LOCUS       NM_002346               1131 bp    mRNA    linear   PRI 29-OCT-2024
DEFINITION  Homo sapiens lymphocyte antigen 6 family member E (LY6E),
            transcript variant 1, mRNA.
ACCESSION   NM_002346
VERSION     NM_002346.3
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 1131)
  AUTHORS   Petta,T.B. and Carlson,J.
  TITLE     Exploring Molecular Drivers of PARPi Resistance in BRCA1-Deficient
            Ovarian Cancer: The Role of LY6E and Immunomodulation
  JOURNAL   Int J Mol Sci 25 (19), 10427 (2024)
   PUBMED   39408764
  REMARK    GeneRIF: Exploring Molecular Drivers of PARPi Resistance in
            BRCA1-Deficient Ovarian Cancer: The Role of LY6E and
            Immunomodulation.
            Publication Status: Online-Only
REFERENCE   2  (bases 1 to 1131)
  AUTHORS   Cao,B., Li,M., Li,X., Ji,X., Wan,L., Jiang,Y., Zhou,L., Gong,F. and
            Chen,X.
  TITLE     Innovative biomarkers TCN2 and LY6E can significantly inhibit
            respiratory syncytial virus infection
  JOURNAL   J Transl Med 22 (1), 854 (2024)
   PUBMED   39313785
  REMARK    GeneRIF: Innovative biomarkers TCN2 and LY6E can significantly
            inhibit respiratory syncytial virus infection.
            Publication Status: Online-Only
REFERENCE   3  (bases 1 to 1131)
  AUTHORS   Kim,D.K., Weller,B., Lin,C.W., Sheykhkarimli,D., Knapp,J.J.,
            Dugied,G., Zanzoni,A., Pons,C., Tofaute,M.J., Maseko,S.B.,
            Spirohn,K., Laval,F., Lambourne,L., Kishore,N., Rayhan,A.,
            Sauer,M., Young,V., Halder,H., la Rosa,N.M., Pogoutse,O.,
            Strobel,A., Schwehn,P., Li,R., Rothballer,S.T., Altmann,M.,
            Cassonnet,P., Cote,A.G., Vergara,L.E., Hazelwood,I., Liu,B.B.,
            Nguyen,M., Pandiarajan,R., Dohai,B., Coloma,P.A.R., Poirson,J.,
            Giuliana,P., Willems,L., Taipale,M., Jacob,Y., Hao,T., Hill,D.E.,
            Brun,C., Twizere,J.C., Krappmann,D., Heinig,M., Falter,C., Aloy,P.,
            Demeret,C., Vidal,M., Calderwood,M.A., Roth,F.P. and
            Falter-Braun,P.
  TITLE     A proteome-scale map of the SARS-CoV-2-human contactome
  JOURNAL   Nat Biotechnol 41 (1), 140-149 (2023)
   PUBMED   36217029
REFERENCE   4  (bases 1 to 1131)
  AUTHORS   Liu,D., Zhu,M., Lin,Y., Li,M., Huang,R., Yang,L., Song,Y., Diao,Y.
            and Yang,C.
  TITLE     LY6E protein facilitates adeno-associated virus crossing in a
            biomimetic chip model of the human blood-brain barrier
  JOURNAL   Lab Chip 22 (21), 4180-4190 (2022)
   PUBMED   36165190
  REMARK    GeneRIF: LY6E protein facilitates adeno-associated virus crossing
            in a biomimetic chip model of the human blood-brain barrier.
            Publication Status: Online-Only
REFERENCE   5  (bases 1 to 1131)
  AUTHORS   Li,T., Liu,W., Wang,C., Wang,M., Hui,W., Lu,J. and Gao,F.
  TITLE     Multidimension Analysis of the Prognostic Value, Immune Regulatory
            Function, and ceRNA Network of LY6E in Individuals with Colorectal
            Cancer
  JOURNAL   J Immunol Res 2022, 5164265 (2022)
   PUBMED   35310607
  REMARK    GeneRIF: Multidimension Analysis of the Prognostic Value, Immune
            Regulatory Function, and ceRNA Network of LY6E in Individuals with
            Colorectal Cancer.
