LOCUS       NM_172732               3216 bp    mRNA    linear   ROD 01-AUG-2024
DEFINITION  Mus musculus C-type lectin domain family 9, member a (Clec9a),
            transcript variant 2, mRNA.
ACCESSION   NM_172732
VERSION     NM_172732.3
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 3216)
  AUTHORS   Xiao,H., Ulmert,I., Bach,L., Huber,J., Narasimhan,H., Kurochkin,I.,
            Chang,Y., Holst,S., Morbe,U., Zhang,L., Schlitzer,A., Pereira,C.F.,
            Schraml,B.U., Baumjohann,D. and Lahl,K.
  TITLE     Genomic deletion of Bcl6 differentially affects conventional
            dendritic cell subsets and compromises Tfh/Tfr/Th17 cell responses
  JOURNAL   Nat Commun 15 (1), 3554 (2024)
   PUBMED   38688934
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 3216)
  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   3  (bases 1 to 3216)
  AUTHORS   Henry,C.M., Castellanos,C.A., Buck,M.D., Giampazolias,E.,
            Frederico,B., Cardoso,A., Rogers,N.C., Schulz,O., Lee,S.,
            Canton,J., Faull,P., Snijders,A.P., Mohapatra,B., Band,H. and Reis
            E Sousa,C.
  TITLE     SYK ubiquitination by CBL E3 ligases restrains cross-presentation
            of dead cell-associated antigens by type 1 dendritic cells
  JOURNAL   Cell Rep 42 (12), 113506 (2023)
   PUBMED   38019655
REFERENCE   4  (bases 1 to 3216)
  AUTHORS   Pereira da Costa,M., Minutti,C.M., Piot,C., Giampazolias,E.,
            Cardoso,A., Cabeza-Cabrerizo,M., Rogers,N.C.,
            Lebrusant-Fernandez,M., Iliakis,C.S., Wack,A. and Reis E Sousa,C.
  TITLE     Interplay between CXCR4 and CCR2 regulates bone marrow exit of
            dendritic cell progenitors
  JOURNAL   Cell Rep 42 (8), 112881 (2023)
   PUBMED   37523265
REFERENCE   5  (bases 1 to 3216)
  AUTHORS   Bayerl,F., Meiser,P., Donakonda,S., Hirschberger,A., Lacher,S.B.,
            Pedde,A.M., Hermann,C.D., Elewaut,A., Knolle,M., Ramsauer,L.,
            Rudolph,T.J., Grassmann,S., Ollinger,R., Kirchhammer,N., Trefny,M.,
            Anton,M., Wohlleber,D., Hochst,B., Zaremba,A., Kruger,A., Rad,R.,
            Obenauf,A.C., Schadendorf,D., Zippelius,A., Buchholz,V.R.,
            Schraml,B.U. and Bottcher,J.P.
  TITLE     Tumor-derived prostaglandin E2 programs cDC1 dysfunction to impair
            intratumoral orchestration of anti-cancer T cell responses
  JOURNAL   Immunity 56 (6), 1341-1358 (2023)
   PUBMED   37315536
REFERENCE   6  (bases 1 to 3216)
  AUTHORS   Joffre,O.P., Sancho,D., Zelenay,S., Keller,A.M. and Reis e Sousa,C.
  TITLE     Efficient and versatile manipulation of the peripheral CD4+ T-cell
            compartment by antigen targeting to DNGR-1/CLEC9A
  JOURNAL   Eur J Immunol 40 (5), 1255-1265 (2010)
   PUBMED   20333625
REFERENCE   7  (bases 1 to 3216)
  AUTHORS   Sancho,D., Joffre,O.P., Keller,A.M., Rogers,N.C., Martinez,D.,
            Hernanz-Falcon,P., Rosewell,I. and Reis e Sousa,C.
  TITLE     Identification of a dendritic cell receptor that couples sensing of
            necrosis to immunity
  JOURNAL   Nature 458 (7240), 899-903 (2009)
   PUBMED   19219027
  REMARK    GeneRIF: CLEC9A functions as a SYK-coupled C-type lectin receptor
            to mediate sensing of necrosis by the principal dendritic-cell
            subset involved in regulating cross-priming to cell-associated
            antigens
REFERENCE   8  (bases 1 to 3216)
  AUTHORS   Caminschi,I., Proietto,A.I., Ahmet,F., Kitsoulis,S., Shin Teh,J.,
            Lo,J.C., Rizzitelli,A., Wu,L., Vremec,D., van Dommelen,S.L.,
            Campbell,I.K., Maraskovsky,E., Braley,H., Davey,G.M., Mottram,P.,
            van de Velde,N., Jensen,K., Lew,A.M., Wright,M.D., Heath,W.R.,
            Shortman,K. and Lahoud,M.H.
