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
Previously 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 ...
Candidate Gene For: Edcs3
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2203,618,853 - 3,621,324 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl203,618,853 - 3,620,859 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx204,318,695 - 4,320,726 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0203,680,759 - 3,682,786 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0204,218,329 - 4,220,348 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
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 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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
adult respiratory distress syndrome  (ISO)
allergic disease  (ISO)
arteriosclerosis  (ISO)
asthma  (ISO)
breast cancer  (ISO)
Cachexia  (ISO)
carotid artery disease  (ISO)
cerebral infarction  (ISO)
cerebral malaria  (ISO)
chorioamnionitis  (ISO)
contact dermatitis  (ISO)
coronary artery disease  (ISO)
cutaneous leishmaniasis  (ISO)
cystic fibrosis  (ISO)
cystitis  (IEP)
dermatitis herpetiformis  (ISO)
Diabetic Nephropathies  (ISO)
diabetic retinopathy  (ISO)
endometrial cancer  (ISO)
erythema nodosum  (ISO)
esophagus squamous cell carcinoma  (ISO)
Experimental Autoimmune Encephalomyelitis  (IEP)
genetic disease  (ISO)
Graves' disease  (ISO)
hepatic encephalopathy  (ISO)
Herpes Simplex Encephalitis  (ISO)
high grade glioma  (ISO)
hyperinsulinism  (ISO)
hypertension  (ISO)
Hypertriglyceridemia  (ISO)
Insulin Resistance  (ISO)
leprosy  (ISO)
lung non-small cell carcinoma  (ISO)
malignant mesothelioma  (ISO)
megacolon  (ISO)
melanoma  (ISO)
mucocutaneous leishmaniasis  (ISO)
myocardial infarction  (ISO)
neovascular inflammatory vitreoretinopathy  (ISO)
proteasome-associated autoinflammatory syndrome 1  (ISO)
psoriasis  (ISO)
psoriatic arthritis  (ISO)
pulmonary sarcoidosis  (ISO)
pulmonary tuberculosis  (ISO)
pustulosis of palm and sole  (ISO)
Sepsis  (ISO)
sinusitis  (ISO)
Sjogren's syndrome  (ISO)
Sudden Hearing Loss  (ISO)
systemic scleroderma  (ISO)
Transplant Rejection  (IEP,IMP)
trichinosis  (ISO)
type 1 diabetes mellitus  (ISO)
type 2 diabetes mellitus  (ISO)
typhoid fever  (ISO)
visceral leishmaniasis  (ISO)

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 A  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (EXP,ISO)
asbestos  (ISO)
asperentin  (ISO)
benzo[a]pyrene  (ISO)
bisphenol A  (EXP,ISO)
bromoacetate  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (EXP,ISO)
CGP 52608  (ISO)
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)
dimethylarsinic acid  (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)
methylarsonic acid  (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)
S-(1,2-dichlorovinyl)-L-cysteine  (ISO)
silicon dioxide  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
sterigmatocystin  (ISO)
tacrolimus hydrate  (ISO)
TMC-120A  (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
# Reference Title Reference Citation
1. Tumor necrosis factor beta gene polymorphisms in Graves' disease. Badenhoop K, etal., J Clin Endocrinol Metab. 1992 Feb;74(2):287-91.
2. Association between genetic variants in the tumour necrosis factor/lymphotoxin alpha/lymphotoxin beta locus and primary Sjogren's syndrome in Scandinavian samples. Bolstad AI, etal., Ann Rheum Dis. 2012 Jun;71(6):981-8. doi: 10.1136/annrheumdis-2011-200446. Epub 2012 Jan 30.
3. TNFA-TNFB haplotypes modify susceptibility to type I diabetes mellitus independently of HLA class II in a Moroccan population. Bouqbis L, etal., Tissue Antigens. 2003 Jan;61(1):72-9.
4. Tumour necrosis factor beta alleles and hyperinsulinaemia in coronary artery disease. Braun J, etal., Eur J Clin Invest. 1998 Jul;28(7):538-42.
