Map2 (microtubule-associated protein 2) - Rat Genome Database

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Gene: Map2 (microtubule-associated protein 2) Rattus norvegicus
Analyze
Symbol: Map2
Name: microtubule-associated protein 2
RGD ID: 3044
Description: Enables actin binding activity; microtubule binding activity; and protein kinase binding activity. Involved in several processes, including negative regulation of axon extension; negative regulation of microtubule polymerization or depolymerization; and positive regulation of vesicle transport along microtubule. Located in several cellular components, including axon; dendrite; and endoplasmic reticulum. Part of protein-containing complex. Used to study Alzheimer's disease and cerebral infarction. Biomarker of arteriovenous malformation; asphyxia neonatorum; brain ischemia; sciatic neuropathy; and temporal lobe epilepsy. Orthologous to human MAP2 (microtubule associated protein 2); INTERACTS WITH (S)-3,5-dihydroxyphenylglycine; 1-naphthyl isothiocyanate; 2,3,7,8-Tetrachlorodibenzofuran.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: MAP-2; MAP2R; microtubule-associated protein 2C; Mtap2
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
mRatBN7.2967,723,422 - 67,981,886 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl967,723,371 - 67,979,809 (+)Ensembl
Rnor_6.0973,204,753 - 73,462,965 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl973,319,710 - 73,462,972 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0973,837,509 - 74,095,431 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4965,174,376 - 65,256,003 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1965,321,360 - 65,402,977 (+)NCBI
Celera965,377,941 - 65,459,391 (+)NCBICelera
RH 3.4 Map9593.2RGD
Cytogenetic Map9q32NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(20S)-ginsenoside Rg3  (ISO)
(S)-3,5-dihydroxyphenylglycine  (EXP)
1,1-dichloroethene  (ISO)
1,2-dimethylhydrazine  (ISO)
1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine  (ISO)
1-naphthyl isothiocyanate  (EXP)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (ISO)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2,5-hexanedione  (EXP)
2-hydroxypropanoic acid  (ISO)
2-methylcholine  (ISO)
3',5'-cyclic AMP  (ISO)
3,3',5,5'-tetrabromobisphenol A  (EXP)
3,4-methylenedioxymethamphetamine  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3-methyladenine  (EXP)
5-fluorouracil  (ISO)
9-cis-retinoic acid  (ISO)
acrylamide  (EXP)
aflatoxin B1  (EXP,ISO)
agomelatine  (EXP)
aldicarb  (ISO)
all-trans-retinoic acid  (EXP,ISO)
aluminium sulfate (anhydrous)  (EXP)
ammonia  (EXP)
ammonium chloride  (EXP)
antimycin A  (ISO)
antirheumatic drug  (ISO)
aristolochic acid  (ISO)
Aroclor 1254  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
azoxystrobin  (ISO)
benzo[a]pyrene  (EXP,ISO)
Benzo[k]fluoranthene  (ISO)
bexarotene  (EXP)
bisphenol A  (EXP,ISO)
bucladesine  (ISO)
butanal  (ISO)
cadmium atom  (ISO)
calcidiol  (EXP)
Calpeptin  (EXP)
capsaicin  (ISO)
carbaryl  (ISO)
chlordecone  (ISO)
chlorohydrocarbon  (EXP)
chloroquine  (EXP)
chlorpromazine  (EXP)
chlorpyrifos  (ISO)
choline  (ISO)
cisplatin  (EXP,ISO)
clobetasol  (ISO)
cobalt dichloride  (ISO)
cocaine  (EXP)
copper atom  (ISO)
copper(0)  (ISO)
Cuprizon  (EXP)
Cyclopamine  (EXP)
cyclosporin A  (ISO)
cypermethrin  (EXP)
cyproconazole  (ISO)
cytarabine  (ISO)
DAPT  (ISO)
DDT  (EXP)
Deguelin  (ISO)
dexamethasone  (EXP)
diarsenic trioxide  (ISO)
dibutyl phthalate  (ISO)
dichlorvos  (EXP)
dieldrin  (ISO)
dihydrolipoic acid  (ISO)
diquat  (ISO)
diuron  (EXP)
dorsomorphin  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
enzalutamide  (ISO)
ethanol  (EXP,ISO)
folic acid  (ISO)
gamma-hexachlorocyclohexane  (ISO)
ginsenoside Rb1  (ISO)
ginsenoside Rd  (ISO)
ginsenoside Re  (ISO)
ginsenoside Rg1  (ISO)
glutathione  (ISO)
haloperidol  (EXP)
heptachlor  (ISO)
hexachlorophene  (ISO)
hydrogen peroxide  (ISO)
isoniazide  (ISO)
ivermectin  (ISO)
kainic acid  (ISO)
L-ascorbic acid  (EXP,ISO)
L-methionine  (ISO)
lead diacetate  (ISO)
leflunomide  (ISO)
LY294002  (ISO)
maneb  (ISO)
manganese(II) chloride  (EXP)
melatonin  (ISO)
methamphetamine  (EXP)
methotrexate  (ISO)
methylmercury chloride  (ISO)
miconazole  (ISO)
morphine  (EXP)
N,N-diethyl-m-toluamide  (EXP)
N-acetyl-L-cysteine  (ISO)
N-nitrosodiethylamine  (EXP)
nickel dichloride  (ISO)
nicotinic acid  (EXP)
nimodipine  (EXP)
nitrofen  (EXP)
olanzapine  (EXP)
oxaliplatin  (ISO)
panobinostat  (ISO)
paracetamol  (ISO)
paraquat  (ISO)
PD123319  (EXP)
permethrin  (EXP)
phenethyl isothiocyanate  (EXP)
phenylmercury acetate  (ISO)
physostigmine  (ISO)
picoxystrobin  (ISO)
potassium chromate  (ISO)
potassium dichromate  (ISO)
progesterone  (EXP,ISO)
pyrimidifen  (ISO)
pyrroloquinoline quinone  (ISO)
rac-lactic acid  (ISO)
resveratrol  (EXP)
risperidone  (EXP)
rotenone  (EXP,ISO)
Salidroside  (ISO)
sarin  (EXP)
SB 431542  (ISO)
scopolamine  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sirolimus  (EXP)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
streptozocin  (ISO)
sulforaphane  (ISO)
tetrachloromethane  (ISO)
thifluzamide  (ISO)
trichostatin A  (ISO)
triclosan  (ISO)
triptonide  (ISO)
Tryptanthrine  (ISO)
valproic acid  (EXP,ISO)
valsartan  (EXP)
venlafaxine hydrochloride  (EXP)
WIN 55212-2  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Molecular Function

References

