Lta (lymphotoxin A) - Rat Genome Database

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Gene: Lta (lymphotoxin A) Mus musculus
Analyze
Symbol: Lta
Name: lymphotoxin A
RGD ID: 733657
MGI Page MGI
Description: Predicted to enable tumor necrosis factor receptor binding activity. Acts upstream of or within several processes, including lymph node development; positive regulation of immune response; and positive regulation of interferon-gamma production. Predicted to be located in extracellular space. Is expressed in several structures, including extraembryonic component; gut; hemolymphoid system; liver; and reproductive system. 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; type 1 diabetes mellitus pathway; INTERACTS WITH 1,2-dichloroethane; 1,2-dimethylhydrazine; 2,2',4,4',5,5'-hexachlorobiphenyl.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: hlb38; hlb382; L; LT; LT-; LT-[; LT-[a]; LT-alpha; LT[; LT[a]; LTalpha; Ltx; lymph; lymphotoxin alpha; lymphotoxin-alpha; MGC117668; Tnf; TNF beta; TNF-be; TNF-beta; Tnfb; Tnfsf; TNFSF1; Tnfsf1b; Tnlg1e; tumor necrosis factor ligand 1e; tumor necrosis factor ligand superfamily member 1
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: GRCm38 - Mouse Genome Assembly GRCm38
Position:
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
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-demecolcine  (ISO)
1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane  (ISO)
1,2-dichloroethane  (EXP)
1,2-dimethylhydrazine  (EXP)
1-nitropyrene  (ISO)
17beta-estradiol  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (EXP,ISO)
2,2',5,5'-tetrachlorobiphenyl  (EXP)
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  (ISO)
amphibole asbestos  (ISO)
aripiprazole  (ISO)
aristolochic acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
asbestos  (ISO)
asperentin  (EXP)
benzo[a]pyrene  (ISO)
bisphenol A  (EXP,ISO)
cadmium dichloride  (ISO)
cisplatin  (EXP,ISO)
cobalt atom  (ISO)
cobalt dichloride  (ISO)
curcumin  (ISO)
cyclosporin A  (ISO)
deoxynivalenol  (EXP)
dextran sulfate  (EXP)
diarsenic trioxide  (ISO)
flavonoids  (ISO)
furosemide  (ISO)
gemcitabine  (ISO)
ibuprofen  (ISO)
indometacin  (ISO)
iron atom  (ISO)
iron(0)  (ISO)
iron(2+) sulfate (anhydrous)  (ISO)
lead nitrate  (EXP)
lipopolysaccharide  (EXP,ISO)
mycophenolic acid  (EXP)
N,N,N',N'-tetrakis(2-pyridylmethyl)ethylenediamine  (ISO)
N-ethyl-N-nitrosourea  (EXP)
nickel atom  (ISO)
ozone  (EXP,ISO)
paracetamol  (EXP,ISO)
paraquat  (ISO)
PCB138  (EXP)
potassium dichromate  (ISO)
progesterone  (EXP)
resveratrol  (ISO)
rifaximin  (ISO)
silicon dioxide  (ISO)
sodium arsenite  (ISO)
sterigmatocystin  (EXP)
tacrolimus hydrate  (ISO)
toluene 2,4-diisocyanate  (EXP)
trichloroethene  (EXP)
troglitazone  (EXP,ISO)
tungsten  (ISO)
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
abnormal circulating tumor necrosis factor level  (IAGP)
abnormal class switch recombination  (IAGP)
abnormal cytokine secretion  (IAGP)
abnormal gamma-delta T cell morphology  (IAGP)
abnormal gut-associated lymphoid tissue morphology  (IAGP)
abnormal heart morphology  (IEA)
abnormal humoral immune response  (IAGP)
abnormal immune serum protein physiology  (IAGP)
abnormal immune system morphology  (IAGP)
abnormal immune system organ morphology  (IAGP)
abnormal leukocyte cell number  (IAGP)
abnormal lymph node morphology  (IAGP)
abnormal lymph node primary follicle morphology  (IAGP)
abnormal lymph organ development  (IAGP)
abnormal lymphocyte morphology  (IAGP)
