyopathy  (ISO)
Heart Block  (ISO)
hemiplegia  (ISO)
hypertrophic cardiomyopathy  (ISO)
hypertrophic cardiomyopathy 1  (ISO)
idiopathic pulmonary fibrosis  (ISO)
Keratosis Palmoplantaris Striata 2  (ISO)
Left Ventricular Hypertrophy  (ISO)
left ventricular noncompaction  (ISO)
long QT syndrome  (ISO)
long QT syndrome 1  (ISO)
Marfanoid Mental Retardation Syndrome, Autosomal  (ISO)
migraine  (ISO)
Paroxysmal Ventricular Fibrillation  (ISO)
progressive familial heart block  (ISO)
pulmonary fibrosis  (ISO)
restrictive cardiomyopathy  (ISO)
Skin Fragility-Woolly Hair Syndrome  (ISO)
subvalvular aortic stenosis  (ISO)
Sudden Cardiac Death  (ISO)
Sudden Death  (ISO)
Sudden Unexpected Nocturnal Death Syndrome  (ISO)
Syncope  (ISO)
systolic heart failure  (ISO)
Ventricular Fibrillation  (ISO)
Ventricular Fibrillation, Paroxysmal Familial, 1  (ISO)
Ventricular Tachycardia  (ISO)
Wolff-Parkinson-White syndrome  (ISO)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,4-dinitrotoluene  (EXP)
2,6-dinitrotoluene  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-aza-2'-deoxycytidine  (ISO)
acrylamide  (EXP)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
amphetamine  (EXP)
Aroclor 1254  (ISO)
arsenous acid  (ISO)
benzo[a]pyrene  (ISO)
bisphenol A  (EXP,ISO)
butanal  (ISO)
cadmium atom  (ISO)
calcitriol  (ISO)
carbon nanotube  (ISO)
cocaine  (ISO)
copper(II) sulfate  (ISO)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
dibenz[a,h]anthracene  (ISO)
dibenzo[a,l]pyrene  (ISO)
dibutyl phthalate  (EXP)
dicrotophos  (ISO)
dihydroartemisinin  (ISO)
dioxygen  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
enzyme inhibitor  (ISO)
ethanol  (EXP,ISO)
folic acid  (ISO)
glafenine  (EXP)
indometacin  (ISO)
lead diacetate  (EXP)
lead(0)  (ISO)
lead(2+)  (ISO)
leflunomide  (ISO)
mercury dibromide  (ISO)
methamphetamine  (ISO)
methylmercury chloride  (ISO)
monosodium L-glutamate  (ISO)
N-acetyl-L-cysteine  (EXP)
nitrofen  (EXP)
Nonylphenol  (EXP)
okadaic acid  (ISO)
paclitaxel  (ISO)
paracetamol  (ISO)
pentachlorophenol  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (ISO)
phenobarbital  (ISO)
phenylmercury acetate  (ISO)
pirinixic acid  (ISO)
potassium chromate  (ISO)
pregnenolone 16alpha-carbonitrile  (ISO)
progesterone  (ISO)
propiconazole  (ISO)
rotenone  (EXP)
SB 431542  (ISO)
silicon dioxide  (ISO)
sodium arsenite  (EXP,ISO)
sodium fluoride  (ISO)
sulforaphane  (ISO)
sunitinib  (ISO)
tetrachloromethane  (ISO)
thioacetamide  (EXP)
topotecan  (ISO)
triadimefon  (ISO)
trichostatin A  (ISO)
triptonide  (ISO)
urethane  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
zinc atom  (ISO)
zinc(0)  (ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Alcalai R, etal., J Am Coll Cardiol. 2003 Jul 16;42(2):319-27.
2. Angst BD, etal., Circ Res. 1997 Jan;80(1):88-94.
3. Atherton BT, etal., J Cell Sci. 1986 Dec;86:233-48.
