Tnc (tenascin C) - Rat Genome Database

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Gene: Tnc (tenascin C) Rattus norvegicus
Analyze
Symbol: Tnc
Name: tenascin C
RGD ID: 621057
Description: Predicted to enable syndecan binding activity. Involved in several processes, including animal organ morphogenesis; cellular response to lipid; and cellular response to prostaglandin D stimulus. Located in extracellular matrix. Used to study pulmonary hypertension. Biomarker of cholangiocarcinoma; high grade glioma; myocardial infarction; polycystic kidney disease; and pulmonary hypertension. Human ortholog(s) of this gene implicated in allergic conjunctivitis; asthma; and autosomal dominant nonsyndromic deafness 56. Orthologous to human TNC (tenascin C); PARTICIPATES IN syndecan signaling pathway; cell-extracellular matrix signaling pathway; INTERACTS WITH (+)-pilocarpine; 1-naphthyl isothiocyanate; 11-deoxycorticosterone.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: tenascin; tenascin-C AD1 domain; Tn-C AD1
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
mRatBN7.2577,375,851 - 77,460,712 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl577,375,851 - 77,460,624 (-)Ensembl
Rnor_6.0579,789,686 - 79,874,555 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl579,789,671 - 79,874,671 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0583,890,952 - 83,950,462 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera576,306,295 - 76,365,869 (-)NCBICelera
Cytogenetic Map5q24NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-pilocarpine  (EXP)
1,2-dimethylhydrazine  (ISO)
1-naphthyl isothiocyanate  (EXP)
11-deoxycorticosterone  (EXP)
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4,6-trinitrobenzenesulfonic acid  (ISO)
2,6-di-tert-butyl-4-methylphenol  (ISO)
2-methylcholine  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3-methylcholanthrene  (ISO)
4,4'-sulfonyldiphenol  (ISO)
5-aza-2'-deoxycytidine  (ISO)
5-azacytidine  (ISO)
6-propyl-2-thiouracil  (EXP)
8-Br-cAMP  (ISO)
acrolein  (ISO)
acrylamide  (EXP,ISO)
aflatoxin B1  (ISO)
alachlor  (EXP)
all-trans-retinoic acid  (ISO)
alpha-pinene  (ISO)
antimycin A  (ISO)
antirheumatic drug  (ISO)
aristolochic acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
azoxystrobin  (ISO)
belinostat  (ISO)
benzene  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
benzo[b]fluoranthene  (ISO)
beta-naphthoflavone  (EXP)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
bleomycin A2  (ISO)
bucladesine  (ISO)
butan-1-ol  (ISO)
butanal  (ISO)
butane-2,3-dione  (EXP)
cadmium atom  (ISO)
calcitriol  (ISO)
capsaicin  (ISO)
carbamazepine  (ISO)
carbon nanotube  (ISO)
carmustine  (ISO)
chloroprene  (ISO)
choline  (ISO)
chrysene  (ISO)
cisplatin  (EXP,ISO)
copper atom  (EXP,ISO)
copper(0)  (EXP,ISO)
corticosterone  (EXP)
Cuprizon  (EXP)
curcumin  (ISO)
cyclosporin A  (ISO)
Deguelin  (ISO)
dexamethasone  (ISO)
diazepam  (ISO)
diethyl malate  (ISO)
diisononyl phthalate  (ISO)
dioxygen  (ISO)
dopamine  (EXP)
dorsomorphin  (ISO)
doxorubicin  (ISO)
entinostat  (ISO)
ethanol  (EXP,ISO)
ethyl methanesulfonate  (ISO)
fenamidone  (ISO)
fenoldopam  (EXP)
fenpyroximate  (ISO)
fenvalerate  (EXP)
folic acid  (ISO)
formaldehyde  (ISO)
furan  (EXP)
genistein  (ISO)
glycidol  (EXP)
hesperidin  (EXP)
ibuprofen  (ISO)
isobutanol  (ISO)
L-methionine  (ISO)
lead diacetate  (EXP,ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
lithium chloride  (ISO)
losartan  (EXP)
medroxyprogesterone acetate  (ISO)
megestrol acetate  (EXP)
methotrexate  (ISO)
methyl methanesulfonate  (ISO)
methylmercury chloride  (ISO)
mifepristone  (EXP)
N-methyl-N'-nitro-N-nitrosoguanidine  (ISO)
N-nitrosodiethylamine  (EXP)
naphthalene  (ISO)
nickel atom  (ISO)
nickel sulfate  (ISO)
nitrofen  (EXP)
oxaliplatin  (EXP)
ozone  (ISO)
paclitaxel  (ISO)
paracetamol  (ISO)
paraquat  (EXP,ISO)
pentane-2,3-dione  (EXP)
phorbol 13-acetate 12-myristate  (ISO)
picoxystrobin  (ISO)
pirinixic acid  (ISO)
progesterone  (ISO)
Ptaquiloside  (ISO)
pyrimidifen  (ISO)
quercetin  (EXP)
raloxifene  (ISO)
rofecoxib  (ISO)
rotenone  (ISO)
Salinomycin  (ISO)
SB 431542  (ISO)
serpentine asbestos  (ISO)
silicon dioxide  (EXP,ISO)
silver atom  (ISO)
silver(0)  (ISO)
simvastatin  (EXP)
sodium arsenite  (ISO)
sodium dodecyl sulfate  (ISO)
sodium fluoride  (ISO)
Soman  (EXP)
spironolactone  (EXP)
sulforaphane  (ISO)
tamoxifen  (ISO)
tebufenpyrad  (ISO)
temozolomide  (ISO)
tert-butyl hydroperoxide  (ISO)
tetrachloromethane  (ISO)
tetraphene  (ISO)
thapsigargin  (ISO)
thifluzamide  (ISO)
titanium dioxide  (ISO)
topotecan  (EXP)
tremolite asbestos  (ISO)
trichostatin A  (ISO)
triptonide  (ISO)
tunicamycin  (ISO)
valproic acid  (ISO)
vorinostat  (ISO)
XL147  (ISO)
zidovudine  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)
zoledronic acid  (ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Alvarez-Dolado M, etal., J Neurosci Res. 1999 Oct 15;58(2):293-300.