References - curated
1. Alexa A, etal., Biochemistry 2002 Oct 15;41(41):12427-35.
2. Bolognin S, etal., Acta Neuropathol. 2012 Jan;123(1):133-51. Epub 2011 Nov 15.
3. Burd I, etal., Reprod Sci. 2011 Sep;18(9):900-7. Epub 2011 Mar 18.
4. Caceres A and Dotti C, Neuroscience. 1985 Sep;16(1):133-50.
5. Camacho-Arroyo I, etal., Life Sci. 2011 Jul 18;89(3-4):123-8. doi: 10.1016/j.lfs.2011.05.008. Epub 2011 Jun 12.
6. Cao MH, etal., Chin Med J (Engl). 2011 Jul;124(14):2184-90.
7. Chen LJ, etal., J Neurotrauma. 2010 Sep;27(9):1657-69.
8. Chubykin AA, etal., Neuron. 2007 Jun 21;54(6):919-31.
9. Doll T, etal., Nucleic Acids Res 1990 Jan 25;18(2):361.
10. Duchossoy Y, etal., Brain Res. 2011 Jul 27;1403:57-66. Epub 2011 Jun 12.
11. Farah CA, etal., J Biol Chem. 2005 Mar 11;280(10):9439-49. Epub 2004 Dec 28.
12. Ferhat L, etal., C R Acad Sci III 1994 Apr;317(4):304-9.
13. Ferreira A, etal., Brain Res Dev Brain Res. 1989 Oct 1;49(2):215-28.
14. Fujimori K, etal., J Comp Neurol 2002 Aug 5;449(4):330-42.
15. Furutani R and Kibayashi K, J Neurotrauma. 2012 Apr 10;29(6):1266-76. Epub 2011 Aug 5.
16. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
17. GOA data from the GO Consortium
18. Gumy LF, etal., Neuron. 2017 Apr 19;94(2):347-362.e7. doi: 10.1016/j.neuron.2017.03.046.
19. Hai J, etal., Acta Neurol Belg. 2010 Jun;110(2):180-5.
20. Harada A, etal., J Cell Biol 2002 Aug 5;158(3):541-9.
21. Kapitein LC, etal., J Neurosci. 2011 Jun 1;31(22):8194-209.
22. Kindler S, etal., Brain Res Mol Brain Res 1996 Feb;36(1):63-9.
23. Kindler S, etal., Nucleic Acids Res 1990 May 11;18(9):2822.
24. Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
25. Malmendal A, etal., Biochem Biophys Res Commun 2003 Jan 31;301(1):136-42.
26. Marechal D, etal., Arch Int Physiol Biochim 1988 Dec;96(5):231-6.
27. Matus A, etal., Neuroscience. 1986 Feb;17(2):371-89.
28. MGD data from the GO Consortium
29. Mukaetova-Ladinska EB, etal., ScientificWorldJournal. 2009 Dec 16;9:1463-75.
30. NCBI rat LocusLink and RefSeq merged data July 26, 2002
31. Obar RA, etal., Neuron. 1989 Nov;3(5):639-45.
32. Ozer RS and Halpain S, Mol Biol Cell. 2000 Oct;11(10):3573-87.
33. Park D, etal., J Neurosci Res. 2012 Feb;90(2):461-7. doi: 10.1002/jnr.22769. Epub 2011 Sep 21.
34. Pellet JB, etal., Eur J Neurosci. 2000 Feb;12(2):621-32.
35. Reyna-Neyra A, etal., Brain Res Bull 2002 Sep 30;58(6):607-12.
36. RGD automated data pipeline
37. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
38. RGD automated import pipeline for gene-chemical interactions
39. Rothe F, etal., Nitric Oxide 2002 Feb;6(1):9-17.
40. Rrapo E, etal., Am J Transl Res. 2009 Jan 1;1(1):72-9.
41. Saraceno GE, etal., Synapse. 2012 Jan;66(1):9-19. doi: 10.1002/syn.20978. Epub 2011 Oct 11.
42. Somenarain L and Jones LB, J Psychiatr Res. 2010 Aug;44(11):694-9. Epub 2010 Jan 22.
43. Suh JG, etal., Neural Plast 2002;9(3):135-46.
44. Tortosa E, etal., Neuron. 2017 May 17;94(4):809-825.e7. doi: 10.1016/j.neuron.2017.04.042.
45. Xiong M, etal., Neurochem Int. 2011 May;58(6):625-33. Epub 2011 Feb 12.
46. Yan XX, etal., Exp Neurol. 2012 May;235(1):228-37. Epub 2012 Jan 11.
47. Yang J, etal., EMBO J. 2011 Jan 5;30(1):165-80. doi: 10.1038/emboj.2010.286. Epub 2010 Nov 30.
48. Yoon KJ, etal., Brain Res. 2012 May 3;1452:61-72. Epub 2012 Mar 5.
Additional References at PubMed
PMID:2174050   PMID:2770869   PMID:3147150   PMID:8282767   PMID:8282771   PMID:8535073   PMID:8631898   PMID:8990203   PMID:10542369   PMID:11145988   PMID:11581286   PMID:11834298  
PMID:11891784   PMID:12074840   PMID:12477932   PMID:12834896   PMID:14989172   PMID:15048929   PMID:15246990   PMID:15255972   PMID:15307151   PMID:15656993   PMID:15834957   PMID:15964096  
PMID:15964665   PMID:15996550   PMID:16000625   PMID:16002213   PMID:16537405   PMID:16597486   PMID:16641100   PMID:16708014   PMID:16892058   PMID:16901895   PMID:16980967   PMID:17114649  
PMID:17141532   PMID:17229541   PMID:17360631   PMID:17573185   PMID:17984326   PMID:18165320   PMID:18268009   PMID:18290605   PMID:18341635   PMID:18359573   PMID:18455509   PMID:18467524  
PMID:18497889   PMID:18584320   PMID:18978811   PMID:19009287   PMID:19141977   PMID:19208628   PMID:19292454   PMID:19447092   PMID:19646951   PMID:19666135   PMID:20513368   PMID:20600662  
PMID:20846339   PMID:20967947   PMID:21869818   PMID:21948316   PMID:22022532   PMID:22456537   PMID:22490839   PMID:22763971   PMID:22871113   PMID:23121659   PMID:23861879   PMID:23877929  