4. Ben-Ze'ev A, etal., Proc Natl Acad Sci U S A. 1988 Apr;85(7):2161-5.
5. Borrmann CM, etal., Eur J Cell Biol. 2006 Jun;85(6):469-85. Epub 2006 Apr 4.
6. Cowin P, etal., J Cell Biol. 1985 Oct;101(4):1442-54.
7. Dulbecco R, etal., Proc Natl Acad Sci U S A. 1984 Sep;81(18):5763-6.
8. Franke WW, etal., Eur J Cell Biol. 2006 Feb;85(2):69-82. Epub 2006 Jan 9.
9. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
10. GOA data from the GO Consortium
11. Green KJ, etal., Exp Cell Res. 1991 Mar;193(1):134-43.
12. Higgins PJ, etal., Int J Cancer. 1987 Dec 15;40(6):792-801.
13. Jazwinska A, etal., BMC Cell Biol. 2003 Aug 4;4:10.
14. Kartenbeck J, etal., EMBO J. 1983;2(5):735-42.
15. Kasper M, etal., Virchows Arch B Cell Pathol Incl Mol Pathol. 1993;64(5):271-9.
16. Kostin S, etal., Circ Res. 1999 Jul 23;85(2):154-67.
17. Matsushita T, etal., Circ Res. 1999 Nov 26;85(11):1046-55.
18. Matsushita T, etal., Circulation. 1999 Nov 9;100(19 Suppl):II262-8.
19. Mochizuki R, etal., J Vet Med Sci. 2002 Feb;64(2):123-7.
20. Nishikawa S, etal., Eur J Cell Biol. 1988 Dec;47(2):222-32.
21. Norgett EE, etal., Hum Mol Genet. 2000 Nov 1;9(18):2761-6.
22. Okada Y, etal., Ophthalmologica. 2001 Jan-Feb;215(1):61-5.
23. OMIM Disease Annotation Pipeline
24. Owaribe K, etal., Cell Tissue Res. 1988 Nov;254(2):301-15.
25. Pipeline to import KEGG annotations from KEGG into RGD
26. Preston AM, etal., Acta Histochem. 2004;106(5):345-51.
27. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
28. RGD automated import pipeline for gene-chemical interactions
29. Savagner P, etal., J Cell Biol 1997 Jun 16;137(6):1403-19.
30. Schmelz M, etal., Cell Tissue Res. 1998 Oct;294(1):11-25.
31. Schmelz M, etal., Differentiation. 1994 Aug;57(2):97-117.
32. Sepp R, etal., Heart. 1996 Nov;76(5):412-7.
33. Shabana AH, etal., Tissue Cell. 1994 Feb;26(1):43-55.
34. Sundberg U, etal., J Cell Sci. 2004 Mar 1;117(Pt 7):1091-104. Epub 2004 Feb 17.
35. Toivola DM, etal., J Cell Sci. 1997 Jan;110 ( Pt 1):23-33.
36. Troyanovsky SM, etal., Cell. 1993 Feb 26;72(4):561-74.
37. Tsukita S and Tsukita S, J Cell Biol. 1989 Jan;108(1):31-41.
38. Uzzaman M, etal., Circ Res. 2000 Apr 28;86(8):871-8.
39. Yan HH and Cheng CY, Proc Natl Acad Sci U S A. 2005 Aug 16;102(33):11722-7. Epub 2005 Aug 5.
40. Yoo S, etal., Circulation. 2006 Sep 26;114(13):1360-71. Epub 2006 Sep 11.
Additional References at PubMed
PMID:9864371   PMID:10852826   PMID:10908733   PMID:11781569   PMID:12373648   PMID:12477932   PMID:12951053   PMID:14673151   PMID:16418220   PMID:16917092   PMID:17535849   PMID:18474624  
PMID:18496566   PMID:19001636   PMID:19056867   PMID:19199708   PMID:19723622   PMID:20458337   PMID:20859650   PMID:21630459   PMID:21700703   PMID:22152112   PMID:22658674   PMID:22781308  
PMID:22889254   PMID:23376485   PMID:23381804   PMID:23979707   PMID:25617501   PMID:26296893   PMID:26403541   PMID:27892606   PMID:29959233  


