LTA (lymphotoxin alpha) - Rat Genome Database

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Gene: LTA (lymphotoxin alpha) Homo sapiens
Analyze
Symbol: LTA
Name: lymphotoxin alpha
RGD ID: 1345394
HGNC Page HGNC
Description: Predicted to have signaling receptor binding activity. Predicted to be involved in apoptotic process; cell-cell signaling; and tumor necrosis factor-mediated signaling pathway. Predicted to localize to plasma membrane. Implicated in several diseases, including artery disease (multiple); autoimmune disease (multiple); glucose metabolism disease (multiple); leishmaniasis (multiple); and lung disease (multiple). Biomarker of allergic disease; autoimmune disease (multiple); lung non-small cell carcinoma; and melanoma.
Type: protein-coding
RefSeq Status: REVIEWED
Also known as: LT; LT-alpha; lymphotoxin-alpha; TNF superfamily, member 1; TNF-beta; TNFB; TNFSF1; TNLG1E; truncated lymphotoxin alpha; tumor necrosis factor beta; tumor necrosis factor ligand 1E; tumor necrosis factor ligand superfamily member 1
RGD Orthologs
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
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
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
adult respiratory distress syndrome  (IAGP)
allergic disease  (IAGP,IEP)
arteriosclerosis  (ISO)
asthma  (IAGP)
breast cancer  (IAGP)
Cachexia  (IAGP)
carotid artery disease  (IAGP)
cerebral infarction  (IAGP)
cerebral malaria  (ISO)
chorioamnionitis  (IAGP)
contact dermatitis  (ISO)
coronary artery disease  (EXP,IAGP)
cutaneous leishmaniasis  (IAGP)
cystic fibrosis  (IAGP)
cystitis  (ISO)
dermatitis herpetiformis  (IAGP)
Diabetic Nephropathies  (IAGP)
diabetic retinopathy  (IAGP)
endometrial cancer  (IAGP)
erythema nodosum  (IAGP)
esophagus squamous cell carcinoma  (EXP)
Experimental Autoimmune Encephalomyelitis  (ISO)
Graves' disease  (IAGP)
hepatic encephalopathy  (EXP)
Herpes Simplex Encephalitis  (ISO)
high grade glioma  (IDA)
hyperinsulinism  (IAGP)
hypertension  (IAGP)
Hypertriglyceridemia  (IAGP)
Insulin Resistance  (IAGP)
leprosy  (EXP,IAGP)
lung non-small cell carcinoma  (IEP)
malignant mesothelioma  (EXP)
melanoma  (IEP)
mucocutaneous leishmaniasis  (IAGP)
myocardial infarction  (EXP,IAGP)
neovascular inflammatory vitreoretinopathy  (IAGP)
psoriasis  (IAGP)
psoriatic arthritis  (EXP,IAGP,IEP)
pulmonary sarcoidosis  (IAGP)
pulmonary tuberculosis  (IAGP)
pustulosis of palm and sole  (IAGP)
Sepsis  (EXP)
sinusitis  (IAGP)
Sjogren's syndrome  (IAGP,IEP,ISO)
Sudden Hearing Loss  (IAGP)
systemic scleroderma  (IAGP)
Transplant Rejection  (ISO)
trichinosis  (ISO)
type 1 diabetes mellitus  (IAGP,IDA,IEP,IMP)
type 2 diabetes mellitus  (IAGP)
typhoid fever  (IAGP)
visceral leishmaniasis  (IAGP,ISO)

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

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

Human Phenotype
References

