LTB (lymphotoxin beta) - Rat Genome Database

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Gene: LTB (lymphotoxin beta) Homo sapiens
Analyze
Symbol: LTB
Name: lymphotoxin beta
RGD ID: 1353964
HGNC Page HGNC:6711
Description: Predicted to enable signaling receptor binding activity. Predicted to be involved in positive regulation of canonical NF-kappaB signal transduction; positive regulation of extrinsic apoptotic signaling pathway; and positive regulation of interleukin-12 production. Predicted to act upstream of or within gene expression; lymph node development; and skin development. Predicted to be located in plasma membrane.
Type: protein-coding
RefSeq Status: REVIEWED
Previously known as: LT-beta; lymphotoxin beta (TNF superfamily, member 3); lymphotoxin-beta; p33; TNF superfamily member 3; TNF-C; TNFC; TNFSF3; TNLG1C; tumor necrosis factor C; tumor necrosis factor ligand 1C; tumor necrosis factor ligand superfamily member 3
RGD Orthologs
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38631,580,558 - 31,582,425 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl631,580,525 - 31,582,522 (-)EnsemblGRCh38hg38GRCh38
GRCh37631,548,335 - 31,550,202 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36631,656,314 - 31,658,181 (-)NCBINCBI36Build 36hg18NCBI36
Build 34631,656,313 - 31,658,181NCBI
Celera633,146,550 - 33,148,417 (-)NCBICelera
Cytogenetic Map6p21.33NCBI
HuRef631,335,069 - 31,336,936 (-)NCBIHuRef
CHM1_1631,550,467 - 31,552,334 (-)NCBICHM1_1
T2T-CHM13v2.0631,433,610 - 31,435,477 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(S)-nicotine  (EXP)
1,2-dimethylhydrazine  (ISO)
1-chloro-2,4-dinitrobenzene  (ISO)
1-naphthyl isothiocyanate  (ISO)
1-nitropyrene  (EXP)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-dinitrotoluene  (ISO)
2,6-dinitrotoluene  (ISO)
2-butoxyethanol  (ISO)
2-naphthylamine  (EXP)
3,3',4,4',5-pentachlorobiphenyl  (EXP)
3-Nitrofluoranthene  (EXP)
4,4'-diaminodiphenylmethane  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-(ethoxymethylene)-2-phenyloxazol-5-one  (ISO)
4-amino-2,6-dinitrotoluene  (ISO)
4-hydroxynon-2-enal  (ISO)
5'-S-methyl-5'-thioadenosine  (ISO)
6-propyl-2-thiouracil  (ISO)
all-trans-retinoic acid  (ISO)
alpha-Zearalanol  (ISO)
antirheumatic drug  (EXP)
aripiprazole  (EXP)
arsane  (EXP)
arsenic atom  (EXP)
arsenous acid  (EXP)
asperentin  (ISO)
benzalkonium chloride  (ISO)
benzene  (ISO)
benzo[a]pyrene  (EXP,ISO)
beta-naphthoflavone  (EXP)
bisphenol A  (ISO)
bisphenol F  (ISO)
Brevianamide A  (ISO)
buta-1,3-diene  (ISO)
cadmium dichloride  (EXP,ISO)
calcitriol  (EXP)
cannabidiol  (EXP)
carbon nanotube  (ISO)
chloroprene  (ISO)
chloroquine  (EXP)
cisplatin  (EXP)
clorgyline  (EXP)
curcumin  (EXP,ISO)
deoxynivalenol  (ISO)
dexamethasone  (EXP,ISO)
diarsenic trioxide  (EXP)
dibenzo[a,l]pyrene  (ISO)
Dibutyl phosphate  (EXP)
dimethylarsinic acid  (ISO)
dioxygen  (ISO)
diquat  (ISO)
disodium selenite  (EXP)
diuron  (EXP)
dorsomorphin  (EXP)
doxorubicin  (ISO)
ethylparaben  (EXP)
fentanyl  (ISO)
fumonisin B1  (ISO)
furan  (ISO)
furosemide  (ISO)
gadolinium trichloride  (ISO)
glafenine  (ISO)
hydrogen peroxide  (EXP)
leflunomide  (EXP)
lipopolysaccharide  (EXP,ISO)
methylarsonic acid  (ISO)
Muraglitazar  (ISO)
mycophenolic acid  (ISO)
mycotoxin  (ISO)
N-methyl-N-nitrosourea  (ISO)
N-nitrosodiethylamine  (ISO)
N-nitrosodimethylamine  (ISO)
neoechinulin A  (ISO)
nickel atom  (EXP)
nickel dichloride  (EXP)
nicotine  (EXP)
oxaliplatin  (ISO)
ozone  (EXP,ISO)
paracetamol  (EXP,ISO)
perfluorohexanesulfonic acid  (EXP)
perfluorononanoic acid  (EXP)
perfluorooctane-1-sulfonic acid  (EXP)
perfluorooctanoic acid  (EXP)
PF-3758309  (EXP)
progesterone  (EXP)
raloxifene  (EXP)
S-adenosyl-L-methioninate  (ISO)
S-adenosyl-L-methionine  (ISO)
sanguinarine  (EXP)
SB 431542  (EXP)
silicon dioxide  (EXP,ISO)
silver atom  (ISO)
silver(0)  (ISO)
simvastatin  (EXP)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
succimer  (ISO)
testosterone  (ISO)
tetrachloromethane  (ISO)
theophylline  (EXP)
titanium dioxide  (ISO)
TMC-120A  (ISO)
toluene 2,4-diisocyanate  (ISO)
topotecan  (ISO)
trichostatin A  (EXP)
triphenyl phosphate  (EXP)
triptonide  (ISO)
valproic acid  (EXP)
vinclozolin  (ISO)
vitamin E  (EXP)
zaragozic acid A  (ISO)
zoledronic acid  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