abnormal lymphopoiesis  (IAGP)
abnormal mucosa-associated lymphoid tissue morphology  (IAGP)
abnormal pancreatic islet morphology  (IAGP)
abnormal retina morphology  (IAGP)
abnormal sleep pattern  (IAGP)
abnormal spleen B cell follicle morphology  (IAGP)
abnormal spleen marginal zone morphology  (IAGP)
abnormal spleen morphology  (IAGP)
abnormal spleen periarteriolar lymphoid sheath morphology  (IAGP)
abnormal spleen white pulp morphology  (IAGP)
abnormal thymus epithelium morphology  (IAGP)
abnormal thymus medulla morphology  (IAGP)
absent axillary lymph nodes  (IAGP)
absent brachial lymph nodes  (IAGP)
absent cervical lymph nodes  (IAGP)
absent inguinal lymph nodes  (IAGP)
absent lymph nodes  (IAGP)
absent marginal zone B cells  (IAGP)
absent mesenteric lymph nodes  (IAGP)
absent peripheral lymph nodes  (IAGP)
absent Peyer's patches  (IAGP)
absent popliteal lymph nodes  (IAGP)
absent spleen germinal center  (IAGP)
absent spleen marginal zone  (IAGP)
decreased body length  (IEA)
decreased circulating insulin level  (IEA)
decreased circulating interferon-gamma level  (IAGP)
decreased IgA level  (IAGP)
decreased IgG level  (IAGP)
decreased IgG1 level  (IAGP)
decreased IgG2a level  (IAGP)
decreased IgG3 level  (IAGP)
decreased immunoglobulin level  (IAGP)
decreased interferon-gamma secretion  (IAGP)
decreased monocyte cell number  (IEA)
decreased NK cell number  (IAGP)
decreased sensitivity to induced morbidity/mortality  (IAGP)
decreased spleen white pulp amount  (IAGP)
decreased susceptibility to endotoxin shock  (IAGP)
decreased susceptibility to experimental autoimmune encephalomyelitis  (IAGP)
decreased susceptibility to induced arthritis  (IAGP)
decreased susceptibility to parasitic infection  (IAGP)
decreased T cell number  (IAGP)
decreased transitional stage B cell number  (IAGP)
decreased tumor necrosis factor secretion  (IAGP)
enlarged heart  (IEA)
enlarged liver  (IAGP)
enlarged spleen  (IAGP)
hepatic steatosis  (IAGP)
impaired macrophage phagocytosis  (IAGP)
increased B cell number  (IAGP)
increased B-1b cell number  (IAGP)
increased body length  (IAGP)
increased body mass index  (IAGP)
increased body weight  (IAGP)
increased bronchoconstrictive response  (IEA)
increased circulating alkaline phosphatase level  (IEA)
increased heart weight  (IAGP)
increased IgM level  (IAGP)
increased leukocyte cell number  (IAGP)
increased liver weight  (IAGP)
increased lymphocyte cell number  (IAGP)
increased neutrophil cell number  (IEA)
increased pulmonary ventilation  (IEA)
increased sensitivity to induced morbidity/mortality  (IAGP)
increased spleen weight  (IAGP)
increased susceptibility to bacterial infection  (IAGP)
increased susceptibility to bacterial infection induced morbidity/mortality  (IAGP)
increased susceptibility to diet-induced obesity  (IAGP)
increased susceptibility to injury  (IAGP)
increased susceptibility to parasitic infection  (IAGP)
increased susceptibility to Poxviridae infection  (IAGP)
increased susceptibility to Riboviria infection  (IAGP)
liver inflammation  (IAGP)
long tibia  (IAGP)
lung inflammation  (IAGP)
retinal photoreceptor degeneration  (IAGP)
small thymus medulla  (IAGP)
thin retinal inner nuclear layer  (IAGP)
thin retinal outer nuclear layer  (IAGP)
References

References - curated
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Additional References at PubMed
PMID:1533632   PMID:1649220   PMID:1673964   PMID:1700275   PMID:1714477   PMID:1732752   PMID:1794054   PMID:2228046   PMID:2450487   PMID:2884262   PMID:2885372   PMID:2937063  
