LOCUS       NM_009646               1993 bp    mRNA    linear   ROD 28-JAN-2025
DEFINITION  Mus musculus autoimmune regulator (Aire), transcript variant 1,
            mRNA.
ACCESSION   NM_009646
VERSION     NM_009646.2
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 1993)
  AUTHORS   Ashby,K.M., Voboril,M., Salgado,O.C., Lee,S.T., Martinez,R.J.,
            O'Connor,C.H., Breed,E.R., Xuan,S., Roll,C.R., Bachigari,S.,
            Heiland,H., Stetson,D.B., Kotenko,S.V. and Hogquist,K.A.
  TITLE     Sterile production of interferons in the thymus affects T cell
            repertoire selection
  JOURNAL   Sci Immunol 9 (97), eadp1139 (2024)
   PUBMED   39058762
REFERENCE   2  (bases 1 to 1993)
  AUTHORS   Seyedsadr,M., Bang,M.F., McCarthy,E.C., Zhang,S., Chen,H.C.,
            Mohebbi,M., Hugo,W., Whitmire,J.K., Lechner,M.G. and Su,M.A.
  TITLE     A pathologically expanded, clonal lineage of IL-21-producing CD4+ T
            cells drives inflammatory neuropathy
  JOURNAL   J Clin Invest 134 (15), e178602 (2024)
   PUBMED   39087473
  REMARK    Publication Status: Online-Only
REFERENCE   3  (bases 1 to 1993)
  AUTHORS   Ribeiro,C., Ferreirinha,P., Landry,J.J.M., Macedo,F., Sousa,L.G.,
            Pinto,R., Benes,V. and Alves,N.L.
  TITLE     Foxo3 regulates cortical and medullary thymic epithelial cell
            homeostasis with implications in T cell development
  JOURNAL   Cell Death Dis 15 (5), 352 (2024)
   PUBMED   38773063
  REMARK    Publication Status: Online-Only
REFERENCE   4  (bases 1 to 1993)
  AUTHORS   Smith,J.A., Yuen,B.T.K., Purtha,W., Balolong,J.M., Phipps,J.D.,
            Crawford,F., Bluestone,J.A., Kappler,J.W. and Anderson,M.S.
  TITLE     Aire mediates tolerance to insulin through thymic trimming of
            high-affinity T cell clones
  JOURNAL   Proc Natl Acad Sci U S A 121 (20), e2320268121 (2024)
   PUBMED   38709934
  REMARK    GeneRIF: Aire mediates tolerance to insulin through thymic trimming
            of high-affinity T cell clones.
REFERENCE   5  (bases 1 to 1993)
  AUTHORS   Ushio,A., Matsuda-Lennikov,M., Kalle-Youngoue,F., Shimizu,A.,
            Abdelmaksoud,A., Kelly,M.C., Ishimaru,N. and Takahama,Y.
  TITLE     Functionally diverse thymic medullary epithelial cells interplay to
            direct central tolerance
  JOURNAL   Cell Rep 43 (4), 114072 (2024)
   PUBMED   38581680
REFERENCE   6  (bases 1 to 1993)
  AUTHORS   Ruan,Q.G., Wang,C.Y., Shi,J.D. and She,J.X.
  TITLE     Expression and alternative splicing of the mouse autoimmune
            regulator gene (Aire)
  JOURNAL   J Autoimmun 13 (3), 307-313 (1999)
   PUBMED   10550218
REFERENCE   7  (bases 1 to 1993)
  AUTHORS   Mittaz,L., Rossier,C., Heino,M., Peterson,P., Krohn,K.J., Gos,A.,
            Morris,M.A., Kudoh,J., Shimizu,N., Antonarakis,S.E. and Scott,H.S.
  TITLE     Isolation and characterization of the mouse Aire gene
  JOURNAL   Biochem Biophys Res Commun 255 (2), 483-490 (1999)
   PUBMED   10049735
REFERENCE   8  (bases 1 to 1993)
  AUTHORS   Wang,C.Y., Shi,J.D., Davoodi-Semiromi,A. and She,J.X.
  TITLE     Cloning of Aire, the mouse homologue of the autoimmune regulator
            (AIRE) gene responsible for autoimmune polyglandular syndrome type
            1 (ASP1)
  JOURNAL   Genomics 55 (3), 322-326 (1999)
   PUBMED   10049587
REFERENCE   9  (bases 1 to 1993)
  AUTHORS   Blechschmidt,K., Schweiger,M., Wertz,K., Poulson,R.,
            Christensen,H.M., Rosenthal,A., Lehrach,H. and Yaspo,M.L.