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

Human Phenotype
Megacolon  (IAGP)
References

References - curated
# Reference Title Reference Citation
1. GOAs Human GO annotations GOA_HUMAN data from the GO Consortium
2. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
3. 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.
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
5. Membrane lymphotoxin contributes to anti-leishmanial immunity by controlling structural integrity of lymphoid organs. Wilhelm P, etal., Eur J Immunol. 2002 Jul;32(7):1993-2003.
6. Lymphotoxin alpha beta 2 (membrane lymphotoxin) is critically important for resistance to Leishmania major infection in mice. Xu G, etal., J Immunol. 2007 Oct 15;179(8):5358-66.
Additional References at PubMed
PMID:1670638   PMID:1671667   PMID:1714477   PMID:2995927   PMID:7590964   PMID:7601445   PMID:7916655   PMID:7995952   PMID:8081366   PMID:8499947   PMID:8586432   PMID:8629302  
PMID:8824804   PMID:9185077   PMID:9235946   PMID:9299492   PMID:9317127   PMID:9480751   PMID:9545284   PMID:10202016   PMID:10318773   PMID:10668961   PMID:11823516   PMID:12474234  
PMID:12477932   PMID:14656967   PMID:15034048   PMID:15077289   PMID:15248211   PMID:15489334   PMID:15857508   PMID:15910501   PMID:15969671   PMID:16702430   PMID:17981284   PMID:18292573  
PMID:18379788   PMID:19115949   PMID:19222863   PMID:19729601   PMID:19735075   PMID:19800575   PMID:19851445   PMID:19913121   PMID:19948975   PMID:20356761   PMID:20628086   PMID:20662065  
PMID:21029472   PMID:21102463   PMID:21211989   PMID:21248773   PMID:21873635   PMID:22294627   PMID:22652080   PMID:22742857   PMID:26646413   PMID:28196873   PMID:35929442   PMID:36348017  
PMID:37919527   PMID:39147874  


