LOCUS       NM_008534               2447 bp    mRNA    linear   ROD 13-JUN-2024
DEFINITION  Mus musculus lymphocyte antigen 9 (Ly9), transcript variant 1,
            mRNA.
ACCESSION   NM_008534
VERSION     NM_008534.4
KEYWORDS    RefSeq; RefSeq Select.
SOURCE      Mus musculus (house mouse)
  ORGANISM  Mus musculus
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
            Muroidea; Muridae; Murinae; Mus; Mus.
REFERENCE   1  (bases 1 to 2447)
  AUTHORS   Li,D., Xiong,W., Wang,Y., Feng,J., He,Y., Du,J., Wang,J., Yang,M.,
            Zeng,H., Yang,Y.G., Wu,N., Chen,S. and Dong,Z.
  TITLE     SLAMF3 and SLAMF4 are immune checkpoints that constrain macrophage
            phagocytosis of hematopoietic tumors
  JOURNAL   Sci Immunol 7 (67), eabj5501 (2022)
   PUBMED   35061505
  REMARK    GeneRIF: SLAMF3 and SLAMF4 are immune checkpoints that constrain
            macrophage phagocytosis of hematopoietic tumors.
REFERENCE   2  (bases 1 to 2447)
  AUTHORS   Wang,N., Yigit,B., van der Poel,C.E., Cuenca,M., Carroll,M.C.,
            Herzog,R.W., Engel,P. and Terhorst,C.
  TITLE     The Checkpoint Regulator SLAMF3 Preferentially Prevents Expansion
            of Auto-Reactive B Cells Generated by Graft-vs.-Host Disease
  JOURNAL   Front Immunol 10, 831 (2019)
   PUBMED   31057553
  REMARK    GeneRIF: The Checkpoint Regulator SLAMF3 Preferentially Prevents
            Expansion of Auto-Reactive B Cells Generated by Graft-vs.-Host
            Disease.
            Publication Status: Online-Only
REFERENCE   3  (bases 1 to 2447)
  AUTHORS   Lu,Y., Zhong,M.C., Qian,J., Calderon,V., Cruz Tleugabulova,M.,
            Mallevaey,T. and Veillette,A.
  TITLE     SLAM receptors foster iNKT cell development by reducing TCR signal
            strength after positive selection
  JOURNAL   Nat Immunol 20 (4), 447-457 (2019)
   PUBMED   30833791
REFERENCE   4  (bases 1 to 2447)
  AUTHORS   Cuenca,M., Punet-Ortiz,J., Ruart,M., Terhorst,C. and Engel,P.
  TITLE     Ly9 (SLAMF3) receptor differentially regulates iNKT cell
            development and activation in mice
  JOURNAL   Eur J Immunol 48 (1), 99-105 (2018)
   PUBMED   28980301
  REMARK    GeneRIF: The authors show that Ly9 influences Invariant natural
            killer T cell lineage differentiation.  Furthermore, treatment of
            wild-type mice with an agonistic monoclonal antibody directed
            against Ly9 impaired IL-4 and IFN-gamma production and reduced by
            half the number of spleen iNKT cells, with a significant decrease
            in the proportion of NKT2 cells.
REFERENCE   5  (bases 1 to 2447)
  AUTHORS   Chen,J., Zhong,M.C., Guo,H., Davidson,D., Mishel,S., Lu,Y.,
            Rhee,I., Perez-Quintero,L.A., Zhang,S., Cruz-Munoz,M.E., Wu,N.,
            Vinh,D.C., Sinha,M., Calderon,V., Lowell,C.A., Danska,J.S. and
            Veillette,A.
  TITLE     SLAMF7 is critical for phagocytosis of haematopoietic tumour cells
            via Mac-1 integrin
  JOURNAL   Nature 544 (7651), 493-497 (2017)
   PUBMED   28424516
REFERENCE   6  (bases 1 to 2447)
  AUTHORS   Sandrin,M.S., Gumley,T.P., Henning,M.M., Vaughan,H.A., Gonez,L.J.,
            Trapani,J.A. and McKenzie,I.F.