References - curated
1. Badenhoop K, etal., J Clin Endocrinol Metab. 1992 Feb;74(2):287-91.
2. Bolstad AI, etal., Ann Rheum Dis. 2012 Jun;71(6):981-8. doi: 10.1136/annrheumdis-2011-200446. Epub 2012 Jan 30.
3. Bouqbis L, etal., Tissue Antigens. 2003 Jan;61(1):72-9.
4. Braun J, etal., Eur J Clin Invest. 1998 Jul;28(7):538-42.
5. Buckova D, etal., J Investig Allergol Clin Immunol. 2002;12(3):192-7.
6. Cabrera M, etal., J Exp Med. 1995 Nov 1;182(5):1259-64.
7. Cavan DA, etal., Hum Immunol. 1994 Jun;40(2):135-7.
8. Corvol H, etal., J Cyst Fibros. 2012 Jan;11(1):63-7. Epub 2011 Oct 10.
9. Dai RP, etal., Eur J Heart Fail. 2004 Oct;6(6):693-703.
10. Diab A, etal., J Neuropathol Exp Neurol. 1997 Jun;56(6):641-50.
11. Dunstan SJ, etal., J Infect Dis. 2001 Jan 15;183(2):261-268. doi: 10.1086/317940. Epub 2000 Dec 21.
12. Engwerda CR, etal., Am J Pathol. 2004 Dec;165(6):2123-33.
13. Engwerda CR, etal., J Exp Med. 2002 May 20;195(10):1371-7.
14. Fernandez-Real JM, etal., Biochem Biophys Res Commun. 1997 Jul 30;236(3):829-32.
15. Feugeas JP, etal., Diabetes Metab. 1997 Sep;23(4):295-301.
16. Garcia-Elorriaga G, etal., Inflammation. 2010 Aug;33(4):267-75.
17. GOA_HUMAN data from the GO Consortium
18. Gong MN, etal., Eur Respir J. 2005 Sep;26(3):382-9.
19. Hamid YH, etal., Diabetologia. 2005 Mar;48(3):445-51. Epub 2005 Feb 24.
20. Hashigucci K, etal., Hum Immunol. 2003 May;64(5):530-7.
21. Huang SC, etal., Pediatr Neonatol. 2008 Apr;49(2):30-4.
22. Hunt PJ, etal., Clin Endocrinol (Oxf). 2001 Oct;55(4):491-9.
23. Ierna MX, etal., Infect Immun. 2009 Sep;77(9):3879-85. doi: 10.1128/IAI.01461-08. Epub 2009 Jun 29.
24. Imagawa DK, etal., J Surg Res. 1990 Apr;48(4):345-8.
25. Issazadeh S, etal., J Neuroimmunol. 1995 Sep;61(2):205-12.
26. Izakovicova Holla L, etal., Clin Exp Allergy. 2001 Sep;31(9):1418-23.
27. Kamali-Sarvestani E, etal., Cytokine. 2006 Aug;35(3-4):159-65. Epub 2006 Sep 6.
28. Kankova K, etal., Ophthalmologica. 2001 Jul-Aug;215(4):294-8.
29. Karplus TM, etal., Infect Immun. 2002 Dec;70(12):6919-25.
30. Kazzi SN, etal., Pediatr Res. 2004 Jul;56(1):94-8. Epub 2004 May 5.
31. Kim TG, etal., Arch Dermatol Res. 2003 Apr;295(1):8-13. Epub 2003 Mar 13.
32. Kohaar I, etal., Breast Cancer Res Treat. 2009 Mar;114(2):347-55. doi: 10.1007/s10549-008-0006-5. Epub 2008 Apr 14.
33. Kumaraguru U, etal., J Immunol. 2001 Jan 15;166(2):1066-74.
34. Laxton R, etal., Genes Immun. 2005 Sep;6(6):539-41.
35. Li FN, etal., Zhonghua Yi Xue Za Zhi. 2008 May 27;88(20):1402-4.
36. Lindholm E, etal., PLoS One. 2008 Jun 25;3(6):e2546.
37. Liu SK, etal., Lymphokine Cytokine Res. 1991 Jun;10(3):189-94.
38. Lowes MA, etal., J Invest Dermatol. 1997 Jun;108(6):914-9.
39. Mak JC, etal., Int Arch Allergy Immunol. 2007;144(2):114-22. Epub 2007 May 24.
40. McDougal KE, etal., J Invest Dermatol. 2009 Aug;129(8):1921-6. doi: 10.1038/jid.2008.456. Epub 2009 Feb 19.
41. Messer G, etal., Dermatology. 1994;189 Suppl 1:135-7.
42. Migita O, etal., Clin Exp Allergy. 2005 Jun;35(6):790-6.
43. Miyaguchi S, etal., Clin Immunol. 2001 Jan;98(1):119-24.
44. Mrazek F, etal., Tissue Antigens. 2005 Feb;65(2):163-71.
45. Murdaca G, etal., J Interferon Cytokine Res. 2012 Jun;32(6):277-9. doi: 10.1089/jir.2011.0120. Epub 2012 Apr 5.
46. Nakayama T, etal., Am J Hypertens. 2004 Nov;17(11 Pt 1):1045-9.
47. Niwa Y, etal., Gynecol Oncol. 2007 Mar;104(3):586-90. Epub 2006 Oct 11.
48. OMIM Disease Annotation Pipeline
49. Ozaki K, etal., Nat Genet. 2002 Dec;32(4):650-4. Epub 2002 Nov 11.
50. Pandey JP and Takeuchi F, Hum Immunol. 1999 Nov;60(11):1128-30.
51. Park KS, etal., Eur J Immunogenet. 2002 Feb;29(1):7-10.
52. Peric A, etal., B-ENT. 2012;8(1):25-32.
53. Pipeline to import KEGG annotations from KEGG into RGD
54. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
55. Pizarro TT, etal., Transplantation. 1993 Aug;56(2):399-404.
56. Rennert PD, etal., J Exp Med. 2001 Jun 4;193(11):1227-38.
57. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
58. RGD automated import pipeline for gene-chemical interactions
59. Rojas J, etal., Ophthalmology. 2010 Dec;117(12):2417-2423.e1-2. doi: 10.1016/j.ophtha.2010.03.059. Epub 2010 Jul 21.
60. Schreyer SA, etal., J Biol Chem. 2002 Apr 5;277(14):12364-8. Epub 2002 Jan 23.
61. Shen L, etal., J Immunol. 2010 Nov 15;185(10):6355-63. doi: 10.4049/jimmunol.1001520. Epub 2010 Oct 15.
62. Shin HD, etal., Ann N Y Acad Sci. 2008 Dec;1150:76-85.
63. Stayoussef M, etal., Clin Vaccine Immunol. 2008 Feb;15(2):379-81. Epub 2007 Nov 7.
64. Suna S, etal., Atherosclerosis. 2013 Apr;227(2):373-9. doi: 10.1016/j.atherosclerosis.2013.01.020. Epub 2013 Jan 25.
65. Takahashi K, etal., Clin Immunol Immunopathol. 1993 Dec;69(3):318-23.
66. Takeuchi K, etal., Laryngoscope. 2000 Oct;110(10 Pt 1):1711-4.
67. Tran TA, etal., Cancer. 1998 Jul 15;83(2):276-82.
68. Um JY, etal., Clin Appl Thromb Hemost. 2010 Oct;16(5):559-62. doi: 10.1177/1076029609348313. Epub 2009 Oct 14.
69. Um JY, etal., J Mol Neurosci. 2003;21(2):167-71.
70. Vendrell J, etal., Metabolism. 1995 Jun;44(6):691-4.
71. Yamada A, etal., J Mol Med. 2004 Jul;82(7):477-83. Epub 2004 Jun 3.
72. Yamasaki Y, etal., Diabetes Care. 2006 Nov;29(11):2445-51.
73. Yoshioka K, etal., Metabolism. 2006 Oct;55(10):1406-10.
74. Zeggini E, etal., Diabetologia. 2005 Oct;48(10):2013-7. Epub 2005 Aug 18.