Genomics

Comparative Map Data
LTB
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38631,580,558 - 31,582,425 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl631,580,525 - 31,582,522 (-)EnsemblGRCh38hg38GRCh38
GRCh37631,548,335 - 31,550,202 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36631,656,314 - 31,658,181 (-)NCBINCBI36Build 36hg18NCBI36
Build 34631,656,313 - 31,658,181NCBI
Celera633,146,550 - 33,148,417 (-)NCBICelera
Cytogenetic Map6p21.33NCBI
HuRef631,335,069 - 31,336,936 (-)NCBIHuRef
CHM1_1631,550,467 - 31,552,334 (-)NCBICHM1_1
T2T-CHM13v2.0631,433,610 - 31,435,477 (-)NCBIT2T-CHM13v2.0
Ltb
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391735,413,483 - 35,415,281 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1735,413,415 - 35,415,296 (+)EnsemblGRCm39 Ensembl
GRCm381735,194,507 - 35,196,305 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1735,194,439 - 35,196,320 (+)EnsemblGRCm38mm10GRCm38
MGSCv371735,331,452 - 35,333,250 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361734,802,574 - 34,804,354 (+)NCBIMGSCv36mm8
Celera1738,291,216 - 38,293,014 (+)NCBICelera
Cytogenetic Map17B1NCBI
cM Map1718.59NCBI
Ltb
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8203,632,209 - 3,634,054 (-)NCBIGRCr8
mRatBN7.2203,627,536 - 3,629,381 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl203,627,537 - 3,629,381 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx204,327,296 - 4,329,142 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0203,689,354 - 3,691,200 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0204,226,971 - 4,228,817 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0205,184,631 - 5,186,476 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl205,184,515 - 5,186,503 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 Ensembl204,861,335 - 4,863,198 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0206,941,753 - 6,943,598 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4203,666,524 - 3,668,369 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1203,666,751 - 3,668,596 (-)NCBI
Celera204,396,109 - 4,397,954 (+)NCBICelera
Cytogenetic Map20p12NCBI
Ltb
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_004955437120,966 - 123,973 (-)NCBIChiLan1.0ChiLan1.0
LTB
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2546,057,500 - 46,060,073 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1642,019,081 - 42,024,574 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0631,241,643 - 31,244,454 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1632,131,607 - 32,133,468 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl632,131,760 - 32,133,467 (-)Ensemblpanpan1.1panPan2
LTB
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1121,079,340 - 1,084,785 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl121,079,358 - 1,081,153 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha121,215,801 - 1,217,596 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0121,224,605 - 1,226,400 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl121,224,605 - 1,226,400 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1121,083,338 - 1,085,125 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0121,151,270 - 1,153,063 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0121,218,053 - 1,219,848 (-)NCBIUU_Cfam_GSD_1.0
Ltb
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494635,628,995 - 35,650,426 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049367271,910,881 - 1,932,356 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049367271,929,533 - 1,932,339 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LTB
