Mtr (5-methyltetrahydrofolate-homocysteine methyltransferase) - Rat Genome Database

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Gene: Mtr (5-methyltetrahydrofolate-homocysteine methyltransferase) Rattus norvegicus
Analyze
Symbol: Mtr
Name: 5-methyltetrahydrofolate-homocysteine methyltransferase
RGD ID: 621283
Description: Enables amino acid binding activity; folic acid binding activity; and methionine synthase activity. Involved in several processes, including alpha-amino acid metabolic process; cellular response to methionine; and cellular response to nitric oxide. Predicted to be active in cytosol. Biomarker of type 2 diabetes mellitus and vitamin B12 deficiency. Human ortholog(s) of this gene implicated in several diseases, including IgA glomerulonephritis; autistic disorder; hematologic cancer (multiple); hyperhomocysteinemia; and methylmalonic aciduria and homocystinuria type cblG. Orthologous to human MTR (5-methyltetrahydrofolate-homocysteine methyltransferase); PARTICIPATES IN folate mediated one-carbon metabolic pathway; folate metabolic pathway; methionine cycle/metabolic pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,6-dinitrotoluene; acetaldehyde.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: 5-methyltetrahydrofolate--homocysteine methyltransferase; cobalamin-dependent methionine synthase; methionine synthase; methioninesynthase; MS; vitamin-B12 dependent methionine synthase
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
mRatBN7.21758,219,998 - 58,308,560 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1758,220,071 - 58,304,822 (+)Ensembl
Rnor_6.01766,210,444 - 66,295,014 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1766,210,461 - 66,295,014 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01767,954,893 - 68,041,488 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41768,782,708 - 68,867,101 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11768,793,540 - 68,877,930 (+)NCBI
Celera1762,230,512 - 62,313,601 (-)NCBICelera
Cytogenetic Map17q12.1NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP)
2,6-dinitrotoluene  (EXP)
3,4-methylenedioxymethamphetamine  (ISO)
5,6,7,8-tetrahydrofolic acid  (ISO)
5-methyltetrahydrofolic acid  (ISO)
acetaldehyde  (EXP)
acetamide  (EXP)
acrylamide  (ISO)
aluminium atom  (ISO)
aluminium(0)  (ISO)
ammonium chloride  (EXP)
amphetamine  (EXP)
antirheumatic drug  (ISO)
aristolochic acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
benazepril  (ISO)
benzimidazoles  (EXP)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bucladesine  (ISO)
butanal  (ISO)
cisplatin  (ISO)
cobalt dichloride  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
cyanocob(III)alamin  (EXP,ISO)
cyclophosphamide  (EXP)
cyclosporin A  (ISO)
D-penicillamine  (ISO)
diarsenic trioxide  (ISO)
dimethylarsinic acid  (ISO)
dinitrogen oxide  (ISO)
dopamine  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
ethanol  (ISO)
folic acid  (EXP,ISO)
formaldehyde  (ISO)
glutathione  (ISO)
glutathionylcobalamin  (ISO)
homocysteine  (EXP,ISO)
hydroxocobalamin  (ISO)
hypoxanthine  (ISO)
ivermectin  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
LY294002  (ISO)
medroxyprogesterone acetate  (ISO)
mercury atom  (ISO)
mercury(0)  (ISO)
methotrexate  (ISO)
methylcobalamin  (ISO)
methylmercury chloride  (ISO)
nitroprusside  (EXP)
paracetamol  (EXP,ISO)
phenylhydrazine  (EXP)
pirinixic acid  (ISO)
progesterone  (ISO)
quercetin  (ISO)
S-adenosyl-L-methioninate  (ISO)
S-adenosyl-L-methionine  (ISO)
S-butyl-DL-homocysteine (S,R)-sulfoximine  (ISO)
sodium arsenite  (EXP)
streptozocin  (EXP,ISO)
sulforaphane  (ISO)
tert-butyl hydroperoxide  (ISO)
thimerosal  (ISO)
thymidine  (ISO)
triazines  (ISO)
trichloroethene  (EXP)
trichostatin A  (ISO)
trimellitic anhydride  (ISO)
urethane  (ISO)
valproic acid  (ISO)
wortmannin  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cellular_component  (ND)
cytosol  (IBA,IEA,ISO)

