LOCUS       NM_001271419             956 bp    mRNA    linear   ROD 28-JAN-2025
DEFINITION  Mus musculus lymphocyte antigen 6 family member A (Ly6a),
            transcript variant 5, mRNA.
ACCESSION   NM_001271419
VERSION     NM_001271419.1
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 956)
  AUTHORS   Coren,L., Zaffryar-Eilot,S., Odeh,A., Kaganovsky,A. and Hasson,P.
  TITLE     Fibroblast diversification is an embryonic process dependent on
            muscle contraction
  JOURNAL   Cell Rep 43 (12), 115034 (2024)
   PUBMED   39636726
REFERENCE   2  (bases 1 to 956)
  AUTHORS   Zhu,Z., Zou,Q., Wang,C., Li,D., Yang,Y., Xiao,Y., Jin,Y., Yan,J.,
            Luo,L., Sun,Y. and Liang,X.
  TITLE     Isl Identifies the Extraembryonic Mesodermal/Allantois Progenitors
            and is Required for Placenta Morphogenesis and Vasculature
            Formation
  JOURNAL   Adv Sci (Weinh) 11 (32), e2400238 (2024)
   PUBMED   38923264
REFERENCE   3  (bases 1 to 956)
  AUTHORS   Rao,J., Djeffal,Y., Chal,J., Marchiano,F., Wang,C.H., Al
            Tanoury,Z., Gapon,S., Mayeuf-Louchart,A., Glass,I., Sefton,E.M.,
            Habermann,B., Kardon,G., Watt,F.M., Tseng,Y.H. and Pourquie,O.
  TITLE     Reconstructing human brown fat developmental trajectory in vitro
  JOURNAL   Dev Cell 58 (21), 2359-2375 (2023)
   PUBMED   37647896
REFERENCE   4  (bases 1 to 956)
  AUTHORS   Ni,Z., Lyu,L., Gong,H., Du,L., Wen,Z., Jiang,H., Yang,H., Hu,Y.,
            Zhang,B., Xu,Q., Guo,X. and Chen,T.
  TITLE     Multilineage commitment of Sca-1+ cells in reshaping vein grafts
  JOURNAL   Theranostics 13 (7), 2154-2175 (2023)
   PUBMED   37153747
  REMARK    Publication Status: Online-Only
REFERENCE   5  (bases 1 to 956)
  AUTHORS   Koren,E., Feldman,A., Yusupova,M., Kadosh,A., Sedov,E., Ankawa,R.,
            Yosefzon,Y., Nasser,W., Gerstberger,S., Kimel,L.B., Priselac,N.,
            Brown,S., Sharma,S., Gorenc,T., Shalom-Feuerstein,R., Steller,H.,
            Shemesh,T. and Fuchs,Y.
  TITLE     Thy1 marks a distinct population of slow-cycling stem cells in the
            mouse epidermis
  JOURNAL   Nat Commun 13 (1), 4628 (2022)
   PUBMED   35941116
  REMARK    Publication Status: Online-Only
REFERENCE   6  (bases 1 to 956)
  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 956)
  AUTHORS   Stanford,W.L., Bruyns,E. and Snodgrass,H.R.
  TITLE     The isolation and sequence of the chromosomal gene and regulatory
            regions of Ly-6A.2
  JOURNAL   Immunogenetics 35 (6), 408-411 (1992)
   PUBMED   1315719
REFERENCE   8  (bases 1 to 956)
  AUTHORS   McGrew,J.T. and Rock,K.L.
  TITLE     Isolation, expression, and sequence of the TAP/Ly-6A.2 chromosomal
            gene
  JOURNAL   J Immunol 146 (10), 3633-3638 (1991)
   PUBMED   1709198
REFERENCE   9  (bases 1 to 956)
  AUTHORS   Khan,K.D., Lindwall,G., Maher,S.E. and Bothwell,A.L.
  TITLE     Characterization of promoter elements of an interferon-inducible
            Ly-6E/A differentiation antigen, which is expressed on activated T
            cells and hematopoietic stem cells
  JOURNAL   Mol Cell Biol 10 (10), 5150-5159 (1990)
   PUBMED   1697928
REFERENCE   10 (bases 1 to 956)
  AUTHORS   Palfree,R.G., LeClair,K.P., Bothwell,A. and Hammerling,U.
  TITLE     cDNA characterization of an Ly-6.2 gene expressed in BW5147 tumor
            cells
  JOURNAL   Immunogenetics 26 (6), 389-391 (1987)
   PUBMED   2822573
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            AC124637.10 and J03636.1.
            
            Transcript Variant: This variant (5) uses two alternate splice
            sites in the 5' UTR, compared to variant 1. Variants 1, 2, 3, 4, 5,
            and 6 encode the same protein.