PMID:3027565   PMID:3147435   PMID:3490653   PMID:3588316   PMID:3684584   PMID:4540898   PMID:6334807   PMID:7495745   PMID:7583355   PMID:7608544   PMID:7636227   PMID:7768593  
PMID:7813906   PMID:7846035   PMID:7916002   PMID:7995944   PMID:8080166   PMID:8097912   PMID:8119735   PMID:8132347   PMID:8138038   PMID:8157957   PMID:8171316   PMID:8171322  
PMID:8228806   PMID:8242763   PMID:8387892   PMID:8387893   PMID:8406442   PMID:8491516   PMID:8499946   PMID:8535974   PMID:8638112   PMID:8642347   PMID:8650181   PMID:8671586  
PMID:8672143   PMID:8684487   PMID:8691140   PMID:8867667   PMID:8912010   PMID:9006341   PMID:9021146   PMID:9036957   PMID:9130661   PMID:9133428   PMID:9159143   PMID:9166104  
PMID:9166595   PMID:9176705   PMID:9182683   PMID:9182689   PMID:9230199   PMID:9256477   PMID:9307073   PMID:9317127   PMID:9317128   PMID:9344502   PMID:9367897   PMID:9368616  
PMID:9379020   PMID:9396768   PMID:9463397   PMID:9521083   PMID:9529317   PMID:9537442   PMID:9565643   PMID:9625757   PMID:9697836   PMID:9697837   PMID:9705956   PMID:9716651  
PMID:9763613   PMID:9782127   PMID:9790725   PMID:9811942   PMID:9834074   PMID:9862349   PMID:9892622   PMID:10064079   PMID:10067894   PMID:10329594   PMID:10339588   PMID:10349636  
PMID:10381864   PMID:10405365   PMID:10415034   PMID:10415052   PMID:10415063   PMID:10453025   PMID:10469308   PMID:10476056   PMID:10477548   PMID:10493167   PMID:10515827   PMID:10540319  
PMID:10562322   PMID:10580607   PMID:10586051   PMID:10608881   PMID:10618409   PMID:10679088   PMID:10684295   PMID:10687308   PMID:10692238   PMID:10698075   PMID:10759375   PMID:10799877  
PMID:10805971   PMID:10843380   PMID:10864873   PMID:10871872   PMID:10878339   PMID:10914503   PMID:10917533   PMID:10940914   PMID:11042159   PMID:11067918   PMID:11076861   PMID:11123309  
PMID:11137582   PMID:11159184   PMID:11160211   PMID:11208864   PMID:11217851   PMID:11239407   PMID:11293812   PMID:11298355   PMID:11433391   PMID:11477542   PMID:11488978   PMID:11489971  
PMID:11518731   PMID:11536150   PMID:11564771   PMID:11672543   PMID:11733579   PMID:11739537   PMID:11751946   PMID:11792852   PMID:11801629   PMID:11805150   PMID:11854219   PMID:11907097  
PMID:11907234   PMID:11920578   PMID:11932402   PMID:11994450   PMID:11994465   PMID:12006975   PMID:12069182   PMID:12093872   PMID:12115617   PMID:12115620   PMID:12147624   PMID:12150889  
PMID:12163535   PMID:12354388   PMID:12391242   PMID:12405187   PMID:12444124   PMID:12446781   PMID:12447768   PMID:12466141   PMID:12466851   PMID:12477932   PMID:12560241   PMID:12603600  
PMID:12614279   PMID:12648490   PMID:12651603   PMID:12682226   PMID:12713579   PMID:12732657   PMID:12734369   PMID:12759424   PMID:12787557   PMID:12794148   PMID:12819136   PMID:12829028  
PMID:12860530   PMID:12882833   PMID:12885938   PMID:14517552   PMID:14581001   PMID:14617751   PMID:14638845   PMID:14656967   PMID:14691481   PMID:14691482   PMID:14732063   PMID:14764671  
PMID:15004164   PMID:15009470   PMID:15071180   PMID:15170228   PMID:15210762   PMID:15245428   PMID:15247480   PMID:15265903   PMID:15270844   PMID:15311275   PMID:15382206   PMID:15470018  
PMID:15521015   PMID:15536567   PMID:15585839   PMID:15592751   PMID:15632007   PMID:15657949   PMID:15661974   PMID:15664785   PMID:15709026   PMID:15793291   PMID:15814693   PMID:15840716  