5. Lack of association between atopic asthma and the tumor necrosis factor alpha-308 gene polymorphism in a Czech population. Buckova D, etal., J Investig Allergol Clin Immunol. 2002;12(3):192-7.
6. Polymorphism in tumor necrosis factor genes associated with mucocutaneous leishmaniasis. Cabrera M, etal., J Exp Med. 1995 Nov 1;182(5):1259-64.
7. Eighteen-month-old Fischer 344 rats fed a spinach-enriched diet show improved delay classical eyeblink conditioning and reduced expression of tumor necrosis factor alpha (TNFalpha ) and TNFbeta in the cerebellum. Cartford MC, etal., J Neurosci 2002 Jul 15;22(14):5813-6.
8. Analysis of a Chinese population suggests that the TNFB gene is not a susceptibility gene for Graves' disease. Cavan DA, etal., Hum Immunol. 1994 Jun;40(2):135-7.
9. Ancestral haplotype 8.1 and lung disease severity in European cystic fibrosis patients. Corvol H, etal., J Cyst Fibros. 2012 Jan;11(1):63-7. Epub 2011 Oct 10.
10. Differential expression of cytokines in the rat heart in response to sustained volume overload. Dai RP, etal., Eur J Heart Fail. 2004 Oct;6(6):693-703.
11. High IL-6 and low IL-10 in the central nervous system are associated with protracted relapsing EAE in DA rats. Diab A, etal., J Neuropathol Exp Neurol. 1997 Jun;56(6):641-50.
12. Genes of the class II and class III major histocompatibility complex are associated with typhoid fever in Vietnam. Dunstan SJ, etal., J Infect Dis. 2001 Jan 15;183(2):261-268. doi: 10.1086/317940. Epub 2000 Dec 21.
13. Distinct roles for lymphotoxin-alpha and tumor necrosis factor in the control of Leishmania donovani infection. Engwerda CR, etal., Am J Pathol. 2004 Dec;165(6):2123-33.
14. Locally up-regulated lymphotoxin alpha, not systemic tumor necrosis factor alpha, is the principle mediator of murine cerebral malaria. Engwerda CR, etal., J Exp Med. 2002 May 20;195(10):1371-7.
15. In situ localization of TNFalpha/beta, TACE and TNF receptors TNF-R1 and TNF-R2 in control and LPS-treated lung tissue. Ermert M, etal., Cytokine. 2003 May;22(3-4):89-100.
16. The TNF-beta gene Nco I polymorphism is not associated with hypertriglyceridemia or insulin resistance in lean and obese subjects. Fernandez-Real JM, etal., Biochem Biophys Res Commun. 1997 Jul 30;236(3):829-32.
17. Influence of metabolic and genetic factors on tumour necrosis factor-alpha and lymphotoxin-alpha production in insulin-dependent diabetes mellitus. Feugeas JP, etal., Diabetes Metab. 1997 Sep;23(4):295-301.
18. Polymorphisms in tumor necrosis factor and lymphotoxin A in tuberculosis without and with response to treatment. Garcia-Elorriaga G, etal., Inflammation. 2010 Aug;33(4):267-75.
19. -308GA and TNFB polymorphisms in acute respiratory distress syndrome. Gong MN, etal., Eur Respir J. 2005 Sep;26(3):382-9.
20. The common T60N polymorphism of the lymphotoxin-alpha gene is associated with type 2 diabetes and other phenotypes of the metabolic syndrome. Hamid YH, etal., Diabetologia. 2005 Mar;48(3):445-51. Epub 2005 Feb 24.
21. A clinical feature associated with polymorphisms of the TNF region in Japanese patients with palmoplantar pustulosis. Hashigucci K, etal., Hum Immunol. 2003 May;64(5):530-7.
22. Association of a lymphotoxin-alpha gene polymorphism and atopic asthma in Taiwanese children. Huang SC, etal., Pediatr Neonatol. 2008 Apr;49(2):30-4.
23. Histocompatibility leucocyte antigens and closely linked immunomodulatory genes in autoimmune thyroid disease. Hunt PJ, etal., Clin Endocrinol (Oxf). 2001 Oct;55(4):491-9.