            Publication Status: Online-Only
REFERENCE   6  (bases 1 to 1131)
  AUTHORS   Kosugi,A., Saitoh,S., Noda,S., Miyake,K., Yamashita,Y., Kimoto,M.,
            Ogata,M. and Hamaoka,T.
  TITLE     Physical and functional association between thymic shared
            antigen-1/stem cell antigen-2 and the T cell receptor complex
  JOURNAL   J Biol Chem 273 (20), 12301-12306 (1998)
   PUBMED   9575182
REFERENCE   7  (bases 1 to 1131)
  AUTHORS   Shan,X., Bourdeau,A., Rhoton,A., Wells,D.E., Cohen,E.H.,
            Landgraf,B.E. and Palfree,R.G.
  TITLE     Characterization and mapping to human chromosome 8q24.3 of
            Ly-6-related gene 9804 encoding an apparent homologue of mouse
            TSA-1
  JOURNAL   J Immunol 160 (1), 197-208 (1998)
   PUBMED   9551972
REFERENCE   8  (bases 1 to 1131)
  AUTHORS   Brakenhoff,R.H., van Dijk,M., Rood-Knippels,E.M. and Snow,G.B.
  TITLE     A gain of novel tissue specificity in the human Ly-6 gene E48
  JOURNAL   J Immunol 159 (10), 4879-4886 (1997)
   PUBMED   9366413
REFERENCE   9  (bases 1 to 1131)
  AUTHORS   Capone,M.C., Gorman,D.M., Ching,E.P. and Zlotnik,A.
  TITLE     Identification through bioinformatics of cDNAs encoding human
            thymic shared Ag-1/stem cell Ag-2. A new member of the human Ly-6
            family
  JOURNAL   J Immunol 157 (3), 969-973 (1996)
   PUBMED   8757598
REFERENCE   10 (bases 1 to 1131)
  AUTHORS   Mao,M., Yu,M., Tong,J.H., Ye,J., Zhu,J., Huang,Q.H., Fu,G., Yu,L.,
            Zhao,S.Y., Waxman,S., Lanotte,M., Wang,Z.Y., Tan,J.Z., Chan,S.J.
            and Chen,Z.
  TITLE     RIG-E, a human homolog of the murine Ly-6 family, is induced by
            retinoic acid during the differentiation of acute promyelocytic
            leukemia cell
  JOURNAL   Proc Natl Acad Sci U S A 93 (12), 5910-5914 (1996)
   PUBMED   8650192
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AC083982.13.
            
            On Nov 23, 2018 this sequence version replaced NM_002346.2.
            
            Summary: This gene belongs to the human Ly6 gene family and encodes
            a glycosylphosphatidyl-inositol (GPI)-anchored cell surface
            protein. The protein plays an important role in T cell physiology,
            oncogenesis and immunological regulation. The protein is also
            involved in modulation of viral infection by coronaviruses,
            SARS-CoV, MERS-CoV and SARS-CoV-2. [provided by RefSeq, Aug 2021].
            
            Transcript Variant: This variant (1) represents the longer
            transcript. 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 :: AK223074.1, SRR5189658.54327.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1965299, SAMEA1966682
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            coronavirus related    :: involved in immune response or antiviral
                                      activity
            MANE Ensembl match     :: ENST00000292494.11/ ENSP00000292494.6
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-58                AC083982.13        29041-29098
            59-167              AC083982.13        31395-31503
            168-287             AC083982.13        31826-31945
            288-1131            AC083982.13        32078-32921
FEATURES             Location/Qualifiers
     source          1..1131
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="8"
                     /map="8q24.3"
     gene            1..1131
                     /gene="LY6E"
                     /gene_synonym="RIG-E; RIGE; SCA-2; SCA2; TSA-1"
                     /note="lymphocyte antigen 6 family member E"
                     /db_xref="GeneID:4061"
