Tyms (thymidylate synthetase) - Rat Genome Database

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Gene: Tyms (thymidylate synthetase) Rattus norvegicus
Analyze
Symbol: Tyms
Name: thymidylate synthetase
RGD ID: 3921
Description: Exhibits several functions, including folic acid binding activity; protein homodimerization activity; and thymidylate synthase activity. Involved in several processes, including nucleobase-containing small molecule metabolic process; response to steroid hormone; and response to vitamin. Localizes to mitochondrion and nucleolus. Used to study urinary bladder cancer. Biomarker of colorectal adenocarcinoma. Human ortholog(s) of this gene implicated in gastrointestinal system cancer (multiple); hematologic cancer (multiple); and rheumatoid arthritis. Orthologous to human TYMS (thymidylate synthetase); PARTICIPATES IN folate mediated one-carbon metabolic pathway; folate metabolic pathway; pyrimidine metabolic pathway; INTERACTS WITH 1-naphthyl isothiocyanate; 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: MGC156654; thymidylate synthase; TS; TSase
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.29113,313,454 - 113,329,551 (-)NCBI
Rnor_6.0 Ensembl9121,918,947 - 121,931,564 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.09121,918,875 - 121,931,564 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.09121,368,418 - 121,381,493 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.49112,604,912 - 112,617,706 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.19112,814,399 - 112,827,186 (-)NCBI
Celera9110,420,900 - 110,433,600 (-)NCBICelera
RH 3.4 Map9866.0RGD
Cytogenetic Map9q38NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-gambogic acid  (ISO)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
1-chloro-2,4-dinitrobenzene  (ISO)
1-naphthyl isothiocyanate  (EXP)
14-Deoxy-11,12-didehydroandrographolide  (ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3-dimethoxynaphthalene-1,4-dione  (ISO)
2,4-dinitrotoluene  (EXP)
2,6-dinitrotoluene  (EXP)
2-methylcholine  (ISO)
2-nitrofluorene  (EXP)
3,3'-diindolylmethane  (ISO)
3,7-dihydropurine-6-thione  (ISO)
3-methylcholanthrene  (ISO)
4-(ethoxymethylene)-2-phenyloxazol-5-one  (ISO)
4-(N-nitrosomethylamino)-1-(3-pyridyl)butan-1-one  (EXP)
4-hydroxyphenyl retinamide  (ISO)
5,6,7,8-tetrahydrofolic acid  (EXP)
5-aza-2'-deoxycytidine  (ISO)
5-fluorouracil  (EXP,ISO)
5-formyltetrahydrofolic acid  (ISO)
5-iodo-2'-deoxyuridine  (ISO)
7,9-dihydro-1H-purine-2,6,8(3H)-trione  (ISO)
acetamide  (EXP)
acetylleucyl-leucyl-norleucinal  (ISO)
acrylamide  (ISO)
aflatoxin B1  (EXP,ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
antimony(0)  (ISO)
antirheumatic drug  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
atrazine  (ISO)
azathioprine  (ISO)
belinostat  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
beta-naphthoflavone  (EXP)
betulinic acid  (ISO)
bicalutamide  (ISO)
Biflorin  (ISO)
bisphenol A  (EXP,ISO)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
cadmium sulfate  (ISO)
caffeine  (EXP)
calcitriol  (ISO)
camptothecin  (ISO)
capecitabine  (ISO)
carboplatin  (ISO)
cefaloridine  (EXP)
chromium atom  (ISO)
cisplatin  (ISO)
cobalt dichloride  (EXP,ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
coumestrol  (ISO)
cycloheximide  (ISO)
cyclosporin A  (ISO)
cytarabine  (ISO)
daunorubicin  (ISO)
DDT  (ISO)
dextran sulfate  (ISO)
diarsenic trioxide  (ISO)
dibutyl phthalate  (ISO)
dichlorine  (EXP)
diethylstilbestrol  (EXP)
dioxygen  (ISO)
dipotassium bis[mu-tartrato(4-)]diantimonate(2-) trihydrate  (ISO)
DISTAMYCIN A  (ISO)
doxifluridine  (ISO)
doxorubicin  (ISO)
dTMP  (ISO)
dUMP  (ISO)
endosulfan  (EXP)
Enterolactone  (ISO)
enzyme inhibitor  (ISO)
erlotinib hydrochloride  (ISO)
ethyl methanesulfonate  (ISO)
etoposide  (ISO)
fipronil  (EXP)
floxuridine  (ISO)
flurbiprofen  (ISO)
folic acid  (EXP,ISO)
furan  (EXP)
gefitinib  (ISO)
genistein  (ISO)
gentamycin  (EXP)
geraniol  (ISO)
Heliotrine  (EXP)
ICI D1694  (ISO)
irinotecan  (ISO)
ketamine  (EXP)
lamivudine  (ISO)
lead(II) chloride  (ISO)
lipopolysaccharide  (ISO)
malathion  (ISO)
menadione  (ISO)
mercaptopurine  (ISO)
mercury atom  (ISO)
mercury(0)  (ISO)
methapyrilene  (EXP)
methcathinone  (ISO)
methotrexate  (EXP,ISO)
methoxyacetic acid  (EXP)
methyl methanesulfonate  (ISO)
methylmercury chloride  (EXP)
methylseleninic acid  (ISO)
mitomycin C  (ISO)
Monobutylphthalate  (EXP)
N,N,N',N'-tetrakis(2-pyridylmethyl)ethylenediamine  (ISO)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
N-nitrosodiethylamine  (EXP)
N-nitrosodimethylamine  (EXP)
N-nitrosomorpholine  (EXP)
nickel atom  (ISO)
nickel dichloride  (EXP)
oxaliplatin  (EXP,ISO)
ozone  (EXP,ISO)
paclitaxel  (ISO)
palbociclib  (ISO)
paracetamol  (ISO)
pemetrexed  (ISO)
phenobarbital  (ISO)
phenolphthalein  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
phytoestrogen  (ISO)
piperonyl butoxide  (EXP)
pirinixic acid  (EXP,ISO)
potassium dichromate  (ISO)
prednisone  (ISO)
progesterone  (ISO)
purine-6-thiol  (ISO)
quercetin  (EXP,ISO)
quinazolines  (ISO)
resveratrol  (ISO)
rotenone  (ISO)
senecionine  (EXP)
Senkirkine  (EXP)
silicon dioxide  (ISO)
simvastatin  (ISO)
sirolimus  (ISO)
sodium arsenite  (ISO)
sodium dichromate  (EXP)
sunitinib  (ISO)
tanespimycin  (ISO)
Tegafur  (ISO)
Temsirolimus  (ISO)
testosterone  (ISO)
tetrachloromethane  (ISO)
thapsigargin  (ISO)
thioacetamide  (EXP)
thymidine  (ISO)
titanium dioxide  (ISO)
toluene 2,4-diisocyanate  (ISO)
topotecan  (EXP)
trichostatin A  (ISO)
triclosan  (ISO)
trimellitic anhydride  (ISO)
triptonide  (ISO)
troglitazone  (ISO)
tungsten  (ISO)
urethane  (ISO)
valproic acid  (ISO)
vincristine  (ISO)
vorinostat  (ISO)
wogonin  (ISO)
zidovudine  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cytoplasm  (ISO,ISS)
cytosol  (IBA)
mitochondrial inner membrane  (ISO,ISS)
mitochondrial matrix  (ISO,ISS)
mitochondrion  (IBA,IDA,ISO)
nucleolus  (IDA)
nucleus  (ISO,ISS)

