LOCUS       NM_000595               1416 bp    mRNA    linear   PRI 03-OCT-2024
DEFINITION  Homo sapiens lymphotoxin alpha (LTA), transcript variant 2, mRNA.
ACCESSION   NM_000595
VERSION     NM_000595.4
KEYWORDS    RefSeq; MANE Select.
SOURCE      Homo sapiens (human)
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
            Catarrhini; Hominidae; Homo.
REFERENCE   1  (bases 1 to 1416)
  AUTHORS   El-Ghamrawy,M., El-Gharbawi,N., Shahin,G., Abdelhady,A., Sayed,R.,
            Diaa,N. and Bishai,I.
  TITLE     Combined tumor necrosis factor-alpha (-308 G/A) and tumor necrosis
            factor-beta (+ 252 A/G) nucleotide polymorphisms and chronicity in
            Egyptian children with immune thrombocytopenia
  JOURNAL   Int J Hematol 117 (6), 856-862 (2023)
   PUBMED   36802017
  REMARK    GeneRIF: Combined tumor necrosis factor-alpha (-308 G/A) and tumor
            necrosis factor-beta (+ 252 A/G) nucleotide polymorphisms and
            chronicity in Egyptian children with immune thrombocytopenia.
REFERENCE   2  (bases 1 to 1416)
  AUTHORS   Alhelf,M., Shoaib,R.M.S., Elsaid,A., Bastawy,N., Elbeltagy,N.S.,
            Salem,E.T., Refaat,S. and Abuelnadar,E.H.
  TITLE     Prognostic significance of the genetic variant of lymphotoxin alpha
            (p.Thr60Asn) in egyptian patients with advanced hepatocellular
            carcinoma
  JOURNAL   Mol Biol Rep 50 (5), 4317-4327 (2023)
   PUBMED   36929286
  REMARK    GeneRIF: Prognostic significance of the genetic variant of
            lymphotoxin alpha (p.Thr60Asn) in egyptian patients with advanced
            hepatocellular carcinoma.
REFERENCE   3  (bases 1 to 1416)
  AUTHORS   Ferroni,P., Palmirotta,R., Egeo,G., Aurilia,C., Valente,M.G.,
            Spila,A., Pierallini,A., Barbanti,P. and Guadagni,F.
  TITLE     Association of LTA and SOD Gene Polymorphisms with Cerebral White
            Matter Hyperintensities in Migraine Patients
  JOURNAL   Int J Mol Sci 23 (22), 13781 (2022)
   PUBMED   36430258
  REMARK    GeneRIF: Association of LTA and SOD Gene Polymorphisms with
            Cerebral White Matter Hyperintensities in Migraine Patients.
            Publication Status: Online-Only
REFERENCE   4  (bases 1 to 1416)
  AUTHORS   Alcais,A., Alter,A., Antoni,G., Orlova,M., Nguyen,V.T., Singh,M.,
            Vanderborght,P.R., Katoch,K., Mira,M.T., Vu,H.T., Ngyuen,T.H.,
            Nguyen,N.B., Moraes,M., Mehra,N., Schurr,E. and Abel,L.
  TITLE     Stepwise replication identifies a low-producing lymphotoxin-alpha
            allele as a major risk factor for early-onset leprosy
  JOURNAL   Nat Genet 39 (4), 517-522 (2007)
   PUBMED   17353895
  REMARK    GeneRIF: LTA is a major gene associated with early-onset leprosy.
REFERENCE   5  (bases 1 to 1416)
  AUTHORS   Seidemann,K., Zimmermann,M., Book,M., Meyer,U., Burkhardt,B.,
            Welte,K., Reiter,A. and Stanulla,M.
  TITLE     Tumor necrosis factor and lymphotoxin alfa genetic polymorphisms
            and outcome in pediatric patients with non-Hodgkin's lymphoma:
            results from Berlin-Frankfurt-Munster Trial NHL-BFM 95
  JOURNAL   J Clin Oncol 23 (33), 8414-8421 (2005)
   PUBMED   16293872
  REMARK    GeneRIF: Observational study of gene-disease association. (HuGE
            Navigator)
REFERENCE   6  (bases 1 to 1416)
  AUTHORS   Ozaki,K., Ohnishi,Y., Iida,A., Sekine,A., Yamada,R., Tsunoda,T.,
            Sato,H., Sato,H., Hori,M., Nakamura,Y. and Tanaka,T.
  TITLE     Functional SNPs in the lymphotoxin-alpha gene that are associated
            with susceptibility to myocardial infarction
  JOURNAL   Nat Genet 32 (4), 650-654 (2002)
   PUBMED   12426569
  REMARK    GeneRIF: Single-nucleotide polymorphisms in the lymphotoxin-alpha
            gene are associated with susceptibility to myocardial infarction.
