LTA (lymphotoxin alpha) - Rat Genome Database

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Gene: LTA (lymphotoxin alpha) Canis lupus familiaris
Analyze
Symbol: LTA
Name: lymphotoxin alpha
RGD ID: 12382647
Description: ENCODES a protein that exhibits cytokine activity (inferred); tumor necrosis factor receptor binding (inferred); INVOLVED IN defense response to Gram-positive bacterium (ortholog); humoral immune response (ortholog); lymph node development (ortholog); PARTICIPATES IN interleukin-4 signaling pathway; ASSOCIATED WITH adult respiratory distress syndrome (ortholog); allergic disease (ortholog); arteriosclerosis (ortholog); FOUND IN extracellular space (ortholog)
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LT-alpha; lymphotoxin alpha (TNF superfamily, member 1); lymphotoxin-alpha; TNF beta; TNF-beta; TNFB; TNFSF1; TNLG1E; tumor necrosis factor ligand 1E; tumor necrosis factor ligand superfamily member 1
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: CanFam3.1 - Dog CanFam3.1 Assembly
Position:
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1121,070,608 - 1,073,053 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl121,071,192 - 1,073,067 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha121,207,912 - 1,208,854 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0121,215,963 - 1,218,298 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl121,216,437 - 1,217,676 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1121,075,453 - 1,076,395 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0121,143,379 - 1,144,321 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0121,210,162 - 1,211,104 (+)NCBIUU_Cfam_GSD_1.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


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

Molecular Pathway Annotations     Click to see Annotation Detail View
References
Additional References at PubMed
PMID:15896203   PMID:22301074   PMID:26646413  


Genomics

Comparative Map Data
LTA
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1121,070,608 - 1,073,053 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl121,071,192 - 1,073,067 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha121,207,912 - 1,208,854 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0121,215,963 - 1,218,298 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl121,216,437 - 1,217,676 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1121,075,453 - 1,076,395 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0121,143,379 - 1,144,321 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0121,210,162 - 1,211,104 (+)NCBIUU_Cfam_GSD_1.0
LTA
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38631,560,610 - 31,574,324 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl631,572,054 - 31,574,324 (+)EnsemblGRCh38hg38GRCh38
GRCh37631,539,876 - 31,542,101 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36631,648,072 - 31,650,077 (+)NCBINCBI36Build 36hg18NCBI36
Build 34631,648,071 - 31,650,077NCBI
Celera633,138,091 - 33,140,313 (+)NCBICelera
Cytogenetic Map6p21.33NCBI
HuRef631,326,608 - 31,328,835 (+)NCBIHuRef
CHM1_1631,542,008 - 31,544,233 (+)NCBICHM1_1
T2T-CHM13v2.0631,424,599 - 31,427,376 (+)NCBIT2T-CHM13v2.0
Lta
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391735,422,141 - 35,424,568 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1735,422,141 - 35,424,327 (-)EnsemblGRCm39 Ensembl
GRCm381735,203,165 - 35,205,578 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1735,203,165 - 35,205,351 (-)EnsemblGRCm38mm10GRCm38
MGSCv371735,340,110 - 35,342,296 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361734,811,215 - 34,813,235 (-)NCBIMGSCv36mm8
Celera1738,299,868 - 38,302,049 (-)NCBICelera
Cytogenetic Map17B1NCBI
cM Map1718.59NCBI
Lta
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8203,622,291 - 3,625,852 (+)NCBIGRCr8
mRatBN7.2203,618,853 - 3,621,324 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl203,618,853 - 3,620,859 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx204,318,695 - 4,320,726 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0203,680,759 - 3,682,786 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0204,218,329 - 4,220,348 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0204,851,889 - 4,854,677 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl204,852,496 - 4,854,677 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0206,932,260 - 6,935,077 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4203,657,842 - 3,659,848 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1203,658,068 - 3,660,075 (+)NCBI
Celera204,404,630 - 4,406,751 (-)NCBICelera
Cytogenetic Map20p12NCBI
Lta
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955437114,640 - 115,529 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955437114,216 - 116,003 (+)NCBIChiLan1.0ChiLan1.0
LTA
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2546,049,233 - 46,051,266 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1642,011,243 - 42,012,833 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0631,233,411 - 31,235,409 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1632,123,353 - 32,125,375 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl632,123,353 - 32,125,375 (+)Ensemblpanpan1.1panPan2
Lta
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494635,620,316 - 35,621,609 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049367271,940,081 - 1,941,022 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049367271,940,081 - 1,941,022 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LTA
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl723,696,040 - 23,698,299 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1723,696,387 - 23,698,280 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2727,553,733 - 27,555,627 (-)NCBISscrofa10.2Sscrofa10.2susScr3
Pig Cytomap7p11-q11NCBI
LTA
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Vero_WHO_p1.0NW_02366604431,473,740 - 31,476,648 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Lta
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462475424,627,318 - 24,628,182 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462475424,626,930 - 24,628,412 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in LTA
30 total Variants