24. Transmembrane tumor necrosis factor alpha is required for enteropathy and is sufficient to promote parasite expulsion in gastrointestinal helminth infection. Ierna MX, etal., Infect Immun. 2009 Sep;77(9):3879-85. doi: 10.1128/IAI.01461-08. Epub 2009 Jun 29.
25. Anti-tumor necrosis factor antibody enhances allograft survival in rats. Imagawa DK, etal., J Surg Res. 1990 Apr;48(4):345-8.
26. Cytokine production in the central nervous system of Lewis rats with experimental autoimmune encephalomyelitis: dynamics of mRNA expression for interleukin-10, interleukin-12, cytolysin, tumor necrosis factor alpha and tumor necrosis factor beta. Issazadeh S, etal., J Neuroimmunol. 1995 Sep;61(2):205-12.
27. The interaction of the polymorphisms in transporter of antigen peptides (TAP) and lymphotoxin alpha (LT-alpha) genes and atopic diseases in the Czech population. Izakovicova Holla L, etal., Clin Exp Allergy. 2001 Sep;31(9):1418-23.
28. Cytokine gene polymorphisms and susceptibility to cutaneous leishmaniasis in Iranian patients. Kamali-Sarvestani E, etal., Cytokine. 2006 Aug;35(3-4):159-65. Epub 2006 Sep 6.
29. Duration of non-Insulin-dependent diabetes mellitus and the TNF-beta NcoI genotype as predictive factors in proliferative diabetic retinopathy. Kankova K, etal., Ophthalmologica. 2001 Jul-Aug;215(4):294-8.
30. Association between the tumor necrosis factor locus and the clinical outcome of Leishmania chagasi infection. Karplus TM, etal., Infect Immun. 2002 Dec;70(12):6919-25.
31. Tumor necrosis factor-alpha allele lymphotoxin-alpha+250 is associated with the presence and severity of placental inflammation among preterm births. Kazzi SN, etal., Pediatr Res. 2004 Jul;56(1):94-8. Epub 2004 May 5.
32. Polymorphisms of tumor necrosis factor (TNF) alpha and beta genes in Korean patients with psoriasis. Kim TG, etal., Arch Dermatol Res. 2003 Apr;295(1):8-13. Epub 2003 Mar 13.
33. Association of single nucleotide polymorphisms (SNPs) in TNF-LTA locus with breast cancer risk in Indian population. 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. Lymphotoxin alpha-/- mice develop functionally impaired CD8+ T cell responses and fail to contain virus infection of the central nervous system. Kumaraguru U, etal., J Immunol. 2001 Jan 15;166(2):1066-74.
35. Cloning and sequence analysis of the rat tumor necrosis factor-encoding genes. Kwon J, etal., Gene 1993 Oct 15;132(2):227-36.
36. Association of the lymphotoxin-alpha gene Thr26Asn polymorphism with severity of coronary atherosclerosis. Laxton R, etal., Genes Immun. 2005 Sep;6(6):539-41.
37. [Association of cytokine gene polymorphisms with cachexia related to sporadic female breast cancer]. Li FN, etal., Zhonghua Yi Xue Za Zhi. 2008 May 27;88(20):1402-4.
38. Association between LTA, TNF and AGER polymorphisms and late diabetic complications. Lindholm E, etal., PLoS One. 2008 Jun 25;3(6):e2546.
39. Effects of intracarotid and intravenous infusion of human TNF and LT on established intracerebral rat gliomas. Liu SK, etal., Lymphokine Cytokine Res. 1991 Jun;10(3):189-94.
40. T helper 1 cytokine mRNA is increased in spontaneously regressing primary melanomas. Lowes MA, etal., J Invest Dermatol. 1997 Jun;108(6):914-9.
41. Polymorphisms in the IL-4, IL-4 receptor alpha chain, TNF-alpha, and lymphotoxin-alpha genes and risk of asthma in Hong Kong Chinese adults. Mak JC, etal., Int Arch Allergy Immunol. 2007;144(2):114-22. Epub 2007 May 24.