            GeneRIF: Observational study of gene-disease association. (HuGE
            Navigator)
            Erratum:[Nat Genet. 2003 Jan;33(1):107.]
REFERENCE   7  (bases 1 to 1416)
  AUTHORS   Buonaguro,L., Barillari,G., Chang,H.K., Bohan,C.A., Kao,V.,
            Morgan,R., Gallo,R.C. and Ensoli,B.
  TITLE     Effects of the human immunodeficiency virus type 1 Tat protein on
            the expression of inflammatory cytokines
  JOURNAL   J Virol 66 (12), 7159-7167 (1992)
   PUBMED   1279199
REFERENCE   8  (bases 1 to 1416)
  AUTHORS   Matsuyama,N., Okawa,N., Tsukii,Y., Endo,T. and Kaji,A.
  TITLE     Nucleotide sequence of a cDNA encoding human tumor necrosis factor
            beta from B lymphoblastoid cell RPMI 1788
  JOURNAL   FEBS Lett 302 (2), 141-144 (1992)
   PUBMED   1353024
REFERENCE   9  (bases 1 to 1416)
  AUTHORS   Evans,A.M., Petersen,J.W., Sekhon,G.S. and DeMars,R.
  TITLE     Mapping of prolactin and tumor necrosis factor-beta genes on human
            chromosome 6p using lymphoblastoid cell deletion mutants
  JOURNAL   Somat Cell Mol Genet 15 (3), 203-213 (1989)
   PUBMED   2567059
REFERENCE   10 (bases 1 to 1416)
  AUTHORS   Gray,P.W., Aggarwal,B.B., Benton,C.V., Bringman,T.S., Henzel,W.J.,
            Jarrett,J.A., Leung,D.W., Moffat,B., Ng,P., Svedersky,L.P. et al.
  TITLE     Cloning and expression of cDNA for human lymphotoxin, a lymphokine
            with tumour necrosis activity
  JOURNAL   Nature 312 (5996), 721-724 (1984)
   PUBMED   6334807
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AL662801.7, BG685356.1,
            D12614.1 and BX108399.1.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Jun 3, 2019 this sequence version replaced NM_000595.3.
            
            Summary: The encoded protein, a member of the tumor necrosis factor
            family, is a cytokine produced by lymphocytes. The protein is
            highly inducible, secreted, and forms heterotrimers with
            lymphotoxin-beta which anchor lymphotoxin-alpha to the cell
            surface. This protein also mediates a large variety of
            inflammatory, immunostimulatory, and antiviral responses, is
            involved in the formation of secondary lymphoid organs during
            development and plays a role in apoptosis. Genetic variations in
            this gene are associated with susceptibility to leprosy type 4,
            myocardial infarction, non-Hodgkin's lymphoma, and psoriatic
            arthritis. Alternatively spliced transcript variants have been
            observed for this gene. [provided by RefSeq, Jul 2012].
            
            Transcript Variant: This variant (2) differs in the 5' UTR compared
            to variant 1. Both variants 1 and 2 encode the same protein.
            
            Publication Note:  This RefSeq record includes a subset of the
            publications that are available for this gene. Please see the Gene
            record to access additional publications.