PMID:15843574   PMID:15845449   PMID:15905567   PMID:15937486   PMID:15937549   PMID:16002734   PMID:16040991   PMID:16141072   PMID:16141073   PMID:16200624   PMID:16210592   PMID:16406654  
PMID:16517718   PMID:16517733   PMID:16582913   PMID:16705172   PMID:16738056   PMID:16751279   PMID:16751400   PMID:16785524   PMID:16887965   PMID:17018858   PMID:17082587   PMID:17082596  
PMID:17119110   PMID:17163957   PMID:17236235   PMID:17266742   PMID:17339474   PMID:17360402   PMID:17392163   PMID:17431181   PMID:17452522   PMID:17456769   PMID:17502664   PMID:17521585  
PMID:17526859   PMID:17692539   PMID:17768379   PMID:17911622   PMID:17947641   PMID:17948268   PMID:17982070   PMID:17989315   PMID:18097025   PMID:18202551   PMID:18212064   PMID:18354186  
PMID:18384745   PMID:18390720   PMID:18403646   PMID:18442881   PMID:18483211   PMID:18490487   PMID:18519649   PMID:18612394   PMID:18769490   PMID:18952083   PMID:19003818   PMID:19089813  
PMID:19100703   PMID:19164352   PMID:19246648   PMID:19249230   PMID:19303389   PMID:19380813   PMID:19380818   PMID:19414773   PMID:19427241   PMID:19468301   PMID:19503106   PMID:19561618  
PMID:19658092   PMID:19681056   PMID:19757439   PMID:19783990   PMID:19789388   PMID:19800575   PMID:19805094   PMID:19822644   PMID:19920180   PMID:20008132   PMID:20207995   PMID:20304952  
PMID:20436484   PMID:20439544   PMID:20494341   PMID:20566898   PMID:20643338   PMID:20720206   PMID:20739675   PMID:20805422   PMID:20817877   PMID:20861360   PMID:21135813   PMID:21153307  
PMID:21267068   PMID:21419662   PMID:21435450   PMID:21436282   PMID:21441458   PMID:21586747   PMID:21666055   PMID:21666689   PMID:21801869   PMID:21871814   PMID:22078797   PMID:22080953  
PMID:22318945   PMID:22357629   PMID:22386268   PMID:22437076   PMID:22770220   PMID:22880094   PMID:22901752   PMID:22906740   PMID:22922363   PMID:23248258   PMID:23277487   PMID:23300712  
PMID:23360826   PMID:23385062   PMID:23704873   PMID:23850656   PMID:23935190   PMID:24194600   PMID:24292710   PMID:24311691   PMID:24440154   PMID:24508087   PMID:24634490   PMID:24684957  
PMID:24759321   PMID:24883436   PMID:24913234   PMID:25252690   PMID:25501629   PMID:25599993   PMID:25600442   PMID:25770220   PMID:25776744   PMID:25968334   PMID:26147686   PMID:26646413  
PMID:27022143   PMID:27323847   PMID:27457277   PMID:27626380   PMID:27939671   PMID:28341747   PMID:28355561   PMID:28455312   PMID:28497779   PMID:28917655   PMID:29186687   PMID:29593265  
PMID:29596840   PMID:29936495   PMID:30277476   PMID:30333312   PMID:31995749   PMID:31999807   PMID:31999809   PMID:32325033   PMID:32591396   PMID:33207209  


Genomics

Comparative Map Data
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
(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
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2203,618,853 - 3,621,324 (+)NCBImRatBN7.2
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
Lta  
Mouse AssemblyChrPosition (strand)SourceJBrowse
MGSCv371735,340,685 - 35,341,340UniSTSGRCm37
MGSCv371735,341,804 - 35,341,943UniSTSGRCm37
MGSCv371735,340,221 - 35,340,605UniSTSGRCm37
MGSCv371735,340,686 - 35,340,903UniSTSGRCm37
MGSCv371735,340,823 - 35,341,369UniSTSGRCm37
Celera1738,299,979 - 38,300,363UniSTS
Celera1738,300,443 - 38,301,098UniSTS
Celera1738,300,444 - 38,300,661UniSTS
Celera1738,300,581 - 38,301,127UniSTS
Celera1738,301,562 - 38,301,696UniSTS
Cytogenetic Map17B1UniSTS
cM Map1719.06UniSTS
cM Map1719.06UniSTS
cM Map1719.06UniSTS
D17Nds3  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381735,204,859 - 35,204,998UniSTSGRCm38