References

References - curated
1. Abolmaali K, etal., Surgery. 2009 Aug;146(2):269-73.
2. Amano M Bull Tokyo Med Dent Univ. 1987 Mar;34(1):1-8.
3. Carl GF and Smith ML, J Nutr. 1995 May;125(5):1245-57.
4. Carlsson G, etal., Biochem Pharmacol. 1995 Oct 26;50(9):1347-51.
5. Chu E, etal., Mol Cell Biol. 1999 Feb;19(2):1582-94.
6. Ciesla J, etal., Biochim Biophys Acta 1995 Apr 4;1261(2):233-42.
7. Fanciullino R, etal., Br J Cancer. 2007 Oct 8;97(7):919-26. Epub 2007 Sep 11.
8. Fraczyk T, etal., Biochim Biophys Acta. 2015 Dec;1854(12):1922-34. doi: 10.1016/j.bbapap.2015.08.007. Epub 2015 Aug 24.
9. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
10. GOA data from the GO Consortium
11. Herzfeld A and Raper SM, Cancer Res. 1980 Mar;40(3):744-50.
12. Iida K, etal., Cancer Detect Prev. 1997;21(5):476-82.
13. Jekic B, etal., Eur J Clin Pharmacol. 2013 Mar;69(3):377-83. doi: 10.1007/s00228-012-1341-3. Epub 2012 Jul 5.
14. Joerger M, etal., Cancer Chemother Pharmacol. 2015 Apr;75(4):763-72. doi: 10.1007/s00280-015-2698-7. Epub 2015 Feb 13.
15. KEGG
16. Kim HN, etal., Leuk Res. 2009 Jan;33(1):82-7. doi: 10.1016/j.leukres.2008.07.026. Epub 2008 Sep 6.
17. Komatsu M and Tsukamoto I, Biochim Biophys Acta. 1998 Feb 2;1379(2):289-96.
18. Kudo H, etal., Oncol Rep. 2000 May-Jun;7(3):621-4.
19. Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
20. Langenbach Biochim Biophys Acta. 1976 Feb 13;422(2):295-301.
21. Lima CS, etal., Leuk Res. 2008 Mar;32(3):401-5. Epub 2007 Jul 25.
22. Maggini V, etal., Leuk Res. 2008 Jan;32(1):49-53. Epub 2007 May 23.
23. Nakayama T, etal., Life Sci. 2001 Aug 17;69(13):1521-9.
24. NCBI rat LocusLink and RefSeq merged data July 26, 2002
25. Ozeki A and Tsukamoto I, Biochim Biophys Acta. 1999 Jul 8;1450(3):308-19.
26. Park DJ, etal., Int J Colorectal Dis 2002 Jan;17(1):46-9.
27. Peterson AM Cell Differ. 1976 Apr;5(1):37-43.
28. Pipeline to import KEGG annotations from KEGG into RGD
29. Pipeline to import SMPDB annotations from SMPDB into RGD
30. RGD automated data pipeline
31. RGD automated import pipeline for gene-chemical interactions
32. Sakamoto S, etal., Anticancer Drugs. 1998 Apr;9(4):351-7.
33. Sakamoto S, etal., Anticancer Res. 1993 May-Jun;13(3):631-4.
34. Sakamoto S, etal., Anticancer Res. 1999 Jan-Feb;19(1A):245-50.
35. Sakamoto S, etal., Oncol Rep. 1999 Nov-Dec;6(6):1321-5.
36. Samsonoff WA, etal., J Biol Chem. 1997 May 16;272(20):13281-5.
37. Sotelo-Mundo RR, etal., Biochemistry 1999 Jan 19;38(3):1087-94.
38. Stover PJ and Field MS, Adv Nutr. 2011 Jul;2(4):325-31. doi: 10.3945/┬┐an.111.000596. Epub 2011 Jun 28.
39. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
40. Tsujimoto S, etal., Int J Clin Oncol. 2008 Apr;13(2):138-43. Epub 2008 May 8.
41. Tsukamoto I and Kojo S, Biochim Biophys Acta. 1991 May 24;1074(1):52-5.
42. Tsukamoto I and Kojo S, Gut. 1989 Mar;30(3):387-90.
43. Tsukamoto I, etal., Biochem Pharmacol. 1996 Sep 27;52(6):879-84.
44. Tsukamoto I, etal., Biochim Biophys Acta. 1988 Feb 17;964(2):254-9.
45. Wang ZH, etal., J Neurooncol. 1998 Feb;36(3):219-29.
46. Yarimizu T, etal., Oncol Rep. 1998 Sep-Oct;5(5):1103-7.
47. Yoshida Y, etal., Biochim Biophys Acta. 1997 Aug 29;1336(2):180-6.
48. Yuan JM, etal., Hepatology. 2007 Sep;46(3):749-58. doi: 10.1002/hep.21735.