Additional References at PubMed
PMID:1279199   PMID:1310388   PMID:1353024   PMID:1451807   PMID:1670638   PMID:1671667   PMID:1733919   PMID:2160731   PMID:2243081   PMID:2545693   PMID:2567059   PMID:2995927  
PMID:3001109   PMID:3001529   PMID:3536896   PMID:3555974   PMID:6334807   PMID:6608523   PMID:7590964   PMID:7601445   PMID:7695626   PMID:7818827   PMID:7916655   PMID:7995952  
PMID:8081366   PMID:8123048   PMID:8139045   PMID:8171323   PMID:8182064   PMID:8288897   PMID:8323280   PMID:8387891   PMID:8499947   PMID:8629302   PMID:8912010   PMID:9153189  
PMID:9185077   PMID:9235946   PMID:9282784   PMID:9307242   PMID:9317127   PMID:9462508   PMID:9480751   PMID:9552007   PMID:10202016   PMID:10668961   PMID:11092520   PMID:11113269  
PMID:11163081   PMID:11164894   PMID:11167813   PMID:11194890   PMID:11196686   PMID:11210078   PMID:11233912   PMID:11243953   PMID:11250044   PMID:11257271   PMID:11258696   PMID:11319038  
PMID:11334675   PMID:11349201   PMID:11371414   PMID:11401880   PMID:11410733   PMID:11544434   PMID:11574100   PMID:11576577   PMID:11732226   PMID:11737072   PMID:11775944   PMID:11781708  
PMID:11800584   PMID:11808761   PMID:11820636   PMID:11823516   PMID:11841484   PMID:11924527   PMID:11975986   PMID:12028020   PMID:12030733   PMID:12047333   PMID:12082592   PMID:12116197  
PMID:12126516   PMID:12149604   PMID:12164325   PMID:12169181   PMID:12351419   PMID:12392859   PMID:12414751   PMID:12439617   PMID:12477932   PMID:12478078   PMID:12519452   PMID:12528108  
PMID:12545006   PMID:12558135   PMID:12559634   PMID:12566517   PMID:12568117   PMID:12648734   PMID:12651071   PMID:12661999   PMID:12679941   PMID:12714268   PMID:12717265   PMID:12746914  
PMID:12768436   PMID:12770792   PMID:12780951   PMID:12828656   PMID:12888330   PMID:12906716   PMID:12915440   PMID:12917036   PMID:12953135   PMID:14566095   PMID:14569193   PMID:14572794  
PMID:14617046   PMID:14635012   PMID:14637275   PMID:14647194   PMID:14656967   PMID:14681301   PMID:14987295   PMID:15009068   PMID:15034015   PMID:15041959   PMID:15052269   PMID:15061799  
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PMID:15306845   PMID:15342556   PMID:15354858   PMID:15380900   PMID:15381184   PMID:15457442   PMID:15489334   PMID:15513316   PMID:15517637   PMID:15526004   PMID:15548263   PMID:15583987  
PMID:15639341   PMID:15639929   PMID:15649304   PMID:15663746   PMID:15667484   PMID:15695296   PMID:15699425   PMID:15718364   PMID:15803361   PMID:15811521   PMID:15843211   PMID:15851552  
PMID:15861005   PMID:15890243   PMID:15932622   PMID:15951664   PMID:15955450   PMID:15976383   PMID:15999154   PMID:16054631   PMID:16095118   PMID:16107511   PMID:16164697   PMID:16186631  
PMID:16193177   PMID:16204594   PMID:16215460   PMID:16246225   PMID:16249504   PMID:16276011   PMID:16293872   PMID:16298864   PMID:16313841   PMID:16323614   PMID:16375755   PMID:16386648  
PMID:16389181   PMID:16447204   PMID:16545485   PMID:16609369   PMID:16643431   PMID:16702430   PMID:16723241   PMID:16728705   PMID:16775170   PMID:16788244   PMID:16814297   PMID:16839190  
PMID:16867312   PMID:16872485   PMID:16874159   PMID:16882065   PMID:16928504   PMID:16931032   PMID:16931544   PMID:16934308   PMID:16939911   PMID:16971410   PMID:16988060   PMID:17014622  
PMID:17018637   PMID:17029750   PMID:17036337   PMID:17040205   PMID:17071996   PMID:17103073   PMID:17113059   PMID:17113632   PMID:17140746   PMID:17174749   PMID:17194634   PMID:17207711  
PMID:17212707   PMID:17216494   PMID:17220333   PMID:17295710   PMID:17311253   PMID:17315188   PMID:17332138   PMID:17335371   PMID:17336158   PMID:17345061   PMID:17348243   PMID:17349875  
PMID:17353895   PMID:17355643   PMID:17380888   PMID:17388919   PMID:17444587   PMID:17444864   PMID:17450233   PMID:17483704   PMID:17485095   PMID:17493152   PMID:17497114   PMID:17517687  
PMID:17521734   PMID:17530646   PMID:17559370   PMID:17595314   PMID:17635597   PMID:17640324   PMID:17640627   PMID:17700210   PMID:17703412   PMID:17767060   PMID:17767555   PMID:17953695  
PMID:17971052   PMID:17981284   PMID:17989341   PMID:18032375   PMID:18062795   PMID:18069935   PMID:18071035   PMID:18190265   PMID:18230628   PMID:18271063   PMID:18273643   PMID:18292573  
PMID:18299433   PMID:18349535   PMID:18354254   PMID:18384488   PMID:18385169   PMID:18394614   PMID:18398039   PMID:18405969   PMID:18442814   PMID:18457972   PMID:18496506   PMID:18504081  
PMID:18513389   PMID:18633131   PMID:18636124   PMID:18676680   PMID:18700950   PMID:18754435   PMID:18797991   PMID:18805892   PMID:18806884   PMID:18819899   PMID:18922873   PMID:18974840  
PMID:18974842   PMID:18977990   PMID:18987644   PMID:18990758   PMID:19000388   PMID:19009622   PMID:19012493   PMID:19013708   PMID:19013788   PMID:19021060   PMID:19028820   PMID:19034549  
PMID:19050632   PMID:19052714   PMID:19074885   PMID:19103156   PMID:19131662   PMID:19143814   PMID:19167443   PMID:19170196   PMID:19182073   PMID:19183163   PMID:19238444   PMID:19242354  
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PMID:19729601   PMID:19735075   PMID:19738620   PMID:19773279   PMID:19773451   PMID:19789445   PMID:19800575   PMID:19837266   PMID:19851445   PMID:19860767   PMID:19889075   PMID:19890662  