PMID:23904609   PMID:24035762   PMID:24554721   PMID:25592752   PMID:25918374   PMID:26071842   PMID:26682524   PMID:27265094   PMID:27335427   PMID:28258221   PMID:29476059   PMID:31168983  
PMID:31471737   PMID:31996007   PMID:32237183  


Genomics

Comparative Map Data
Map2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2967,723,422 - 67,981,886 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl967,723,371 - 67,979,809 (+)Ensembl
Rnor_6.0973,204,753 - 73,462,965 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl973,319,710 - 73,462,972 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0973,837,509 - 74,095,431 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4965,174,376 - 65,256,003 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1965,321,360 - 65,402,977 (+)NCBI
Celera965,377,941 - 65,459,391 (+)NCBICelera
RH 3.4 Map9593.2RGD
Cytogenetic Map9q32NCBI
MAP2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2209,424,047 - 209,734,118 (+)EnsemblGRCh38hg38GRCh38
GRCh382209,424,047 - 209,734,118 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh372210,288,771 - 210,598,836 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362209,997,016 - 210,307,079 (+)NCBINCBI36hg18NCBI36
Build 342210,269,908 - 210,421,484NCBI
Celera2204,056,618 - 204,366,628 (+)NCBI
Cytogenetic Map2q34NCBI
HuRef2202,133,889 - 202,443,633 (+)NCBIHuRef
CHM1_12210,294,619 - 210,604,654 (+)NCBICHM1_1
Map2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39166,214,337 - 66,481,742 (+)NCBIGRCm39mm39
GRCm39 Ensembl166,214,432 - 66,481,742 (+)Ensembl
GRCm38166,175,202 - 66,442,583 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl166,175,273 - 66,442,583 (+)EnsemblGRCm38mm10GRCm38
MGSCv37166,221,903 - 66,489,157 (+)NCBIGRCm37mm9NCBIm37
MGSCv36166,108,521 - 66,375,797 (+)NCBImm8
Celera166,699,319 - 66,964,492 (+)NCBICelera
Cytogenetic Map1C3NCBI
cM Map133.49NCBI
Map2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554575,678,436 - 5,875,024 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554575,678,826 - 5,816,114 (-)NCBIChiLan1.0ChiLan1.0
MAP2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12B215,085,476 - 215,395,439 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2B215,314,857 - 215,391,728 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02B96,681,268 - 96,991,650 (+)NCBIMhudiblu_PPA_v0panPan3
MAP2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13717,316,899 - 17,611,360 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3717,466,678 - 17,607,803 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3718,197,871 - 18,492,089 (+)NCBI
ROS_Cfam_1.03717,252,304 - 17,547,172 (+)NCBI
UMICH_Zoey_3.13717,357,768 - 17,502,660 (+)NCBI
UNSW_CanFamBas_1.03717,171,196 - 17,465,399 (+)NCBI
UU_Cfam_GSD_1.03717,188,565 - 17,479,742 (+)NCBI
Map2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405303165,843,181 - 166,122,293 (+)NCBI
SpeTri2.0NW_004936845475,406 - 752,600 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
MAP2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl15112,156,578 - 112,460,171 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.115112,156,578 - 112,462,932 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.215124,033,358 - 124,184,546 (+)NCBISscrofa10.2Sscrofa10.2susScr3
MAP2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11095,319,649 - 95,431,106 (+)NCBI
ChlSab1.1 Ensembl1095,349,157 - 95,431,320 (+)Ensembl
Vero_WHO_p1.0NW_023666040103,915,685 - 104,226,077 (-)NCBI
Map2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247656,476,544 - 6,758,959 (-)NCBI

Position Markers
D10Chm45  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2967,979,993 - 67,980,297 (+)MAPPERmRatBN7.2
Rnor_6.0973,461,080 - 73,461,383NCBIRnor6.0
Rnor_5.0973,839,091 - 73,839,394UniSTSRnor5.0
RGSC_v3.4965,257,702 - 65,258,005UniSTSRGSC3.4
Celera965,461,090 - 65,461,393UniSTS
Cytogenetic Map9q32UniSTS
D10Chm64  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2967,980,006 - 67,980,297 (+)MAPPERmRatBN7.2
Rnor_6.0973,461,093 - 73,461,383NCBIRnor6.0
Rnor_5.0973,839,091 - 73,839,381UniSTSRnor5.0
RGSC_v3.4965,257,715 - 65,258,005UniSTSRGSC3.4
Celera965,461,103 - 65,461,393UniSTS
Cytogenetic Map9q32UniSTS
D9Wox30  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2967,981,231 - 67,981,318 (+)MAPPERmRatBN7.2
Rnor_6.0973,462,318 - 73,462,404NCBIRnor6.0
Rnor_5.0973,838,070 - 73,838,156UniSTSRnor5.0
RGSC_v3.4965,258,940 - 65,259,026UniSTSRGSC3.4