Molecular Function

References

References - curated
1. Blaise S, etal., Pediatr Res 2005 Jun;57(6):777-82. Epub 2005 Apr 21.
2. Blom HJ and Smulders Y, J Inherit Metab Dis. 2011 Feb;34(1):75-81. doi: 10.1007/s10545-010-9177-4. Epub 2010 Sep 4.
3. Brunaud L, etal., Digestion. 2003;68(2-3):133-40. Epub 2003 Nov 28.
4. Cheng FW, etal., Br J Haematol. 1975 Nov;31(3):323-36.
5. de Lima EL, etal., Pediatr Blood Cancer. 2010 Jul 1;54(7):904-8. doi: 10.1002/pbc.22472.
6. Doolin MT, etal., Am J Hum Genet 2002 Nov;71(5):1222-6. Epub 2002 Oct 09.
7. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
8. Gemmati D, etal., Cancer Epidemiol Biomarkers Prev. 2004 May;13(5):787-94.
9. GOA data from the GO Consortium
10. Gross M, etal., Audiol Neurootol. 2006;11(5):287-93. Epub 2006 Jun 14.
11. Huang L, etal., Anal Biochem. 2001 Dec 15;299(2):253-9.
12. Iskandar BJ, etal., J Clin Invest. 2010 May;120(5):1603-16. doi: 10.1172/JCI40000. Epub 2010 Apr 26.
13. KEGG
14. Lima CS, etal., Leuk Res. 2008 Mar;32(3):401-5. Epub 2007 Jul 25.
15. Lu SC and Mato JM, Physiol Rev. 2012 Oct;92(4):1515-42. doi: 10.1152/physrev.00047.2011.
16. MGD data from the GO Consortium
17. Mohammad NS, etal., Psychiatr Genet. 2009 Aug;19(4):171-6.
18. NCBI rat LocusLink and RefSeq merged data July 26, 2002
19. Nikbakht M, etal., Exp Oncol. 2012;34(1):43-8.
20. OMIM Disease Annotation Pipeline
21. Pipeline to import KEGG annotations from KEGG into RGD
22. Pipeline to import SMPDB annotations from SMPDB into RGD
23. RGD automated data pipeline
24. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
25. RGD automated import pipeline for gene-chemical interactions
26. Rouissi K, etal., Cancer Genet Cytogenet. 2009 Nov;195(1):43-53.
27. Sepe DM, etal., Pediatr Blood Cancer. 2012 May;58(5):695-700. doi: 10.1002/pbc.23192. Epub 2011 May 25.
28. Stover PJ J Nutrigenet Nutrigenomics. 2011;4(5):293-305. doi: 10.1159/000334586. Epub 2012 Feb 22.
29. Suzuki T, etal., Cancer Epidemiol Biomarkers Prev. 2008 Oct;17(10):2742-7.
30. Uchida Y, etal., BMC Med Genet. 2011 Mar 7;12:35. doi: 10.1186/1471-2350-12-35.
31. Vujkovic M, etal., Leuk Res Rep. 2015 Jul 21;4(2):47-50. doi: 10.1016/j.lrr.2015.05.005. eCollection 2015.
32. Waly MI, etal., Alcohol Clin Exp Res. 2011 Feb;35(2):277-83. doi: 10.1111/j.1530-0277.2010.01343.x. Epub 2010 Dec 1.
33. Wang L, etal., Zhonghua Liu Xing Bing Xue Za Zhi. 2006 Jan;27(1):50-4.
34. Watkins D and Rosenblatt DS, J Inherit Metab Dis. 2012 Jul;35(4):665-70. doi: 10.1007/s10545-011-9418-1. Epub 2011 Nov 23.
35. Watkins D, etal., Am J Hum Genet. 2002 Jul;71(1):143-53. Epub 2002 May 30.
36. Williams KT and Schalinske KL, Diabetes Metab Res Rev. 2012 Feb;28(2):123-31. doi: 10.1002/dmrr.1281.
37. Williams KT, etal., J Nutr. 2008 Nov;138(11):2064-9. doi: 10.3945/jn.108.094144.
38. Yamada K, etal., Biosci Biotechnol Biochem 1998 Nov;62(11):2155-60.
39. Yamamoto R, etal., Nephrol Dial Transplant. 2012 Mar;27(3):1020-30. doi: 10.1093/ndt/gfr369. Epub 2011 Jul 7.
40. Zhang Y, etal., J Hum Genet. 2004;49(6):296-301. Epub 2004 May 18.
41. Zhu WL, etal., Biomed Environ Sci. 2004 Mar;17(1):57-64.
Additional References at PubMed
PMID:11158293   PMID:14760703   PMID:16769880   PMID:23825108   PMID:25467853  


