Tymp (thymidine phosphorylase) - Rat Genome Database

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Gene: Tymp (thymidine phosphorylase) Rattus norvegicus
Analyze
Symbol: Tymp
Name: thymidine phosphorylase
RGD ID: 1305756
Description: Predicted to enable protein homodimerization activity and thymidine phosphorylase activity. Predicted to be involved in several processes, including nucleobase-containing small molecule metabolic process; regulation of gastric motility; and regulation of myelination. Predicted to be active in cytosol. Human ortholog(s) of this gene implicated in lung non-small cell carcinoma; mitochondrial DNA depletion syndrome 1; mitochondrial encephalomyopathy; pancreatic cancer; and transitional cell carcinoma. Orthologous to human TYMP (thymidine phosphorylase); PARTICIPATES IN beta-ureidopropionase deficiency pathway; capecitabine pharmacodynamics pathway; capecitabine pharmacokinetics pathway; INTERACTS WITH 1-naphthyl isothiocyanate; 17alpha-ethynylestradiol; 17beta-estradiol 3-benzoate.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: Ecgf1; endothelial cell growth factor 1 (platelet-derived); LOC315219; MGC108801; MGC112734; tdRPase; TP
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Squirrel
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
mRatBN7.27120,438,768 - 120,444,088 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl7120,438,770 - 120,443,874 (-)Ensembl
mRatBN7.2 Ensembl7120,438,125 - 120,447,429 (-)Ensembl
Rnor_6.07130,342,481 - 130,347,845 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7130,342,483 - 130,347,587 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.07130,027,662 - 130,033,050 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47127,666,518 - 127,671,624 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.17127,700,749 - 127,705,854 (-)NCBI
Celera7116,911,732 - 116,916,838 (-)NCBICelera
Cytogenetic Map7q34NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (ISO)
1-naphthyl isothiocyanate  (EXP)
17alpha-ethynylestradiol  (EXP)
17beta-estradiol 3-benzoate  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-dinitrotoluene  (EXP)
2-amino-4,6-dinitrotoluene  (EXP)
2-deoxy-alpha-D-ribose 1-phosphate  (ISO)
2-deoxy-D-ribofuranose 1-phosphate  (ISO)
4'-epidoxorubicin  (ISO)
4-amino-2,6-dinitrotoluene  (EXP)
5-fluorouracil  (ISO)
5-formyltetrahydrofolic acid  (ISO)
acetamide  (EXP)
acetylleucyl-leucyl-norleucinal  (ISO)
acetylsalicylic acid  (ISO)
actinomycin D  (ISO)
antirheumatic drug  (ISO)
arsenous acid  (ISO)
Aurothioglucose  (ISO)
benzo[a]pyrene  (ISO)
beta-carotene  (ISO)
bisphenol A  (EXP,ISO)
calcitriol  (ISO)
chromium(6+)  (ISO)
cisplatin  (ISO)
Cuprizon  (EXP)
curcumin  (ISO)
cycloheximide  (ISO)
cyclophosphamide  (ISO)
cyclosporin A  (ISO)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
dibenz[a,h]anthracene  (ISO)
dioxygen  (ISO)
doxifluridine  (EXP,ISO)
doxorubicin  (ISO)
elemental selenium  (ISO)
fipronil  (EXP)
folic acid  (ISO)
formaldehyde  (ISO)
fumonisin B1  (ISO)
furan  (EXP)
gemcitabine  (ISO)
glyphosate  (EXP)
gossypol  (ISO)
hydrazine  (ISO)
irinotecan  (ISO)
ivermectin  (ISO)
Lasiocarpine  (ISO)
mitomycin C  (ISO)
N-acetyl-L-cysteine  (ISO)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
N-nitrosodiethylamine  (EXP)
nickel atom  (ISO)
nickel sulfate  (ISO)
nitrofen  (EXP)
nocodazole  (ISO)
obeticholic acid  (ISO)
oxaliplatin  (ISO)
ozone  (ISO)
paclitaxel  (ISO)
paracetamol  (ISO)
pemetrexed  (ISO)
phenobarbital  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
pirinixic acid  (ISO)
propiconazole  (ISO)
rotenone  (EXP)
Salinomycin  (ISO)
SB 203580  (ISO)
selenium atom  (ISO)
silicon dioxide  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sodium dodecyl sulfate  (ISO)
stavudine  (ISO)
sulfasalazine  (ISO)
tanespimycin  (ISO)
temozolomide  (ISO)
tert-butyl hydroperoxide  (ISO)
testosterone  (ISO)
thioacetamide  (EXP)
thymidine  (ISO)
thymine  (ISO)
titanium dioxide  (ISO)
triclosan  (ISO)
valproic acid  (ISO)
vincristine  (ISO)
vitamin E  (ISO)
zalcitabine  (ISO)
zidovudine  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