42. Changes in urinary bladder cytokine mRNA and protein after cyclophosphamide-induced cystitis. Malley SE and Vizzard MA, Physiol Genomics. 2002;9(1):5-13.
43. Variation in the lymphotoxin-alpha/tumor necrosis factor locus modifies risk of erythema nodosum in sarcoidosis. McDougal KE, etal., J Invest Dermatol. 2009 Aug;129(8):1921-6. doi: 10.1038/jid.2008.456. Epub 2009 Feb 19.
44. Polymorphism of the tumor necrosis factor genes in patients with dermatitis herpetiformis. Messer G, etal., Dermatology. 1994;189 Suppl 1:135-7.
45. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
46. Haplotype analysis of a 100 kb region spanning TNF-LTA identifies a polymorphism in the LTA promoter region that is associated with atopic asthma susceptibility in Japan. Migita O, etal., Clin Exp Allergy. 2005 Jun;35(6):790-6.
47. Human LT-alpha-mediated resistance to autoimmune diabetes is induced in NOD, but not NOD-scid, mice and abrogated by IL-12. Miyaguchi S, etal., Clin Immunol. 2001 Jan;98(1):119-24.
48. Association of tumour necrosis factor-alpha, lymphotoxin-alpha and HLA-DRB1 gene polymorphisms with Lofgren's syndrome in Czech patients with sarcoidosis. Mrazek F, etal., Tissue Antigens. 2005 Feb;65(2):163-71.
49. Determination of lymphotoxin-alpha levels in patients with psoriatic arthritis undergoing etanercept treatment. Murdaca G, etal., J Interferon Cytokine Res. 2012 Jun;32(6):277-9. doi: 10.1089/jir.2011.0120. Epub 2012 Apr 5.
50. An association study in essential hypertension using functional polymorphisms in lymphotoxin-alpha gene. Nakayama T, etal., Am J Hypertens. 2004 Nov;17(11 Pt 1):1045-9.
51. Regulatory substances produced by lymphocytes. II. Lymphotoxin in the rat. Namba Y and Waksman BH, J Immunol. 1975 Oct;115(4):1018-22.
52. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
53. Lymphotoxin-alpha polymorphisms and the risk of endometrial cancer in Japanese subjects. Niwa Y, etal., Gynecol Oncol. 2007 Mar;104(3):586-90. Epub 2006 Oct 11.
54. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
55. Functional SNPs in the lymphotoxin-alpha gene that are associated with susceptibility to myocardial infarction. Ozaki K, etal., Nat Genet. 2002 Dec;32(4):650-4. Epub 2002 Nov 11.
56. TNF-alpha and TNF-beta gene polymorphisms in systemic sclerosis. Pandey JP and Takeuchi F, Hum Immunol. 1999 Nov;60(11):1128-30.
57. Polymorphisms of tumour necrosis factors A and B in breast cancer. Park KS, etal., Eur J Immunogenet. 2002 Feb;29(1):7-10.
58. Influence of allergy on clinical, immunological and histological characteristics of nasal polyposis. Peric A, etal., B-ENT. 2012;8(1):25-32.
59. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
60. PID Annotation Import Pipeline Pipeline to import Pathway Interaction Database annotations from NCI into RGD
61. Induction of TNF alpha and TNF beta gene expression in rat cardiac transplants during allograft rejection. Pizarro TT, etal., Transplantation. 1993 Aug;56(2):399-404.
62. Effects of NF-kappaB oligonucleotide "decoys" on gene expression in P7 rat hippocampus after hypoxia/ischemia. Qiu J, etal., J Neurosci Res. 2004 Jul 1;77(1):108-18.
63. Essential role of lymph nodes in contact hypersensitivity revealed in lymphotoxin-alpha-deficient mice. Rennert PD, etal., J Exp Med. 2001 Jun 4;193(11):1227-38.