Genomics

Comparative Map Data
Mtr
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21758,219,998 - 58,308,560 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1758,220,071 - 58,304,822 (+)Ensembl
Rnor_6.01766,210,444 - 66,295,014 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1766,210,461 - 66,295,014 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01767,954,893 - 68,041,488 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41768,782,708 - 68,867,101 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11768,793,540 - 68,877,930 (+)NCBI
Celera1762,230,512 - 62,313,601 (-)NCBICelera
Cytogenetic Map17q12.1NCBI
MTR
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1236,795,260 - 236,921,278 (+)EnsemblGRCh38hg38GRCh38
GRCh381236,794,304 - 236,903,981 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371236,958,581 - 237,067,281 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361235,025,341 - 235,130,585 (+)NCBINCBI36hg18NCBI36
Build 341233,284,758 - 233,390,001NCBI
Celera1210,207,757 - 210,316,611 (+)NCBI
Cytogenetic Map1q43NCBI
HuRef1207,414,687 - 207,523,271 (+)NCBIHuRef
CHM1_11238,230,032 - 238,338,720 (+)NCBICHM1_1
Mtr
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391312,196,217 - 12,273,090 (-)NCBIGRCm39mm39
GRCm39 Ensembl1312,197,598 - 12,272,999 (-)Ensembl
GRCm381312,181,331 - 12,258,199 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1312,182,712 - 12,258,113 (-)EnsemblGRCm38mm10GRCm38
MGSCv371312,279,086 - 12,350,267 (-)NCBIGRCm37mm9NCBIm37
MGSCv361312,240,869 - 12,312,428 (-)NCBImm8
Celera1312,106,428 - 12,177,671 (-)NCBICelera
Cytogenetic Map13A1NCBI
cM Map134.52NCBI
Mtr
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554923,376,512 - 3,474,180 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554923,372,915 - 3,474,173 (-)NCBIChiLan1.0ChiLan1.0
MTR
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11217,352,707 - 217,461,313 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1217,358,050 - 217,460,946 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01212,353,195 - 212,463,304 (+)NCBIMhudiblu_PPA_v0panPan3
MTR
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.143,219,851 - 3,328,000 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl43,215,090 - 3,328,115 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha43,267,770 - 3,375,365 (-)NCBI
ROS_Cfam_1.043,240,178 - 3,347,933 (-)NCBI
ROS_Cfam_1.0 Ensembl43,243,029 - 3,347,943 (-)Ensembl
UMICH_Zoey_3.143,239,421 - 3,346,967 (-)NCBI
UNSW_CanFamBas_1.043,370,826 - 3,478,490 (-)NCBI
UU_Cfam_GSD_1.043,591,890 - 3,699,525 (-)NCBI
Mtr
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934439,925,911 - 40,014,880 (-)NCBI
SpeTri2.0NW_00493648416,087,924 - 16,180,089 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
MTR
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1454,546,981 - 54,652,759 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11454,546,978 - 54,652,780 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21458,497,706 - 58,627,105 (-)NCBISscrofa10.2Sscrofa10.2susScr3
MTR
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12573,935,666 - 74,039,872 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl2573,935,225 - 74,038,741 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366605576,034,340 - 76,141,359 (+)NCBIVero_WHO_p1.0
Mtr
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462477513,791,690 - 13,903,888 (-)NCBIHetGla_female_1.0hetGla2


