LOCUS       NM_001164036            2326 bp    mRNA    linear   ROD 06-NOV-2024
DEFINITION  Mus musculus lymphocyte antigen 6 family member E (Ly6e),
            transcript variant 1, mRNA.
ACCESSION   NM_001164036
VERSION     NM_001164036.2
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 2326)
  AUTHORS   Adams,D.J., Barlas,B., McIntyre,R.E., Salguero,I., van der
            Weyden,L., Barros,A., Vicente,J.R., Karimpour,N., Haider,A.,
            Ranzani,M., Turner,G., Thompson,N.A., Harle,V., Olvera-Leon,R.,
            Robles-Espinoza,C.D., Speak,A.O., Geisler,N., Weninger,W.J.,
            Geyer,S.H., Hewinson,J., Karp,N.A., Fu,B., Yang,F., Kozik,Z.,
            Choudhary,J., Yu,L., van Ruiten,M.S., Rowland,B.D., Lelliott,C.J.,
            Del Castillo Velasco-Herrera,M., Verstraten,R., Bruckner,L.,
            Henssen,A.G., Rooimans,M.A., de Lange,J., Mohun,T.J., Arends,M.J.,
            Kentistou,K.A., Coelho,P.A., Zhao,Y., Zecchini,H., Perry,J.R.B.,
            Jackson,S.P. and Balmus,G.
  CONSRTM   Sanger Mouse Genetics Project
  TITLE     Genetic determinants of micronucleus formation in vivo
  JOURNAL   Nature 627 (8002), 130-136 (2024)
   PUBMED   38355793
REFERENCE   2  (bases 1 to 2326)
  AUTHORS   Mar,K.B., Wells,A.I., Caballero Van Dyke,M.C., Lopez,A.H.,
            Eitson,J.L., Fan,W., Hanners,N.W., Evers,B.M., Shelton,J.M. and
            Schoggins,J.W.
  TITLE     LY6E is a pan-coronavirus restriction factor in the respiratory
            tract
  JOURNAL   Nat Microbiol 8 (8), 1587-1599 (2023)
   PUBMED   37443277
REFERENCE   3  (bases 1 to 2326)
  AUTHORS   Gao,M., Liu,X., Guo,P., Wang,J., Li,J., Wang,W., Stoddart,M.J.,
            Grad,S., Li,Z., Wu,H., Li,B., He,Z., Zhou,G., Liu,S., Zhu,W.,
            Chen,D., Zou,X. and Zhou,Z.
  TITLE     Deciphering postnatal limb development at single-cell resolution
  JOURNAL   iScience 26 (1), 105808 (2022)
   PUBMED   36619982
  REMARK    Publication Status: Online-Only
REFERENCE   4  (bases 1 to 2326)
  AUTHORS   Sandovici,I., Georgopoulou,A., Perez-Garcia,V., Hufnagel,A.,
            Lopez-Tello,J., Lam,B.Y.H., Schiefer,S.N., Gaudreau,C., Santos,F.,
            Hoelle,K., Yeo,G.S.H., Burling,K., Reiterer,M., Fowden,A.L.,
            Burton,G.J., Branco,C.M., Sferruzzi-Perri,A.N. and Constancia,M.
  TITLE     The imprinted Igf2-Igf2r axis is critical for matching placental
            microvasculature expansion to fetal growth
  JOURNAL   Dev Cell 57 (1), 63-79 (2022)
   PUBMED   34963058
REFERENCE   5  (bases 1 to 2326)
  AUTHORS   Bedogni,F. and Hevner,R.F.
  TITLE     Cell-Type-Specific Gene Expression in Developing Mouse Neocortex:
            Intermediate Progenitors Implicated in Axon Development
  JOURNAL   Front Mol Neurosci 14, 686034 (2021)
   PUBMED   34321999
  REMARK    Publication Status: Online-Only
REFERENCE   6  (bases 1 to 2326)
  AUTHORS   Bamezai,A.
  TITLE     Mouse Ly-6 proteins and their extended family: markers of cell
            differentiation and regulators of cell signaling
  JOURNAL   Arch Immunol Ther Exp (Warsz) 52 (4), 255-266 (2004)
   PUBMED   15467490
  REMARK    Review article
REFERENCE   7  (bases 1 to 2326)
  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   8  (bases 1 to 2326)
  AUTHORS   Classon,B.J. and Coverdale,L.
  TITLE     Genomic organization and expression of mouse thymic shared
            antigen-1 (TSA-1): evidence for a processed pseudogene
  JOURNAL   Immunogenetics 44 (3), 222-226 (1996)
   PUBMED   8662090
REFERENCE   9  (bases 1 to 2326)
  AUTHORS   Classon,B.J. and Coverdale,L.
