Human Gene LTA (ENST00000418386.3_4) from GENCODE V47lift37
  Description: lymphotoxin alpha, transcript variant 2 (from RefSeq NM_000595.4)
Gencode Transcript: ENST00000418386.3_4
Gencode Gene: ENSG00000226979.9_7
Transcript (Including UTRs)
   Position: hg19 chr6:31,540,066-31,542,101 Size: 2,036 Total Exon Count: 4 Strand: +
Coding Region
   Position: hg19 chr6:31,540,520-31,541,470 Size: 951 Coding Exon Count: 3 

Page IndexSequence and LinksPrimersMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr6:31,540,066-31,542,101)mRNA (may differ from genome)Protein (205 aa)
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-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: LTA
Diseases sorted by gene-association score: psoriatic arthritis* (619), leprosy 4* (550), myocardial infarction* (217), transient hypogammaglobulinemia (22), toxic shock syndrome (20), leprosy (20), tonsillitis (16), sympathetic ophthalmia (16), null-cell leukemia (16), shigellosis (14), acute respiratory distress syndrome (13), streptococcal toxic-shock syndrome (13), monoclonal gammopathy of uncertain significance (12), juvenile spondyloarthropathy (12), arthritis (12), hantavirus pulmonary syndrome (10), hodgkin lymphoma (10), spondylitis (10), selective iga deficiency disease (9), optic neuritis (9), tetanus (9), spondylarthropathy (8), chronic venous leg ulcers (7), necrotizing fasciitis (7), listeria meningitis (7), duodenal ulcer (7), post-transplant lymphoproliferative disease (6), idiopathic achalasia (6), mucocutaneous leishmaniasis (6), typhoid fever (5), behcet syndrome (5), rheumatoid arthritis, systemic juvenile (5), psoriasis (5), malignant histiocytosis (4), sarcoidosis 1 (4), systemic lupus erythematosus (3), malaria (2), multiple sclerosis, disease progression, modifier of (2), lung cancer susceptibility 3 (1), diabetes mellitus, insulin-dependent (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 127.97 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 145.49 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -66.00167-0.395 Picture PostScript Text
3' UTR -197.30631-0.313 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR006052 - TNF
IPR006053 - TNF_a/b/c
IPR002960 - TNF_beta
IPR021184 - TNF_CS
IPR008983 - Tumour_necrosis_fac-like

Pfam Domains:
PF00229 - TNF(Tumour Necrosis Factor) family

SCOP Domains:
49842 - TNF-like

ModBase Predicted Comparative 3D Structure on Q5STV3
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005125 cytokine activity
GO:0005164 tumor necrosis factor receptor binding

Biological Process:
GO:0001666 response to hypoxia
GO:0002876 positive regulation of chronic inflammatory response to antigenic stimulus
GO:0002925 positive regulation of humoral immune response mediated by circulating immunoglobulin
GO:0006955 immune response
GO:0006959 humoral immune response
GO:0007584 response to nutrient
GO:0010469 regulation of receptor activity
GO:0032496 response to lipopolysaccharide
GO:0032729 positive regulation of interferon-gamma production
GO:0042493 response to drug
GO:0043065 positive regulation of apoptotic process
GO:0044130 negative regulation of growth of symbiont in host
GO:0048147 negative regulation of fibroblast proliferation
GO:0048535 lymph node development
GO:0050830 defense response to Gram-positive bacterium
GO:0060252 positive regulation of glial cell proliferation

Cellular Component:
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0016020 membrane