MGSCv371735,341,804 - 35,341,943UniSTSGRCm37
Celera1738,301,562 - 38,301,696UniSTS
Cytogenetic Map17B1UniSTS
cM Map1719.06UniSTS
Lta  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381735,203,878 - 35,204,424UniSTSGRCm38
MGSCv371735,340,823 - 35,341,369UniSTSGRCm37
Celera1738,300,581 - 38,301,127UniSTS
Cytogenetic Map17B1UniSTS
cM Map1719.06UniSTS
Lta  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381735,204,859 - 35,204,998UniSTSGRCm38
MGSCv371735,341,804 - 35,341,943UniSTSGRCm37
Celera1738,301,562 - 38,301,696UniSTS
Cytogenetic Map17B1UniSTS
cM Map1719.06UniSTS
Lta  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381735,203,276 - 35,203,660UniSTSGRCm38
MGSCv371735,340,221 - 35,340,605UniSTSGRCm37
Celera1738,299,979 - 38,300,363UniSTS
Cytogenetic Map17B1UniSTS
cM Map1719.06UniSTS
Lta  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381735,203,740 - 35,204,395UniSTSGRCm38
MGSCv371735,340,685 - 35,341,340UniSTSGRCm37
Celera1738,300,443 - 38,301,098UniSTS
Cytogenetic Map17B1UniSTS
Lta  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381735,203,741 - 35,203,958UniSTSGRCm38
MGSCv371735,340,686 - 35,340,903UniSTSGRCm37
Celera1738,300,444 - 38,300,661UniSTS
Cytogenetic Map17B1UniSTS


QTLs in Region (GRCm38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10412276Leci2_mleukocyte endothelial cell interactions 2 (mouse)Not determined17312791337128037Mouse
1300890Bhr3_mbronchial hyperresponsiveness 3 (mouse)Not determined17392461548559063Mouse
4141215Mnic1_mmacronutrient intake, carbohydrate 1 (mouse)Not determined480447745359340Mouse
1300706Alan1_malloantigen response 1 (mouse)Not determined17480447746158776Mouse
1357789Kdnw3_mkidney weight 3 (mouse)Not determined17480447747574740Mouse
4141272Tfv1_mtotal food volume 1 (mouse)Not determined480447765330362Mouse
10043949Pbft7_mpercent body fat 7 (mouse)Not determined17667496240674962Mouse
1301935Skull24_mskull morphology 24 (mouse)Not determined17836594042366175Mouse
1300787Cd8mts5_mCD8 memory T cell subset 5 (mouse)Not determined17836594042366175Mouse
1301338Lmr1_mleishmaniasis resistance 1 (mouse)Not determined17986241186688972Mouse
1302028Asbb3_mautoimmune susceptibility in C57BL/6J and BALB/c 3 (mouse)Not determined171065914544659245Mouse
4142342Lfnq4_mlung function QTL 4 (mouse)Not determined1098759739053168Mouse
4141067Hbnr2_mHeligmosomoides bakeri nematode resistance 2 (mouse)Not determined1166699745667145Mouse
14747010Mancz14_mmandible centroid size 14 (mouse)171177921045779210Mouse
4142150Stheal11_msoft tissue heal 11 (mouse)Not determined171206732483054339Mouse
12904946Tammq8_mtibialis anterior muscle mass QTL 8 (mouse)171223281346232813Mouse
13524847Asrq8a_macoustic startle response 8a (mouse)171242798746427987Mouse
11081168Tir7_mtrypanosome infection response 7 (mouse)171390439847904522Mouse
1300914Pcir4_mperiosteal circumference 4 (mouse)Not determined171484267848842786Mouse
1558886Lgth9_mbody length 9 (mouse)Not determined171484267848842786Mouse
1302070Tbbmd7_mtotal body bone mineral density 7 (mouse)Not determined171484267848842786Mouse
1300995Fembrs4_mfemur breaking strength 4 (mouse)Not determined171484267848842786Mouse
1302140Wta4_mweight adult 4 (mouse)Not determined171660074750600869Mouse
1302152Skull25_mskull morphology 25 (mouse)Not determined171660074750600869Mouse
1301505Tir1_mtrypanosome infection response 1 (mouse)Not determined171660074750600869Mouse
10412083Sm2_msusceptibility to Schistosoma mansoni infection 2 (mouse)Not determined171681096950811104Mouse