2. Andrews MR, etal., J Neurosci. 2009 Apr 29;29(17):5546-57.
3. Avivi-Green C, etal., Am J Respir Crit Care Med. 2006 Aug 15;174(4):420-7. Epub 2006 May 11.
4. Carey WA, etal., Am J Physiol Lung Cell Mol Physiol. 2010 Sep 10.
5. Correia-Pinto J, etal., Basic Res Cardiol. 2009 Sep;104(5):535-45. Epub 2009 Mar 14.
6. Deckner M, etal., Exp Neurol. 2000 Dec;166(2):350-62.
7. Dumur CI, etal., Exp Mol Pathol. 2010 Dec;89(3):227-35. Epub 2010 Sep 9.
8. Eliasson P, etal., J Appl Physiol. 2009 Aug;107(2):399-407. Epub 2009 Jun 18.
9. Hisatomi K, etal., Intern Med. 2009;48(17):1501-7. Epub 2009 Sep 1.
10. Ihida-Stansbury K, etal., Am J Physiol Lung Cell Mol Physiol. 2006 Oct;291(4):L694-702. Epub 2006 Jun 16.
11. Imanaka-Yoshida K, etal., Lab Invest. 2001 Jul;81(7):1015-24.
12. Kaarteenaho-Wiik R, etal., Histopathology. 2003 Mar;42(3):280-91.
13. Kaarteenaho-Wiik R, etal., J Histochem Cytochem. 2000 Sep;48(9):1257-68.
14. Kaarteenaho-Wiik R, etal., Lung. 1998;176(6):371-80.
15. LaFleur DW, etal., J Biol Chem 1994 Aug 12;269(32):20757-63.
16. Laitinen A, etal., Am J Respir Crit Care Med. 1997 Sep;156(3 Pt 1):951-8.
17. Matias MA, etal., Arch Oral Biol. 2003 Oct;48(10):709-16.
18. Matsuda A, etal., Hum Mol Genet. 2005 Oct 1;14(19):2779-86. Epub 2005 Aug 22.
19. Nakahara H, etal., Eur J Immunol. 2006 Dec;36(12):3334-45.
20. NCBI rat LocusLink and RefSeq merged data July 26, 2002
21. Nishimura T, etal., Histol Histopathol. 2008 Feb;23(2):157-66.
22. OMIM Disease Annotation Pipeline
23. Orsmark-Pietras C, etal., Hum Mol Genet. 2008 Jun 1;17(11):1673-82. Epub 2008 Feb 27.
24. Pipeline to import KEGG annotations from KEGG into RGD
25. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
26. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
27. RGD automated import pipeline for gene-chemical interactions
28. RGD comprehensive gene curation
29. Schermuly RT, etal., Am J Respir Crit Care Med. 2005 Aug 1;172(3):358-63. Epub 2005 May 5.
30. Schumann C, etal., Biomarkers. 2010 Sep;15(6):523-32.
31. Silacci M, etal., Protein Eng Des Sel. 2006 Oct;19(10):471-8. Epub 2006 Aug 22.
32. Sun G, etal., Lin Chuang Er Bi Yan Hou Ke Za Zhi. 2003 May;17(5):279-80.
33. Suzuki H, etal., Neurol Res. 2010 Mar;32(2):179-84. Epub 2009 Jul 8.
34. Suzuki S, etal., Neuroreport. 2002 Jun 12;13(8):1041-5.
35. Taki J, etal., J Nucl Med. 2010 Jul;51(7):1116-22. Epub 2010 Jun 16.
36. Tang X, etal., J Neurosci Res 2003 Feb 1;71(3):427-44.
37. Turan Akay M and Arzu Kockaya E, Cell Biochem Funct. 2005 Nov-Dec;23(6):435-45.
38. Whitehead GS, etal., Immunogenetics. 2006 Oct;58(10):793-804. Epub 2006 Sep 26.
Additional References at PubMed
PMID:7512960   PMID:7687262   PMID:8769660   PMID:8856503   PMID:9013311   PMID:9182584   PMID:9593587   PMID:11767049   PMID:11882319   PMID:14568337   PMID:14604154   PMID:15178565  
PMID:15196921   PMID:15646290   PMID:15655118   PMID:15780469   PMID:16210410   PMID:16262655   PMID:16452087   PMID:16461331   PMID:16502470   PMID:16551009   PMID:16891397   PMID:18294871  
PMID:18950615   PMID:19459213   PMID:19690384   PMID:19710535   PMID:20451518   PMID:20551380   PMID:20592347   PMID:21423176   PMID:21586275   PMID:21792920   PMID:21968644   PMID:23099153  
PMID:23658023   PMID:24006456   PMID:24998028   PMID:25028133   PMID:25445237   PMID:25957016   PMID:26770971   PMID:27031437   PMID:27068509   PMID:27374750   PMID:27559042   PMID:28363952  
PMID:28447748   PMID:31494663   PMID:31706751  


Genomics

Comparative Map Data
Tnc
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2577,375,851 - 77,460,712 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl577,375,851 - 77,460,624 (-)Ensembl
Rnor_6.0579,789,686 - 79,874,555 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl579,789,671 - 79,874,671 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0583,890,952 - 83,950,462 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera576,306,295 - 76,365,869 (-)NCBICelera
Cytogenetic Map5q24NCBI