PMID:19894308   PMID:19900796   PMID:19913121   PMID:19933216   PMID:19948975   PMID:19958618   PMID:20014019   PMID:20035431   PMID:20047977   PMID:20070603   PMID:20080841   PMID:20145925  
PMID:20177654   PMID:20188863   PMID:20189261   PMID:20214763   PMID:20237496   PMID:20307689   PMID:20335604   PMID:20356761   PMID:20395963   PMID:20396759   PMID:20416077   PMID:20452482  
PMID:20453000   PMID:20459604   PMID:20463618   PMID:20472930   PMID:20485444   PMID:20491592   PMID:20500087   PMID:20503287   PMID:20536507   PMID:20536609   PMID:20537163   PMID:20548340  
PMID:20568250   PMID:20578820   PMID:20587610   PMID:20603037   PMID:20608170   PMID:20627040   PMID:20628086   PMID:20644561   PMID:20662065   PMID:20668555   PMID:20673868   PMID:20811626  
PMID:20835611   PMID:20848459   PMID:20854863   PMID:20878356   PMID:20933106   PMID:20957367   PMID:21029472   PMID:21067489   PMID:21102463   PMID:21271873   PMID:21319595   PMID:21323572  
PMID:21366408   PMID:21459939   PMID:21482522   PMID:21544635   PMID:21628868   PMID:21765051   PMID:21793721   PMID:22001640   PMID:22100609   PMID:22177457   PMID:22193458   PMID:22225620  
PMID:22243485   PMID:22310064   PMID:22311026   PMID:22427961   PMID:22464751   PMID:22507624   PMID:22568977   PMID:22748850   PMID:22882567   PMID:22897480   PMID:22901152   PMID:23051989  
PMID:23159874   PMID:23289732   PMID:23299818   PMID:23364796   PMID:23377953   PMID:23524463   PMID:23547113   PMID:23550407   PMID:23683942   PMID:23824834   PMID:23834030   PMID:23840460  
PMID:23884763   PMID:23931336   PMID:23953530   PMID:24035239   PMID:24054031   PMID:24136744   PMID:24197700   PMID:24233435   PMID:24244632   PMID:24259423   PMID:24283517   PMID:24312346  
PMID:24349304   PMID:24420856   PMID:24598699   PMID:24610621   PMID:24642747   PMID:24696164   PMID:24796628   PMID:24896334   PMID:24959879   PMID:25003989   PMID:25063351   PMID:25139349  
PMID:25140780   PMID:25173940   PMID:25735143   PMID:25910212   PMID:25915535   PMID:25931031   PMID:25980610   PMID:25981594   PMID:26076780   PMID:26108796   PMID:26114114   PMID:26221924  
PMID:26554163   PMID:26561241   PMID:26646413   PMID:26707826   PMID:26761582   PMID:26821796   PMID:26932696   PMID:27056089   PMID:27102235   PMID:27312561   PMID:27411794   PMID:27592234  
PMID:27647233   PMID:27819528   PMID:27838362   PMID:27914457   PMID:28106707   PMID:28476335   PMID:28489756   PMID:28514442   PMID:28620227   PMID:28738973   PMID:28740106   PMID:28865603  
PMID:29484035   PMID:29786123   PMID:30129153   PMID:30244922   PMID:30284722   PMID:30334603   PMID:30627222   PMID:31049794   PMID:31054364   PMID:31539146   PMID:31570816   PMID:31996699  
PMID:32102503   PMID:32296183   PMID:32420584   PMID:32884945   PMID:32986381  


Genomics

Comparative Map Data
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
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2203,618,853 - 3,621,324 (+)NCBI
Rnor_6.0 Ensembl204,852,496 - 4,854,677 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0204,851,889 - 4,854,677 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
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
(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 (+)NCBI
Lta
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475424,626,930 - 24,628,412 (-)NCBI

Position Markers
GDB:182383  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37631,540,365 - 31,540,523UniSTSGRCh37
Build 36631,648,344 - 31,648,502RGDNCBI36
Celera633,138,580 - 33,138,738RGD
Cytogenetic Map6p21.33UniSTS
Cytogenetic Map6p21.3UniSTS
HuRef631,327,097 - 31,327,257UniSTS
PMC32163P1  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37631,540,175 - 31,540,543UniSTSGRCh37
Build 36631,648,154 - 31,648,522RGDNCBI36
Celera633,138,390 - 33,138,758RGD
Cytogenetic Map6p21.33UniSTS
Cytogenetic Map6p21.3UniSTS
HuRef631,326,907 - 31,327,277UniSTS
LTA_189  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37631,541,432 - 31,542,274UniSTSGRCh37
Build 36631,649,411 - 31,650,253RGDNCBI36
Celera633,139,647 - 33,140,489RGD
HuRef631,328,166 - 31,329,008UniSTS
D6S2791  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37631,540,361 - 31,540,542UniSTSGRCh37
Build 36631,648,340 - 31,648,521RGDNCBI36
Celera633,138,576 - 33,138,757RGD
HuRef631,327,093 - 31,327,276UniSTS
RH71008  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37631,540,441 - 31,540,536UniSTSGRCh37
Build 36631,648,420 - 31,648,515RGDNCBI36
Celera633,138,656 - 33,138,751RGD
Cytogenetic Map6p21.33UniSTS
Cytogenetic Map6p21.3UniSTS
HuRef631,327,173 - 31,327,270UniSTS
GeneMap99-GB4 RH Map6145.45UniSTS
RH17367  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37631,541,606 - 31,541,740UniSTSGRCh37
Build 36631,649,585 - 31,649,719RGDNCBI36
Celera633,139,821 - 33,139,955RGD
Cytogenetic Map6p21.33UniSTS
Cytogenetic Map6p21.3UniSTS
HuRef631,328,340 - 31,328,474UniSTS
GeneMap99-GB4 RH Map6119.82UniSTS
GDB:192948  
Human AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map6p21.3UniSTS

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1149
Count of miRNA genes:432
Interacting mature miRNAs:470
Transcripts:ENST00000418386, ENST00000454783, ENST00000471842, ENST00000489638
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system sensory system adipose tissue appendage entire extraembryonic component pharyngeal arch