References

References - curated
1. Aishima S, etal., Int J Surg Pathol. 2002 Jan;10(1):47-56.
2. Brown NS, etal., Br J Cancer. 2005 May 9;92(9):1696-701.
3. Engels K, etal., J Pathol. 1997 Aug;182(4):414-20.
4. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
5. GOA data from the GO Consortium
6. Harino Y, etal., Int J Clin Oncol. 2008 Oct;13(5):452-7. Epub 2008 Oct 23.
7. Hong SP, etal., Hepatogastroenterology. 2009 Jul-Aug;56(93):1178-82.
8. Jones A, etal., BJU Int. 2000 Jul;86(1):80-6.
9. Kubiak R, etal., Z Naturforsch C. 1999 Dec;54(12):1096-102.
10. Lu H, etal., Clin Cancer Res. 2009 Aug 15;15(16):5136-44. Epub 2009 Aug 11.
11. Mazurek A, etal., Neoplasma. 2008;55(3):261-5.
12. MGD data from the GO Consortium
13. Miszczak-Zaborska E, etal., Gynecol Oncol. 2004 Jul;94(1):86-92.
14. Morimoto Y, etal., Gan To Kagaku Ryoho. 2004 Dec;31(13):2195-8.
15. Nakashima M, etal., Int J Gynecol Cancer. 2006 May-Jun;16(3):1309-13.
16. Nishino I, etal., Science. 1999 Jan 29;283(5402):689-92.
17. Nonomura N, etal., Int J Clin Oncol. 2006 Aug;11(4):297-302.
18. OMIM Disease Annotation Pipeline
19. Pipeline to import KEGG annotations from KEGG into RGD
20. Pipeline to import SMPDB annotations from SMPDB into RGD
21. Puglisi F, etal., Ann Oncol. 2008 Apr 25;.
22. RGD automated data pipeline
23. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
24. RGD automated import pipeline for gene-chemical interactions
25. RGD comprehensive gene curation
26. Takayama T, etal., Jpn J Clin Oncol. 2006 Sep;36(9):564-9. Epub 2006 Jul 22.
27. Wada S, etal., BJU Int. 2003 Jan;91(1):105-8.
28. Yanagi Y, etal., Invest Ophthalmol Vis Sci. 2003 Feb;44(2):751-4.
29. Yu ZG, etal., Zhonghua Yi Xue Za Zhi. 2006 Jun 13;86(22):1558-63.
30. Zhao B, etal., Jpn J Cancer Res. 2000 Mar;91(3):331-6.
Additional References at PubMed
PMID:1590793   PMID:7284378   PMID:12477932   PMID:17681069  