64. GOA pipeline RGD automated data pipeline
65. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
66. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
67. Comprehensive gene review and curation RGD comprehensive gene curation
68. A strong genetic association between the tumor necrosis factor locus and proliferative vitreoretinopathy: the retina 4 project. 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. Loss of lymphotoxin-alpha but not tumor necrosis factor-alpha reduces atherosclerosis in mice. Schreyer SA, etal., J Biol Chem. 2002 Apr 5;277(14):12364-8. Epub 2002 Jan 23.
70. A role for lymphotoxin in primary Sjogren's disease. Shen L, etal., J Immunol. 2010 Nov 15;185(10):6355-63. doi: 10.4049/jimmunol.1001520. Epub 2010 Oct 15.
71. Independent association of tumor necrosis factor polymorphism with type 1 diabetes susceptibility. Shin HD, etal., Ann N Y Acad Sci. 2008 Dec;1150:76-85.
72. Modulation of type 1 diabetes susceptibility by tumor necrosis factor alpha -308 G/A and lymphotoxin alpha +249 A/G haplotypes and lack of linkage disequilibrium with predisposing DQB1-DRB1 haplotypes in Bahraini patients. Stayoussef M, etal., Clin Vaccine Immunol. 2008 Feb;15(2):379-81. Epub 2007 Nov 7.
73. Decreased mortality associated with statin treatment in patients with acute myocardial infarction and lymphotoxin-alpha C804A polymorphism. Suna S, etal., Atherosclerosis. 2013 Apr;227(2):373-9. doi: 10.1016/j.atherosclerosis.2013.01.020. Epub 2013 Jan 25.
74. Prevention of type I diabetes with lymphotoxin in BB rats. Takahashi K, etal., Clin Immunol Immunopathol. 1993 Dec;69(3):318-23.
75. Tumor necrosis factor gene polymorphism in chronic sinusitis. Takeuchi K, etal., Laryngoscope. 2000 Oct;110(10 Pt 1):1711-4.
76. Prognostic significance of tumor necrosis factors and their receptors in nonsmall cell lung carcinoma. Tran TA, etal., Cancer. 1998 Jul 15;83(2):276-82.
77. Thyroid hormone induces cerebellar astrocytes and C6 glioma cells to secrete mitogenic growth factors. Trentin AG, etal., Am J Physiol Endocrinol Metab. 2001 Nov;281(5):E1088-94.
78. Candidate genes of cerebrovascular disease and sudden sensorineural hearing loss. Um JY, etal., Clin Appl Thromb Hemost. 2010 Oct;16(5):559-62. doi: 10.1177/1076029609348313. Epub 2009 Oct 14.
79. TNF-alpha and TNF-beta gene polymorphisms in cerebral infarction. Um JY, etal., J Mol Neurosci. 2003;21(2):167-71.
80. A tumor necrosis factor-beta polymorphism associated with hypertriglyceridemia in non-insulin-dependent diabetes mellitus. Vendrell J, etal., Metabolism. 1995 Jun;44(6):691-4.
81. Salicylate-induced degeneration of cochlea spiral ganglion neurons-apoptosis signaling. Wei L, etal., Neuroscience. 2010 Jun 16;168(1):288-99. Epub 2010 Mar 15.
82. Lack of association of polymorphisms of the lymphotoxin alpha gene with myocardial infarction in Japanese. Yamada A, etal., J Mol Med. 2004 Jul;82(7):477-83. Epub 2004 Jun 3.
83. Tumor necrosis factor-beta is associated with thymic apoptosis during acute rejection. Yamaguchi Y, etal., Transplantation. 1998 Oct 15;66(7):894-902.
84. Combination of multiple genetic risk factors is synergistically associated with carotid atherosclerosis in Japanese subjects with type 2 diabetes. Yamasaki Y, etal., Diabetes Care. 2006 Nov;29(11):2445-51.
85. Relationship between polymorphisms 804C/A and 252A/G of lymphotoxin-alpha gene and -308G/A of tumor necrosis factor alpha gene and diabetic retinopathy in Japanese patients with type 2 diabetes mellitus. Yoshioka K, etal., Metabolism. 2006 Oct;55(10):1406-10.