  TITLE     Isolation and characterization of cDNA clones for mouse Ly-9
  JOURNAL   J Immunol 149 (5), 1636-1641 (1992)
   PUBMED   1506686
REFERENCE   7  (bases 1 to 2447)
  AUTHORS   Gough,N.M., Lipkowitz,S., Kirsch,I.R. and Begley,C.G.
  TITLE     Localization of murine HLH gene NSCL to chromosome 1 by use of
            recombinant inbred strains
  JOURNAL   Mamm Genome 3 (3), 182-183 (1992)
   PUBMED   1617226
REFERENCE   8  (bases 1 to 2447)
  AUTHORS   You,K.H., Hsieh,C.L., Hayes,C., Stahl,N., Francke,U. and Popko,B.
  TITLE     DNA sequence, genomic organization, and chromosomal localization of
            the mouse peripheral myelin protein zero gene: identification of
            polymorphic alleles
  JOURNAL   Genomics 9 (4), 751-757 (1991)
   PUBMED   1709914
REFERENCE   9  (bases 1 to 2447)
  AUTHORS   Opdenakker,G., Snoddy,J., Choubey,D., Toniato,E., Pravtcheva,D.D.,
            Seldin,M.F., Ruddle,F.H. and Lengyel,P.
  TITLE     Interferons as gene activators: a cluster of six
            interferon-activatable genes is linked to the erythroid
            alpha-spectrin locus on murine chromosome 1
  JOURNAL   Virology 171 (2), 568-578 (1989)
   PUBMED   2474894
REFERENCE   10 (bases 1 to 2447)
  AUTHORS   Durda,P.J., Boos,S.C. and Gottlieb,P.D.
  TITLE     T100: a new murine cell surface glycoprotein detected by
            anti-Lyt-2.1 serum
  JOURNAL   J Immunol 122 (4), 1407-1412 (1979)
   PUBMED   312840
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            AC083892.19.
            
            On Oct 17, 2022 this sequence version replaced NM_008534.3.
            
            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 :: BC066212.1, M84412.1 [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMN00849374,
                                           SAMN00849375 [ECO:0006172]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on expression, longest protein
            ##RefSeq-Attributes-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-150               AC083892.19        40632-40781
            151-480             AC083892.19        42662-42991
            481-756             AC083892.19        45919-46194
            757-1095            AC083892.19        46661-46999
            1096-1365           AC083892.19        48065-48334
            1366-1464           AC083892.19        50199-50297
            1465-1518           AC083892.19        51438-51491
            1519-1853           AC083892.19        53792-54126
            1854-1925           AC083892.19        54487-54558
            1926-2447           AC083892.19        58856-59377
FEATURES             Location/Qualifiers
     source          1..2447
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="1"
                     /map="1 79.54 cM"
     gene            1..2447
                     /gene="Ly9"
                     /gene_synonym="CD229; Lgp100; Ly-9; SLAMF3; T100"
                     /note="lymphocyte antigen 9"
                     /db_xref="GeneID:17085"
                     /db_xref="MGI:MGI:96885"
     exon            1..150
                     /gene="Ly9"
                     /gene_synonym="CD229; Lgp100; Ly-9; SLAMF3; T100"
                     /inference="alignment:Splign:2.1.0"
     CDS             27..1991
                     /gene="Ly9"
                     /gene_synonym="CD229; Lgp100; Ly-9; SLAMF3; T100"
                     /note="isoform 1 precursor is encoded by transcript