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 reproductive system respiratory system adipose tissue
High
Medium
Low 4 1 6 5 5
Below cutoff 1 2 16 6 6 1 1 11 7 3 4

Sequence


RefSeq Acc Id: ENSCAFT00000000802   ⟹   ENSCAFP00000000737
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl121,071,192 - 1,073,067 (+)Ensembl
RefSeq Acc Id: ENSCAFT00845018517   ⟹   ENSCAFP00845014444
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl121,216,437 - 1,217,676 (+)Ensembl
RefSeq Acc Id: NM_001313849   ⟹   NP_001300778
RefSeq Status: VALIDATED
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1121,071,469 - 1,072,411 (+)NCBI
Dog10K_Boxer_Tasha121,207,912 - 1,208,854 (+)NCBI
ROS_Cfam_1.0121,216,714 - 1,217,656 (+)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
Sequence:
RefSeq Acc Id: XM_038682767   ⟹   XP_038538695
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0121,215,963 - 1,218,298 (+)NCBI
RefSeq Acc Id: NP_001300778   ⟸   NM_001313849
- Peptide Label: precursor
- UniProtKB: Q5WR07 (UniProtKB/Swiss-Prot),   A0A0U5J7M4 (UniProtKB/TrEMBL),   A0A8C0LAW4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSCAFP00000000737   ⟸   ENSCAFT00000000802
RefSeq Acc Id: XP_038538695   ⟸   XM_038682767
- Peptide Label: isoform X1
- UniProtKB: Q5WR07 (UniProtKB/Swiss-Prot),   A0A0U5J7M4 (UniProtKB/TrEMBL),   A0A8C0LAW4 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSCAFP00845014444   ⟸   ENSCAFT00845018517
Protein Domains
TNF family profile


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCAFG00000000515 Ensembl, UniProtKB/Swiss-Prot
  ENSCAFG00030005134 UniProtKB/Swiss-Prot
  ENSCAFG00040009649 UniProtKB/Swiss-Prot
  ENSCAFG00805014243 UniProtKB/Swiss-Prot
  ENSCAFG00845010521 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSCAFT00000000802.3 UniProtKB/Swiss-Prot
  ENSCAFT00030009403.1 UniProtKB/Swiss-Prot
  ENSCAFT00040017906.1 UniProtKB/Swiss-Prot
  ENSCAFT00805025897 UniProtKB/Swiss-Prot
  ENSCAFT00845018517 ENTREZGENE
  ENSCAFT00845018517.1 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 cfa:607183 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene LTA ENTREZGENE
PANTHER LYMPHOTOXIN-ALPHA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TUMOR NECROSIS FACTOR FAMILY MEMBER UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam TNF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
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 A0A0U5J7M4 ENTREZGENE, UniProtKB/TrEMBL
  A0A8C0LAW4 ENTREZGENE
  Q5WR07 ENTREZGENE, UniProtKB/Swiss-Prot
VGNC ID VGNC:42852 ENTREZGENE