49. Zgheib NK, etal., Pharmacogenet Genomics. 2014 Aug;24(8):387-96. doi: 10.1097/FPC.0000000000000069.
Additional References at PubMed
PMID:1924359   PMID:8845352   PMID:11278511   PMID:12477932   PMID:15093541   PMID:16079077   PMID:21876188  


Genomics

Comparative Map Data
Tyms
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.29113,313,454 - 113,329,551 (-)NCBI
Rnor_6.0 Ensembl9121,918,947 - 121,931,564 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.09121,918,875 - 121,931,564 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.09121,368,418 - 121,381,493 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.49112,604,912 - 112,617,706 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.19112,814,399 - 112,827,186 (-)NCBI
Celera9110,420,900 - 110,433,600 (-)NCBICelera
RH 3.4 Map9866.0RGD
Cytogenetic Map9q38NCBI
TYMS
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl18657,653 - 673,578 (+)EnsemblGRCh38hg38GRCh38
GRCh3818657,653 - 673,578 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh3718657,653 - 673,578 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3618647,651 - 663,492 (+)NCBINCBI36hg18NCBI36
Build 3418647,650 - 663,492NCBI
Celera18532,413 - 547,810 (+)NCBI
Cytogenetic Map18p11.32NCBI
HuRef18617,665 - 633,936 (+)NCBIHuRef
CHM1_118656,968 - 672,692 (+)NCBICHM1_1
Tyms
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39530,243,544 - 30,279,261 (-)NCBIGRCm39mm39
GRCm39 Ensembl530,263,200 - 30,278,615 (-)Ensembl
GRCm38530,038,546 - 30,073,645 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl530,058,202 - 30,073,617 (-)EnsemblGRCm38mm10GRCm38
MGSCv37530,384,740 - 30,400,165 (-)NCBIGRCm37mm9NCBIm37
MGSCv36530,389,614 - 30,404,368 (-)NCBImm8
Celera527,575,630 - 27,591,037 (-)NCBICelera
Cytogenetic Map5B1NCBI
cM Map515.81NCBI
Tyms
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554029,296,321 - 9,306,631 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554029,295,862 - 9,304,952 (-)NCBIChiLan1.0ChiLan1.0
TYMS
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11817,295,182 - 17,310,311 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1817,295,182 - 17,310,320 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01813,653,085 - 13,668,478 (-)NCBIMhudiblu_PPA_v0panPan3
TYMS
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1767,487,927 - 67,497,747 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl767,487,927 - 67,497,747 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha766,941,464 - 66,951,243 (+)NCBI
ROS_Cfam_1.0767,553,912 - 67,563,695 (+)NCBI
UMICH_Zoey_3.1767,230,668 - 67,240,435 (+)NCBI
UNSW_CanFamBas_1.0767,242,107 - 67,251,886 (+)NCBI
UU_Cfam_GSD_1.0767,544,017 - 67,553,794 (+)NCBI
Tyms
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494463,774,083 - 63,783,067 (+)NCBI
SpeTri2.0NW_00493655033,797 - 42,233 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TYMS
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl6105,640,031 - 105,660,601 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.16105,642,730 - 105,660,279 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
TYMS
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11860,030,640 - 60,043,297 (+)NCBI
ChlSab1.1 Ensembl1860,030,658 - 60,041,856 (+)Ensembl
Tyms
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462477011,138,673 - 11,149,600 (+)NCBI