High 6
Medium 20 61 3 722 1 1 3 1 144 4 1
Low 500 848 388 132 1084 118 1029 238 1335 132 701 772 14 377 694 1 2
Below cutoff 1774 1925 1257 468 122 324 3113 1831 2295 237 574 751 155 817 2002 2

Sequence

Nucleotide Sequences
RefSeq Transcripts NG_007462 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NG_012010 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_000595 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001159740 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_011514615 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_011514616 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_011514617 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_011514618 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide A06316 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB088112 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB103618 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB202113 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF037255 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF129756 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AL662801 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AL662847 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AL929587 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY070490 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY216498 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY274903 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY274904 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY274905 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY274906 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY274907 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY274908 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY274909 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY274910 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY274911 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY274912 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY274913 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY274914 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY274915 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY274916 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY274917 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY274918 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY274919 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY274920 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY274921 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY274922 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY274923 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY274924 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY274925 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY274926 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BA000025 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC034729 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BG685356 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BP338937 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BX108399 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BX248516 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BX248519 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BX927320 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH471081 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CR542253 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CR542273 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CR753892 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CR942185 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CS081477 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  D00102 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  D12614 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DQ123821 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DQ123822 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DQ123823 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DQ123824 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DQ123825 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DQ123826 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DQ123827 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  EU338448 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  EU338449 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  EU338450 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  EU338451 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KF809957 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KF809958 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KF809959 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KF809960 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KF809961 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KF809962 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KF809963 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KF809964 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KF809965 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KF833316 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KF833317 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KF833318 