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
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
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
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
61394Bp8Blood pressure QTL 82.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)172308056759555013Rat
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
4889955Bss93Bone structure and strength QTL 934.4tibia size trait (VT:0100001)tibia cortical bone volume to tibia total bone volume ratio (CMO:0001727)172702794960463643Rat
8552928Pigfal9Plasma insulin-like growth factor 1 level QTL 99blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)172840914773409147Rat
9590107Sffal7Serum free fatty acids level QTL 74.810.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)172840914773409147Rat
10450503Bp386Blood pressure QTL 3860.28arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)173136839162109574Rat
2324621Coatc5Coat color QTL 5coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)173136839173951021Rat
724549Niddm56Non-insulin dependent diabetes mellitus QTL 560.03blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)173199078476990784Rat
1354663Bvd5Brain ventricular dilatation QTL 53.510.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)173199078481292925Rat
1300148Bp192Blood pressure QTL 1923.47arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)173455084373951021Rat
724528Uae4Urinary albumin excretion QTL 44.90.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)173583708569599340Rat
2301412Kidm40Kidney mass QTL 400.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)173747984782479847Rat
2317054Aia12Adjuvant induced arthritis QTL 124.24joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)173828150983281509Rat
2317060Aia26Adjuvant induced arthritis QTL 263.22joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)173828150983281509Rat
1598871Memor5Memory QTL 55.3exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)174054004180387013Rat
1358295Aocep1Aortic cell protein QTL 16.10.00000071thoracic aorta cellular protein amount (VT:0010598)aortic cell percentage174099000585990005Rat
631497Bp98Blood pressure QTL 983.66arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)174135465160463643Rat
1354635Bp245Blood pressure QTL 2456arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)174207316069599340Rat
1354635Bp245Blood pressure QTL 2456arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)174207316069599340Rat
7411575Bw140Body weight QTL 14030.20.001body mass (VT:0001259)body weight gain (CMO:0000420)174856093586533673Rat
8694181Bw151Body weight QTL 1514.360.001body mass (VT:0001259)body weight gain (CMO:0000420)174856093586533673Rat
2317038Ginf3Gastrointestinal inflammation QTL 32.890.005liver integrity trait (VT:0010547)liver granuloma severity score (CMO:0002157)174992015486533673Rat
2303580Gluco49Glucose level QTL 492blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)175004027186533673Rat
1354629Scl31Serum cholesterol level QTL 314.1blood cholesterol amount (VT:0000180)blood total cholesterol level (CMO:0000051)175089090860781592Rat
1354654Spl7Serum phospholipid level QTL 75.5blood phospholipid amount (VT:0006084)blood phospholipid level (CMO:0001169)175089090860781592Rat
4889894Eae33Experimental allergic encephalomyelitis QTL 335.20.0001nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)175090909986022412Rat
2317053Aia25Adjuvant induced arthritis QTL 252.69joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)175090919660781426Rat
1354588Bvd4Brain ventricular dilatation QTL 45.310.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)175349882882479847Rat
61466Niddm12Non-insulin dependent diabetes mellitus QTL 123.20.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)175402992960463637Rat
70210Cm15Cardiac mass QTL 156.5heart right ventricle mass (VT:0007033)heart right ventricle wet weight (CMO:0000072)175724672370156904Rat
1600398Edcs5Endometrial carcinoma susceptibility QTL 52.2uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)175724672370852846Rat
2302365Gluco40Glucose level QTL 404.79blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)175724684382046127Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:476
Count of miRNA genes:242
Interacting mature miRNAs:287
Transcripts:ENSRNOT00000023974
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 27 31 15 17 15 1 1 50 35 37 9 1
Low 3 16 26 26 2 26 7 10 24 4 2 7
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000023974   ⟹   ENSRNOP00000023973
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1758,220,071 - 58,304,822 (+)Ensembl
Rnor_6.0 Ensembl1766,210,461 - 66,295,014 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000083172   ⟹   ENSRNOP00000071254
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1766,210,885 - 66,288,202 (-)Ensembl
RefSeq Acc Id: NM_030864   ⟹   NP_110491
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21758,220,071 - 58,304,839 (+)NCBI
Rnor_6.01766,210,444 - 66,295,014 (-)NCBI
Rnor_5.01767,954,893 - 68,041,488 (-)NCBI
RGSC_v3.41768,782,708 - 68,867,101 (+)RGD
Celera1762,230,512 - 62,313,601 (-)RGD
Sequence:
RefSeq Acc Id: XM_039096105   ⟹   XP_038952033
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21758,219,998 - 58,308,560 (+)NCBI
RefSeq Acc Id: XM_039096106   ⟹   XP_038952034
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21758,220,018 - 58,308,560 (+)NCBI
RefSeq Acc Id: XM_039096107   ⟹   XP_038952035
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21758,220,018 - 58,308,560 (+)NCBI
RefSeq Acc Id: XM_039096108   ⟹   XP_038952036
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21758,220,018 - 58,290,676 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_110491   ⟸   NM_030864
- Sequence:
RefSeq Acc Id: ENSRNOP00000023973   ⟸   ENSRNOT00000023974
RefSeq Acc Id: ENSRNOP00000071254   ⟸   ENSRNOT00000083172
RefSeq Acc Id: XP_038952033   ⟸   XM_039096105
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038952035   ⟸   XM_039096107
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038952034   ⟸   XM_039096106
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038952036   ⟸   XM_039096108
- Peptide Label: isoform X3
Protein Domains
AdoMet activation   B12-binding   B12-binding N-terminal   Hcy-binding   Pterin-binding