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl723,704,841 - 23,706,745 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1723,704,842 - 23,707,036 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2727,545,187 - 27,547,163 (+)NCBISscrofa10.2Sscrofa10.2susScr3
LTB
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Vero_WHO_p1.0NW_02366604431,482,890 - 31,485,770 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ltb
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475424,618,888 - 24,620,448 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in LTB
5 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
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
NM_002341.2(LTB):c.259C>T (p.Leu87Phe) single nucleotide variant not provided [RCV000958836] Chr6:31581580 [GRCh38]
Chr6:31549357 [GRCh37]
Chr6:6p21.33
benign
NM_002341.2(LTB):c.365C>T (p.Ala122Val) single nucleotide variant not provided [RCV000949290] Chr6:31581079 [GRCh38]
Chr6:31548856 [GRCh37]
Chr6:6p21.33
benign
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
NC_000006.11:g.(?_30695893)_(31937492_?)dup duplication not provided [RCV003107453] Chr6:30695893..31937492 [GRCh37]
Chr6:6p21.33
uncertain significance
NC_000006.11:g.28005012_31683185del deletion Megacolon [RCV001290055] Chr6:28005012..31683185 [GRCh37]
Chr6:6p22.1-21.33
likely pathogenic
GRCh37/hg19 6p21.33(chr6:31384577-31902308) copy number gain not specified [RCV002053564] Chr6:31384577..31902308 [GRCh37]
Chr6:6p21.33
uncertain significance
NC_000006.11:g.(?_30695893)_(36953949_?)dup duplication Proteasome-associated autoinflammatory syndrome 1 [RCV003113679] Chr6:30695893..36953949 [GRCh37]
Chr6:6p21.33-21.2
uncertain significance
NM_002341.2(LTB):c.194C>A (p.Ala65Asp) single nucleotide variant not specified [RCV004112901] Chr6:31581828 [GRCh38]
Chr6:31549605 [GRCh37]
Chr6:6p21.33
uncertain significance
NM_002341.2(LTB):c.464G>C (p.Arg155Pro) single nucleotide variant not specified [RCV004408236] Chr6:31580980 [GRCh38]
Chr6:31548757 [GRCh37]
Chr6:6p21.33
likely benign
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1005
Count of miRNA genes:583
Interacting mature miRNAs:669
Transcripts:ENST00000429299, ENST00000446745, ENST00000482429, ENST00000483972
Prediction methods: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 (GRCh38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1358854MULTSCL4_HMultiple sclerosis susceptibility QTL 4 (human)Multiple sclerosis susceptibility6691196032911960Human
1358839MULTSCL5_HMultiple sclerosis susceptibility QTL 5 (human)Multiple sclerosis susceptibility61958431145584311Human
1643377BW325_HBody weight QTL 325 (human)2.320.0005Body fat amount6691196032911960Human
1643569GLUCO21_HGlucose level QTL 21 (human)0.021Glucose levelnon-insulin-dependent6691196032911960Human
1298458BW9_HBody weight QTL 9 (human)2.70.0002Body fat amount6691196032911960Human
1298431RA11_HRheumatoid arthritis QTL 11 (human)0.0000024Joint/bone inflammationrheumatoid arthritis61991188340191709Human
1358857MULTSCL19_HMultiple sclerosis susceptibility QTL 19 (human)Multiple sclerosis susceptibility61958431145584311Human
1643399BMD5_HBone mineral density QTL 5 (human)2.320.0005Bone mineral density6691196032911960Human
406906126GWAS555102_Htrait in response to apixaban QTL GWAS555102 (human)6e-08trait in response to apixaban63158177931581780Human
407139562GWAS788538_Hbody height QTL GWAS788538 (human)1e-08body height (VT:0001253)body height (CMO:0000106)63158177931581780Human