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KF833319 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KY500410 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KY500411 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KY500412 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KY500413 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  LC461700 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  LN874316 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M16441 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M55913 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  MF477884 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  MF477885 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  MF477886 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  MF477887 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  MF477888 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X01393 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X02911 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  Y14768 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  Z15026 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENST00000418386   ⟹   ENSP00000413450
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl631,572,283 - 31,574,324 (+)Ensembl
RefSeq Acc Id: ENST00000454783   ⟹   ENSP00000403495
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl631,572,054 - 31,574,324 (+)Ensembl
RefSeq Acc Id: ENST00000471842
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl631,572,294 - 31,574,324 (+)Ensembl
RefSeq Acc Id: ENST00000489638
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl631,572,270 - 31,574,324 (+)Ensembl
RefSeq Acc Id: NM_000595   ⟹   NP_000586
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38631,572,289 - 31,574,324 (+)NCBI
GRCh37631,539,876 - 31,542,101 (+)NCBI
Build 36631,648,072 - 31,650,077 (+)NCBI Archive
HuRef631,326,608 - 31,328,835 (+)NCBI
CHM1_1631,542,203 - 31,544,233 (+)NCBI
Sequence:
RefSeq Acc Id: NM_001159740   ⟹   NP_001153212
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38631,572,099 - 31,574,324 (+)NCBI
GRCh37631,539,876 - 31,542,101 (+)NCBI
HuRef631,326,608 - 31,328,835 (+)NCBI
CHM1_1631,542,008 - 31,544,233 (+)NCBI
Sequence:
RefSeq Acc Id: XM_011514615   ⟹   XP_011512917
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38631,560,615 - 31,574,324 (+)NCBI
Sequence:
RefSeq Acc Id: XM_011514616   ⟹   XP_011512918
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38631,560,615 - 31,574,324 (+)NCBI
Sequence:
RefSeq Acc Id: XM_011514617   ⟹   XP_011512919
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38631,560,615 - 31,574,324 (+)NCBI
Sequence:
RefSeq Acc Id: XM_011514618   ⟹   XP_011512920
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38631,560,550 - 31,574,324 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_000586 (Get FASTA)   NCBI Sequence Viewer  
  NP_001153212 (Get FASTA)   NCBI Sequence Viewer  
  XP_011512917 (Get FASTA)   NCBI Sequence Viewer  
  XP_011512918 (Get FASTA)   NCBI Sequence Viewer  
  XP_011512919 (Get FASTA)   NCBI Sequence Viewer  
  XP_011512920 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA61199 (Get FASTA)   NCBI Sequence Viewer  
  AAB59455 (Get FASTA)   NCBI Sequence Viewer  
  AAD18092 (Get FASTA)   NCBI Sequence Viewer  
  AAH34729 (Get FASTA)   NCBI Sequence Viewer  
  AAL49956 (Get FASTA)   NCBI Sequence Viewer  
  AAO21135 (Get FASTA)   NCBI Sequence Viewer  
  AAP51421 (Get FASTA)   NCBI Sequence Viewer  
  AAP51422 (Get FASTA)   NCBI Sequence Viewer  
  AAP51423 (Get FASTA)   NCBI Sequence Viewer  
  AAP51424 (Get FASTA)   NCBI Sequence Viewer  
  AAP51425 (Get FASTA)   NCBI Sequence Viewer  
  AAP51426 (Get FASTA)   NCBI Sequence Viewer  
  AAP51427 (Get FASTA)   NCBI Sequence Viewer  
  AAP51428 (Get FASTA)   NCBI Sequence Viewer  
  AAP51429 (Get FASTA)   NCBI Sequence Viewer  
  AAP51430 (Get FASTA)   NCBI Sequence Viewer  
  AAP51431 (Get FASTA)   NCBI Sequence Viewer  
  AAP51432 (Get FASTA)   NCBI Sequence Viewer  
  AAP51433 (Get FASTA)   NCBI Sequence Viewer  
  AAP51434 (Get FASTA)   NCBI Sequence Viewer  
  AAP51435 (Get FASTA)   NCBI Sequence Viewer  
  AAP51436 (Get FASTA)   NCBI Sequence Viewer  
  AAP51437 (Get FASTA)   NCBI Sequence Viewer  
  AAP51438 (Get FASTA)   NCBI Sequence Viewer  
  AAP51439 (Get FASTA)   NCBI Sequence Viewer  
  AAP51440 (Get FASTA)   NCBI Sequence Viewer  
  AAP51441 (Get FASTA)   NCBI Sequence Viewer  
  AAP51442 (Get FASTA)   NCBI Sequence Viewer  
  AAP51443 (Get FASTA)   NCBI Sequence Viewer  
  AAP51444 (Get FASTA)   NCBI Sequence Viewer  
  AAZ32914 (Get FASTA)   NCBI Sequence Viewer  
  AAZ32915 (Get FASTA)   NCBI Sequence Viewer  
  AAZ32916 (Get FASTA)   NCBI Sequence Viewer  
  AAZ32917 (Get FASTA)   NCBI Sequence Viewer  
  AAZ32918 (Get FASTA)   NCBI Sequence Viewer  
  AAZ32919 (Get FASTA)   NCBI Sequence Viewer  
  AAZ32920 (Get FASTA)   NCBI Sequence Viewer  
  ACA64643 (Get FASTA)   NCBI Sequence Viewer  
  ACA64644 (Get FASTA)   NCBI Sequence Viewer  
  ACA64645 (Get FASTA)   NCBI Sequence Viewer  
  ACA64646 (Get FASTA)   NCBI Sequence Viewer  
  AHH34316 (Get FASTA)   NCBI Sequence Viewer  
  AHH34317 (Get FASTA)   NCBI Sequence Viewer  
  AHH34318 (Get FASTA)   NCBI Sequence Viewer  