Celera965,462,328 - 65,462,414UniSTS
Cytogenetic Map9q32UniSTS
RH94590  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2967,978,164 - 67,978,264 (+)MAPPERmRatBN7.2
Rnor_6.0973,459,251 - 73,459,350NCBIRnor6.0
Rnor_5.0973,841,124 - 73,841,223UniSTSRnor5.0
RGSC_v3.4965,255,873 - 65,255,972UniSTSRGSC3.4
Celera965,459,261 - 65,459,360UniSTS
RH 3.4 Map9593.2UniSTS
Cytogenetic Map9q32UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10054125Srcrt7Stress Responsive Cort QTL 73.330.0011blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)9187073594Rat
70186Niddm26Non-insulin dependent diabetes mellitus QTL 263.87blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)92207116986369743Rat
7207814Bmd91Bone mineral density QTL 913.5femur size trait (VT:1000369)femoral neck cross-sectional area (CMO:0001697)92375414483851531Rat
70218Cm28Cardiac mass QTL 288.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)92526804479271759Rat
724544Uae9Urinary albumin excretion QTL 94.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)925268044114175309Rat
731164Uae25Urinary albumin excretion QTL 253.50.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)925661188100929786Rat
1641894Alcrsp12Alcohol response QTL 12response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)92746863972468639Rat
7411656Foco26Food consumption QTL 269.80.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)93253550577535505Rat
7411571Bw138Body weight QTL 13814.30.001body mass (VT:0001259)body weight gain (CMO:0000420)93253550577535505Rat
1598834Memor11Memory QTL 112.5exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)93696235977814038Rat
8662828Vetf6Vascular elastic tissue fragility QTL 63.9artery integrity trait (VT:0010639)patent ductus arteriosus score (CMO:0002566)93696235992058970Rat
2290450Scl57Serum cholesterol level QTL 574.15blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)93696235995410867Rat
6903941Pur31Proteinuria QTL 310.036total urine protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)94019418885194188Rat
11353949Bp393Blood pressure QTL 393arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)94019418885194188Rat
61352Bp34Blood pressure QTL 345arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)94249534379271511Rat
10058949Gmadr5Adrenal mass QTL 520.014adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)94279151387976209Rat
11353951Bp394Blood pressure QTL 394arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)94464992189649921Rat
12879506Pur33Proteinuria QTL 33total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)94464992189649921Rat
11353957Bmd92Bone mineral density QTL 920.01tibia mineral mass (VT:1000283)volumetric bone mineral density (CMO:0001553)94611419991114199Rat
631656Bp108Blood pressure QTL 1085.970.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)94859825193598251Rat
1598849Memor17Memory QTL 172.2exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)94996854671098346Rat
2303170Bp332Blood pressure QTL 3323.730.027arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)95584784177026453Rat
2303180Bp333Blood pressure QTL 3330.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)95662771378595166Rat
2303180Bp333Blood pressure QTL 3330.001arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)95662771378595166Rat
2303180Bp333Blood pressure QTL 3330.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)95662771378595166Rat
1578760Cm53Cardiac mass QTL 533.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)956771635101771635Rat
724515Uae16Urinary albumin excretion QTL 168urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)958163035100929646Rat
1300134Bp185Blood pressure QTL 1853.73arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)961381434104821652Rat
1581580Uae34Urinary albumin excretion QTL 34urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)96207227596470995Rat
1578757Pur6Proteinuria QTL 63.30.005total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)96207227596470995Rat
61385Edpm9Estrogen-dependent pituitary mass QTL 93.430.05pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)963869687108869687Rat
731171Glom6Glomerulus QTL 62.80.0003kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)964573531109573531Rat

miRNA Target Status

Confirmed Target Of
miRNA GeneMature miRNAMethod NameResult TypeData TypeSupport TypePMID
Mir26arno-miR-26a-5pMirtarbaseexternal_infoWestern blotFunctional MTI17592044

Predicted Target Of