  TITLE     Mouse stem cell antigen Sca-2 is a member of the Ly-6 family of
            cell surface proteins
  JOURNAL   Proc Natl Acad Sci U S A 91 (12), 5296-5300 (1994)
   PUBMED   8202484
REFERENCE   10 (bases 1 to 2326)
  AUTHORS   MacNeil,I., Kennedy,J., Godfrey,D.I., Jenkins,N.A.,
            Masciantonio,M., Mineo,C., Gilbert,D.J., Copeland,N.G., Boyd,R.L.
            and Zlotnik,A.
  TITLE     Isolation of a cDNA encoding thymic shared antigen-1. A new member
            of the Ly6 family with a possible role in T cell development
  JOURNAL   J Immunol 151 (12), 6913-6923 (1993)
   PUBMED   8258699
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            AC124637.10.
            
            On Sep 11, 2019 this sequence version replaced NM_001164036.1.
            
            Transcript Variant: This variant (1) represents the longest
            transcript. Variants 1 to 7 all encode the same protein.
            
            Sequence Note: The RefSeq transcript and protein were derived from
            genomic sequence to make the sequence consistent with the reference
            genome assembly. The genomic coordinates used for the transcript
            record were based on alignments.
            
            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 :: AK014207.1, BC005684.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN00849374, SAMN00849375
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            CDS uses downstream in-frame AUG :: upstream AUG and CDS extension
                                                is not conserved
            RefSeq Select criteria           :: based on conservation,
                                                expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-693               AC124637.10        65507-66199
            694-794             AC124637.10        68259-68359
            795-914             AC124637.10        68751-68870
            915-2326            AC124637.10        68975-70386
FEATURES             Location/Qualifiers
     source          1..2326
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="15"
                     /map="15 34.29 cM"
     gene            1..2326
                     /gene="Ly6e"
                     /gene_synonym="Ly67; RIG-E; Sca-2; TSA-1; Tsa1"
                     /note="lymphocyte antigen 6 family member E"
                     /db_xref="GeneID:17069"
                     /db_xref="MGI:MGI:106651"
     exon            1..693
                     /gene="Ly6e"
                     /gene_synonym="Ly67; RIG-E; Sca-2; TSA-1; Tsa1"
                     /inference="alignment:Splign:2.1.0"
     exon            694..794
                     /gene="Ly6e"
                     /gene_synonym="Ly67; RIG-E; Sca-2; TSA-1; Tsa1"
                     /inference="alignment:Splign:2.1.0"
     CDS             743..1135
                     /gene="Ly6e"
                     /gene_synonym="Ly67; RIG-E; Sca-2; TSA-1; Tsa1"
                     /note="lymphocyte antigen 6E; stem cell antigen 2; thymic
                     shared antigen 1; lymphocyte antigen 6 complex, locus E"
                     /codon_start=1
                     /product="lymphocyte antigen 6E precursor"
                     /protein_id="NP_001157508.2"
                     /db_xref="CCDS:CCDS27538.1"
                     /db_xref="GeneID:17069"
                     /db_xref="MGI:MGI:106651"
                     /translation="MRVFLPVLLAALLGMEQVHSLMCFSCTDQKNNINCLWPVSCQEK
                     DHYCITLSAAAGFGNVNLGYTLNKGCSPICPSENVNLNLGVASVNSYCCQSSFCNFSA
                     AGLGLRASIPLLGLGLLLSLLALLQLSP"
     exon            795..914
                     /gene="Ly6e"
                     /gene_synonym="Ly67; RIG-E; Sca-2; TSA-1; Tsa1"
                     /inference="alignment:Splign:2.1.0"