  AHH34319 (Get FASTA)   NCBI Sequence Viewer  
  AHH34320 (Get FASTA)   NCBI Sequence Viewer  
  AHH34321 (Get FASTA)   NCBI Sequence Viewer  
  AHH34322 (Get FASTA)   NCBI Sequence Viewer  
  AHH34323 (Get FASTA)   NCBI Sequence Viewer  
  AHH34324 (Get FASTA)   NCBI Sequence Viewer  
  AHI45173 (Get FASTA)   NCBI Sequence Viewer  
  AHI45174 (Get FASTA)   NCBI Sequence Viewer  
  AHI45175 (Get FASTA)   NCBI Sequence Viewer  
  AHI45176 (Get FASTA)   NCBI Sequence Viewer  
  AQY76897 (Get FASTA)   NCBI Sequence Viewer  
  AQY76898 (Get FASTA)   NCBI Sequence Viewer  
  AQY76899 (Get FASTA)   NCBI Sequence Viewer  
  AQY76900 (Get FASTA)   NCBI Sequence Viewer  
  ASZ70071 (Get FASTA)   NCBI Sequence Viewer  
  ASZ70072 (Get FASTA)   NCBI Sequence Viewer  
  ASZ70073 (Get FASTA)   NCBI Sequence Viewer  
  ASZ70074 (Get FASTA)   NCBI Sequence Viewer  
  ASZ70075 (Get FASTA)   NCBI Sequence Viewer  
  BAA00064 (Get FASTA)   NCBI Sequence Viewer  
  BAA02139 (Get FASTA)   NCBI Sequence Viewer  
  BAB63397 (Get FASTA)   NCBI Sequence Viewer  
  BAC54943 (Get FASTA)   NCBI Sequence Viewer  
  BAE78638 (Get FASTA)   NCBI Sequence Viewer  
  BAF31278 (Get FASTA)   NCBI Sequence Viewer  
  CAA00536 (Get FASTA)   NCBI Sequence Viewer  
  CAA25649 (Get FASTA)   NCBI Sequence Viewer  
  CAA26670 (Get FASTA)   NCBI Sequence Viewer  
  CAA75071 (Get FASTA)   NCBI Sequence Viewer  
  CAA78746 (Get FASTA)   NCBI Sequence Viewer  
  CAG47049 (Get FASTA)   NCBI Sequence Viewer  
  CAG47069 (Get FASTA)   NCBI Sequence Viewer  
  CAI95949 (Get FASTA)   NCBI Sequence Viewer  
  CTQ86081 (Get FASTA)   NCBI Sequence Viewer  
  EAX03422 (Get FASTA)   NCBI Sequence Viewer  
  EAX03423 (Get FASTA)   NCBI Sequence Viewer  
  P01374 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001153212   ⟸   NM_001159740
- Peptide Label: precursor
- UniProtKB: P01374 (UniProtKB/Swiss-Prot),   Q5STV3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_000586   ⟸   NM_000595
- Peptide Label: precursor
- UniProtKB: P01374 (UniProtKB/Swiss-Prot),   Q5STV3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_011512920   ⟸   XM_011514618
- Peptide Label: isoform X1
- UniProtKB: P01374 (UniProtKB/Swiss-Prot),   Q5STV3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_011512917   ⟸   XM_011514615
- Peptide Label: isoform X1
- UniProtKB: P01374 (UniProtKB/Swiss-Prot),   Q5STV3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_011512918   ⟸   XM_011514616
- Peptide Label: isoform X1
- UniProtKB: P01374 (UniProtKB/Swiss-Prot),   Q5STV3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_011512919   ⟸   XM_011514617
- Peptide Label: isoform X1
- UniProtKB: P01374 (UniProtKB/Swiss-Prot),   Q5STV3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSP00000403495   ⟸   ENST00000454783
RefSeq Acc Id: ENSP00000413450   ⟸   ENST00000418386
Protein Domains
TNF_2

Promoters
RGD ID:6872514
Promoter ID:EPDNEW_H9422
Type:initiation region
Name:LTA_1
Description:lymphotoxin alpha
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H9423  
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh38631,572,289 - 31,572,349EPDNEW
RGD ID:6872516
Promoter ID:EPDNEW_H9423
Type:initiation region
Name:LTA_2
Description:lymphotoxin alpha
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H9422  
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh38631,572,513 - 31,572,573EPDNEW
RGD ID:6804419
Promoter ID:HG_KWN:52935
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:CD4+TCell,   K562,   Lymphoblastoid
Transcripts:ENST00000396143,   OTTHUMT00000076237,   OTTHUMT00000076238,   OTTHUMT00000259098,   UC003NUD.1,   UC003NUF.1,   UC003NUG.1,   UC003NUH.1,   UC010JSR.1
Position:
Human AssemblyChrPosition (strand)Source
Build 36631,647,856 - 31,648,356 (+)MPROMDB
RGD ID:6850160
Promoter ID:EP11159
Type:multiple initiation site
Name:HS_LTA
Description:Tumor necrosis factor-beta, LTA or TNFB gene.
SO ACC ID:SO:0000170
Source:EPD (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Notes:homology_group=Homology group 127; Mammalian tumor necrosis factor beta
Experiment Methods:Nuclease protection with homologous sequence ladder
Regulation:T (repressed by or weakly expressed in) lymphocytes; (induced by or strongly expressed in) antigen, (induced by or strongly expressed in) mitogen
Position:
Human AssemblyChrPosition (strand)Source
Build 36631,648,041 - 31,648,101EPD

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
NM_000595.4(LTA):c.-10+90A>G single nucleotide variant Myocardial infarction [RCV000015456]|Psoriatic arthritis, susceptibility to [RCV000015457] Chr6:31572536 [GRCh38]
Chr6:31540313 [GRCh37]
Chr6:6p21.33
risk factor
NM_000595.4(LTA):c.-92= single nucleotide variant Leprosy, early-onset, susceptibility to [RCV000015458] Chr6:31572364 [GRCh38]
Chr6:31540141 [GRCh37]
Chr6:6p21.33
risk factor
NM_000595.4(LTA):c.179C>A (p.Thr60Asn) single nucleotide variant Myocardial infarction [RCV000015455] Chr6:31573007 [GRCh38]
Chr6:31540784 [GRCh37]
Chr6:6p21.33
risk factor
NM_001159740.2(LTA):c.556G>A (p.Asp186Asn) single nucleotide variant Malignant melanoma [RCV000067284] Chr6:31573631 [GRCh38]
Chr6:31541408 [GRCh37]
Chr6:31649387 [NCBI36]
Chr6:6p21.33
not provided
GRCh38/hg38 6p25.3-12.3(chr6:156974-46789291)x3 copy number gain See cases [RCV000143497] Chr6:156974..46789291 [GRCh38]