Summary Value
Count of predictions:181
Count of miRNA genes:109
Interacting mature miRNAs:117
Transcripts:ENSRNOT00000037974, ENSRNOT00000043627, ENSRNOT00000045766
Prediction methods:Microtar, 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 8 74 6 16
Low 25 32 24 19 24 8 8 29 25 11 8
Below cutoff 3 17 16 16 16 2

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_013066 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006245100 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008767197 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008767198 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008767199 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008767200 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008767201 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008767202 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008767205 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008767206 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008767207 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008767208 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017596291 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017596292 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017596293 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017596294 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017596295 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017596296 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017596297 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017596298 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017596299 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083074 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083075 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083076 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083077 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083078 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083079 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083080 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083081 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083082 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083083 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083084 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083085 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083086 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083087 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083088 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083089 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AB075604 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC081835 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH474044 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ213599 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ213746 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000215 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U30937 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U30938 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X17682 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X51842 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X54100 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X71487 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X74211 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000037974   ⟹   ENSRNOP00000031915
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl967,723,371 - 67,979,809 (+)Ensembl
Rnor_6.0 Ensembl973,378,111 - 73,459,278 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000043627   ⟹   ENSRNOP00000042029
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl967,897,011 - 67,978,285 (+)Ensembl
Rnor_6.0 Ensembl973,378,057 - 73,459,386 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000045766   ⟹   ENSRNOP00000050877
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl967,896,967 - 67,978,285 (+)Ensembl
Rnor_6.0 Ensembl973,378,063 - 73,459,295 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000092319
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl973,404,871 - 73,418,612 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000092376
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl973,404,996 - 73,446,962 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000092445   ⟹   ENSRNOP00000075849
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl967,896,967 - 67,978,285 (+)Ensembl
