LOCUS       NM_194447               1179 bp    mRNA    linear   PRI 07-APR-2024
DEFINITION  Homo sapiens C-type lectin domain family 4 member A (CLEC4A),
            transcript variant 3, mRNA.
ACCESSION   NM_194447
VERSION     NM_194447.3
KEYWORDS    RefSeq.
SOURCE      Homo sapiens (human)
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
            Catarrhini; Hominidae; Homo.
REFERENCE   1  (bases 1 to 1179)
  AUTHORS   Trimaglio,G., Sneperger,T., Raymond,B.B.A., Gilles,N., Naser,E.,
            Locard-Paulet,M., Ijsselsteijn,M.E., Brouwer,T.P., Ecalard,R.,
            Roelands,J., Matsumoto,N., Colom,A., Habch,M., de Miranda,N.F.C.C.,
            Vergnolle,N., Devaud,C., Neyrolles,O. and Rombouts,Y.
  TITLE     The C-type lectin DCIR contributes to the immune response and
            pathogenesis of colorectal cancer
  JOURNAL   Sci Rep 14 (1), 7199 (2024)
   PUBMED   38532110
  REMARK    GeneRIF: The C-type lectin DCIR contributes to the immune response
            and pathogenesis of colorectal cancer.
            Publication Status: Online-Only
REFERENCE   2  (bases 1 to 1179)
  AUTHORS   Kaifu,T., Maruhashi,T., Chung,S.H., Shimizu,K., Nakamura,A. and
            Iwakura,Y.
  TITLE     DCIR suppresses osteoclastic proliferation and resorption by
            downregulating M-CSF and RANKL signaling
  JOURNAL   Front Immunol 14, 1159058 (2023)
   PUBMED   37266426
  REMARK    GeneRIF: DCIR suppresses osteoclastic proliferation and resorption
            by downregulating M-CSF and RANKL signaling.
            Publication Status: Online-Only
REFERENCE   3  (bases 1 to 1179)
  AUTHORS   Pakvisal,N., Kongkavitoon,P., Sathitruangsak,C., Pornpattanarak,N.,
            Boonsirikamchai,P., Ouwongprayoon,P., Aporntewan,C.,
            Chantranuwatana,P., Mutirangura,A. and Vinayanuwattikun,C.
  TITLE     Differential expression of immune-regulatory proteins C5AR1, CLEC4A
            and NLRP3 on peripheral blood mononuclear cells in early-stage
            non-small cell lung cancer patients
  JOURNAL   Sci Rep 12 (1), 18439 (2022)
   PUBMED   36323738
  REMARK    GeneRIF: Differential expression of immune-regulatory proteins
            C5AR1, CLEC4A and NLRP3 on peripheral blood mononuclear cells in
            early-stage non-small cell lung cancer patients.
            Publication Status: Online-Only
REFERENCE   4  (bases 1 to 1179)
  AUTHORS   Kaifu,T., Yabe,R., Maruhashi,T., Chung,S.H., Tateno,H.,
            Fujikado,N., Hirabayashi,J. and Iwakura,Y.
  TITLE     DCIR and its ligand asialo-biantennary N-glycan regulate DC
            function and osteoclastogenesis
  JOURNAL   J Exp Med 218 (12) (2021)
   PUBMED   34817551
  REMARK    GeneRIF: DCIR and its ligand asialo-biantennary N-glycan regulate
            DC function and osteoclastogenesis.
REFERENCE   5  (bases 1 to 1179)
  AUTHORS   Nasu,J., Uto,T., Fukaya,T., Takagi,H., Fukui,T., Miyanaga,N.,
            Nishikawa,Y., Yamasaki,S., Yamashita,Y. and Sato,K.
  TITLE     Pivotal role of the carbohydrate recognition domain in
            self-interaction of CLEC4A to elicit the ITIM-mediated inhibitory
            function in murine conventional dendritic cells in vitro
  JOURNAL   Int Immunol 32 (10), 673-682 (2020)
   PUBMED   32415968
  REMARK    GeneRIF: Pivotal role of the carbohydrate recognition domain in
            self-interaction of CLEC4A to elicit the ITIM-mediated inhibitory
            function in murine conventional dendritic cells in vitro.
REFERENCE   6  (bases 1 to 1179)
  AUTHORS   Ebner,S., Sharon,N. and Ben-Tal,N.