            
            Sequence Note: This RefSeq record was created from transcript and
            genomic sequence data to make the sequence consistent with the
            reference genome assembly. The genomic coordinates used for the
            transcript record were based on transcript 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 :: DV059778.1, BI655938.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN01164133 [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on expression, longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-127               AC124637.10        108387-108513       c
            128-841             J03636.1           7-720
            842-956             AC124637.10        105359-105473       c
FEATURES             Location/Qualifiers
     source          1..956
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="15"
                     /map="15 34.29 cM"
     gene            1..956
                     /gene="Ly6a"
                     /gene_synonym="Ly-6A.2; Ly-6A/E; Ly-6E.1; Sca-1; Sca1;
                     TAP"
                     /note="lymphocyte antigen 6 family member A"
                     /db_xref="GeneID:110454"
                     /db_xref="MGI:MGI:107527"
     exon            1..153
                     /gene="Ly6a"
                     /gene_synonym="Ly-6A.2; Ly-6A/E; Ly-6E.1; Sca-1; Sca1;
                     TAP"
                     /inference="alignment:Splign:2.1.0"
     exon            154..236
                     /gene="Ly6a"
                     /gene_synonym="Ly-6A.2; Ly-6A/E; Ly-6E.1; Sca-1; Sca1;
                     TAP"
                     /inference="alignment:Splign:2.1.0"
     CDS             167..571
                     /gene="Ly6a"
                     /gene_synonym="Ly-6A.2; Ly-6A/E; Ly-6E.1; Sca-1; Sca1;
                     TAP"
                     /note="lymphocyte antigen 6A-2/6E-1; stem cell antigen 1;
                     T-cell-activating protein; lymphocyte antigen 6 complex,
                     locus A"
                     /codon_start=1
                     /product="lymphocyte antigen 6A-2/6E-1 precursor"
                     /protein_id="NP_001258348.1"
                     /db_xref="CCDS:CCDS27540.1"
                     /db_xref="GeneID:110454"
                     /db_xref="MGI:MGI:107527"
                     /translation="MDTSHTTKSCLLILLVALLCAERAQGLECYQCYGVPFETSCPSI
                     TCPYPDGVCVTQEAAVIVDSQTRKVKNNLCLPICPPNIESMEILGTKVNVKTSCCQED
                     LCNVAVPNGGSTWTMAGVLLFSLSSVLLQTLL"
     exon            237..353
                     /gene="Ly6a"
                     /gene_synonym="Ly-6A.2; Ly-6A/E; Ly-6E.1; Sca-1; Sca1;
                     TAP"
                     /inference="alignment:Splign:2.1.0"
     exon            354..956
                     /gene="Ly6a"
                     /gene_synonym="Ly-6A.2; Ly-6A/E; Ly-6E.1; Sca-1; Sca1;
                     TAP"
                     /inference="alignment:Splign:2.1.0"
     regulatory      936..941
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Ly6a"
                     /gene_synonym="Ly-6A.2; Ly-6A/E; Ly-6E.1; Sca-1; Sca1;
                     TAP"
                     /note="hexamer: AATAAA"
     polyA_site      956
                     /gene="Ly6a"
                     /gene_synonym="Ly-6A.2; Ly-6A/E; Ly-6E.1; Sca-1; Sca1;
                     TAP"
                     /note="major polyA site"
ORIGIN      
        1 cttaaccaat aaacatgatg gcctggaaaa ggttaagtac tgaaacccct ccctcttcag
       61 gatgccagct gggaggagct gaaggaaatt aaagtacttc agtccacatc tgacagaact
      121 tgccactgtg cctgcaacct tgtctgagag gaacccttct ctgaggatgg acacttctca
      181 cactacaaag tcctgtttgc tgattcttct tgtggcccta ctgtgtgcag aaagagctca
      241 gggactggag tgttaccagt gctatggagt cccatttgag acttcttgcc catcaattac
      301 ctgcccctac cctgatggag tctgtgttac tcaggaggca gcagttattg tggattctca
      361 aacaaggaaa gtaaagaaca atctttgctt acccatctgc cctcctaata ttgaaagtat
      421 ggagatcctg ggtactaagg tcaacgtgaa gacttcctgt tgccaggaag acctctgcaa
      481 tgtagcagtt cccaatggag gcagcacctg gaccatggca ggggtgcttc tgttcagcct
      541 gagctcagtc ctcctgcaga ccttgctctg atggtcctcc caatgacctc cacccttgtc
      601 cttttatcct catgtgcaac aattcttcct ggagccctct agtgatgaat tatgagttat
      661 agaagctcca aggtgggagt agtgtgtgaa ataccatgtt ttgcctttat agcccctgct
      721 gggtaggtag gtgctctaat cctctctagg gctttcaagt ctgtacttcc tagaatgtca
      781 ttttgttgtg gattgctgct catgaccctg gaggcacaca gccagcacag tgaagaggca
      841 gaattccaag gtattatgct atcaccatcc acacataagt atctggggtc ctgcaatgtt
      901 cccacatgta tcctgaatgt ccccctgttg agtccaataa accctttgtt ctccca
//