Rnor_6.0 Ensembl973,378,094 - 73,462,972 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000092485   ⟹   ENSRNOP00000075883
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl967,723,371 - 67,979,809 (+)Ensembl
Rnor_6.0 Ensembl973,319,710 - 73,459,579 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000092540   ⟹   ENSRNOP00000075766
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl967,923,934 - 67,978,285 (+)Ensembl
Rnor_6.0 Ensembl973,433,252 - 73,458,471 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000092547   ⟹   ENSRNOP00000075888
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl973,418,607 - 73,429,555 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000092602
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl973,405,033 - 73,446,795 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000092717   ⟹   ENSRNOP00000075908
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl973,334,618 - 73,418,591 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000110600   ⟹   ENSRNOP00000089734
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl967,896,967 - 67,978,285 (+)Ensembl
RefSeq Acc Id: NM_013066   ⟹   NP_037198
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2967,896,967 - 67,978,295 (+)NCBI
Rnor_6.0973,378,057 - 73,459,381 (+)NCBI
Rnor_5.0973,837,509 - 74,095,431 (-)NCBI
RGSC_v3.4965,174,376 - 65,256,003 (+)RGD
Celera965,377,941 - 65,459,391 (+)RGD
Sequence:
RefSeq Acc Id: XM_006245100   ⟹   XP_006245162
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2967,923,463 - 67,981,886 (+)NCBI
Rnor_6.0973,403,748 - 73,462,965 (+)NCBI
Rnor_5.0973,837,509 - 74,095,431 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008767198   ⟹   XP_008765420
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2967,853,351 - 67,981,886 (+)NCBI
Rnor_6.0973,334,494 - 73,462,965 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008767199   ⟹   XP_008765421
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2967,853,351 - 67,981,886 (+)NCBI
Rnor_6.0973,334,495 - 73,462,965 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008767200   ⟹   XP_008765422
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2967,853,187 - 67,981,886 (+)NCBI
Rnor_6.0973,334,494 - 73,462,965 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008767201   ⟹   XP_008765423
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2967,853,351 - 67,981,886 (+)NCBI
Rnor_6.0973,334,494 - 73,462,965 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008767202   ⟹   XP_008765424
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2967,853,351 - 67,981,886 (+)NCBI
Rnor_6.0973,334,495 - 73,462,965 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008767205   ⟹   XP_008765427
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2967,853,351 - 67,981,886 (+)NCBI
Rnor_6.0973,334,496 - 73,462,965 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008767206   ⟹   XP_008765428
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2967,853,351 - 67,981,886 (+)NCBI
Rnor_6.0973,334,498 - 73,462,965 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008767207   ⟹   XP_008765429
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2967,853,351 - 67,981,886 (+)NCBI
Rnor_6.0973,334,501 - 73,462,965 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008767208   ⟹   XP_008765430
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2967,853,351 - 67,981,886 (+)NCBI
Rnor_6.0973,334,502 - 73,462,965 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017596291   ⟹   XP_017451780
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2967,853,351 - 67,981,886 (+)NCBI
Rnor_6.0973,334,495 - 73,462,965 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017596293   ⟹   XP_017451782
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2967,723,422 - 67,981,886 (+)NCBI
Rnor_6.0973,204,753 - 73,462,965 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017596297   ⟹   XP_017451786
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2967,853,351 - 67,981,886 (+)NCBI
Rnor_6.0973,334,496 - 73,462,965 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017596298   ⟹   XP_017451787
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2967,853,351 - 67,981,886 (+)NCBI
Rnor_6.0973,334,497 - 73,462,965 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017596299   ⟹   XP_017451788
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2967,853,351 - 67,981,886 (+)NCBI