Genomics

Comparative Map Data
Tymp
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.27120,438,768 - 120,444,088 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl7120,438,770 - 120,443,874 (-)Ensembl
mRatBN7.2 Ensembl7120,438,125 - 120,447,429 (-)Ensembl
Rnor_6.07130,342,481 - 130,347,845 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7130,342,483 - 130,347,587 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.07130,027,662 - 130,033,050 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47127,666,518 - 127,671,624 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.17127,700,749 - 127,705,854 (-)NCBI
Celera7116,911,732 - 116,916,838 (-)NCBICelera
Cytogenetic Map7q34NCBI
TYMP
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2250,525,752 - 50,530,032 (-)EnsemblGRCh38hg38GRCh38
GRCh382250,525,752 - 50,530,085 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh372250,964,181 - 50,968,514 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362249,311,047 - 49,315,321 (-)NCBINCBI36hg18NCBI36
Build 342249,254,324 - 49,258,599NCBI
Celera2234,840,208 - 34,844,541 (-)NCBI
Cytogenetic Map22q13.33ENTREZGENE
HuRef2233,855,199 - 33,859,532 (-)NCBIHuRef
CHM1_12250,922,918 - 50,927,220 (-)NCBICHM1_1
Tymp
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391589,255,834 - 89,261,239 (-)NCBIGRCm39mm39
GRCm39 Ensembl1589,256,134 - 89,261,242 (-)Ensembl
GRCm381589,371,631 - 89,377,036 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1589,371,931 - 89,377,039 (-)EnsemblGRCm38mm10GRCm38
MGSCv371589,202,362 - 89,207,467 (-)NCBIGRCm37mm9NCBIm37
MGSCv361589,199,698 - 89,204,803 (-)NCBImm8
Celera1591,501,072 - 91,506,177 (-)NCBICelera
Cytogenetic Map15E3NCBI
cM Map1544.86NCBI
Tymp
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541333,505,446 - 33,508,748 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495541333,505,424 - 33,509,095 (-)NCBIChiLan1.0ChiLan1.0
TYMP
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12249,883,129 - 49,886,996 (-)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v02230,772,088 - 30,776,618 (-)NCBIMhudiblu_PPA_v0panPan3
LOC101977033
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404945315,033 - 319,093 (+)NCBI
SpeTri2.0NW_004936629315,609 - 320,356 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LOC103223569
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11932,997,337 - 33,001,558 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1932,997,304 - 33,001,215 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604592,341,070 - 92,345,265 (+)NCBIVero_WHO_p1.0
Tymp
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624752251,670 - 256,243 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
RH128722  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27120,438,507 - 120,438,709 (+)MAPPERmRatBN7.2
Rnor_6.07130,342,221 - 130,342,422NCBIRnor6.0
Rnor_5.07130,027,402 - 130,027,603UniSTSRnor5.0
RGSC_v3.47127,666,258 - 127,666,459UniSTSRGSC3.4
Celera7116,911,472 - 116,911,673UniSTS
RH 3.4 Map7948.7UniSTS
Cytogenetic Map7q34UniSTS
RH129073  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27120,439,749 - 120,439,903 (+)MAPPERmRatBN7.2
Rnor_6.07130,343,463 - 130,343,616NCBIRnor6.0
Rnor_5.07130,028,644 - 130,028,797UniSTSRnor5.0
RGSC_v3.47127,667,500 - 127,667,653UniSTSRGSC3.4
Celera7116,912,714 - 116,912,867UniSTS
RH 3.4 Map7958.5UniSTS
Cytogenetic Map7q34UniSTS
RH139883  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27120,438,861 - 120,439,050 (+)MAPPERmRatBN7.2
Rnor_6.07130,342,575 - 130,342,763NCBIRnor6.0
Rnor_5.07130,027,756 - 130,027,944UniSTSRnor5.0
RGSC_v3.47127,666,612 - 127,666,800UniSTSRGSC3.4
Celera7116,911,826 - 116,912,014UniSTS
RH 3.4 Map7961.8UniSTS
Cytogenetic Map7q34UniSTS
RH136025  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27120,439,191 - 120,439,377 (+)MAPPERmRatBN7.2
Rnor_6.07130,342,905 - 130,343,090NCBIRnor6.0
Rnor_5.07130,028,086 - 130,028,271UniSTSRnor5.0
RGSC_v3.47127,666,942 - 127,667,127UniSTSRGSC3.4
Celera7116,912,156 - 116,912,341UniSTS
Cytogenetic Map7q34UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1300179Kidm5Kidney mass QTL 53.51kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)743747012135012528Rat
70173Niddm19Non-insulin dependent diabetes mellitus QTL 194.330.00005blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)764002457135012528Rat
634331Pia17Pristane induced arthritis QTL 174.7joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)773829340130221005Rat
7411654Foco25Food consumption QTL 259.30.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)775918751120918751Rat
7411607Foco15Food consumption QTL 150.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)775918751120918751Rat
1331728Bp214Blood pressure QTL 2142.825arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)780221299124373579Rat
1331768Kidm10Kidney mass QTL 104.62096kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)780221299125221299Rat
2317052Aia17Adjuvant induced arthritis QTL 172.13joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)781737938126737938Rat
634322Bw12Body weight QTL 120body mass (VT:0001259)body weight (CMO:0000012)783153392128153392Rat
1358891Bp265Blood pressure QTL 2652.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)783591953134666232Rat
1358914Bp266Blood pressure QTL 266arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)783591953134666232Rat
71114Niddm14Non-insulin dependent diabetes mellitus QTL 144.5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)784257275129257275Rat
2298475Eau6Experimental allergic uveoretinitis QTL 60.0029uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)784257275129257275Rat
1558655Swd4Spike wave discharge measurement QTL 43.680.0002brain electrophysiology trait (VT:0010557)brain spike-and-wave discharge severity grade (CMO:0001988)786983365131983365Rat
1549899Stresp8Stress response QTL 84.370.0008stress-related behavior trait (VT:0010451)defensive burying duration (CMO:0001961)790482196135012528Rat
2299163Iddm34Insulin dependent diabetes mellitus QTL 342.71blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)791281130135012528Rat
631687Hcas1Hepatocarcinoma susceptibility QTL 13.90.001liver integrity trait (VT:0010547)liver tumorous lesion volume to total liver volume ratio (CMO:0001082)791412594129807172Rat
731176Glom5Glomerulus QTL 52.50.0035kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)796670164135012528Rat
1331731Bp216Blood pressure QTL 2162.851arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7102297359133492884Rat
731174Uae23Urinary albumin excretion QTL 232.40.0042urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)7104603555135012528Rat