TNC
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl9115,019,575 - 115,118,257 (-)EnsemblGRCh38hg38GRCh38
GRCh389115,019,575 - 115,118,244 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh379117,781,854 - 117,880,436 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 369116,822,626 - 116,920,307 (-)NCBINCBI36hg18NCBI36
Build 349114,862,366 - 114,959,993NCBI
Celera988,430,273 - 88,527,747 (-)NCBI
Cytogenetic Map9q33.1NCBI
HuRef987,386,539 - 87,484,951 (-)NCBIHuRef
CHM1_19117,928,574 - 118,027,020 (-)NCBICHM1_1
Tnc
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39463,878,022 - 63,965,554 (-)NCBIGRCm39mm39
GRCm39 Ensembl463,878,022 - 63,965,252 (-)Ensembl
GRCm38463,959,785 - 64,047,015 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl463,959,785 - 64,047,015 (-)EnsemblGRCm38mm10GRCm38
MGSCv37463,620,819 - 63,681,760 (-)NCBIGRCm37mm9NCBIm37
MGSCv36463,446,149 - 63,507,087 (-)NCBImm8
Celera462,620,454 - 62,681,423 (-)NCBICelera
Cytogenetic Map4C1NCBI
cM Map434.06NCBI
Tnc
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541912,569,547 - 12,662,958 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495541912,569,620 - 12,662,897 (+)NCBIChiLan1.0ChiLan1.0
LOC100977568
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.19114,486,778 - 114,584,297 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl9114,486,778 - 114,584,299 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0986,125,672 - 86,222,804 (-)NCBIMhudiblu_PPA_v0panPan3
TNC
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11169,077,532 - 69,169,673 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1169,077,535 - 69,170,281 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1167,478,996 - 67,543,867 (-)NCBI
ROS_Cfam_1.01170,201,293 - 70,293,471 (-)NCBI
UMICH_Zoey_3.11168,715,128 - 68,780,124 (-)NCBI
UNSW_CanFamBas_1.01168,756,416 - 68,820,385 (-)NCBI
UU_Cfam_GSD_1.01169,487,404 - 69,552,684 (-)NCBI
Tnc
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947184,403,727 - 184,487,858 (-)NCBI
SpeTri2.0NW_0049364874,172,263 - 4,256,780 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TNC
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1255,532,449 - 255,630,377 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11255,533,235 - 255,630,381 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21286,732,751 - 286,813,962 (-)NCBISscrofa10.2Sscrofa10.2susScr3
Pig Cytomap1q21.1-q21.3NCBI
TNC
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11224,457,616 - 24,556,194 (+)NCBI
ChlSab1.1 Ensembl1224,457,738 - 24,556,451 (+)Ensembl
Vero_WHO_p1.0NW_02366603518,276,825 - 18,375,675 (-)NCBI
Tnc
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462476020,044,900 - 20,137,260 (+)NCBI

Position Markers
RH130033  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2577,375,961 - 77,376,141 (+)MAPPERmRatBN7.2
Rnor_6.0579,789,797 - 79,789,976NCBIRnor6.0
Rnor_5.0583,890,474 - 83,890,653UniSTSRnor5.0
Celera576,305,817 - 76,305,996UniSTS
RH 3.4 Map5581.6UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1331756Rf34Renal function QTL 344.16275kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5190450412Rat
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51131345958Rat
1331771Rf35Renal function QTL 354.36965kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)572947086724018Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
7394712Emca13Estrogen-induced mammary cancer QTL 13mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)5982326699753708Rat
634305Mamtr1Mammary tumor resistance QTL 10.0001mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)512789751113558310Rat
2290448Scl54Serum cholesterol level QTL 542.93blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)531663789131345958Rat
1598807Glom12Glomerulus QTL 122.7kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)53321566578215665Rat
1298067Scl15Serum cholesterol level QTL 154.80.001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)53321566578215665Rat