Position Markers
RH94514  
Rat AssemblyChrPosition (strand)SourceJBrowse
Celera9110,420,954 - 110,421,052UniSTS
RH 3.4 Map9866.0UniSTS
Cytogenetic Map9q38UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724544Uae9Urinary albumin excretion QTL 94.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)929075079122095297Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:172
Count of miRNA genes:134
Interacting mature miRNAs:147
Transcripts:ENSRNOT00000056243
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 3 34 48 32 19 32 1 1 69 34 35 11 1
Low 9 9 9 9 7 10 5 1 6 7
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000056243   ⟹   ENSRNOP00000053086
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl9121,918,947 - 121,931,564 (-)Ensembl
RefSeq Acc Id: NM_019179   ⟹   NP_062052
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.29113,316,779 - 113,329,478 (-)NCBI
Rnor_6.09121,918,875 - 121,931,564 (-)NCBI
Rnor_5.09121,368,418 - 121,381,493 (-)NCBI
RGSC_v3.49112,604,912 - 112,617,706 (-)RGD
Celera9110,420,900 - 110,433,600 (-)RGD
Sequence:
RefSeq Acc Id: XM_008767421   ⟹   XP_008765643
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.29113,313,454 - 113,328,322 (-)NCBI
Rnor_6.09121,919,276 - 121,930,981 (-)NCBI
Sequence:
RefSeq Acc Id: XR_005488858
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.29113,313,454 - 113,329,551 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_062052   ⟸   NM_019179
- UniProtKB: P45352 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_008765643   ⟸   XM_008767421
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000053086   ⟸   ENSRNOT00000056243

Transcriptome

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

Promoters
RGD ID:13696918
Promoter ID:EPDNEW_R7443
Type:initiation region
Name:Tyms_1
Description:thymidylate synthetase
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_6.09121,931,588 - 121,931,648EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
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 (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/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 (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)
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
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
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/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
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 (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
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
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
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
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
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 (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
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
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 (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 (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
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 (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 (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 (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:3921 AgrOrtholog
Ensembl Genes ENSRNOG00000037225 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000053086 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000056243 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 3.30.572.10 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:8362547 IMAGE-MGC_LOAD
InterPro Thymidate_synth/dCMP_Mease UniProtKB/Swiss-Prot
  Thymidate_synth/dCMP_Mease_sf UniProtKB/Swiss-Prot
  Thymidylate_synthase UniProtKB/Swiss-Prot
  Thymidylate_synthase_AS UniProtKB/Swiss-Prot
KEGG Report rno:29261 UniProtKB/Swiss-Prot
MGC_CLONE MGC:156654 IMAGE-MGC_LOAD
NCBI Gene 29261 ENTREZGENE
Pfam Thymidylat_synt UniProtKB/Swiss-Prot
PharmGKB TYMS RGD
PhenoGen Tyms PhenoGen
PRINTS THYMDSNTHASE UniProtKB/Swiss-Prot
PROSITE THYMIDYLATE_SYNTHASE UniProtKB/Swiss-Prot
Superfamily-SCOP SSF55831 UniProtKB/Swiss-Prot
TIGR TC239473
TIGRFAMs thym_sym UniProtKB/Swiss-Prot
UniProt P45352 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary A0JN23 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-10-23 Tyms  thymidylate synthetase  Tyms  thymidylate synthase  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-06-10 Tyms  thymidylate synthase      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_protein 307 amino acids; 35 kDa 70045