  TITLE     The dendritic cell subtype-restricted C-type lectin Clec9A is a
            target for vaccine enhancement
  JOURNAL   Blood 112 (8), 3264-3273 (2008)
   PUBMED   18669894
  REMARK    GeneRIF: analysis of differences between mouse and human Clec9A
REFERENCE   9  (bases 1 to 3216)
  AUTHORS   Huysamen,C., Willment,J.A., Dennehy,K.M. and Brown,G.D.
  TITLE     CLEC9A is a novel activation C-type lectin-like receptor expressed
            on BDCA3+ dendritic cells and a subset of monocytes
  JOURNAL   J Biol Chem 283 (24), 16693-16701 (2008)
   PUBMED   18408006
  REMARK    GeneRIF: CLEC9A functions as an activation receptor
REFERENCE   10 (bases 1 to 3216)
  AUTHORS   Sancho,D., Mourao-Sa,D., Joffre,O.P., Schulz,O., Rogers,N.C.,
            Pennington,D.J., Carlyle,J.R. and Reis e Sousa,C.
  TITLE     Tumor therapy in mice via antigen targeting to a novel,
            DC-restricted C-type lectin
  JOURNAL   J Clin Invest 118 (6), 2098-2110 (2008)
   PUBMED   18497879
  REMARK    GeneRIF: DC, NK lectin group receptor-1 (DNGR-1) is a C-type lectin
            of the NK cell receptor group
            GeneRIF: characterization of human and mouse CLEC9A (a.k.a DNGR-1)
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            AC138620.4 and AK041288.1.
            
            On Apr 19, 2011 this sequence version replaced NM_172732.2.
            
            Transcript Variant: This variant (2) lacks an exon in the coding
            region, but maintains the reading frame, compared to variant 1. The
            encoded isoform (2) is shorter than isoform 1.
            
            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 :: AK041288.1, EU339277.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN00849385, SAMN01164134
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on expression
            ##RefSeq-Attributes-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-1                 AC138620.4         139620-139620
            2-1021              AK041288.1         2-1021
            1022-3216           AC138620.4         153328-155522
FEATURES             Location/Qualifiers
     source          1..3216
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="6"
                     /map="6 63.3 cM"
     gene            1..3216
                     /gene="Clec9a"
                     /gene_synonym="9830005G06Rik; DNGR-1"
                     /note="C-type lectin domain family 9, member a"
                     /db_xref="GeneID:232414"
                     /db_xref="MGI:MGI:2444608"
     exon            1..184
                     /gene="Clec9a"
                     /gene_synonym="9830005G06Rik; DNGR-1"
                     /inference="alignment:Splign:2.1.0"
     exon            185..265
                     /gene="Clec9a"
                     /gene_synonym="9830005G06Rik; DNGR-1"
                     /inference="alignment:Splign:2.1.0"
     exon            266..406
                     /gene="Clec9a"
                     /gene_synonym="9830005G06Rik; DNGR-1"
                     /inference="alignment:Splign:2.1.0"
     exon            407..558
                     /gene="Clec9a"
                     /gene_synonym="9830005G06Rik; DNGR-1"
                     /inference="alignment:Splign:2.1.0"
     exon            559..677
                     /gene="Clec9a"
                     /gene_synonym="9830005G06Rik; DNGR-1"
                     /inference="alignment:Splign:2.1.0"
     exon            678..3216
                     /gene="Clec9a"
                     /gene_synonym="9830005G06Rik; DNGR-1"
                     /inference="alignment:Splign:2.1.0"
     regulatory      1139..1144
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Clec9a"
                     /gene_synonym="9830005G06Rik; DNGR-1"
                     /note="hexamer: AGTAAA"
     polyA_site      1165
                     /gene="Clec9a"
                     /gene_synonym="9830005G06Rik; DNGR-1"
     regulatory      3195..3200
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Clec9a"
                     /gene_synonym="9830005G06Rik; DNGR-1"
                     /note="hexamer: AATAAA"
     polyA_site      3215
                     /gene="Clec9a"