1302786Kidm8Kidney mass QTL 828.15kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)53321566578215665Rat
1576317Eutr2Estrogen induced uterine response QTL 20.01uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)534730116104251008Rat
2316959Gluco59Glucose level QTL 594.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)534944474113558310Rat
1641912Alcrsp18Alcohol response QTL 18response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)535189153141643988Rat
1549845Scl44Serum cholesterol level QTL 446blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)540128307148607290Rat
1331773Scl26Serum cholesterol level QTL 263.065blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)54372665686724018Rat
1331801Rf33Renal function QTL 334.149kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)543726656129132602Rat
1578766Tcas11Tongue tumor susceptibility QTL 114.12tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)546711509161317411Rat
1300115Hrtrt7Heart rate QTL 72.76heart pumping trait (VT:2000009)heart rate (CMO:0000002)54786906290099692Rat
9589025Epfw7Epididymal fat weight QTL 720.660.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)54946360094463600Rat
7411561Bw134Body weight QTL 134240.001body mass (VT:0001259)body weight gain (CMO:0000420)54946360094463600Rat
1576312Emca8Estrogen-induced mammary cancer QTL 84.1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)550328551141643988Rat
2303615Vencon7Ventilatory control QTL 70.001respiration trait (VT:0001943)respiration rate (CMO:0000289)55098389595983895Rat
2303574Gluco42Glucose level QTL 422blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)55349671998496719Rat
61359EaexExperimental allergic encephalomyelitis QTL x3nervous system integrity trait (VT:0010566)post-insult time to onset of experimental autoimmune encephalomyelitis (CMO:0001422)555715622100715622Rat
70189Mcs5Mammary carcinoma susceptibility QTL 510.51mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)555805606132207589Rat
1358895Bp254Blood pressure QTL 2543.60.0003arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)558829236128034027Rat
61426Scl2Serum cholesterol level QTL 27.30.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)559793399143070159Rat
2316954Rf57Renal function QTL 570kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)55979352890450144Rat
2316957Pur21Proteinuria QTL 216.2urine protein amount (VT:0005160)urine protein level (CMO:0000591)559793528113558156Rat
61386Bp49Blood pressure QTL 4916.6cerebrum integrity trait (VT:0010549)brain infarction volume (CMO:0001013)56029343498603051Rat
61393Bp7Blood pressure QTL 74.50.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)560293434161481680Rat
2290005Mcs24Mammary carcinoma susceptibility QTL 24mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)564719390109719390Rat
2306971Anxrr21Anxiety related response QTL 219.47fear/anxiety-related behavior trait (VT:1000241)number of entries into a discrete space in an experimental apparatus (CMO:0000960)566174080124160948Rat
2312671Scl64Serum cholesterol level QTL 640.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)568984307104251008Rat
61380Edpm5Estrogen-dependent pituitary mass QTL 54.50.92pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)568984307104251008Rat
1357396Bw44Body weight QTL 444.19body mass (VT:0001259)body weight (CMO:0000012)568984307104251008Rat
1357402Bw46Body weight QTL 464.47body mass (VT:0001259)body mass index (BMI) (CMO:0000105)568984307104251008Rat
2302381Bw84Body weight QTL 844.47body mass (VT:0001259)body mass index (BMI) (CMO:0000105)568984307104251008Rat
1354598Srn6Serum renin concentration QTL 63.8blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)569540295151018848Rat
1598845Mcs14Mammary carcinoma susceptibility QTL 140.0001mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)57636977680813390Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:87