  TITLE     The mouse Aire gene: comparative genomic sequencing, gene
            organization, and expression
  JOURNAL   Genome Res 9 (2), 158-166 (1999)
   PUBMED   10022980
REFERENCE   10 (bases 1 to 1993)
  AUTHORS   Shi,J.D., Wang,C.Y., Marron,M.P., Ruan,Q.G., Huang,Y.Q.,
            Detter,J.C. and She,J.X.
  TITLE     Chromosomal localization and complete genomic sequence of the
            murine autoimmune regulator gene (Aire)
  JOURNAL   Autoimmunity 31 (1), 47-53 (1999)
   PUBMED   10593569
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            AK153690.1, AF079536.1 and AJ243821.1.
            
            On Oct 18, 2012 this sequence version replaced NM_009646.1.
            
            Transcript Variant: This variant (1) represents the longest
            transcript and encodes the longest isoform (1).
            
            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 :: AJ243821.1, AF079536.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN00849383 [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-30                AK153690.1         2-31
            31-1959             AF079536.1         1-1929
            1960-1993           AJ243821.1         1873-1906
FEATURES             Location/Qualifiers
     source          1..1993
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="10"
                     /map="10 39.72 cM"
     gene            1..1993
                     /gene="Aire"
                     /note="autoimmune regulator"
                     /db_xref="GeneID:11634"
                     /db_xref="MGI:MGI:1338803"
     exon            1..222
                     /gene="Aire"
                     /inference="alignment:Splign:2.1.0"
     CDS             88..1746
                     /gene="Aire"
                     /note="isoform 1 is encoded by transcript variant 1;
                     autoimmune regulator AIRE1a; autoimmune polyendocrinopathy
                     candidiasis ectodermal dystrophy protein homolog; APECED
                     protein homolog; autoimmune regulator (autoimmune
                     polyendocrinopathy candidiasis ectodermal dystrophy)"
                     /codon_start=1
                     /product="autoimmune regulator isoform 1"
                     /protein_id="NP_033776.1"
                     /db_xref="CCDS:CCDS23961.1"
                     /db_xref="GeneID:11634"
                     /db_xref="MGI:MGI:1338803"
                     /translation="MAGGDGMLRRLLRLHRTEIAVAIDSAFPLLHALADHDVVPEDKF
                     QETLRLKEKEGCPQAFHALLSWLLTRDSGAILDFWRILFKDYNLERYSRLHSILDGFP
                     KDVDLNQSRKGRKPLAGPKAAVLPPRPPTKRKALEEPRATPPATLASKSVSSPGSHLK
                     TKPPKKPDGNLESQHLPLGNGIQTMAASVQRAVTVASGDVPGTRGAVEGILIQQVFES
                     GRSKKCIQVGGEFYTPNKFEDPSGNLKNKARSGSSLKPVVRAKGAQVTIPGRDEQKVG
                     QQCGVPPLPSLPSEPQVNQKNEDECAVCHDGGELICCDGCPRAFHLACLSPPLQEIPS
                     GLWRCSCCLQGRVQQNLSQPEVSRPPELPAETPILVGLRSASEKTRGPSRELKASSDA
                     AVTYVNLLAPHPAAPLLEPSALCPLLSAGNEGRPGPAPSARCSVCGDGTEVLRCAHCA
                     AAFHWRCHFPTAAARPGTNLRCKSCSADSTPTPGTPGEAVPTSGPRPAPGLAKVGDDS
                     ASHDPVLHRDDLESLLNEHSFDGILQWAIQSMSRPLAETPPFSS"
     exon            223..397
                     /gene="Aire"
                     /inference="alignment:Splign:2.1.0"
     exon            398..553
                     /gene="Aire"
                     /inference="alignment:Splign:2.1.0"
     exon            554..628
                     /gene="Aire"
                     /inference="alignment:Splign:2.1.0"
     exon            629..742
                     /gene="Aire"
                     /inference="alignment:Splign:2.1.0"
     exon            743..891
                     /gene="Aire"
