Lta (lymphotoxin alpha) - Rat Genome Database

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Gene: Lta (lymphotoxin alpha) Rattus norvegicus
Analyze
Symbol: Lta
Name: lymphotoxin alpha
RGD ID: 3020
Description: Predicted to enable cytokine activity and tumor necrosis factor receptor binding activity. Involved in several processes, including negative regulation of fibroblast proliferation; positive regulation of glial cell proliferation; and response to lipopolysaccharide. Located in extracellular space. Biomarker of cystitis. Human ortholog(s) of this gene implicated in several diseases, including artery disease (multiple); autoimmune disease (multiple); glucose metabolism disease (multiple); leishmaniasis (multiple); and lung disease (multiple). Orthologous to human LTA (lymphotoxin alpha); PARTICIPATES IN interleukin-4 signaling pathway; cytokine mediated signaling pathway; type 1 diabetes mellitus pathway; INTERACTS WITH 1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane; 2,3,7,8-tetrachlorodibenzodioxine; ammonium chloride.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: LOC103690381; LT-alpha; lymphotoxin A; Lymphotoxin alpha (formerly tumor necrosis factor beta); Lymphotoxin alpha (formerly tumor necrosis factor, beta); lymphotoxin alpha (TNF superfamily, member 1); lymphotoxin-alpha; lymphotoxin-alpha-like; TNF-beta; Tnfb; tumor necrosis factor beta; tumor necrosis factor ligand superfamily member 1
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
mRatBN7.2203,618,853 - 3,621,324 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl203,618,853 - 3,620,859 (+)Ensembl
Rnor_6.0204,851,889 - 4,854,677 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl204,852,496 - 4,854,677 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0206,932,260 - 6,935,077 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4203,657,842 - 3,659,848 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1203,658,068 - 3,660,075 (+)NCBI
Celera204,404,630 - 4,406,751 (-)NCBICelera
Cytogenetic Map20p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-demecolcine  (ISO)
1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane  (EXP)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
1-nitropyrene  (ISO)
17beta-estradiol  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,6-dichloroindophenol  (ISO)
3-chloropropane-1,2-diol  (ISO)
3-phenylprop-2-enal  (ISO)
acetylsalicylic acid  (ISO)
acrylamide  (ISO)
ammonium chloride  (EXP)
amphibole asbestos  (ISO)
aripiprazole  (ISO)
aristolochic acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (EXP,ISO)
asbestos  (ISO)
asperentin  (ISO)
benzo[a]pyrene  (ISO)
bisphenol A  (EXP,ISO)
cadmium dichloride  (EXP)
cisplatin  (ISO)
cobalt atom  (EXP)
cobalt dichloride  (ISO)
Cuprizon  (EXP)
curcumin  (ISO)
cyclosporin A  (EXP,ISO)
deoxynivalenol  (ISO)
dextran sulfate  (ISO)
diarsenic trioxide  (EXP,ISO)
flavonoids  (EXP)
furosemide  (EXP)
gemcitabine  (ISO)
ibuprofen  (ISO)
indometacin  (ISO)
iron atom  (EXP)
iron(0)  (EXP)
iron(2+) sulfate (anhydrous)  (ISO)
lead nitrate  (ISO)
lipopolysaccharide  (ISO)
mycophenolic acid  (ISO)
N,N,N',N'-tetrakis(2-pyridylmethyl)ethylenediamine  (ISO)
N-ethyl-N-nitrosourea  (ISO)
nickel atom  (EXP)
ozone  (ISO)
paracetamol  (ISO)
paraquat  (ISO)
PCB138  (ISO)
potassium dichromate  (ISO)
progesterone  (ISO)
resveratrol  (ISO)
rifaximin  (ISO)
silicon dioxide  (ISO)
sodium arsenite  (ISO)
sterigmatocystin  (ISO)
tacrolimus hydrate  (ISO)
toluene 2,4-diisocyanate  (ISO)
trichloroethene  (ISO)
troglitazone  (ISO)
tungsten  (EXP)
usnic acid  (ISO)
vincristine  (ISO)
zinc dichloride  (ISO)
zinc pyrithione  (ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References

References - curated
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15. Ermert M, etal., Cytokine. 2003 May;22(3-4):89-100.
