CLC9A_MOUSE
ID CLC9A_MOUSE Reviewed; 238 AA.
AC Q8BRU4; B0ZBM3; B0ZBM5; B0ZBM6; B0ZBM7; Q5M8M6; Q8CBB4;
DT 30-AUG-2005, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2003, sequence version 1.
DT 03-AUG-2022, entry version 132.
DE RecName: Full=C-type lectin domain family 9 member A;
DE AltName: Full=Dendritic cell natural killer lectin group receptor 1;
DE AltName: CD_antigen=CD370;
GN Name=Clec9a; Synonyms=Dngr-1;
OS Mus musculus (Mouse).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC Murinae; Mus; Mus.
OX NCBI_TaxID=10090;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1; 2; 3; 4 AND 5), TISSUE SPECIFICITY,
RP SUBUNIT, FUNCTION, AND SUBCELLULAR LOCATION.
RC TISSUE=Spleen;
RX PubMed=18408006; DOI=10.1074/jbc.m709923200;
RA Huysamen C., Willment J.A., Dennehy K.M., Brown G.D.;
RT "CLEC9A is a novel activation C-type lectin-like receptor expressed on
RT BDCA3+ dendritic cells and a subset of monocytes.";
RL J. Biol. Chem. 283:16693-16701(2008).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 4).
RC STRAIN=C57BL/6J; TISSUE=Aorta, and Vein;
RX PubMed=16141072; DOI=10.1126/science.1112014;
RA Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N.,
RA Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K.,
RA Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.,
RA Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R.,
RA Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T.,
RA Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A.,
RA Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B.,
RA Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M.,
RA Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S.,
RA Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E.,
RA Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D.,
RA Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M.,
RA Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H.,
RA Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V.,
RA Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S.,
RA Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H.,
RA Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N.,
RA Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F.,
RA Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G.,
RA Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z.,
RA Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C.,
RA Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y.,
RA Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S.,
RA Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K.,
RA Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R.,
RA van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H.,
RA Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M.,
RA Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C.,
RA Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S.,
RA Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K.,
RA Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M.,
RA Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C.,
RA Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A.,
RA Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.;
RT "The transcriptional landscape of the mammalian genome.";
RL Science 309:1559-1563(2005).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RA Mural R.J., Adams M.D., Myers E.W., Smith H.O., Venter J.C.;
RL Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RC TISSUE=Kidney;
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA project:
RT the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [5]
RP ALTERNATIVE SPLICING (ISOFORM 4), TISSUE SPECIFICITY, SUBUNIT, AND
RP FUNCTION.
RX PubMed=18497879; DOI=10.1172/jci34584;
RA Sancho D., Mourao-Sa D., Joffre O.P., Schulz O., Rogers N.C.,
RA Pennington D.J., Carlyle J.R., Reis e Sousa C.;
RT "Tumor therapy in mice via antigen targeting to a novel, DC-restricted C-
RT type lectin.";
RL J. Clin. Invest. 118:2098-2110(2008).
RN [6]
RP FUNCTION, MUTAGENESIS OF TYR-7, AND DISRUPTION PHENOTYPE.
RX PubMed=19219027; DOI=10.1038/nature07750;
RA Sancho D., Joffre O.P., Keller A.M., Rogers N.C., Martinez D.,
RA Hernanz-Falcon P., Rosewell I., Reis e Sousa C.;
RT "Identification of a dendritic cell receptor that couples sensing of
RT necrosis to immunity.";
RL Nature 458:899-903(2009).
RN [7]
RP FUNCTION.
RX PubMed=22483802; DOI=10.1016/j.immuni.2012.03.009;
RA Zhang J.G., Czabotar P.E., Policheni A.N., Caminschi I., Wan S.S.,
RA Kitsoulis S., Tullett K.M., Robin A.Y., Brammananth R., van Delft M.F.,
RA Lu J., O'Reilly L.A., Josefsson E.C., Kile B.T., Chin W.J., Mintern J.D.,
RA Olshina M.A., Wong W., Baum J., Wright M.D., Huang D.C., Mohandas N.,
RA Coppel R.L., Colman P.M., Nicola N.A., Shortman K., Lahoud M.H.;
RT "The dendritic cell receptor Clec9A binds damaged cells via exposed actin
RT filaments.";
RL Immunity 36:646-657(2012).
CC -!- FUNCTION: Functions as an endocytic receptor on a small subset of
CC myeloid cells specialized for the uptake and processing of material
CC from dead cells. Recognizes filamentous form of actin in association
CC with particular actin-binding domains of cytoskeletal proteins,
CC including spectrin, exposed when cell membranes are damaged, and
CC mediate the cross-presentation of dead-cell associated antigens in a
CC Syk-dependent manner. {ECO:0000269|PubMed:18408006,
CC ECO:0000269|PubMed:18497879, ECO:0000269|PubMed:19219027,
CC ECO:0000269|PubMed:22483802}.