                     variant 1; T-lymphocyte surface antigen Ly-9; cell surface
                     molecule Ly-9; SLAM family member 3; signaling lymphocytic
                     activation molecule 3"
                     /codon_start=1
                     /product="T-lymphocyte surface antigen Ly-9 isoform 1
                     precursor"
                     /protein_id="NP_032560.2"
                     /db_xref="CCDS:CCDS35779.1"
                     /db_xref="GeneID:17085"
                     /db_xref="MGI:MGI:96885"
                     /translation="MADLKRYWCDWALGPLSENPRMSQQQIFSPILWIPLLFLLMGLG
                     ASGKETPPTVISGMLGGSVTFSLNISKDAEIEHIIWNCPPKALALVFYKKDITILDKG
                     YNGRLKVSEDGYSLYMSNLTKSDSGSYHAQINQKNVILTTNKEFTLHIYEKLQKPQII
                     VESVTPSDTDSCTFTLICTVKGTKDSVQYSWTREDTHLNTYDGSHTLRVSQSVCDPDL
                     PYTCKAWNPVSQNSSQPVRIWQFCTGASRRKTAAGKTVVGILGEPVTLPLEFRATRAT
                     KNVVWVFNTSVISQERRGAATADSRRKPKGSEERRVRTSDQDQSLKISQLKMEDAGPY
                     HAYVCSEASRDPSVRHFTLLVYKRLEKPSVTKSPVHMMNGICEVVLTCSVDGGGNNVT
                     YTWMPLQNKAVMSQGKSHLNVSWESGEHLPNFTCTAHNPVSNSSSQFSSGTICSGPER
                     NKRFWLLLLLVLLLLMLIGGYFILRKKKQCSSLATRYRQAEVPAEIPETPTGHGQFSV
                     LSQRYEKLDMSAKTTRHQPTPTSDTSSESSATTEEDDEKTRMHSTANSRNQVYDLVTH
                     QDIAHALAYEGQVEYEAITPYDKVDGSMDEEDMAYIQVSLNVQGETPLPQKKEDSNTI
                     YCSVQKPKKTAQTPQQDAESPETPTYENFT"
     exon            151..480
                     /gene="Ly9"
                     /gene_synonym="CD229; Lgp100; Ly-9; SLAMF3; T100"
                     /inference="alignment:Splign:2.1.0"
     exon            481..756
                     /gene="Ly9"
                     /gene_synonym="CD229; Lgp100; Ly-9; SLAMF3; T100"
                     /inference="alignment:Splign:2.1.0"
     exon            757..1095
                     /gene="Ly9"
                     /gene_synonym="CD229; Lgp100; Ly-9; SLAMF3; T100"
                     /inference="alignment:Splign:2.1.0"
     exon            1096..1365
                     /gene="Ly9"
                     /gene_synonym="CD229; Lgp100; Ly-9; SLAMF3; T100"
                     /inference="alignment:Splign:2.1.0"
     exon            1366..1464
                     /gene="Ly9"
                     /gene_synonym="CD229; Lgp100; Ly-9; SLAMF3; T100"
                     /inference="alignment:Splign:2.1.0"
     exon            1465..1518
                     /gene="Ly9"
                     /gene_synonym="CD229; Lgp100; Ly-9; SLAMF3; T100"
                     /inference="alignment:Splign:2.1.0"
     exon            1519..1853
                     /gene="Ly9"
                     /gene_synonym="CD229; Lgp100; Ly-9; SLAMF3; T100"
                     /inference="alignment:Splign:2.1.0"
     exon            1854..1925
                     /gene="Ly9"
                     /gene_synonym="CD229; Lgp100; Ly-9; SLAMF3; T100"
                     /inference="alignment:Splign:2.1.0"
     exon            1926..2447
                     /gene="Ly9"
                     /gene_synonym="CD229; Lgp100; Ly-9; SLAMF3; T100"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2417..2422
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Ly9"
                     /gene_synonym="CD229; Lgp100; Ly-9; SLAMF3; T100"
                     /note="hexamer: ATTAAA"
     regulatory      2426..2431
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Ly9"
                     /gene_synonym="CD229; Lgp100; Ly-9; SLAMF3; T100"