-  Descriptions from all associated GenBank mRNAs
  DQ123821 - Homo sapiens lymphotoxin alpha transcript variant 2 (LTA) mRNA, partial cds, alternatively spliced.
E01275 - cDNA encoding human lymphotoxin polypeptide.
D12614 - Homo sapiens LT mRNA for lymphotoxin (TNF-beta), complete cds.
DQ123822 - Homo sapiens lymphotoxin alpha transcript variant 3 (LTA) mRNA, complete cds, alternatively spliced.
JD405587 - Sequence 386611 from Patent EP1572962.
JD255149 - Sequence 236173 from Patent EP1572962.
JD399627 - Sequence 380651 from Patent EP1572962.
JD271056 - Sequence 252080 from Patent EP1572962.
JD537200 - Sequence 518224 from Patent EP1572962.
X01393 - Human mRNA for lymphotoxin.
JD477089 - Sequence 458113 from Patent EP1572962.
JD487611 - Sequence 468635 from Patent EP1572962.
D00102 - Homo sapiens mRNA for lymphotoxin, complete cds.
E01241 - cDNA encoding a polypeptide having a lymphotoxin activity.
E01481 - cDNA encoding human lymphotoxin.
E01482 - cDNA encoding human lymphotoxin.
E01804 - cDNA encoding human polypeptide having lymphotoxin activity.
JD099807 - Sequence 80831 from Patent EP1572962.
A06316 - H.sapiens mRNA for lymphotoxin.
JD403468 - Sequence 384492 from Patent EP1572962.
DQ894298 - Synthetic construct Homo sapiens clone IMAGE:100008758; FLH169474.01L; RZPDo839C1095D lymphotoxin alpha (TNF superfamily, member 1) (LTA) gene, encodes complete protein.
DQ891119 - Synthetic construct clone IMAGE:100003749; FLH169478.01X; RZPDo839C1096D lymphotoxin alpha (TNF superfamily, member 1) (LTA) gene, encodes complete protein.
BC034729 - Homo sapiens lymphotoxin alpha (TNF superfamily, member 1), mRNA (cDNA clone MGC:17018 IMAGE:4341621), complete cds.
AB590443 - Synthetic construct DNA, clone: pFN21AE1386, Homo sapiens LTA gene for lymphotoxin alpha, without stop codon, in Flexi system.
CU689954 - Synthetic construct Homo sapiens gateway clone IMAGE:100020241 5' read LTA mRNA.
KJ897146 - Synthetic construct Homo sapiens clone ccsbBroadEn_06540 LTA gene, encodes complete protein.
KR709601 - Synthetic construct Homo sapiens clone CCSBHm_00003905 LTA (LTA) mRNA, encodes complete protein.
KR712263 - Synthetic construct Homo sapiens clone CCSBHm_00900227 LTA (LTA) mRNA, encodes complete protein.
CR542273 - Homo sapiens full open reading frame cDNA clone RZPDo834H0626D for gene LTA, lymphotoxin alpha (TNF superfamily, member 1); complete cds, without stopcodon.
CR542253 - Homo sapiens full open reading frame cDNA clone RZPDo834D0626D for gene LTA, lymphotoxin alpha (TNF superfamily, member 1); complete cds, incl. stopcodon.
E01474 - cDNA encoding human lymphotoxin.
E01539 - DNA encoding lymphotoxin.
E02166 - DNA encoding human lympho toxin.
E02581 - Human lymphotoxin gene.
E01538 - DNA encoding lymphotoxin.
E03042 - DNA encoding improved human lymphotoxin.
E09028 - cDNA encoding novel recombinant lymphotoxin as antitumor agent.
DQ123823 - Homo sapiens lymphotoxin alpha transcript variant 4 (LTA) mRNA, partial cds, alternatively spliced.
DQ123827 - Homo sapiens lymphotoxin alpha transcript variant 8 (LTA) mRNA, partial cds, alternatively spliced.
DQ123824 - Homo sapiens lymphotoxin alpha transcript variant 5 (LTA) mRNA, partial cds, alternatively spliced.
DQ123826 - Homo sapiens lymphotoxin alpha transcript variant 7 (LTA) mRNA, partial cds, alternatively spliced.
DQ123825 - Homo sapiens lymphotoxin alpha transcript variant 6 (LTA) mRNA, partial cds, alternatively spliced.
JD286854 - Sequence 267878 from Patent EP1572962.
JD113623 - Sequence 94647 from Patent EP1572962.
JD099536 - Sequence 80560 from Patent EP1572962.
JD321880 - Sequence 302904 from Patent EP1572962.
JD268147 - Sequence 249171 from Patent EP1572962.
JD484773 - Sequence 465797 from Patent EP1572962.
JD540819 - Sequence 521843 from Patent EP1572962.
JD303478 - Sequence 284502 from Patent EP1572962.
JD441170 - Sequence 422194 from Patent EP1572962.
JD386845 - Sequence 367869 from Patent EP1572962.
JD475133 - Sequence 456157 from Patent EP1572962.
JD154691 - Sequence 135715 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000418386.1, ENST00000418386.2, hCG_43681 , LTA , NM_000595, Q5HYS4, Q5STV3, Q5STV3_HUMAN, TNLG1E , uc319nzn.1, uc319nzn.2
UCSC ID: ENST00000418386.3_4
RefSeq Accession: NM_000595.4
Protein: Q5STV3

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.