Markers in Region
RH75844  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37631,548,335 - 31,548,490UniSTSGRCh37
Build 36631,656,314 - 31,656,469RGDNCBI36
Celera633,146,550 - 33,146,705RGD
Cytogenetic Map6p21.3UniSTS
HuRef631,335,069 - 31,335,224UniSTS
UniSTS:483258  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37631,548,911 - 31,550,200UniSTSGRCh37
Celera633,147,126 - 33,148,415UniSTS
HuRef631,335,645 - 31,336,934UniSTS


Expression

RNA-SEQ Expression

adipose tissue
alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
entire extraembryonic component
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
pharyngeal arch
renal system
reproductive system
respiratory system
sensory system
visual system
1204 2405 2763 2233 4906 1724 2320 5 624 1943 465 2241 7231 6434 36 3691 1 842 1727 1586 173 1

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_002341 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_009588 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AB088106 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB103612 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB202114 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF129756 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK312210 (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
  AY070219 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY216497 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BA000025 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC055090 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC055094 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC069330 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC093783 (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
  CP068272 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CR753892 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CR759886 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CR942185 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CS081478 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KY500414 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  L11015 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  L11016 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  LN874314 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U79029 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U89922 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  Y14768 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Ensembl Acc Id: ENST00000429299   ⟹   ENSP00000410481
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl631,580,558 - 31,582,424 (-)Ensembl
Ensembl Acc Id: ENST00000446745   ⟹   ENSP00000416113
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl631,580,555 - 31,582,427 (-)Ensembl
Ensembl Acc Id: ENST00000482429
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl631,580,624 - 31,582,406 (-)Ensembl
Ensembl Acc Id: ENST00000483972
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl631,580,525 - 31,582,522 (-)Ensembl
RefSeq Acc Id: NM_002341   ⟹   NP_002332
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38631,580,558 - 31,582,424 (-)NCBI
GRCh37631,548,335 - 31,550,202 (-)ENTREZGENE
Build 36631,656,314 - 31,658,181 (-)NCBI Archive
HuRef631,335,069 - 31,336,936 (-)ENTREZGENE
CHM1_1631,550,467 - 31,552,334 (-)NCBI
T2T-CHM13v2.0631,433,610 - 31,435,476 (-)NCBI
Sequence:
RefSeq Acc Id: NM_009588   ⟹   NP_033666
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38631,580,558 - 31,582,425 (-)NCBI
GRCh37631,548,335 - 31,550,202 (-)ENTREZGENE
Build 36631,656,314 - 31,658,181 (-)NCBI Archive
HuRef631,335,069 - 31,336,936 (-)ENTREZGENE
CHM1_1631,550,467 - 31,552,334 (-)NCBI
T2T-CHM13v2.0631,433,610 - 31,435,477 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_002332 (Get FASTA)   NCBI Sequence Viewer  
  NP_033666 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA36191 (Get FASTA)   NCBI Sequence Viewer  
  AAA99888 (Get FASTA)   NCBI Sequence Viewer  
  AAB37342 (Get FASTA)   NCBI Sequence Viewer  
  AAC51769 (Get FASTA)   NCBI Sequence Viewer  
  AAD18089 (Get FASTA)   NCBI Sequence Viewer  
  AAH69330 (Get FASTA)   NCBI Sequence Viewer  
  AAH93783 (Get FASTA)   NCBI Sequence Viewer  
  AAL49954 (Get FASTA)   NCBI Sequence Viewer  
  AAL49955 (Get FASTA)   NCBI Sequence Viewer  
  AAO21134 (Get FASTA)   NCBI Sequence Viewer  
  AQY76901 (Get FASTA)   NCBI Sequence Viewer  
  BAB63395 (Get FASTA)   NCBI Sequence Viewer  
  BAC54938 (Get FASTA)   NCBI Sequence Viewer  
  BAE78640 (Get FASTA)   NCBI Sequence Viewer  
  BAF31273 (Get FASTA)   NCBI Sequence Viewer  
  BAG35143 (Get FASTA)   NCBI Sequence Viewer  
  CAA75069 (Get FASTA)   NCBI Sequence Viewer  
  CAI95950 (Get FASTA)   NCBI Sequence Viewer  
  CTQ86079 (Get FASTA)   NCBI Sequence Viewer  
  EAX03425 (Get FASTA)   NCBI Sequence Viewer  
  EAX03426 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSP00000365285.3
  ENSP00000372985.2
  ENSP00000393693.2
  ENSP00000395102.2
  ENSP00000398741.2
  ENSP00000404014.2
  ENSP00000404450.2
  ENSP00000410481
  ENSP00000410481.3
  ENSP00000416113
  ENSP00000416113.2
GenBank Protein Q06643 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_033666   ⟸   NM_009588
- Peptide Label: isoform b
- UniProtKB: Q06643 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_002332   ⟸   NM_002341
- Peptide Label: isoform a
- UniProtKB: Q52LU8 (UniProtKB/Swiss-Prot),   P78370 (UniProtKB/Swiss-Prot),   Q99761 (UniProtKB/Swiss-Prot),   Q06643 (UniProtKB/Swiss-Prot),   Q5STB2 (UniProtKB/TrEMBL),   A8MQV6 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSP00000410481   ⟸   ENST00000429299
Ensembl Acc Id: ENSP00000416113   ⟸   ENST00000446745
Protein Domains
THD