Transcriptome

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

Promoters
RGD ID:13700536
Promoter ID:EPDNEW_R11060
Type:multiple initiation site
Name:Mtr_1
Description:5-methyltetrahydrofolate-homocysteine methyltransferase
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_6.01766,295,049 - 66,295,109EPDNEW

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)
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)
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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)
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)
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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)
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)
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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)
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)
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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)
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)
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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)
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)
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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)
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)
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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)
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)
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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)
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)
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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)
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)
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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)
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)
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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)
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)
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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)
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)
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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)
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: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (MCW)
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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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621283 AgrOrtholog
Ensembl Genes ENSRNOG00000017593 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000023973 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000071254 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000023974 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000083172 UniProtKB/TrEMBL
Gene3D-CATH 1.10.1240.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.10.196.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.20.20.20 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.20.20.330 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Cbl-bd_cap UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cobalamin-bd UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cobalamin-bd_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Dihydropteroate_synth-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HCY_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HCY_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Met_synthase_B12-bd UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MetH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Meth_synthase_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Pterin-binding_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  VitB12-dep_Met_synth_activ_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  VitB12-dep_Met_synth_activ_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:81522 UniProtKB/Swiss-Prot
NCBI Gene 81522 ENTREZGENE
Pfam B12-binding UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  B12-binding_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Met_synt_B12 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Pterin_bind UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  S-methyl_trans UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB MTR RGD
PhenoGen Mtr PhenoGen
PIRSF MetH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE ADOMET_ACTIVATION UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  B12_BINDING UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  B12_BINDING_NTER UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HCY UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTERIN_BINDING UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART B12-binding_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF47644 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF51717 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF52242 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF56507 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF82282 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGRFAMs metH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt G3V8A4_RAT UniProtKB/TrEMBL
  METH_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-09-10 Mtr  5-methyltetrahydrofolate-homocysteine methyltransferase    methionine synthase  Name updated 1299863 APPROVED
2002-08-07 Mtr  methionine synthase      Symbol and Name status set to provisional 70820 PROVISIONAL