Count of miRNA genes:74
Interacting mature miRNAs:76
Transcripts:ENSRNOT00000075051
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 2 26 11 4 7 4 3 4 51 26 32 11 3
Low 1 13 34 25 11 25 5 7 23 9 8 5
Below cutoff 4 11 11 1 11 1

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_053861 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008763754 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008763755 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008763756 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008763757 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008763758 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039109145 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039109146 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039109147 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039109148 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039109150 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC229945 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC229948 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DQ916292 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  EU596506 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FN665804 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000161 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U09361 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U09400 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U09401 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U15550 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000084563   ⟹   ENSRNOP00000071884
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl577,375,851 - 77,460,624 (-)Ensembl
Rnor_6.0 Ensembl579,789,671 - 79,874,671 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000102414   ⟹   ENSRNOP00000089121
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl577,376,440 - 77,436,038 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000107729   ⟹   ENSRNOP00000093442
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl577,376,440 - 77,436,038 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000109041   ⟹   ENSRNOP00000091808
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl577,376,440 - 77,436,038 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000117346   ⟹   ENSRNOP00000096828
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl577,375,851 - 77,460,624 (-)Ensembl
RefSeq Acc Id: NM_053861   ⟹   NP_446313
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2577,376,440 - 77,436,038 (-)NCBI
Rnor_6.0579,790,275 - 79,849,865 (-)NCBI
Rnor_5.0583,890,952 - 83,950,462 (-)NCBI
Celera576,306,295 - 76,365,869 (-)RGD
Sequence:
RefSeq Acc Id: XM_008763754   ⟹   XP_008761976
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2577,375,851 - 77,460,712 (-)NCBI
Rnor_6.0579,789,686 - 79,874,555 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008763755   ⟹   XP_008761977
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2577,375,851 - 77,460,712 (-)NCBI
Rnor_6.0579,789,686 - 79,874,555 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008763756   ⟹   XP_008761978
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2577,375,851 - 77,460,712 (-)NCBI
Rnor_6.0579,789,686 - 79,874,554 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008763757   ⟹   XP_008761979
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2577,375,851 - 77,460,711 (-)NCBI
Rnor_6.0579,789,686 - 79,874,553 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008763758   ⟹   XP_008761980
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2577,375,851 - 77,460,709 (-)NCBI
Rnor_6.0579,789,686 - 79,874,549 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039109145   ⟹   XP_038965073
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2577,375,851 - 77,460,711 (-)NCBI
RefSeq Acc Id: XM_039109146   ⟹   XP_038965074