2306821Bp335Blood pressure QTL 3350.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7106571501135012528Rat
631663Bw6Body weight QTL 63.4body mass (VT:0001259)body weight (CMO:0000012)7111075573134976056Rat
1300112Bp183Blood pressure QTL 1833.51arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)7111182207135012528Rat
1331748Bp215Blood pressure QTL 2154.043arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7112308254133492884Rat
1357339Stl14Serum triglyceride level QTL 143.450.0001blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)7112729683133492707Rat
1582240Sffal1Serum free fatty acids level QTL 13.40.0021blood free fatty acid amount (VT:0001553)serum free fatty acids level (CMO:0000547)7116677010124049952Rat
631201Panci1Pancreas inflammation QTL 100.001pancreas integrity trait (VT:0010560)percentage of study population displaying chronic pancreatitis at a point in time (CMO:0001214)7116677189127103496Rat
1354582Stl11Serum triglyceride level QTL 113.42blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)7119513385135012528Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:100
Count of miRNA genes:84
Interacting mature miRNAs:88
Transcripts:ENSRNOT00000040541
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 3 3 41 25 19 25 1 3 50 12 15 11 1
Low 40 16 16 16 7 8 24 23 26 7
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001012122 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006242209 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008765730 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008765734 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017594882 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017594883 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017594884 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079309 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079310 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079311 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079312 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079313 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079314 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079315 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005486647 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005486648 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005486649 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC125982 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC089830 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH474027 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000187 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000040541   ⟹   ENSRNOP00000039935
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7120,438,770 - 120,443,874 (-)Ensembl
Rnor_6.0 Ensembl7130,342,483 - 130,347,587 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000095915   ⟹   ENSRNOP00000091776
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7120,438,125 - 120,441,206 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000096628   ⟹   ENSRNOP00000084065
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7120,438,125 - 120,447,429 (-)Ensembl
RefSeq Acc Id: NM_001012122   ⟹   NP_001012122
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27120,438,768 - 120,443,874 (-)NCBI
Rnor_6.07130,342,481 - 130,347,587 (-)NCBI
Rnor_5.07130,027,662 - 130,033,050 (-)NCBI
RGSC_v3.47127,666,518 - 127,671,624 (-)RGD
Celera7116,911,732 - 116,916,838 (-)RGD
Sequence:
RefSeq Acc Id: XM_006242209   ⟹   XP_006242271
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27120,438,768 - 120,444,088 (-)NCBI
Rnor_6.07130,342,481 - 130,347,685 (-)NCBI
Rnor_5.07130,027,662 - 130,033,050 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008765730   ⟹   XP_008763952
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27120,438,768 - 120,444,088 (-)NCBI
Rnor_6.07130,342,481 - 130,347,685 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008765734   ⟹   XP_008763956
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27120,438,768 - 120,440,844 (-)NCBI
Rnor_6.07130,342,481 - 130,344,356 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039079309   ⟹   XP_038935237
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27120,438,768 - 120,444,088 (-)NCBI
RefSeq Acc Id: XM_039079310   ⟹   XP_038935238
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27120,438,768 - 120,444,088 (-)NCBI
RefSeq Acc Id: XM_039079311   ⟹   XP_038935239
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27120,438,768 - 120,442,030 (-)NCBI
RefSeq Acc Id: XM_039079312   ⟹   XP_038935240
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27120,439,463 - 120,444,088 (-)NCBI
RefSeq Acc Id: XM_039079313   ⟹   XP_038935241
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27120,439,462 - 120,444,088 (-)NCBI
RefSeq Acc Id: XM_039079314   ⟹   XP_038935242
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27120,439,462 - 120,444,088 (-)NCBI
RefSeq Acc Id: XM_039079315   ⟹   XP_038935243
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27120,438,768 - 120,442,036 (-)NCBI
RefSeq Acc Id: XR_005486647
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27120,439,462 - 120,444,088 (-)NCBI
RefSeq Acc Id: XR_005486648
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27120,439,463 - 120,444,088 (-)NCBI
RefSeq Acc Id: XR_005486649
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27120,439,463 - 120,444,088 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001012122   ⟸   NM_001012122
- UniProtKB: Q5FVR2 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006242271   ⟸   XM_006242209
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_008763952   ⟸   XM_008765730
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008763956   ⟸   XM_008765734
- Peptide Label: isoform X9
- Sequence:
RefSeq Acc Id: ENSRNOP00000039935   ⟸   ENSRNOT00000040541
RefSeq Acc Id: XP_038935238   ⟸   XM_039079310
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038935237   ⟸   XM_039079309
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038935243   ⟸   XM_039079315
- Peptide Label: isoform X9
RefSeq Acc Id: XP_038935239   ⟸   XM_039079311
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038935242   ⟸   XM_039079314
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038935241   ⟸   XM_039079313
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038935240   ⟸   XM_039079312
- Peptide Label: isoform X6
RefSeq Acc Id: ENSRNOP00000091776   ⟸   ENSRNOT00000095915
RefSeq Acc Id: ENSRNOP00000084065   ⟸   ENSRNOT00000096628