CC -!- SUBUNIT: Isoform 1: Monomer. Isoform 4: Homodimer.
CC {ECO:0000269|PubMed:18408006, ECO:0000269|PubMed:18497879}.
CC -!- SUBCELLULAR LOCATION: Membrane {ECO:0000269|PubMed:18408006}; Single-
CC pass type II membrane protein {ECO:0000269|PubMed:18408006}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=5;
CC Name=1;
CC IsoId=Q8BRU4-1; Sequence=Displayed;
CC Name=2; Synonyms=Gamma;
CC IsoId=Q8BRU4-2; Sequence=VSP_041500, VSP_041501;
CC Name=3; Synonyms=Delta;
CC IsoId=Q8BRU4-3; Sequence=VSP_041504, VSP_041505;
CC Name=4; Synonyms=Beta;
CC IsoId=Q8BRU4-4; Sequence=VSP_041501;
CC Name=5; Synonyms=Epsilon;
CC IsoId=Q8BRU4-5; Sequence=VSP_041502, VSP_041503;
CC -!- TISSUE SPECIFICITY: Isoform 4 expressed at high levels by CD8(+)
CC dendritic cells (DCs), and at low levels by plasmacytoid DCs but not by
CC other hematopoietic cells. {ECO:0000269|PubMed:18408006,
CC ECO:0000269|PubMed:18497879}.
CC -!- PTM: [Isoform 1]: Not glycosylated.
CC -!- PTM: [Isoform 4]: N-glycosylated.
CC -!- DISRUPTION PHENOTYPE: Deficient mice shown no alteration of dendritic
CC cell phenotype and numbers and the response of dendritic cells to
CC innate stimuli is not altered. No alterations are found in leukocyte
CC numbers or frequencies in spleen, lymph node or thymus, and mice appear
CC normal and do not develop any obvious symptoms of autoimmune disease.
CC {ECO:0000269|PubMed:19219027}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAC29411.1; Type=Frameshift; Evidence={ECO:0000305};
CC -!- WEB RESOURCE: Name=Functional Glycomics Gateway - Glycan Binding;
CC Note=mCLEC9;
CC URL="http://www.functionalglycomics.org/glycomics/GBPServlet?&operationType=view&cbpId=cbp_mou_Ctlect_817";
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DR EMBL; EU339277; ABZ04558.1; -; mRNA.
DR EMBL; EU339278; ABZ04559.1; -; mRNA.
DR EMBL; EU339279; ABZ04560.1; -; mRNA.
DR EMBL; EU339280; ABZ04561.1; -; mRNA.
DR EMBL; EU339281; ABZ04562.1; -; mRNA.
DR EMBL; AK036399; BAC29411.1; ALT_FRAME; mRNA.
DR EMBL; AK041288; BAC30890.1; -; mRNA.
DR EMBL; CH466523; EDK99924.1; -; Genomic_DNA.
DR EMBL; BC087955; AAH87955.1; -; mRNA.
DR CCDS; CCDS39658.1; -. [Q8BRU4-1]
DR CCDS; CCDS57454.1; -. [Q8BRU4-4]
DR CCDS; CCDS57455.1; -. [Q8BRU4-2]
DR RefSeq; NP_001192292.1; NM_001205363.1. [Q8BRU4-4]
DR RefSeq; NP_001192293.1; NM_001205364.1. [Q8BRU4-2]
DR RefSeq; NP_001192294.1; NM_001205365.1.
DR RefSeq; NP_766320.2; NM_172732.3. [Q8BRU4-1]
DR PDB; 3J82; EM; 7.70 A; A=108-238.
DR PDBsum; 3J82; -.
DR AlphaFoldDB; Q8BRU4; -.
DR SMR; Q8BRU4; -.
DR BioGRID; 231256; 2.
DR STRING; 10090.ENSMUSP00000085394; -.
DR TCDB; 1.C.111.1.12; the regiiiGama (regiiiGama) family.
DR GlyGen; Q8BRU4; 2 sites.
DR iPTMnet; Q8BRU4; -.
DR PhosphoSitePlus; Q8BRU4; -.
DR PRIDE; Q8BRU4; -.
DR ProteomicsDB; 283566; -. [Q8BRU4-1]
DR ProteomicsDB; 283567; -. [Q8BRU4-2]
DR ProteomicsDB; 283568; -. [Q8BRU4-3]
DR ProteomicsDB; 283569; -. [Q8BRU4-4]
DR ProteomicsDB; 283570; -. [Q8BRU4-5]
DR ABCD; Q8BRU4; 1 sequenced antibody.