                     /db_xref="HGNC:HGNC:6727"
                     /db_xref="MIM:601384"
     exon            1..58
                     /gene="LY6E"
                     /gene_synonym="RIG-E; RIGE; SCA-2; SCA2; TSA-1"
                     /inference="alignment:Splign:2.1.0"
     exon            59..167
                     /gene="LY6E"
                     /gene_synonym="RIG-E; RIGE; SCA-2; SCA2; TSA-1"
                     /inference="alignment:Splign:2.1.0"
     CDS             116..511
                     /gene="LY6E"
                     /gene_synonym="RIG-E; RIGE; SCA-2; SCA2; TSA-1"
                     /note="retinoic acid induced gene E; lymphocyte antigen
                     6E; ly-6E; stem cell antigen 2; thymic shared antigen 1;
                     retinoic acid-induced gene E protein; lymphocyte antigen 6
                     complex, locus E"
                     /codon_start=1
                     /product="lymphocyte antigen 6E precursor"
                     /protein_id="NP_002337.1"
                     /db_xref="CCDS:CCDS6394.1"
                     /db_xref="GeneID:4061"
                     /db_xref="HGNC:HGNC:6727"
                     /db_xref="MIM:601384"
                     /translation="MKIFLPVLLAALLGVERASSLMCFSCLNQKSNLYCLKPTICSDQ
                     DNYCVTVSASAGIGNLVTFGHSLSKTCSPACPIPEGVNVGVASMGISCCQSFLCNFSA
                     ADGGLRASVTLLGAGLLLSLLPALLRFGP"
     exon            168..287
                     /gene="LY6E"
                     /gene_synonym="RIG-E; RIGE; SCA-2; SCA2; TSA-1"
                     /inference="alignment:Splign:2.1.0"
     exon            288..1131
                     /gene="LY6E"
                     /gene_synonym="RIG-E; RIGE; SCA-2; SCA2; TSA-1"
                     /inference="alignment:Splign:2.1.0"
     regulatory      1111..1116
                     /regulatory_class="polyA_signal_sequence"
                     /gene="LY6E"
                     /gene_synonym="RIG-E; RIGE; SCA-2; SCA2; TSA-1"
                     /note="hexamer: AATAAA"
     polyA_site      1131
                     /gene="LY6E"
                     /gene_synonym="RIG-E; RIGE; SCA-2; SCA2; TSA-1"
                     /note="major polyA site"
ORIGIN      
        1 agagcgcgcg aggttcgggg agctcggcca ggctgctggt acctgcgtcc gcccggcgag
       61 caggacaggc tgctttggtt tgtgacctcc aggcaggacg gccatcctct ccagaatgaa
      121 gatcttcttg ccagtgctgc tggctgccct tctgggtgtg gagcgagcca gctcgctgat
      181 gtgcttctcc tgcttgaacc agaagagcaa tctgtactgc ctgaagccga ccatctgctc
      241 cgaccaggac aactactgcg tgactgtgtc tgctagtgcc ggcattggga atctcgtgac
      301 atttggccac agcctgagca agacctgttc cccggcctgc cccatcccag aaggcgtcaa
      361 tgttggtgtg gcttccatgg gcatcagctg ctgccagagc tttctgtgca atttcagtgc
      421 ggccgatggc gggctgcggg caagcgtcac cctgctgggt gccgggctgc tgctgagcct
      481 gctgccggcc ctgctgcggt ttggcccctg accgcccaga ccctgtcccc cgatccccca
      541 gctcaggaag gaaagcccag ccctttctgg atcccacagt gtatgggagc ccctgactcc
      601 tcacgtgcct gatctgtgcc cttggtccca ggtcaggccc accccctgca cctccacctg
      661 ccccagcccc tgcctctgcc ccaagtgggg ccagctgccc tcacttctgg ggtggatgat
      721 gtgaccttcc ttgggggacc gcggaaggga cgagggttcc ctggagtctt acggtccaac
      781 atcaggacca agtcccatgg acatgctgac agggtcccca gggagaccgt gtcagtaggg
      841 atgtgtgcct ggctgtgtac gtgggtgtgc agtgcacgtg agagcacgtg gcggcttctg
      901 ggggccatgt ttggggaggg aggtgtgcca gcagcctgga gagcctcagt ccctgtagcc
      961 ccctgccctg gcacagctgc atgcacttca agggcagcct ttgggggttg gggtttctgc
     1021 cacttccggg tctaggccct gccccaaatc cagccagtcc tgccccagcc cacccccaca
     1081 ttggagccct cctgctgctt tggtgcctca aataaataca gatgtccccc a
//