Rnor_6.0973,334,497 - 73,462,965 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039083074   ⟹   XP_038939002
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2967,853,679 - 67,981,886 (+)NCBI
RefSeq Acc Id: XM_039083075   ⟹   XP_038939003
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2967,723,434 - 67,981,886 (+)NCBI
RefSeq Acc Id: XM_039083076   ⟹   XP_038939004
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2967,723,540 - 67,981,886 (+)NCBI
RefSeq Acc Id: XM_039083077   ⟹   XP_038939005
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2967,853,351 - 67,981,886 (+)NCBI
RefSeq Acc Id: XM_039083078   ⟹   XP_038939006
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2967,853,351 - 67,981,886 (+)NCBI
RefSeq Acc Id: XM_039083079   ⟹   XP_038939007
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2967,853,351 - 67,981,886 (+)NCBI
RefSeq Acc Id: XM_039083080   ⟹   XP_038939008
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2967,853,351 - 67,981,886 (+)NCBI
RefSeq Acc Id: XM_039083081   ⟹   XP_038939009
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2967,853,351 - 67,981,886 (+)NCBI
RefSeq Acc Id: XM_039083082   ⟹   XP_038939010
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2967,853,351 - 67,981,886 (+)NCBI
RefSeq Acc Id: XM_039083083   ⟹   XP_038939011
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2967,853,351 - 67,981,886 (+)NCBI
RefSeq Acc Id: XM_039083084   ⟹   XP_038939012
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2967,853,351 - 67,981,886 (+)NCBI
RefSeq Acc Id: XM_039083085   ⟹   XP_038939013
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2967,853,351 - 67,981,886 (+)NCBI
RefSeq Acc Id: XM_039083086   ⟹   XP_038939014
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2967,853,351 - 67,981,886 (+)NCBI
RefSeq Acc Id: XM_039083087   ⟹   XP_038939015
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2967,923,788 - 67,981,886 (+)NCBI
RefSeq Acc Id: XM_039083088   ⟹   XP_038939016
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2967,923,788 - 67,981,886 (+)NCBI
RefSeq Acc Id: XM_039083089   ⟹   XP_038939017
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2967,853,351 - 67,981,886 (+)NCBI
Protein Sequences
Protein RefSeqs NP_037198 (Get FASTA)   NCBI Sequence Viewer  
  XP_006245162 (Get FASTA)   NCBI Sequence Viewer  
  XP_008765420 (Get FASTA)   NCBI Sequence Viewer  
  XP_008765421 (Get FASTA)   NCBI Sequence Viewer  
  XP_008765422 (Get FASTA)   NCBI Sequence Viewer  
  XP_008765423 (Get FASTA)   NCBI Sequence Viewer  
  XP_008765424 (Get FASTA)   NCBI Sequence Viewer  
  XP_008765427 (Get FASTA)   NCBI Sequence Viewer  
  XP_008765428 (Get FASTA)   NCBI Sequence Viewer  
  XP_008765429 (Get FASTA)   NCBI Sequence Viewer  
  XP_008765430 (Get FASTA)   NCBI Sequence Viewer  
  XP_017451780 (Get FASTA)   NCBI Sequence Viewer  
  XP_017451782 (Get FASTA)   NCBI Sequence Viewer  
  XP_017451786 (Get FASTA)   NCBI Sequence Viewer  
  XP_017451787 (Get FASTA)   NCBI Sequence Viewer  
  XP_017451788 (Get FASTA)   NCBI Sequence Viewer  
  XP_038939002 (Get FASTA)   NCBI Sequence Viewer  
  XP_038939003 (Get FASTA)   NCBI Sequence Viewer  
  XP_038939004 (Get FASTA)   NCBI Sequence Viewer  
  XP_038939005 (Get FASTA)   NCBI Sequence Viewer  
  XP_038939006 (Get FASTA)   NCBI Sequence Viewer  
  XP_038939007 (Get FASTA)   NCBI Sequence Viewer  
  XP_038939008 (Get FASTA)   NCBI Sequence Viewer  
  XP_038939009 (Get FASTA)   NCBI Sequence Viewer  
  XP_038939010 (Get FASTA)   NCBI Sequence Viewer  
  XP_038939011 (Get FASTA)   NCBI Sequence Viewer  
  XP_038939012 (Get FASTA)   NCBI Sequence Viewer  
  XP_038939013 (Get FASTA)   NCBI Sequence Viewer  
  XP_038939014 (Get FASTA)   NCBI Sequence Viewer  
  XP_038939015 (Get FASTA)   NCBI Sequence Viewer  
  XP_038939016 (Get FASTA)   NCBI Sequence Viewer  
  XP_038939017 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH81835 (Get FASTA)   NCBI Sequence Viewer  
  CAA35667 (Get FASTA)   NCBI Sequence Viewer  
  CAA36135 (Get FASTA)   NCBI Sequence Viewer  
  CAA38034 (Get FASTA)   NCBI Sequence Viewer  
  CAA50588 (Get FASTA)   NCBI Sequence Viewer  
  CAA52283 (Get FASTA)   NCBI Sequence Viewer  
  EDL75300 (Get FASTA)   NCBI Sequence Viewer  
  EDL75301 (Get FASTA)   NCBI Sequence Viewer  
  EDL75302 (Get FASTA)   NCBI Sequence Viewer  
  EDL75303 (Get FASTA)   NCBI Sequence Viewer  
  EDL75304 (Get FASTA)   NCBI Sequence Viewer  