16. Fernandez-Real JM, etal., Biochem Biophys Res Commun. 1997 Jul 30;236(3):829-32.
17. Feugeas JP, etal., Diabetes Metab. 1997 Sep;23(4):295-301.
18. Garcia-Elorriaga G, etal., Inflammation. 2010 Aug;33(4):267-75.
19. Gong MN, etal., Eur Respir J. 2005 Sep;26(3):382-9.
20. Hamid YH, etal., Diabetologia. 2005 Mar;48(3):445-51. Epub 2005 Feb 24.
21. Hashigucci K, etal., Hum Immunol. 2003 May;64(5):530-7.
22. Huang SC, etal., Pediatr Neonatol. 2008 Apr;49(2):30-4.
23. Hunt PJ, etal., Clin Endocrinol (Oxf). 2001 Oct;55(4):491-9.
24. Ierna MX, etal., Infect Immun. 2009 Sep;77(9):3879-85. doi: 10.1128/IAI.01461-08. Epub 2009 Jun 29.
25. Imagawa DK, etal., J Surg Res. 1990 Apr;48(4):345-8.
26. Issazadeh S, etal., J Neuroimmunol. 1995 Sep;61(2):205-12.
27. Izakovicova Holla L, etal., Clin Exp Allergy. 2001 Sep;31(9):1418-23.
28. Kamali-Sarvestani E, etal., Cytokine. 2006 Aug;35(3-4):159-65. Epub 2006 Sep 6.
29. Kankova K, etal., Ophthalmologica. 2001 Jul-Aug;215(4):294-8.
30. Karplus TM, etal., Infect Immun. 2002 Dec;70(12):6919-25.
31. Kazzi SN, etal., Pediatr Res. 2004 Jul;56(1):94-8. Epub 2004 May 5.
32. Kim TG, etal., Arch Dermatol Res. 2003 Apr;295(1):8-13. Epub 2003 Mar 13.
33. Kohaar I, etal., Breast Cancer Res Treat. 2009 Mar;114(2):347-55. doi: 10.1007/s10549-008-0006-5. Epub 2008 Apr 14.
34. Kumaraguru U, etal., J Immunol. 2001 Jan 15;166(2):1066-74.
35. Kwon J, etal., Gene 1993 Oct 15;132(2):227-36.
36. Laxton R, etal., Genes Immun. 2005 Sep;6(6):539-41.
37. Li FN, etal., Zhonghua Yi Xue Za Zhi. 2008 May 27;88(20):1402-4.
38. Lindholm E, etal., PLoS One. 2008 Jun 25;3(6):e2546.
39. Liu SK, etal., Lymphokine Cytokine Res. 1991 Jun;10(3):189-94.
40. Lowes MA, etal., J Invest Dermatol. 1997 Jun;108(6):914-9.
41. Mak JC, etal., Int Arch Allergy Immunol. 2007;144(2):114-22. Epub 2007 May 24.
42. Malley SE and Vizzard MA, Physiol Genomics. 2002;9(1):5-13.
43. McDougal KE, etal., J Invest Dermatol. 2009 Aug;129(8):1921-6. doi: 10.1038/jid.2008.456. Epub 2009 Feb 19.
44. Messer G, etal., Dermatology. 1994;189 Suppl 1:135-7.
45. MGD data from the GO Consortium
46. Migita O, etal., Clin Exp Allergy. 2005 Jun;35(6):790-6.
47. Miyaguchi S, etal., Clin Immunol. 2001 Jan;98(1):119-24.
48. Mrazek F, etal., Tissue Antigens. 2005 Feb;65(2):163-71.
49. Murdaca G, etal., J Interferon Cytokine Res. 2012 Jun;32(6):277-9. doi: 10.1089/jir.2011.0120. Epub 2012 Apr 5.
50. Nakayama T, etal., Am J Hypertens. 2004 Nov;17(11 Pt 1):1045-9.
51. Namba Y and Waksman BH, J Immunol. 1975 Oct;115(4):1018-22.
52. NCBI rat LocusLink and RefSeq merged data July 26, 2002
53. Niwa Y, etal., Gynecol Oncol. 2007 Mar;104(3):586-90. Epub 2006 Oct 11.
54. OMIM Disease Annotation Pipeline
55. Ozaki K, etal., Nat Genet. 2002 Dec;32(4):650-4. Epub 2002 Nov 11.
56. Pandey JP and Takeuchi F, Hum Immunol. 1999 Nov;60(11):1128-30.
57. Park KS, etal., Eur J Immunogenet. 2002 Feb;29(1):7-10.
58. Peric A, etal., B-ENT. 2012;8(1):25-32.
59. Pipeline to import KEGG annotations from KEGG into RGD
60. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
61. Pizarro TT, etal., Transplantation. 1993 Aug;56(2):399-404.
62. Qiu J, etal., J Neurosci Res. 2004 Jul 1;77(1):108-18.
63. Rennert PD, etal., J Exp Med. 2001 Jun 4;193(11):1227-38.
64. RGD automated data pipeline
65. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
66. RGD automated import pipeline for gene-chemical interactions
67. RGD comprehensive gene curation
68. Rojas J, etal., Ophthalmology. 2010 Dec;117(12):2417-2423.e1-2. doi: 10.1016/j.ophtha.2010.03.059. Epub 2010 Jul 21.
69. Schreyer SA, etal., J Biol Chem. 2002 Apr 5;277(14):12364-8. Epub 2002 Jan 23.
70. Shen L, etal., J Immunol. 2010 Nov 15;185(10):6355-63. doi: 10.4049/jimmunol.1001520. Epub 2010 Oct 15.
71. Shin HD, etal., Ann N Y Acad Sci. 2008 Dec;1150:76-85.
72. Stayoussef M, etal., Clin Vaccine Immunol. 2008 Feb;15(2):379-81. Epub 2007 Nov 7.