Chr6:156974..46757028 [GRCh37]
Chr6:101974..46864987 [NCBI36]
Chr6:6p25.3-12.3
pathogenic
GRCh37/hg19 6p21.33(chr6:31384577-31902308)x3 copy number gain See cases [RCV000448679] Chr6:31384577..31902308 [GRCh37]
Chr6:6p21.33
uncertain significance
GRCh37/hg19 6p25.3-q27(chr6:156975-170919482)x3 copy number gain See cases [RCV000512067] Chr6:156975..170919482 [GRCh37]
Chr6:6p25.3-q27
pathogenic
GRCh37/hg19 6p25.3-q27(chr6:156975-170919482) copy number gain See cases [RCV000510595] Chr6:156975..170919482 [GRCh37]
Chr6:6p25.3-q27
pathogenic
GRCh37/hg19 6p25.3-q27(chr6:108666-170980171)x3 copy number gain not provided [RCV000745403] Chr6:108666..170980171 [GRCh37]
Chr6:6p25.3-q27
pathogenic
GRCh37/hg19 6p25.3-q27(chr6:60107-171054786)x3 copy number gain not provided [RCV000745400] Chr6:60107..171054786 [GRCh37]
Chr6:6p25.3-q27
pathogenic
GRCh37/hg19 6p25.3-q27(chr6:165632-170919470)x3 copy number gain not provided [RCV000745404] Chr6:165632..170919470 [GRCh37]
Chr6:6p25.3-q27
pathogenic
GRCh37/hg19 6p22.1-21.32(chr6:28130359-32108367)x3 copy number gain not provided [RCV000745592] Chr6:28130359..32108367 [GRCh37]
Chr6:6p22.1-21.32
uncertain significance
GRCh37/hg19 6p22.1-q14.1(chr6:29455465-81447367) copy number gain not provided [RCV000767714] Chr6:29455465..81447367 [GRCh37]
Chr6:6p22.1-q14.1
pathogenic
GRCh37/hg19 6p21.33-21.31(chr6:31036397-34088832)x3 copy number gain not provided [RCV001005791] Chr6:31036397..34088832 [GRCh37]
Chr6:6p21.33-21.31
likely pathogenic

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:6709 AgrOrtholog
COSMIC LTA COSMIC
Ensembl Genes ENSG00000173503 UniProtKB/TrEMBL
  ENSG00000223919 UniProtKB/TrEMBL
  ENSG00000226275 UniProtKB/TrEMBL
  ENSG00000226979 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
  ENSG00000230279 UniProtKB/Swiss-Prot
  ENSG00000231408 UniProtKB/Swiss-Prot
  ENSG00000238130 UniProtKB/TrEMBL
Ensembl Protein ENSP00000372791 UniProtKB/TrEMBL
  ENSP00000372793 UniProtKB/TrEMBL
  ENSP00000372991 UniProtKB/TrEMBL
  ENSP00000383131 UniProtKB/TrEMBL
  ENSP00000387924 UniProtKB/TrEMBL
  ENSP00000395895 UniProtKB/TrEMBL
  ENSP00000395976 UniProtKB/Swiss-Prot
  ENSP00000402413 UniProtKB/Swiss-Prot
  ENSP00000403495 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSP00000407133 UniProtKB/TrEMBL
  ENSP00000412555 UniProtKB/Swiss-Prot
  ENSP00000413450 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSP00000416337 UniProtKB/TrEMBL
  ENSP00000416509 UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000383303 UniProtKB/TrEMBL
  ENST00000383304 UniProtKB/TrEMBL
  ENST00000383499 UniProtKB/TrEMBL
  ENST00000400272 UniProtKB/TrEMBL
  ENST00000412851 UniProtKB/Swiss-Prot
  ENST00000418386 ENTREZGENE, UniProtKB/Swiss-Prot
  ENST00000426845 UniProtKB/Swiss-Prot
  ENST00000432632 UniProtKB/TrEMBL
  ENST00000436519 UniProtKB/Swiss-Prot
  ENST00000441939 UniProtKB/TrEMBL
  ENST00000448630 UniProtKB/TrEMBL
  ENST00000454550 UniProtKB/Swiss-Prot
  ENST00000454783 ENTREZGENE, UniProtKB/Swiss-Prot
  ENST00000456789 UniProtKB/TrEMBL
Gene3D-CATH 2.60.120.40 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
GTEx ENSG00000173503 GTEx
  ENSG00000223919 GTEx
  ENSG00000226275 GTEx
  ENSG00000226979 GTEx
  ENSG00000230279 GTEx
  ENSG00000231408 GTEx
  ENSG00000238130 GTEx
HGNC ID HGNC:6709 ENTREZGENE
Human Proteome Map LTA Human Proteome Map
InterPro TNF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TNF_beta UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TNF_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TNF_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Tumour_necrosis_fac-like_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report hsa:4049 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 4049 ENTREZGENE
OMIM 153440 OMIM
  607507 OMIM
  608446 OMIM
  610988 OMIM
Pfam TNF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB LTA RGD, PharmGKB
PRINTS TNECROSISFCT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TNFBETA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE TNF_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TNF_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART TNF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF49842 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A286SD60_HUMAN UniProtKB/TrEMBL
  A0A286SD61_HUMAN UniProtKB/TrEMBL
  A0A286SD62_HUMAN UniProtKB/TrEMBL
  A0A286SD66_HUMAN UniProtKB/TrEMBL
  A0A286SD73_HUMAN UniProtKB/TrEMBL
  P01374 ENTREZGENE
  Q45NE3_HUMAN UniProtKB/TrEMBL
  Q45NE4_HUMAN UniProtKB/TrEMBL
  Q45NE5_HUMAN UniProtKB/TrEMBL
  Q45NE6_HUMAN UniProtKB/TrEMBL
  Q45NE7_HUMAN UniProtKB/TrEMBL
  Q45NE8_HUMAN UniProtKB/TrEMBL
  Q45NE9_HUMAN UniProtKB/TrEMBL
  Q5ST95_HUMAN UniProtKB/TrEMBL
  Q5STV3 ENTREZGENE, UniProtKB/TrEMBL
  Q6FG55_HUMAN UniProtKB/TrEMBL
  Q6WQT9_HUMAN UniProtKB/TrEMBL
  Q6WQU7_HUMAN UniProtKB/TrEMBL
  Q6WQV4_HUMAN UniProtKB/TrEMBL
  Q6WQV6_HUMAN UniProtKB/TrEMBL
  Q6WQV7_HUMAN UniProtKB/TrEMBL
  TNFB_HUMAN UniProtKB/Swiss-Prot
  W6A1P7_HUMAN UniProtKB/TrEMBL
UniProt Secondary Q5HYS4 UniProtKB/TrEMBL
  Q8N4C3 UniProtKB/Swiss-Prot
  Q9UKS8 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-07-30 LTA  lymphotoxin alpha    lymphotoxin alpha (TNF superfamily, member 1)  Symbol and/or name change 5135510 APPROVED