  P15146 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_037198   ⟸   NM_013066
- UniProtKB: Q64715 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006245162   ⟸   XM_006245100
- Peptide Label: isoform X21
- Sequence:
RefSeq Acc Id: XP_008765429   ⟸   XM_008767207
- Peptide Label: isoform X22
- UniProtKB: Q78DZ1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008765430   ⟸   XM_008767208
- Peptide Label: isoform X23
- UniProtKB: P15146 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_008765420   ⟸   XM_008767198
- Peptide Label: isoform X1
- UniProtKB: F1LNK0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008765428   ⟸   XM_008767206
- Peptide Label: isoform X15
- UniProtKB: A0A0U1RRX4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008765422   ⟸   XM_008767200
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_008765424   ⟸   XM_008767202
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: XP_008765421   ⟸   XM_008767199
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_008765427   ⟸   XM_008767205
- Peptide Label: isoform X13
- Sequence:
RefSeq Acc Id: XP_008765423   ⟸   XM_008767201
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017451782   ⟸   XM_017596293
- Peptide Label: isoform X1
- UniProtKB: F1LNK0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017451780   ⟸   XM_017596291
- Peptide Label: isoform X1
- UniProtKB: F1LNK0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017451786   ⟸   XM_017596297
- Peptide Label: isoform X7
- Sequence:
RefSeq Acc Id: XP_017451787   ⟸   XM_017596298
- Peptide Label: isoform X11
- Sequence:
RefSeq Acc Id: XP_017451788   ⟸   XM_017596299
- Peptide Label: isoform X18
- UniProtKB: F1MAQ5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000050877   ⟸   ENSRNOT00000045766
RefSeq Acc Id: ENSRNOP00000075908   ⟸   ENSRNOT00000092717
RefSeq Acc Id: ENSRNOP00000075888   ⟸   ENSRNOT00000092547
RefSeq Acc Id: ENSRNOP00000075766   ⟸   ENSRNOT00000092540
RefSeq Acc Id: ENSRNOP00000075883   ⟸   ENSRNOT00000092485
RefSeq Acc Id: ENSRNOP00000075849   ⟸   ENSRNOT00000092445
RefSeq Acc Id: ENSRNOP00000042029   ⟸   ENSRNOT00000043627
RefSeq Acc Id: ENSRNOP00000031915   ⟸   ENSRNOT00000037974
RefSeq Acc Id: XP_038939003   ⟸   XM_039083075
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038939004   ⟸   XM_039083076
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038939006   ⟸   XM_039083078
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038939007   ⟸   XM_039083079
- Peptide Label: isoform X9
RefSeq Acc Id: XP_038939008   ⟸   XM_039083080
- Peptide Label: isoform X10
RefSeq Acc Id: XP_038939011   ⟸   XM_039083083
- Peptide Label: isoform X16
RefSeq Acc Id: XP_038939014   ⟸   XM_039083086
- Peptide Label: isoform X20
RefSeq Acc Id: XP_038939017   ⟸   XM_039083089
- Peptide Label: isoform X24
RefSeq Acc Id: XP_038939005   ⟸   XM_039083077
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038939009   ⟸   XM_039083081
- Peptide Label: isoform X12
RefSeq Acc Id: XP_038939012   ⟸   XM_039083084
- Peptide Label: isoform X17
RefSeq Acc Id: XP_038939010   ⟸   XM_039083082
- Peptide Label: isoform X14
RefSeq Acc Id: XP_038939013   ⟸   XM_039083085
- Peptide Label: isoform X19
RefSeq Acc Id: XP_038939002   ⟸   XM_039083074
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038939015   ⟸   XM_039083087
- Peptide Label: isoform X21
RefSeq Acc Id: XP_038939016   ⟸   XM_039083088
- Peptide Label: isoform X21
RefSeq Acc Id: ENSRNOP00000089734   ⟸   ENSRNOT00000110600
Protein Domains
MAP2_projctn   RII_binding_1

Transcriptome

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

Promoters
RGD ID:13696731
Promoter ID:EPDNEW_R7247
Type:initiation region
Name:Map2_1
Description:microtubule-associated protein 2
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_6.0973,334,536 - 73,334,596EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
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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
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
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)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
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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)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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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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