86. Large-scale studies of the association between variation at the TNF/LTA locus and susceptibility to type 2 diabetes. 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   PMID:35776111  


Genomics

Comparative Map Data
Lta
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2203,618,853 - 3,621,324 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl203,618,853 - 3,620,859 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx204,318,695 - 4,320,726 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0203,680,759 - 3,682,786 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0204,218,329 - 4,220,348 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
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 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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
GRCh38631,560,610 - 31,574,324 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl631,572,054 - 31,574,324 (+)EnsemblGRCh38hg38GRCh38
GRCh37631,539,876 - 31,542,101 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36631,648,072 - 31,650,077 (+)NCBINCBI36Build 36hg18NCBI36
Build 34631,648,071 - 31,650,077NCBI
Celera633,138,091 - 33,140,313 (+)NCBICelera
Cytogenetic Map6p21.33NCBI
HuRef631,326,608 - 31,328,835 (+)NCBIHuRef
CHM1_1631,542,008 - 31,544,233 (+)NCBICHM1_1
T2T-CHM13v2.0631,424,599 - 31,427,376 (+)NCBIT2T-CHM13v2.0
Lta
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391735,422,141 - 35,424,568 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1735,422,141 - 35,424,327 (-)EnsemblGRCm39 Ensembl
GRCm381735,203,165 - 35,205,578 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1735,203,165 - 35,205,351 (-)EnsemblGRCm38mm10GRCm38
MGSCv371735,340,110 - 35,342,296 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361734,811,215 - 34,813,235 (-)NCBIMGSCv36mm8
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
NHGRI_mPanPan1642,011,243 - 42,012,833 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0631,233,411 - 31,235,409 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1632,123,353 - 32,125,375 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl632,123,353 - 32,125,375 (+)Ensemblpanpan1.1panPan2
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 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0121,215,963 - 1,218,298 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl121,216,437 - 1,217,676 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1121,075,453 - 1,076,395 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0121,143,379 - 1,144,321 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0121,210,162 - 1,211,104 (+)NCBIUU_Cfam_GSD_1.0
Lta
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494635,620,316 - 35,621,609 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049367271,940,081 - 1,941,022 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049367271,940,081 - 1,941,022 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LTA
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl723,696,040 - 23,698,299 (+)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_p1.0Vero_WHO_p1.0
Lta
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462475424,627,318 - 24,628,182 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462475424,626,930 - 24,628,412 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Lta
31 total Variants
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.


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

Markers in Region
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


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


RefSeq Acc Id: ENSRNOT00000001111   ⟹   ENSRNOP00000001111
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
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
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2203,618,859 - 3,621,324 (+)NCBI
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
- UniProtKB: Q06332 (UniProtKB/Swiss-Prot)

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q06332-F1-model_v2 AlphaFold Q06332 1-202 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3020 AgrOrtholog
BioCyc Gene G2FUF-4661 BioCyc
Ensembl Genes ENSRNOG00000000838 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOG00055007875 UniProtKB/Swiss-Prot
  ENSRNOG00060004710 UniProtKB/Swiss-Prot
  ENSRNOG00065031221 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000001111 ENTREZGENE
  ENSRNOT00000001111.3 UniProtKB/Swiss-Prot
  ENSRNOT00055013228 UniProtKB/Swiss-Prot
  ENSRNOT00060007870 UniProtKB/Swiss-Prot
  ENSRNOT00065053840 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
PANTHER LYMPHOTOXIN-ALPHA UniProtKB/Swiss-Prot
  TUMOR NECROSIS FACTOR FAMILY MEMBER UniProtKB/Swiss-Prot
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
RatGTEx ENSRNOG00000000838 RatGTEx
  ENSRNOG00055007875 RatGTEx
  ENSRNOG00060004710 RatGTEx
  ENSRNOG00065031221 RatGTEx
SMART TNF UniProtKB/Swiss-Prot
Superfamily-SCOP SSF49842 UniProtKB/Swiss-Prot
UniProt A6KTW9_RAT UniProtKB/TrEMBL
  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 from RGD:9369310 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