                     /note="hexamer: AATAAA"
     polyA_site      2436
                     /gene="Ly9"
                     /gene_synonym="CD229; Lgp100; Ly-9; SLAMF3; T100"
                     /note="major polyA site"
     polyA_site      2447
                     /gene="Ly9"
                     /gene_synonym="CD229; Lgp100; Ly-9; SLAMF3; T100"
                     /note="major polyA site"
ORIGIN      
        1 aatttgaaat ctggaagtac accatcatgg cggatctaaa gagatattgg tgtgactggg
       61 ctctaggtcc actctctgaa aatccaagaa tgagtcagca gcagatattt tctcccattc
      121 tttggattcc tctcctcttc ctactcatgg ggctcggagc ctctggaaag gaaacacctc
      181 caacagtgat atcagggatg ctagggggtt ctgtgacttt ctccctaaac atctcaaagg
      241 atgcagagat tgagcatatc atctggaatt gtcccccaaa ggctcttgct ttagtattct
      301 acaaaaaaga tataactatt ctggacaaag gatataatgg cagactcaaa gtcagcgaag
      361 atggctactc cttgtacatg agcaacctaa ccaaaagtga ttcaggatcc taccatgctc
      421 agataaacca aaagaatgtt atcctcacca caaataaaga gttcacactg cacatctatg
      481 agaagctcca gaagcctcag atcatcgtgg aatctgtgac cccatccgat actgattcct
      541 gcaccttcac cctaatctgc actgtaaagg ggacaaagga cagtgtccag tacagctgga
      601 cccgagagga cacccattta aatacatacg atggaagcca caccctcagg gtttcccaga
      661 gtgtctgtga ccccgaccta ccctatacct gcaaagcctg gaatccagtc agccaaaaca
      721 gctcccaacc tgtccgcatc tggcaattct gcacaggagc ctccagaaga aaaacagcag
      781 cggggaagac tgtggtagga atcctgggag agccagtgac cctgcccttg gaatttcggg
      841 ccactcgggc cacaaagaat gttgtctggg tgtttaacac gtcggttatc agccaagaac
      901 ggagaggagc agcaacagcg gattctcgcc gtaagcccaa aggttctgaa gaacggaggg
      961 tgaggacctc tgaccaggac caatccctga agatcagcca gctgaagatg gaggacgcgg
     1021 gcccctacca tgcctatgtg tgctcagagg cctcccgaga ccccagtgtg agacatttca
     1081 ccttgcttgt ctacaagaga ctggagaagc ccagtgtcac caagagtcct gtgcacatga
     1141 tgaacggaat ctgcgaggtt gtcctgacct gttcagtgga cggtggtgga aacaatgtga
     1201 catacacatg gatgcctcta caaaacaaag ctgtcatgtc ccaagggaag tcgcacctca
     1261 acgtctcctg ggaaagtggt gaacacctgc ccaacttcac atgcacagcc cataaccctg
     1321 tcagcaacag ctccagccag ttttcttctg ggaccatctg ttcaggccct gagagaaaca
     1381 agaggttttg gctcctgctc ctcctggttt tgctcttgtt gatgctcatt ggcggttact
     1441 tcattttgag gaaaaagaag cagtgttcgt ctttggccac caggtacaga caagcggagg
     1501 tcccagctga aataccagaa accccaactg gccatggaca attttctgtg ctctcccaac
     1561 ggtatgagaa actagacatg tctgctaaga ccaccaggca tcagcctaca cccacctcag
     1621 ataccagctc tgagagcagc gcaacaacag aagaggatga cgaaaagacc agaatgcaca
     1681 gcactgctaa tagtagaaat caggtgtatg acttggtcac ccatcaggac attgcacatg
     1741 ccttggccta tgaggggcaa gtagaatatg aagcaatcac tccatatgat aaagtggatg
     1801 ggtctatgga tgaagaggac atggcatata tacaagtgtc cctgaatgtg cagggagaga
     1861 ccccacttcc tcagaagaaa gaagactcaa atacaatcta ctgctctgtg cagaagccta
     1921 aaaagacggc acaaacacca cagcaagatg ctgagtctcc tgaaacccct acctatgaaa
     1981 atttcacctg aagggaaaag cggctgctac ttccggggtg aggatttgga gaaaaacaga
     2041 catcataaat cctcctgttt ctgcagaaag aacacatcag aatttcctgc catggcttag
     2101 actagcctga atttgatgcc ttcctcttct tgtcatcctc cttaccccat gagcccattc
     2161 acaggtcagg cagagtctcc ttggagccta caggctttga acaccctgcc tttggatctc
     2221 tttttcttat ctggactgcc ttgtctgcct cagtggggga ggatgcactt agtcctgttg
     2281 ggacttgatg tgccagggtg ggttggtacc gtctctgagg agaaggggag atgggaattg
     2341 ggggagggat gtgagggagg gatgggaggc ctgtggtcaa tatgtaaagt gaataaataa
     2401 actaataaag aaaaaaatta aaaaaaataa agcccctcat aagttca
//