1302042Acsns3_mAngiostrongylus costaricensis nematode susceptibility 3 (mouse)Not determined171724323451243371Mouse
1300535Char3_mP. chabaudi malaria resistance QTL 3 (mouse)Not determined171724323451243371Mouse
10412214Sxbq3_mSGC/Knj cross B6 QTL 3 (mouse)Not determined171724323451243371Mouse
13452396Leusq3_mleucocytosis susceptibility QTL 3 (mouse)171724323451243371Mouse
13452399Leusq6_mleucocytosis susceptibility QTL 6 (mouse)171724323451243371Mouse
1301840Ssial4_msusceptibility to sialadenitiss 4 (mouse)Not determined171795643651959238Mouse
1301331Lbw1_mlupus NZB x NZW 1 (mouse)Not determined171819938152202007Mouse
1301056Pas2_mpulmonary adenoma susceptibility 2 (mouse)Not determined171820316552205351Mouse
15039354Nmrs36_mNAFLD-associated magnetic resonance shift 36 (mouse)171883413352834133Mouse
1301454Eae5_msusceptibility to experimental allergic encephalomyelitis 5 (mouse)Not determined172430185958301973Mouse
10412198Sst5_msusceptibility to tuberculosis 5 (mouse)Not determined172485760955405969Mouse
10412196Bbaa28_mB.burgdorferi-associated arthritis 28 (mouse)Not determined172536594043665344Mouse
10412204Bbaa29_mB.burgdorferi-associated arthritis 29 (mouse)Not determined172574029459740461Mouse
1558758Kcal2_mkilocalorie 2 (mouse)Not determined172618203852604676Mouse
1300602Eye2_meye weight 2 (mouse)Not determined172628636340794146Mouse
1302005Loco2_mlocomotor activity 2 (mouse)Not determined172657408160574223Mouse
11075105Modc1_mmodifier of Odc1 (mouse)172749681845311728Mouse
15039348Nmrs37_mNAFLD-associated magnetic resonance shift 37 (mouse)172750432261504322Mouse
10045977Tir9_mtrypanosome infection response 9 (mouse)Not determined172765914543574223Mouse
1300703Uvbi2_mUVB induced immunosuppression 2 (mouse)Not determined172831148062311728Mouse
1300589Myaa2_mmodifier of Yaa 2 (mouse)Not determined172982162963821740Mouse
4140955Plgr1_mplague resistance locus 1 (mouse)Not determined3072257564722705Mouse
4141357Mrdq1_mmodifier of retinal degeneration QTL 1 (mouse)Not determined3076892947728778Mouse
1300692Blmpf1_mbleomycin-induced pulmonary fibrosis 1 (mouse)Not determined173184267837333884Mouse
25394538Skmw84_mskeletal muscle weight 84, TA (mouse)173244145235301060Mouse
26884379Skwq5_mskull length QTL 5, 5 week (mouse)173290000053800000Mouse
1302189Dps3_mdelta power in slow-wave sleep 3 (mouse)Not determined173360074735939288Mouse
1300885Mbis4_mMycobacterium bovis-induced systemic lupus erythematosus 4 (mouse)Not determined173495684169858931Mouse

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:633
Count of miRNA genes:370
Interacting mature miRNAs:429
Transcripts:ENSMUST00000025266
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


Sequence

Nucleotide Sequences
RefSeq Transcripts NM_010735 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006523731 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AF109719 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK080308 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK153694 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK156659 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC099464 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH466666 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CR974444 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CU407309 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CU466548 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  LN874394 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M16819 