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2577,375,851 - 77,460,710 (-)NCBI
RefSeq Acc Id: XM_039109147   ⟹   XP_038965075
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2577,375,851 - 77,460,709 (-)NCBI
RefSeq Acc Id: XM_039109148   ⟹   XP_038965076
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2577,375,851 - 77,460,709 (-)NCBI
RefSeq Acc Id: XM_039109150   ⟹   XP_038965078
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2577,375,851 - 77,460,708 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_446313   ⟸   NM_053861
- Peptide Label: precursor
- Sequence:
RefSeq Acc Id: XP_008761977   ⟸   XM_008763755
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_008761976   ⟸   XM_008763754
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008761978   ⟸   XM_008763756
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_008761979   ⟸   XM_008763757
- Peptide Label: isoform X4
- UniProtKB: A0A0G2K1L0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008761980   ⟸   XM_008763758
- Peptide Label: isoform X9
- Sequence:
RefSeq Acc Id: ENSRNOP00000071884   ⟸   ENSRNOT00000084563
RefSeq Acc Id: XP_038965073   ⟸   XM_039109145
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038965074   ⟸   XM_039109146
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038965076   ⟸   XM_039109148
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038965075   ⟸   XM_039109147
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038965078   ⟸   XM_039109150
- Peptide Label: isoform X10
RefSeq Acc Id: ENSRNOP00000093442   ⟸   ENSRNOT00000107729
RefSeq Acc Id: ENSRNOP00000091808   ⟸   ENSRNOT00000109041
RefSeq Acc Id: ENSRNOP00000089121   ⟸   ENSRNOT00000102414
RefSeq Acc Id: ENSRNOP00000096828   ⟸   ENSRNOT00000117346
Transcriptome

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

Promoters
RGD ID:13693805
Promoter ID:EPDNEW_R4329
Type:initiation region
Name:Tnc_1
Description:tenascin C
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_6.0579,874,476 - 79,874,536EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
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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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
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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)
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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
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)
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:621057 AgrOrtholog
Ensembl Genes ENSRNOG00000058645 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000071884 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000084563 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/TrEMBL
InterPro EG-like_dom UniProtKB/TrEMBL
  EGF_extracell UniProtKB/TrEMBL
  EGF_Tenascin UniProtKB/TrEMBL
  Fibrinogen-like_C UniProtKB/TrEMBL
  Fibrinogen_a/b/g_C_dom UniProtKB/TrEMBL
  Fibronectin_type3 UniProtKB/TrEMBL
  FN3_sf UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/TrEMBL
  TNC UniProtKB/TrEMBL
KEGG Report rno:116640 UniProtKB/TrEMBL
NCBI Gene 116640 ENTREZGENE
PANTHER PTHR46708:SF1 UniProtKB/TrEMBL
Pfam EGF_2 UniProtKB/TrEMBL
  EGF_Tenascin UniProtKB/TrEMBL
  Fibrinogen_C UniProtKB/TrEMBL
  fn3 UniProtKB/TrEMBL
PhenoGen Tnc PhenoGen
PROSITE EGF_1 UniProtKB/TrEMBL
  EGF_2 UniProtKB/TrEMBL
  EGF_3 UniProtKB/TrEMBL
  FIBRINOGEN_C_2 UniProtKB/TrEMBL
  FN3 UniProtKB/TrEMBL
SMART EGF UniProtKB/TrEMBL
  FBG UniProtKB/TrEMBL
  FN3 UniProtKB/TrEMBL
Superfamily-SCOP Fibrinogen_a/b/g_C UniProtKB/TrEMBL
  FN_III-like UniProtKB/TrEMBL
UniProt A0A0G2K1L0 ENTREZGENE, UniProtKB/TrEMBL
  B2LYI9_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-07-08 Tnc  tenascin C      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Tnc  tenascin C      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_regulation expression of splicing variants is upregulated by PDGF-BB 634489