Genomics

Comparative Map Data
Dsp
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21726,623,602 - 26,671,692 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1726,623,588 - 26,671,800 (-)Ensembl
Rnor_6.01727,286,811 - 27,334,453 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1727,286,796 - 27,334,379 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01729,201,872 - 29,249,490 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41732,848,313 - 32,896,044 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11732,851,800 - 32,898,885 (-)NCBI
Celera1726,257,726 - 26,305,766 (-)NCBICelera
Cytogenetic Map17p12NCBI
DSP
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl67,541,617 - 7,586,714 (+)EnsemblGRCh38hg38GRCh38
GRCh3867,541,671 - 7,586,714 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh3767,541,904 - 7,586,947 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3667,486,869 - 7,531,945 (+)NCBINCBI36hg18NCBI36
Build 3467,486,868 - 7,531,945NCBI
Celera68,771,623 - 8,816,711 (+)NCBI
Cytogenetic Map6p24.3NCBI
HuRef67,419,476 - 7,464,417 (+)NCBIHuRef
CHM1_167,544,023 - 7,589,106 (+)NCBICHM1_1
Dsp
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391338,335,270 - 38,382,553 (+)NCBIGRCm39mm39
GRCm39 Ensembl1338,335,270 - 38,382,553 (+)Ensembl
GRCm381338,151,294 - 38,198,577 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1338,151,294 - 38,198,577 (+)EnsemblGRCm38mm10GRCm38
MGSCv371338,243,163 - 38,290,446 (+)NCBIGRCm37mm9NCBIm37
MGSCv361338,158,760 - 38,206,043 (+)NCBImm8
Celera1339,265,897 - 39,313,259 (+)NCBICelera
Cytogenetic Map13A3.3NCBI
Dsp
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554656,356,863 - 6,392,207 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554656,356,970 - 6,391,206 (-)NCBIChiLan1.0ChiLan1.0
DSP
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.167,664,399 - 7,709,391 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl67,664,211 - 7,709,391 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v067,381,046 - 7,426,408 (+)NCBIMhudiblu_PPA_v0panPan3
DSP
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1357,479,628 - 7,524,732 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl357,479,643 - 7,524,044 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha357,483,107 - 7,528,345 (+)NCBI
ROS_Cfam_1.0357,562,265 - 7,607,463 (+)NCBI
UMICH_Zoey_3.1357,415,316 - 7,460,024 (+)NCBI
UNSW_CanFamBas_1.0357,441,523 - 7,486,395 (+)NCBI
UU_Cfam_GSD_1.0358,773,585 - 8,819,012 (+)NCBI
LOC101968918
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494616,760,022 - 16,807,481 (-)NCBI
SpeTri2.0NW_0049365345,029,008 - 5,076,467 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
DSP
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl74,862,649 - 4,915,615 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.174,862,649 - 4,915,626 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.274,968,344 - 5,021,222 (+)NCBISscrofa10.2Sscrofa10.2susScr3
LOC103222210
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11764,611,243 - 64,656,297 (-)NCBI
ChlSab1.1 Ensembl1764,611,103 - 64,656,366 (-)Ensembl
Vero_WHO_p1.0NW_0236660447,495,774 - 7,541,054 (+)NCBI
Dsp
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475618,036,103 - 18,083,379 (-)NCBI