Transcriptome

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

Promoters
RGD ID:13695587
Promoter ID:EPDNEW_R6111
Type:multiple initiation site
Name:Tymp_1
Description:thymidine phosphorylase
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_6.07130,347,611 - 130,347,671EPDNEW

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)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (MCW)
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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
Damaging Variants


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
7 130346957 130346958 A G snv WKY/N (MCW)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
7 127670994 127670995 A G snv WKY/N (KNAW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1305756 AgrOrtholog
Ensembl Genes ENSRNOG00000032394 Ensembl, UniProtKB/Swiss-Prot
  ENSRNOG00000066458 Ensembl
Ensembl Protein ENSRNOP00000039935 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000040541 UniProtKB/Swiss-Prot
Gene3D-CATH 3.40.1030.10 UniProtKB/Swiss-Prot
  3.90.1170.30 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7323197 IMAGE-MGC_LOAD
InterPro Glycosyl_Trfase_fam3 UniProtKB/Swiss-Prot
  Glycosyl_Trfase_fam3_N_dom UniProtKB/Swiss-Prot
  Glycosyl_Trfase_fam3_N_dom)sf UniProtKB/Swiss-Prot
  Nuc_phospho_transferase UniProtKB/Swiss-Prot
  PYNP-like_C_sf UniProtKB/Swiss-Prot
  PYNP_C UniProtKB/Swiss-Prot
  Pyrmidine_PPas_bac/euk UniProtKB/Swiss-Prot
  Thymidine/pyrmidine_PPase UniProtKB/Swiss-Prot
KEGG Report rno:315219 UniProtKB/Swiss-Prot
MGC_CLONE MGC:108801 IMAGE-MGC_LOAD
NCBI Gene 315219 ENTREZGENE
PANTHER PTHR10515 UniProtKB/Swiss-Prot
Pfam Glycos_trans_3N UniProtKB/Swiss-Prot
  Glycos_transf_3 UniProtKB/Swiss-Prot
  PYNP_C UniProtKB/Swiss-Prot
PharmGKB TYMP RGD
PhenoGen Tymp PhenoGen
PIRSF TP_PyNP UniProtKB/Swiss-Prot
SMART PYNP_C UniProtKB/Swiss-Prot
Superfamily-SCOP SSF47648 UniProtKB/Swiss-Prot
  SSF52418 UniProtKB/Swiss-Prot
  SSF54680 UniProtKB/Swiss-Prot
TIGRFAMs Y_phosphoryl UniProtKB/Swiss-Prot
UniProt Q5FVR2 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-04 Tymp  thymidine phosphorylase  Ecgf1  endothelial cell growth factor 1 (platelet-derived)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 Ecgf1  endothelial cell growth factor 1 (platelet-derived)  Ecgf1_predicted  endothelial cell growth factor 1 (platelet-derived) (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Ecgf1_predicted  endothelial cell growth factor 1 (platelet-derived) (predicted)      Symbol and Name status set to approved 70820 APPROVED