73. Suna S, etal., Atherosclerosis. 2013 Apr;227(2):373-9. doi: 10.1016/j.atherosclerosis.2013.01.020. Epub 2013 Jan 25.
74. Takahashi K, etal., Clin Immunol Immunopathol. 1993 Dec;69(3):318-23.
75. Takeuchi K, etal., Laryngoscope. 2000 Oct;110(10 Pt 1):1711-4.
76. Tran TA, etal., Cancer. 1998 Jul 15;83(2):276-82.
77. Trentin AG, etal., Am J Physiol Endocrinol Metab. 2001 Nov;281(5):E1088-94.
78. Um JY, etal., Clin Appl Thromb Hemost. 2010 Oct;16(5):559-62. doi: 10.1177/1076029609348313. Epub 2009 Oct 14.
79. Um JY, etal., J Mol Neurosci. 2003;21(2):167-71.
80. Vendrell J, etal., Metabolism. 1995 Jun;44(6):691-4.
81. Wei L, etal., Neuroscience. 2010 Jun 16;168(1):288-99. Epub 2010 Mar 15.
82. Yamada A, etal., J Mol Med. 2004 Jul;82(7):477-83. Epub 2004 Jun 3.
83. Yamaguchi Y, etal., Transplantation. 1998 Oct 15;66(7):894-902.
84. Yamasaki Y, etal., Diabetes Care. 2006 Nov;29(11):2445-51.
85. Yoshioka K, etal., Metabolism. 2006 Oct;55(10):1406-10.
86. Zeggini E, etal., Diabetologia. 2005 Oct;48(10):2013-7. Epub 2005 Aug 18.
Additional References at PubMed
PMID:7636227   PMID:8171322   PMID:9368616   PMID:9565643   PMID:9834074   PMID:10415063   PMID:15060004   PMID:20092780   PMID:33441130  


Genomics

Candidate Gene Status
Lta is a candidate Gene for QTL Edcs3
Comparative Map Data
Lta
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2203,618,853 - 3,621,324 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl203,618,853 - 3,620,859 (+)Ensembl
Rnor_6.0204,851,889 - 4,854,677 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl204,852,496 - 4,854,677 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0206,932,260 - 6,935,077 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4203,657,842 - 3,659,848 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1203,658,068 - 3,660,075 (+)NCBI
Celera204,404,630 - 4,406,751 (-)NCBICelera
Cytogenetic Map20p12NCBI
LTA
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl631,572,054 - 31,574,324 (+)EnsemblGRCh38hg38GRCh38
GRCh38631,560,550 - 31,574,324 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37631,539,876 - 31,542,101 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36631,648,072 - 31,650,077 (+)NCBINCBI36hg18NCBI36
Build 34631,648,071 - 31,650,077NCBI
Celera633,138,091 - 33,140,313 (+)NCBI
Cytogenetic Map6p21.33NCBI
HuRef631,326,608 - 31,328,835 (+)NCBIHuRef
CHM1_1631,542,008 - 31,544,233 (+)NCBICHM1_1
Lta
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391735,422,141 - 35,424,568 (-)NCBIGRCm39mm39
GRCm39 Ensembl1735,422,141 - 35,424,327 (-)Ensembl
GRCm381735,203,165 - 35,205,578 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1735,203,165 - 35,205,351 (-)EnsemblGRCm38mm10GRCm38
MGSCv371735,340,110 - 35,342,296 (-)NCBIGRCm37mm9NCBIm37
MGSCv361734,811,215 - 34,813,235 (-)NCBImm8
Celera1738,299,868 - 38,302,049 (-)NCBICelera
Cytogenetic Map17B1NCBI
cM Map1718.59NCBI
Lta
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955437114,640 - 115,529 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955437114,216 - 116,003 (+)NCBIChiLan1.0ChiLan1.0
LTA
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1632,123,353 - 32,125,375 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl632,123,353 - 32,125,375 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0631,233,411 - 31,235,409 (+)NCBIMhudiblu_PPA_v0panPan3
LTA
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1121,070,608 - 1,073,053 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl121,071,192 - 1,073,067 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha121,207,912 - 1,208,854 (+)NCBI
ROS_Cfam_1.0121,215,963 - 1,218,298 (+)NCBI
UMICH_Zoey_3.1121,075,453 - 1,076,395 (+)NCBI
UNSW_CanFamBas_1.0121,143,379 - 1,144,321 (+)NCBI
UU_Cfam_GSD_1.0121,210,162 - 1,211,104 (+)NCBI
Lta
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494635,620,316 - 35,621,609 (+)NCBI