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M17015 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M60586 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U06950 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X06216 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X06217 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X06218 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X14800 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  Y00137 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  Y00467 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSMUST00000025266   ⟹   ENSMUSP00000025266
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl1735,203,165 - 35,205,351 (-)Ensembl
RefSeq Acc Id: NM_010735   ⟹   NP_034865
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391735,422,141 - 35,424,327 (-)NCBI
GRCm381735,203,165 - 35,205,351 (-)NCBI
MGSCv371735,340,110 - 35,342,296 (-)RGD
Celera1738,299,868 - 38,302,049 (-)RGD
cM Map17 ENTREZGENE
Sequence:
RefSeq Acc Id: XM_006523731   ⟹   XP_006523794
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391735,422,378 - 35,424,568 (-)NCBI
GRCm381735,203,402 - 35,205,578 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_034865   ⟸   NM_010735
- Peptide Label: precursor
- UniProtKB: P09225 (UniProtKB/Swiss-Prot),   Q542S2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006523794   ⟸   XM_006523731
- Peptide Label: isoform X1
- UniProtKB: P09225 (UniProtKB/Swiss-Prot),   Q542S2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSMUSP00000025266   ⟸   ENSMUST00000025266
Protein Domains
TNF_2

Promoters
RGD ID:13675846
Promoter ID:EPDNEW_M22072
Type:multiple initiation site
Name:Lta_1
Description:Mus musculus lymphotoxin A , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm381735,204,676 - 35,204,736EPDNEW
RGD ID:13675848
Promoter ID:EPDNEW_M22073
Type:initiation region
Name:TNFB_1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm381735,205,175 - 35,205,235EPDNEW
RGD ID:6828313
Promoter ID:MM_KWN:23289
Type:Non-CpG
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:Lung,   Spleen
Transcripts:NM_010735_LTA,   UC008CGU.1
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv361735,341,921 - 35,342,421 (-)MPROMDB
RGD ID:6850158
Promoter ID:EP24027
Type:single initiation site
Name:MM_TNFB
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; experiments; performed with closely related gene
Regulation:T (repressed by or weakly expressed in) lymphocytes; (induced by or strongly expressed in) antigen, (induced by or strongly expressed in) mitogen
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv371735,342,120 - 35,342,180EPD
MGSCv361735,342,120 - 35,342,180EPD

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:104797 AgrOrtholog
Ensembl Genes ENSMUSG00000024402 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSMUSP00000025266 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSMUST00000025266 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 2.60.120.40 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
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 mmu:16992 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGD MGI:104797 ENTREZGENE
NCBI Gene 16992 ENTREZGENE
Pfam TNF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB LTA RGD
PhenoGen Lta PhenoGen
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 P09225 ENTREZGENE
  Q3U0Q5_MOUSE UniProtKB/TrEMBL
  Q542S2 ENTREZGENE, UniProtKB/TrEMBL
  TNFB_MOUSE UniProtKB/Swiss-Prot