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q06643-F1-model_v2 AlphaFold Q06643 1-244 view protein structure

Promoters
RGD ID:6872606
Promoter ID:EPDNEW_H9427
Type:initiation region
Name:LTB_1
Description:lymphotoxin beta
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H9432  
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh38631,582,424 - 31,582,484EPDNEW
RGD ID:6872534
Promoter ID:EPDNEW_H9432
Type:initiation region
Name:LTB_2
Description:lymphotoxin beta
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H9427  
Experiment Methods:Single-end sequencing.; Paired-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh38631,586,915 - 31,586,975EPDNEW
RGD ID:6804420
Promoter ID:HG_KWN:52938
Type:Non-CpG
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:CD4+TCell,   CD4+TCell_2Hour,   K562,   Lymphoblastoid,   NB4
Transcripts:OTTHUMT00000076239,   OTTHUMT00000076240,   OTTHUMT00000259102
Position:
Human AssemblyChrPosition (strand)Source
Build 36631,657,921 - 31,658,567 (-)MPROMDB

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:6711 AgrOrtholog
COSMIC LTB COSMIC
Ensembl Genes ENSG00000204487 UniProtKB/Swiss-Prot
  ENSG00000206437 UniProtKB/Swiss-Prot
  ENSG00000223448 UniProtKB/Swiss-Prot
  ENSG00000227507 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
  ENSG00000231314 UniProtKB/Swiss-Prot
  ENSG00000236237 UniProtKB/Swiss-Prot
  ENSG00000236925 UniProtKB/Swiss-Prot
  ENSG00000238114 UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000376117.3 UniProtKB/Swiss-Prot
  ENST00000383493.2 UniProtKB/Swiss-Prot
  ENST00000420402.2 UniProtKB/Swiss-Prot
  ENST00000421268.2 UniProtKB/Swiss-Prot
  ENST00000429299 ENTREZGENE
  ENST00000429299.3 UniProtKB/Swiss-Prot
  ENST00000444479.2 UniProtKB/Swiss-Prot
  ENST00000446745 ENTREZGENE
  ENST00000446745.2 UniProtKB/Swiss-Prot
  ENST00000456113.2 UniProtKB/Swiss-Prot
  ENST00000457552.2 UniProtKB/Swiss-Prot
Gene3D-CATH 2.60.120.40 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
GTEx ENSG00000204487 GTEx
  ENSG00000206437 GTEx
  ENSG00000223448 GTEx
  ENSG00000227507 GTEx
  ENSG00000231314 GTEx
  ENSG00000236237 GTEx
  ENSG00000236925 GTEx
  ENSG00000238114 GTEx
HGNC ID HGNC:6711 ENTREZGENE
Human Proteome Map LTB Human Proteome Map
InterPro TNF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TNF_C 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:4050 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 4050 ENTREZGENE
OMIM 600978 OMIM
PANTHER PTHR11471:SF29 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TUMOR NECROSIS FACTOR FAMILY MEMBER UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam TNF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA30475 PharmGKB
PRINTS TNECROSISFCT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TNFC 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 A8MQV6 ENTREZGENE
  P78370 ENTREZGENE
  Q06643 ENTREZGENE
  Q52LU8 ENTREZGENE
  Q5STB2 ENTREZGENE, UniProtKB/TrEMBL
  Q99761 ENTREZGENE
  TNFC_HUMAN UniProtKB/Swiss-Prot
UniProt Secondary A8MQV6 UniProtKB/TrEMBL
  P78370 UniProtKB/Swiss-Prot
  Q52LU8 UniProtKB/Swiss-Prot
  Q99761 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-11-24 LTB  lymphotoxin beta  LTB  lymphotoxin beta (TNF superfamily, member 3)  Symbol and/or name change 5135510 APPROVED