SpeTri2.0NW_0049367271,940,081 - 1,941,022 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LTA
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl723,696,039 - 23,698,302 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1723,696,387 - 23,698,280 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2727,553,733 - 27,555,627 (-)NCBISscrofa10.2Sscrofa10.2susScr3
Pig Cytomap7p11-q11NCBI
LTA
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Vero_WHO_p1.0NW_02366604431,473,740 - 31,476,648 (+)NCBIVero_WHO_p1.0
Lta
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475424,626,930 - 24,628,412 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
AI113237  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2203,620,478 - 3,620,693 (+)MAPPERmRatBN7.2
mRatBN7.2203,620,478 - 3,620,693 (-)MAPPERmRatBN7.2
Rnor_6.0205,193,318 - 5,193,532NCBIRnor6.0
Rnor_6.0204,854,297 - 4,854,511NCBIRnor6.0
Rnor_5.0206,934,697 - 6,934,911UniSTSRnor5.0
RGSC_v3.4203,659,468 - 3,659,682UniSTSRGSC3.4
Celera204,404,796 - 4,405,010UniSTS
Cytogenetic Map20p12UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724519Bp144Blood pressure QTL 1440.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2013624629Rat
1354642Despr15Despair related QTL 150.0027locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)20124159021Rat
1600382Edcs3Endometrial carcinoma susceptibility QTL33.50.003uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)20125159026Rat
2317851Alcrsp22Alcohol response QTL 223.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127339237Rat
1641893Alcrsp7Alcohol response QTL 7response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127339237Rat
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20129191651Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20129191651Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20129191651Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20129191651Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20129191651Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20132578807Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20136600972Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20136600972Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20152784246527842Rat
2306850Pia40Pristane induced arthritis QTL 400.0001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)2015279595304575Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20153065546530655Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)20260683647606836Rat
61448Ciaa1CIA Autoantibody QTL 1300.001blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)2026463954597031Rat
61472Aia1Adjuvant induced arthritis QTL 1180.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)2026463954597031Rat
2317057Aia27Adjuvant induced arthritis QTL 272.83joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)20289259726381954Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:184
Count of miRNA genes:125
Interacting mature miRNAs:140
Transcripts:ENSRNOT00000001111
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 musculoskeletal system nervous system renal system reproductive system respiratory system
High
Medium 2 3
Low 8 16 2 7
Below cutoff 1 15 7 7 7 1 40 12 29 4

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000001111   ⟹   ENSRNOP00000001111
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl203,618,853 - 3,620,859 (+)Ensembl
Rnor_6.0 Ensembl204,852,671 - 4,854,677 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000088936   ⟹   ENSRNOP00000069608
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl204,852,496 - 4,854,294 (+)Ensembl
RefSeq Acc Id: NM_080769   ⟹   NP_542947
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2203,618,853 - 3,620,859 (+)NCBI
Rnor_6.0204,852,671 - 4,854,677 (+)NCBI
Rnor_5.0206,932,260 - 6,935,077 (+)NCBI
RGSC_v3.4203,657,842 - 3,659,848 (+)RGD