            
            ##Evidence-Data-START##
            Transcript exon combination :: D12614.1, SRR1163657.434742.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1965299, SAMEA1966682
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000418386.3/ ENSP00000413450.2
            RefSeq Select criteria :: based on conservation, longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-5                 AL662801.7         44960-44964
            6-27                BG685356.1         2-23
            28-1413             D12614.1           1-1386
            1414-1416           BX108399.1         539-541
FEATURES             Location/Qualifiers
     source          1..1416
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="6"
                     /map="6p21.33"
     gene            1..1416
                     /gene="LTA"
                     /gene_synonym="LT; TNFB; TNFSF1; TNLG1E"
                     /note="lymphotoxin alpha"
                     /db_xref="GeneID:4049"
                     /db_xref="HGNC:HGNC:6709"
                     /db_xref="MIM:153440"
     exon            1..158
                     /gene="LTA"
                     /gene_synonym="LT; TNFB; TNFSF1; TNLG1E"
                     /inference="alignment:Splign:2.1.0"
     exon            159..266
                     /gene="LTA"
                     /gene_synonym="LT; TNFB; TNFSF1; TNLG1E"
                     /inference="alignment:Splign:2.1.0"
     CDS             168..785
                     /gene="LTA"
                     /gene_synonym="LT; TNFB; TNFSF1; TNLG1E"
                     /note="tumor necrosis factor beta; LT-alpha; TNF-beta; TNF
                     superfamily, member 1; tumor necrosis factor ligand
                     superfamily member 1; tumor necrosis factor ligand 1E"
                     /codon_start=1
                     /product="lymphotoxin-alpha precursor"
                     /protein_id="NP_000586.2"
                     /db_xref="CCDS:CCDS4701.1"
                     /db_xref="GeneID:4049"
                     /db_xref="HGNC:HGNC:6709"
                     /db_xref="MIM:153440"
                     /translation="MTPPERLFLPRVCGTTLHLLLLGLLLVLLPGAQGLPGVGLTPSA
                     AQTARQHPKMHLAHSTLKPAAHLIGDPSKQNSLLWRANTDRAFLQDGFSLSNNSLLVP
                     TSGIYFVYSQVVFSGKAYSPKATSSPLYLAHEVQLFSSQYPFHVPLLSSQKMVYPGLQ
                     EPWLHSMYHGAAFQLTQGDQLSTHTDGIPHLVLSPSTVFFGAFAL"
     exon            267..372
                     /gene="LTA"
                     /gene_synonym="LT; TNFB; TNFSF1; TNLG1E"
                     /inference="alignment:Splign:2.1.0"
     exon            373..1416
                     /gene="LTA"
                     /gene_synonym="LT; TNFB; TNFSF1; TNLG1E"
                     /inference="alignment:Splign:2.1.0"
     regulatory      1395..1400
                     /regulatory_class="polyA_signal_sequence"
                     /gene="LTA"
                     /gene_synonym="LT; TNFB; TNFSF1; TNLG1E"
                     /note="hexamer: AATAAA"
     polyA_site      1416
                     /gene="LTA"
                     /gene_synonym="LT; TNFB; TNFSF1; TNLG1E"
                     /note="major polyA site"
ORIGIN      
        1 gctccgcaca gcaggtgagg ctctcctgcc ccatctcctt gggctgcccg tgcttcgtgc
       61 tttggactac cgcccagcag tgtcctgccc tctgcctggg cctcggtccc tcctgcacct
      121 gctgcctgga tccccggcct gcctgggcct gggccttggt tctccccatg acaccacctg
      181 aacgtctctt cctcccaagg gtgtgtggca ccaccctaca cctcctcctt ctggggctgc
      241 tgctggttct gctgcctggg gcccaggggc tccctggtgt tggcctcaca ccttcagctg
      301 cccagactgc ccgtcagcac cccaagatgc atcttgccca cagcaccctc aaacctgctg
      361 ctcacctcat tggagacccc agcaagcaga actcactgct ctggagagca aacacggacc
      421 gtgccttcct ccaggatggt ttctccttga gcaacaattc tctcctggtc cccaccagtg
      481 gcatctactt cgtctactcc caggtggtct tctctgggaa agcctactct cccaaggcca
      541 cctcctcccc actctacctg gcccatgagg tccagctctt ctcctcccag taccccttcc
      601 atgtgcctct cctcagctcc cagaagatgg tgtatccagg gctgcaggaa ccctggctgc
      661 actcgatgta ccacggggct gcgttccagc tcacccaggg agaccagcta tccacccaca
      721 cagatggcat cccccaccta gtcctcagcc ctagtactgt cttctttgga gccttcgctc
      781 tgtagaactt ggaaaaatcc agaaagaaaa aataattgat ttcaagacct tctccccatt
      841 ctgcctccat tctgaccatt tcaggggtcg tcaccacctc tcctttggcc attccaacag
      901 ctcaagtctt ccctgatcaa gtcaccggag ctttcaaaga aggaattcta ggcatcccag
      961 gggaccacac ctccctgaac catccctgat gtctgtctgg ctgaggattt caagcctgcc
     1021 taggaattcc cagcccaaag ctgttggtct gtcccaccag ctaggtgggg cctagatcca
     1081 cacacagagg aagagcaggc acatggagga gcttggggga tgactagagg cagggagggg
     1141 actatttatg aaggcaaaaa aattaaatta tttatttatg gaggatggag agaggggaat
     1201 aatagaagaa catccaagga gaaacagaga caggcccaag agatgaagag tgagagggca
     1261 tgcgcacaag gctgaccaag agagaaagaa gtaggcatga gggatcacag ggccccagaa
     1321 ggcagggaaa ggctctgaaa gccagctgcc gaccagagcc ccacacggag gcatctgcac
     1381 cctcgatgaa gcccaataaa cctcttttct ctgaaa
//