     exon            915..2326
                     /gene="Ly6e"
                     /gene_synonym="Ly67; RIG-E; Sca-2; TSA-1; Tsa1"
                     /inference="alignment:Splign:2.1.0"
     regulatory      1734..1739
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Ly6e"
                     /gene_synonym="Ly67; RIG-E; Sca-2; TSA-1; Tsa1"
                     /note="hexamer: AATAAA"
     polyA_site      1753
                     /gene="Ly6e"
                     /gene_synonym="Ly67; RIG-E; Sca-2; TSA-1; Tsa1"
                     /note="major polyA site"
     regulatory      2307..2312
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Ly6e"
                     /gene_synonym="Ly67; RIG-E; Sca-2; TSA-1; Tsa1"
                     /note="hexamer: ATTAAA"
     polyA_site      2326
                     /gene="Ly6e"
                     /gene_synonym="Ly67; RIG-E; Sca-2; TSA-1; Tsa1"
ORIGIN      
        1 agatctgttc aaaccagtgc tgcaatgacc tccttcccga ggaatttctg tcctgccgcc
       61 tcatccccaa aagagggatg gcccagacgg gctcagccca gagggacctg acaacctgaa
      121 gggcgggtga tgaggcatcc ttggtccagg acttcctcag ccttacagca gcagagattc
      181 ccatgagcgt ttcaggatgc agtctgtccc ctcactcctt ccggaagcaa gctaagcctg
      241 cgcacaggtc ttagtatcgg tgattgccag aagccctggc ctttccaccc tccctaggtc
      301 tgtcctgaaa ggtaaggtag acatgctaca ccagaagcca cgccagggct ctgatgccac
      361 attgtgtgcg gtggggcact tagggcggtc tcagccaggc ttctgggtac caccggggac
      421 cgccgccgtg ggcgcatagc ttgggacccc tgtcgtagtc tcagaggagc agttgtgcag
      481 ccaagccaag ggcacagccg gagttgccag aggccagcag ccagggtcgt tctccccacc
      541 agccagagac ccgcccacag cccatgaaac gccccgcctg cagcccgccc ccgccatctg
      601 tgctccgctc cgcctgcttg ggtgcattca gcctttggtg atcctccagg acctaaggtt
      661 tcggtattat cttcggggcc tcttcacccg gagtaggctt ctttggcttg cgaaccttca
      721 gcagatgtct gccacttcca acatgagagt cttcctgcct gtgctgttgg cagcccttct
      781 gggcatggag caagttcatt ccctgatgtg cttctcatgt accgatcaga agaacaatat
      841 aaactgcctg tggccagttt catgccagga gaaagaccat tactgtatca cgttatctgc
      901 cgctgcgggc tttgggaatg tcaaccttgg ctacaccctg aacaagggct gctccccgat
      961 ctgccccagt gaaaatgtca atctcaatct cggtgtggcg tccgtgaaca gctactgctg
     1021 ccaaagctcc ttctgcaact tcagcgcagc tggcctcgga cttcgtgcca gtatcccact
     1081 actgggcctt ggactcctgc ttagcttgtt ggctctgctg cagctgagcc cctgaccatc
     1141 ccccatgtgt tctccatatc cccccagctc aggaaaagcc cagctccttt taggtcccag
     1201 gggaccctag gaaccttcag ctcctcctgg gtgtgtctag ttccccctcc acactctctc
     1261 aacgtcaggg ctaagtacca aactcaccca tacctgctct gttgaagtgg tactggctac
     1321 ccttgcttcc agagccaatc ctataacctc ccttggggaa ccagcgaagg ggtgaagatc
     1381 tccttggagt ctcaagagta ccagagtcag cgccgaatct tgtggacaca ctgacaagga
     1441 tgtctaatcc aaatagatgt atatctgtgt gctcagtgta tccctgtgtg aatgaagcca
     1501 cttggattct ggggtgggca aagaagacct gaaaagattc tacagcagaa ggcctgtgtc
     1561 gccaccaaaa cccctccccc tggtatcatt gtacccacct tgtactctgt tcaggaggct
     1621 gcccatggag gactgccacc cctccagatg aaggctccca ctacccgatg cagttgagtc
     1681 ccatcctgcc ctctctgccc acactggctt cctgctgcta ttctagtgcc tcaaataaac
     1741 cgttcacacc ctttcctgct atgtcctggt tgtccttaac ccgtcttccc cctccggtcc
     1801 aaagggacct ggggatcctg caggcccaca gccctgctta agcgattctg aaagaccaac
     1861 cccgatacag tgatacattc ctatgatgcc atcatagcag aagcagaggt ctctgggagg
     1921 ccagcctggt gcatagcaaa tcccaggaat ctaggcccat ttagtgagac aggcctgaga
     1981 gaaaagagag agagcaaagg cagagagaac ttgaaagtgt gctgtctcag gctgaaagct
     2041 gagaagtaca gctacccata aaggcaggcc catcaggctg gtcacacatt cccaagcttt
     2101 gtctgcccca gagacttcag aggcctgctg ttgccacttg tccttcataa actaccctgt
     2161 agtctaagcc atgggagtct ggcccaggca agtgatactt gtccacccta taactggctt
     2221 tgctttgctt tctggtattt taagacggtc tcgctatgtt aagactagct gccccaaacc
     2281 cagagcaatc ctctttgagt gctggaatta aaggcatgca ccacca
//