Celera204,404,630 - 4,406,751 (-)RGD
Sequence:
RefSeq Acc Id: XM_039098430   ⟹   XP_038954358
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2203,618,859 - 3,621,324 (+)NCBI
Protein Sequences
Protein RefSeqs NP_542947 (Get FASTA)   NCBI Sequence Viewer  
  XP_038954358 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA16276 (Get FASTA)   NCBI Sequence Viewer  
  CAE84004 (Get FASTA)   NCBI Sequence Viewer  
  EDL83549 (Get FASTA)   NCBI Sequence Viewer  
  Q06332 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_542947   ⟸   NM_080769
- Peptide Label: precursor
- UniProtKB: Q06332 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000069608   ⟸   ENSRNOT00000088936
RefSeq Acc Id: ENSRNOP00000001111   ⟸   ENSRNOT00000001111
RefSeq Acc Id: XP_038954358   ⟸   XM_039098430
- Peptide Label: isoform X1

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
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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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
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
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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
SHRSP/Gcrc (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
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)
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: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (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
SS/Jr (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
SS/JrHsdMcwi (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
SS/JrHsdMcwi (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)
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)
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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3020 AgrOrtholog
Ensembl Genes ENSRNOG00000000838 Ensembl, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000001111 UniProtKB/Swiss-Prot
  ENSRNOP00000069608 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000001111 UniProtKB/Swiss-Prot
  ENSRNOT00000088936 UniProtKB/Swiss-Prot
Gene3D-CATH 2.60.120.40 UniProtKB/Swiss-Prot
InterPro TNF UniProtKB/Swiss-Prot
  TNF_beta UniProtKB/Swiss-Prot
  TNF_CS UniProtKB/Swiss-Prot
  TNF_dom UniProtKB/Swiss-Prot
  Tumour_necrosis_fac-like_dom UniProtKB/Swiss-Prot
KEGG Report rno:25008 UniProtKB/Swiss-Prot
NCBI Gene 25008 ENTREZGENE
Pfam TNF UniProtKB/Swiss-Prot
PharmGKB LTA RGD
PhenoGen Lta PhenoGen
PRINTS TNECROSISFCT UniProtKB/Swiss-Prot
  TNFBETA UniProtKB/Swiss-Prot
PROSITE TNF_1 UniProtKB/Swiss-Prot
  TNF_2 UniProtKB/Swiss-Prot
SMART TNF UniProtKB/Swiss-Prot
Superfamily-SCOP SSF49842 UniProtKB/Swiss-Prot
UniProt Q06332 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Lta  lymphotoxin alpha  LOC103690381  lymphotoxin-alpha-like  Data Merged 737654 PROVISIONAL
2014-08-25 LOC103690381  lymphotoxin-alpha-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2013-08-14 Lta  lymphotoxin alpha  Lta  lymphotoxin alpha (TNF superfamily, member 1)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-18 Lta  lymphotoxin alpha (TNF superfamily, member 1)  Lta  lymphotoxin A  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-11-06 Lta  lymphotoxin A    Lymphotoxin alpha (formerly tumor necrosis factor, beta)  Name updated 625702 APPROVED
2002-06-10 Lta  Lymphotoxin alpha (formerly tumor necrosis factor, beta)      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_mapping found within the rat major histocompatibility RT1 complex 1300431
gene_regulation expression decreased in cerebellum from F344 animals (20-month-old) on 6 weeks of a spinach-enriched diet 628312
gene_regulation expression was decreased in cerebellum from F344 animals (20-month-old) on 6 weeks of a spinach-enriched diet 628312
gene_transcript gene is tandemly arranged 5' to TNF-alpha 729032