  TITLE     Evolutionary analysis reveals collective properties and specificity
            in the C-type lectin and lectin-like domain superfamily
  JOURNAL   Proteins 53 (1), 44-55 (2003)
   PUBMED   12945048
REFERENCE   7  (bases 1 to 1179)
  AUTHORS   Richard,M., Veilleux,P., Rouleau,M., Paquin,R. and Beaulieu,A.D.
  TITLE     The expression pattern of the ITIM-bearing lectin CLECSF6 in
            neutrophils suggests a key role in the control of inflammation
  JOURNAL   J Leukoc Biol 71 (5), 871-880 (2002)
   PUBMED   11994513
REFERENCE   8  (bases 1 to 1179)
  AUTHORS   Huang,X., Yuan,Z., Chen,G., Zhang,M., Zhang,W., Yu,Y. and Cao,X.
  TITLE     Cloning and characterization of a novel ITIM containing lectin-like
            immunoreceptor LLIR and its two transmembrane region deletion
            variants
  JOURNAL   Biochem Biophys Res Commun 281 (1), 131-140 (2001)
   PUBMED   11178971
REFERENCE   9  (bases 1 to 1179)
  AUTHORS   Drickamer,K.
  TITLE     C-type lectin-like domains
  JOURNAL   Curr Opin Struct Biol 9 (5), 585-590 (1999)
   PUBMED   10508765
  REMARK    Review article
REFERENCE   10 (bases 1 to 1179)
  AUTHORS   Bates,E.E., Fournier,N., Garcia,E., Valladeau,J., Durand,I.,
            Pin,J.J., Zurawski,S.M., Patel,S., Abrams,J.S., Lebecque,S.,
            Garrone,P. and Saeland,S.
  TITLE     APCs express DCIR, a novel C-type lectin surface receptor
            containing an immunoreceptor tyrosine-based inhibitory motif
  JOURNAL   J Immunol 163 (4), 1973-1983 (1999)
   PUBMED   10438934
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AC006511.5, AF067800.1,
            AJ133532.1 and AI400631.1.
            
            On Aug 11, 2020 this sequence version replaced NM_194447.2.
            
            Summary: This gene encodes a member of the C-type lectin/C-type
            lectin-like domain (CTL/CTLD) superfamily. Members of this family
            share a common protein fold and have diverse functions, such as
            cell adhesion, cell-cell signalling, glycoprotein turnover, and
            roles in inflammation and immune response. The encoded type 2
            transmembrane protein may play a role in inflammatory and immune
            response. Multiple transcript variants encoding distinct isoforms
            have been identified for this gene. This gene is closely linked to
            other CTL/CTLD superfamily members on chromosome 12p13 in the
            natural killer gene complex region. [provided by RefSeq, Jul 2008].
            
            Transcript Variant: This variant (3), also known as LLIRv1, lacks
            an in-frame segment of the coding region, compared to variant 1. It
            encodes a shorter isoform (3), that is missing the transmembrane
            domain compared to 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##
            RNAseq introns :: single sample supports all introns SAMEA1965299,
                              SAMEA1968540 [ECO:0000348]
            ##Evidence-Data-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-15                AC006511.5         6788-6802           c
            16-219              AF067800.1         22-225
            220-220             AC006511.5         6583-6583           c
            221-344             AJ133532.1         200-323
            345-1002            AJ133532.1         441-1098
            1003-1130           AF067800.1         1126-1253
            1131-1179           AI400631.1         4-52                c
FEATURES             Location/Qualifiers
     source          1..1179
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="12"
                     /map="12p13.31"
     gene            1..1179
                     /gene="CLEC4A"
                     /gene_synonym="CD367; CLECSF6; DCIR; DDB27; HDCGC13P;
                     hDCIR; LLIR"
                     /note="C-type lectin domain family 4 member A"
                     /db_xref="GeneID:50856"
                     /db_xref="HGNC:HGNC:13257"
                     /db_xref="MIM:605306"
     exon            1..344
                     /gene="CLEC4A"
                     /gene_synonym="CD367; CLECSF6; DCIR; DDB27; HDCGC13P;
                     hDCIR; LLIR"