                     /inference="alignment:Splign:2.1.0"
     exon            892..972
                     /gene="Aire"
                     /inference="alignment:Splign:2.1.0"
     exon            973..1088
                     /gene="Aire"
                     /inference="alignment:Splign:2.1.0"
     exon            1089..1188
                     /gene="Aire"
                     /inference="alignment:Splign:2.1.0"
     exon            1189..1365
                     /gene="Aire"
                     /inference="alignment:Splign:2.1.0"
     exon            1366..1487
                     /gene="Aire"
                     /inference="alignment:Splign:2.1.0"
     exon            1488..1596
                     /gene="Aire"
                     /inference="alignment:Splign:2.1.0"
     exon            1597..1665
                     /gene="Aire"
                     /inference="alignment:Splign:2.1.0"
     exon            1666..1968
                     /gene="Aire"
                     /inference="alignment:Splign:2.1.0"
     regulatory      1939..1944
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Aire"
                     /note="hexamer: ATTAAA"
     polyA_site      1958
                     /gene="Aire"
                     /note="major polyA site"
ORIGIN      
        1 agcaccacga cacccaagga agggagaagg gaacgcaagc gcgcgtgggc cagcaggggg
       61 cgccgaggcg cagcccctgt gaggaagatg gcaggtgggg atggaatgct acgccgtctg
      121 ctgaggctgc accgcaccga gatcgcggtg gccatagaca gtgcctttcc gctgctgcat
      181 gctctagccg accacgacgt ggtccctgag gacaagttcc aggagacgct ccgtctgaag
      241 gagaaggaag gctgccccca ggccttccac gccctgctgt cctggctcct gacccgggac
      301 agtggggcca tcctggattt ctggaggatt ctctttaagg actacaatct ggagcggtac
      361 agccgcctgc atagcatcct ggacggcttc ccaaaagatg tggacctaaa ccagtcccgg
      421 aaagggagaa agccccttgc tggtcccaag gccgcggtac tgccacccag accccccacc
      481 aagagaaaag cactggagga gcctcgagcc accccaccag caactctggc ctcaaagagc
      541 gtctccagcc caggctccca cctgaagact aagcccccta agaagccaga tggcaacttg
      601 gagtcacagc accttcctct tggaaacgga attcagacca tggcagcttc tgtccagaga
      661 gctgtgaccg tggcctctgg ggatgttcca ggaacccgag gggccgtgga agggatcctt
      721 atccagcagg tgtttgagtc aggaagatcc aagaagtgca ttcaggttgg gggagagttt
      781 tatacaccca acaagttcga agaccccagt ggcaatttga agaacaaggc ccggagtggt
      841 agcagcctaa agccagtggt ccgagccaag ggagcccagg tcactatacc tggtagagat
      901 gagcagaaag tgggccagca gtgtggggtt cctccccttc catccctccc cagtgagccc
      961 caggttaacc agaagaacga ggatgagtgt gccgtgtgcc acgacggagg tgagctcatc
     1021 tgttgtgacg gctgtccccg ggccttccac ctggcttgcc tgtccccacc tctgcaggag
     1081 atccccagtg gcctctggag atgctcctgc tgcctccagg gcagagtcca acagaacctg
     1141 tcccagcctg aggtgtccag gcccccggag ctacctgcag agaccccgat cctcgtggga
     1201 ctgaggtcag cttcagagaa aaccaggggc ccatccaggg agctcaaagc cagctctgat
     1261 gctgctgtca catatgtgaa cctgctggcc ccgcaccctg cagctcctct gctggagcct
     1321 tcagcactgt gccctctact gagtgctggg aatgaggggc ggccaggtcc agcaccaagc
     1381 gcgcgatgca gtgtgtgtgg cgatggcacc gaggtgttgc ggtgtgcaca ctgtgccgct
     1441 gccttccact ggcgctgcca cttcccgacg gccgccgccc ggccggggac caatctccgc
     1501 tgcaaatcct gctctgcaga ctcgactccc acgccaggca caccgggcga agctgtaccc
     1561 acctctgggc cccgtccagc acctgggctt gccaaggtag gggacgactc tgctagtcac
     1621 gaccctgttc tacataggga cgacctggag tccctcctca atgagcactc atttgacggc
     1681 atcctgcagt gggccatcca gagcatgtca cgcccgctgg ccgagacacc acccttctct
     1741 tcctgatgac aggtggccca ggaaggggtg ggcagcacag cattggctcc ctccccaccc
     1801 agccccatcg gatgaggcac tctgttctga gaggcctggg ctgattagga ccaagagctg
     1861 gcaggttctg gcctgctgga ctcagcttgc agatggccct gatctttgta gagatgcaag
     1921 gccaccccat atcctggaat taaagtcact tctatgtact ttgaggtaaa aaaaaaaaaa
     1981 aaaaaaaaaa aaa
//