                     /gene_synonym="9830005G06Rik; DNGR-1"
                     /note="major polyA site"
ORIGIN      
        1 ccatttcttg taccaaccta ctcctaacta caaccgaagt tctttgtgcc aggctcctat
       61 gtagactgct tcaccactcc aagcaccttc agcatgcatg cggaagaaat atatacctct
      121 cttcagtggg acattcctac ctcagaggcc tctcagaagt gccaatcccc tagcaaatgt
      181 tcaggagcat ggtgtgttgt gacgatgatt tcctgtgtgg tctgtatggg cttgttagca
      241 acgtccattt tcttgggcat caagttcttc caggtatcct ctcttgtctt ggagcagcag
      301 gaaagactca tccaacagga cacagcattg gtgaacctta cacagtggca gaggaaatac
      361 acactggaat actgccaagc cttactgcag agatctctcc attcaggtag tgactgcagc
      421 ccttgtccac acaactggat tcagaatgga aaaagttgtt actatgtctt tgaacgctgg
      481 gaaatgtgga acatcagtaa gaagagctgt ttaaaagagg gcgctagtct ctttcaaata
      541 gacagcaaag aagaaatgga gttcatcagc agtataggga aactcaaagg aggaaataaa
      601 tattgggtgg gagtgtttca agatggaatc agtggatctt ggttctggga agatggctct
      661 tctcctctct ctgacttgtt gccagcagaa agacagcgat cagccggcca gatctgtgga
      721 tacctcaaag attctactct catctcagat aagtgcgata gctggaaata ttttatctgt
      781 gagaagaagg catttggatc ctgcatctga aagatacaac tcaaagctac ctgttacaca
      841 agtgtttgaa agaggccaaa gagcaaacac aggaggagat tgatgtgaga ctatgaaggc
      901 aagcttgatt ttttatttac acttggcaat agtctgtaac gctttgcaga tttcagttga
      961 ccttgtccat tgtgccaagg aaaaaattga tttagagcta cagaagatct gactcagtga
     1021 gaacaaagaa gagaaaataa tttcctgtgt gtttgaaagt ccaaagtgac gatccatacc
     1081 acaccgagat ctagctgtcc ttgtgggagt ttttatgcaa tccttggttt gtacttttag
     1141 taaacaattc tatctactat acttacaact gacaaaattt tcttcaggtc accttccagt
     1201 aattatagat cataagatca cacactgaga ggagagagat ggatttctaa actgtagtat
     1261 taccaccaat catacgccag gggtcctttg gctctaggta aaaatgagca gaatggggac
     1321 ctccagtgtt tttaatcttc ttctgaggcc cagggcctgg gggatgacct cacagatata
     1381 gagatttaca gtttctaacc cttggagcta gggggctatt gctccgggat ctgagtgctc
     1441 aggttgaagg cttatagctt ttcgttttaa tcactactgg ctctgggtct tggcagcttt
     1501 tacaatccct aacctttagc agcaatacca gacagcagtc agtagcagca agcagctccc
     1561 actagtgtta tagctcttgg atggctttag ggtggtgggg cattaactct gcagtgacta
     1621 ctattacagt cctctggtct agaatgcagg aatctcccat cagcccttgt tggctgttag
     1681 tgttacagct ctcagcatag gttttctgtg atccttggtt ccaaagactg cagctgcttg
     1741 gcactcttcc aggtctccaa gcccgtgttt ctccttcctg gttggccaca gtcttctgtc
     1801 tttactcagc cttgcttttc tgccttctct catttctcta actctaccat tcctcagtct
     1861 ctctgtttct gctgcccatc ctttctgcca tgacccatct ctggaatttt tcaggtgttc
     1921 tcttgtctgt cgactgccac ggtaactgct gtcaccacta gagctgcttg ctctgcttgg
     1981 ttgcctttgc tcccatcttg tgcttctgca tcttctcttt gtgttagcag ctcaggctac
     2041 tcttctaatg cagggcaaag gaggagaaaa aggaccattc gggaagtctt ttattggtgt
     2101 taatgttaca gcatcaggag tgtcagagga gggggtgtcc tggctgactc taaaactgaa
     2161 ctaaacagcc catttaatag ataagaagtg ggtgtagtgc gggtgtctgc accttcacag
     2221 tagctcttca aggactgtgt ttgcaccaat cacagcacag actcttgttt acagtcacag
     2281 atcttcccta ggttcatggt tggaagtgct ccctctctgg cccaaatgag aactgcagga
     2341 caggctgggc cttgggcaat ttgccaaaag gcttcccttg cttagttaga gtgctgtttt
     2401 ccataggcta ttccagttgt gggagcagtc acaactggag catgtcttca gccatggggt
     2461 ggtggtattc ttcagtagct agaggggctt cagagtaaag tgcccaaact gctggctgga
     2521 ctgtcatgag ggcagtctgg ccagatgtta gtaaaaaggc tgcttggctg atagcttgaa
     2581 ttcacgttca cagacaataa aagtgtgttt acaataaata cttaataaaa ccccagtaca
     2641 tgacaattcg aatagcactt agcagtactt cataaaaatg aacatttaac agggtttaac
     2701 ttctgcccca aagctgtaga gtcattgagt ccctctgatc tgcctcagaa ggaaccaggg
     2761 ctttttctgt ctatggtgct tttcagactg cagagttctg ctgggaaagg tactctttga
     2821 atttcatgta ggggaaggat tagcatggac atcagcatgt cccattgtgt aggtggagcc
     2881 ttccatccta ttgctcacag atcaaacggc tcagtctgcg ctgacaagat gaacaagatg
     2941 aacaacctag ttcctctaac tgcctgtgtc tcaaccttcc tgctataaaa ctgtaataca
     3001 attcacttca aaatactgct taagaacacc atccaaatat tacatgcaaa ctataaaaaa
     3061 tgatacttta gataagaaag ggtaaatgaa aatgagtgct atctaccaga agaaaaatta
     3121 gctaattata gttatcatgt tccgtactta taatgtgtca tctctaaatc atactacata
     3181 cataacatgc tcttaataaa tatttgataa attcag
//