Position Markers
RH130644  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21726,623,710 - 26,623,906 (+)MAPPERmRatBN7.2
Rnor_6.01727,286,920 - 27,287,115NCBIRnor6.0
Rnor_5.01729,201,981 - 29,202,176UniSTSRnor5.0
RGSC_v3.41732,848,422 - 32,848,617UniSTSRGSC3.4
Celera1726,257,835 - 26,258,030UniSTS
RH 3.4 Map17341.4UniSTS
Cytogenetic Map17p12UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10401807Kidm52Kidney mass QTL 52kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)17131701463Rat
70184BpQTLcluster14Blood pressure QTL cluster 143.38arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)17131990913Rat
631207Niddm41Non-insulin dependent diabetes mellitus QTL 41blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)17137830672Rat
1354658Spl8Serum phospholipid level QTL 83.8blood VLDL phospholipid amount (VT:0010507)blood very low density lipoprotein phospholipid level (CMO:0001571)17160781592Rat
1354581Bp247Blood pressure QTL 2474.5arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)17169599340Rat
1354662Rf49Renal function QTL 492.9blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)17169599340Rat
1300123Bp194Blood pressure QTL 1942.82arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)17211514934551001Rat
631499Stl1Serum triglyceride level QTL 13.6blood triglyceride amount (VT:0002644)blood triglyceride level (CMO:0000118)17327139827389946Rat
1354613Kidm14Kidney mass QTL 146.2kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)17429913035837242Rat
1354596Bw32Body weight QTL 324.5body mass (VT:0001259)body weight (CMO:0000012)17429913060781592Rat
1354630Cm34Cardiac mass QTL 348.7heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)17429913069599340Rat
1354638Insul1Insulin level QTL 14.8blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)17429913069599340Rat
1354651Lmblg2Limb length QTL 26tibia length (VT:0004357)tibia length (CMO:0000450)17429913069599340Rat
2293648Bmd31Bone mineral density QTL 314.50.0001femur size trait (VT:1000369)femoral neck cortical cross-sectional area (CMO:0001702)17435448727028127Rat
2293664Bmd28Bone mineral density QTL 285.10.0001femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)17435448727028127Rat
2303627Vencon8Ventilatory control QTL 80.001respiration trait (VT:0001943)tidal volume (CMO:0000222)17452803849528038Rat
10054088Scort28Serum corticosterone level QTL 282.040.0102blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)17452803849528038Rat
2303561Bw91Body weight QTL 912body mass (VT:0001259)body weight (CMO:0000012)17886846253868462Rat
2300002Iddm36Insulin dependent diabetes mellitus QTL 361.98blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)17999128640540197Rat
1331765Hrtrt15Heart rate QTL 154.094heart pumping trait (VT:2000009)heart rate (CMO:0000002)171533061355836425Rat
1354640Scl32Serum cholesterol level QTL 325.4blood HDL cholesterol amount (VT:0000184)blood high density lipoprotein cholesterol level (CMO:0000052)171578159260781592Rat
1354659Scl68Serum cholesterol level QTL 683.9blood VLDL cholesterol amount (VT:0005144)blood very low density lipoprotein cholesterol level (CMO:0000648)171578159260781592Rat
7394837Memor18Memory QTL 18exploratory behavior trait (VT:0010471)measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)171864018263640182Rat
1354628Stl13Serum triglyceride level QTL 133.8blood triglyceride amount (VT:0002644)blood triglyceride level (CMO:0000118)172129303960781592Rat
70157Niddm32Non-insulin dependent diabetes mellitus QTL 324.34blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)172245492450909196Rat
61394Bp8Blood pressure QTL 82.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)172308056759555013Rat
7488966Bp370Blood pressure QTL 3700.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)172365318457246843Rat
12903978Cm118Cardiac mass QTL 1180.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)172365318468653184Rat
12903979Cm119Cardiac mass QTL 1190.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)172365318468653184Rat
12903980Cm120Cardiac mass QTL 1200.002heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)172365318468653184Rat
12903981Am17Aortic mass QTL 170.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)172365318468653184Rat
1559055Bp278Blood pressure QTL 2780.04arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)172365318468653184Rat
12903982Kidm70Kidney mass QTL 700.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)172365318470974005Rat
1354619Bp242Blood pressure QTL 2426.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)172459934069599340Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:16
Count of miRNA genes:16
Interacting mature miRNAs:16
Transcripts:ENSRNOT00000018649
Prediction methods:Miranda, Rnahybrid
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 43 41 25 8 25 35 23 11
Low 16 16 11 16 8 8 50 17 8
Below cutoff 3 24 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000018649   ⟹   ENSRNOP00000018649
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1726,623,588 - 26,671,800 (-)Ensembl
Rnor_6.0 Ensembl1727,286,796 - 27,334,379 (-)Ensembl
RefSeq Acc Id: XM_017600713   ⟹   XP_017456202
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21726,623,602 - 26,671,692 (-)NCBI
Rnor_6.01727,286,811 - 27,334,452 (-)NCBI
Sequence:
RefSeq Acc Id: XM_225259   ⟹   XP_225259
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21726,623,602 - 26,671,691 (-)NCBI
Rnor_6.01727,286,811 - 27,334,453 (-)NCBI
Rnor_5.01729,201,872 - 29,249,490 (-)NCBI
RGSC_v3.41732,848,313 - 32,896,044 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs XP_017456202 (Get FASTA)   NCBI Sequence Viewer  
  XP_225259 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH98071 (Get FASTA)   NCBI Sequence Viewer  
  EDL98260 (Get FASTA)   NCBI Sequence Viewer  
  EDL98261 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: XP_225259   ⟸   XM_225259
- Peptide Label: isoform X1
- UniProtKB: F1LMV6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017456202   ⟸   XM_017600713
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSRNOP00000018649   ⟸   ENSRNOT00000018649
Protein Domains
SH3

Transcriptome

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

Promoters
RGD ID:13700401
Promoter ID:EPDNEW_R10917
Type:initiation region
Name:Dsp_1
Description:desmoplakin
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_6.01727,334,318 - 27,334,378EPDNEW

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)
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)
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
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)
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
PVG/Seac (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
SBH/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)