                     /inference="alignment:Splign:2.1.0"
     CDS             263..859
                     /gene="CLEC4A"
                     /gene_synonym="CD367; CLECSF6; DCIR; DDB27; HDCGC13P;
                     hDCIR; LLIR"
                     /note="isoform 3 is encoded by transcript variant 3;
                     C-type (calcium dependent, carbohydrate-recognition
                     domain) lectin, superfamily member 6; lectin-like
                     immunoreceptor; dendritic cell immunoreceptor; C-type
                     lectin DDB27; C-type lectin superfamily member 6"
                     /codon_start=1
                     /product="C-type lectin domain family 4 member A isoform
                     3"
                     /protein_id="NP_919429.2"
                     /db_xref="CCDS:CCDS41745.1"
                     /db_xref="GeneID:50856"
                     /db_xref="HGNC:HGNC:13257"
                     /db_xref="MIM:605306"
                     /translation="MTSEITYAEVRFKNEFKSSGINTASSAVFFQKYSQLLEKKTTKE
                     LVHTTLECVKKNMPVEETAWSCCPKNWKSFSSNCYFISTESASWQDSEKDCARMEAHL
                     LVINTQEEQDFIFQNLQEESAYFVGLSDPEGQRHWQWVDQTPYNESSTFWHPREPSDP
                     NERCVVLNFRKSPKRWGWNDVNCLGPQRSVCEMMKIHL"
     exon            345..443
                     /gene="CLEC4A"
                     /gene_synonym="CD367; CLECSF6; DCIR; DDB27; HDCGC13P;
                     hDCIR; LLIR"
                     /inference="alignment:Splign:2.1.0"
     exon            444..595
                     /gene="CLEC4A"
                     /gene_synonym="CD367; CLECSF6; DCIR; DDB27; HDCGC13P;
                     hDCIR; LLIR"
                     /inference="alignment:Splign:2.1.0"
     exon            596..711
                     /gene="CLEC4A"
                     /gene_synonym="CD367; CLECSF6; DCIR; DDB27; HDCGC13P;
                     hDCIR; LLIR"
                     /inference="alignment:Splign:2.1.0"
     exon            712..1179
                     /gene="CLEC4A"
                     /gene_synonym="CD367; CLECSF6; DCIR; DDB27; HDCGC13P;
                     hDCIR; LLIR"
                     /inference="alignment:Splign:2.1.0"
     regulatory      1154..1159
                     /regulatory_class="polyA_signal_sequence"
                     /gene="CLEC4A"
                     /gene_synonym="CD367; CLECSF6; DCIR; DDB27; HDCGC13P;
                     hDCIR; LLIR"
                     /note="hexamer: AATAAA"
     polyA_site      1179
                     /gene="CLEC4A"
                     /gene_synonym="CD367; CLECSF6; DCIR; DDB27; HDCGC13P;
                     hDCIR; LLIR"
                     /note="major polyA site"
ORIGIN      
        1 gcatttgttt caaggctgtg attctcacta tactggtcct gaggaaaggg cttctgtgaa
       61 ctgcggtttt tagtttttat tgtggttctt agttctcatg agacccctct tgaggatatg
      121 tgcctatctg gtgcctctgc tctccactag ttgagtgaaa ggaaggaggt aatttaccac
      181 catgtttggt tcctgtttat aagatgtttt aagaaagatc tgaaacagat tttctgaaga
      241 aagcagaagc tctcttccca ttatgacttc ggaaatcact tatgctgaag tgaggttcaa
      301 aaatgaattc aagtcctcag gcatcaacac agcctcttct gcagttttct ttcaaaaata
      361 ttctcagctt cttgaaaaaa agactacaaa agagctggtt catacaacat tggagtgtgt
      421 gaaaaaaaat atgcccgtgg aagagacagc ctggagctgt tgcccaaaga attggaagtc
      481 atttagttcc aactgctact ttatttctac tgaatcagca tcttggcaag acagtgagaa
      541 ggactgtgct agaatggagg ctcacctgct ggtgataaac actcaagaag agcaggattt
      601 catcttccag aatctgcaag aagaatctgc ttattttgtg gggctctcag atccagaagg
      661 tcagcgacat tggcaatggg ttgatcagac accatacaat gaaagttcca cattctggca
      721 tccacgtgag cccagtgatc ccaatgagcg ctgcgttgtg ctaaattttc gtaaatcacc
      781 caaaagatgg ggctggaatg atgttaattg tcttggtcct caaaggtcag tttgtgagat
      841 gatgaagatc cacttatgaa ctgaacattc tccatgaaca ggtggttgga ttggtatctg
      901 tcattgtagg gatagataat aagctcttct tattcatgtg taagggaggt ccatagaatt
      961 taggtggtct gtcaactatt ctacttatga gagaattggt ctgtacattg actgattcac
     1021 tttttcataa agtgagcatt tattgagcat tttttcatgt gccagagcct gtactggagg
     1081 cccccattgt gcacacatgg agagaacatg agtctctctt aatttttatc tggttgctaa
     1141 agaattattt accaataaaa ttatatgatg tggtgtctc
//