DR Antibodypedia; 23221; 455 antibodies from 29 providers.
DR DNASU; 232414; -.
DR Ensembl; ENSMUST00000058352; ENSMUSP00000056625; ENSMUSG00000046080. [Q8BRU4-4]
DR Ensembl; ENSMUST00000088075; ENSMUSP00000085394; ENSMUSG00000046080. [Q8BRU4-1]
DR Ensembl; ENSMUST00000164513; ENSMUSP00000128622; ENSMUSG00000046080. [Q8BRU4-2]
DR Ensembl; ENSMUST00000204860; ENSMUSP00000144990; ENSMUSG00000046080. [Q8BRU4-5]
DR GeneID; 232414; -.
DR KEGG; mmu:232414; -.
DR UCSC; uc009efr.2; mouse. [Q8BRU4-1]
DR UCSC; uc009efs.2; mouse. [Q8BRU4-4]
DR UCSC; uc012etj.2; mouse. [Q8BRU4-2]
DR UCSC; uc012etk.2; mouse. [Q8BRU4-5]
DR CTD; 283420; -.
DR MGI; MGI:2444608; Clec9a.
DR VEuPathDB; HostDB:ENSMUSG00000046080; -.
DR eggNOG; KOG4297; Eukaryota.
DR GeneTree; ENSGT00940000161796; -.
DR HOGENOM; CLU_049894_9_0_1; -.
DR InParanoid; Q8BRU4; -.
DR OMA; SCIFCMG; -.
DR OrthoDB; 1201127at2759; -.
DR TreeFam; TF336674; -.
DR BioGRID-ORCS; 232414; 0 hits in 71 CRISPR screens.
DR PRO; PR:Q8BRU4; -.
DR Proteomes; UP000000589; Chromosome 6.
DR RNAct; Q8BRU4; protein.
DR Bgee; ENSMUSG00000046080; Expressed in spleen and 42 other tissues.
DR GO; GO:0009986; C:cell surface; IDA:UniProtKB.
DR GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
DR GO; GO:0030246; F:carbohydrate binding; IEA:UniProtKB-KW.
DR GO; GO:0001819; P:positive regulation of cytokine production; ISS:UniProtKB.
DR GO; GO:0006898; P:receptor-mediated endocytosis; IDA:UniProtKB.
DR CDD; cd03593; CLECT_NK_receptors_like; 1.
DR Gene3D; 3.10.100.10; -; 1.
DR InterPro; IPR001304; C-type_lectin-like.
DR InterPro; IPR016186; C-type_lectin-like/link_sf.
DR InterPro; IPR018378; C-type_lectin_CS.
DR InterPro; IPR043315; CLEC9A.
DR InterPro; IPR016187; CTDL_fold.
DR InterPro; IPR033992; NKR-like_CTLD.
DR PANTHER; PTHR47727; PTHR47727; 1.
DR Pfam; PF00059; Lectin_C; 1.
DR SMART; SM00034; CLECT; 1.
DR SUPFAM; SSF56436; SSF56436; 1.
DR PROSITE; PS00615; C_TYPE_LECTIN_1; 1.
DR PROSITE; PS50041; C_TYPE_LECTIN_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Alternative splicing; Disulfide bond; Glycoprotein; Lectin;
KW Membrane; Receptor; Reference proteome; Signal-anchor; Transmembrane;
KW Transmembrane helix.
FT CHAIN 1..238
FT /note="C-type lectin domain family 9 member A"
FT /id="PRO_0000046638"
FT TOPO_DOM 1..35
FT /note="Cytoplasmic"
FT /evidence="ECO:0000255"
FT TRANSMEM 36..56
FT /note="Helical; Signal-anchor for type II membrane protein"
FT /evidence="ECO:0000255"
FT TOPO_DOM 57..238
FT /note="Extracellular"
FT /evidence="ECO:0000255"
FT DOMAIN 118..230
FT /note="C-type lectin"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00040"
FT MOTIF 5..10
FT /note="ITAM-like"
FT CARBOHYD 81
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 133
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT DISULFID 111..122
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00040"
FT DISULFID 139..229
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00040"
FT DISULFID 208..221
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00040"
FT VAR_SEQ 31..58
FT /note="GAWCVVTMISCVVCMGLLATSIFLGIKF -> V (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:18408006"
FT /id="VSP_041500"
FT VAR_SEQ 105
FT /note="G -> GTDASTGPVLLTSPQMVPQTLDSKETG (in isoform 2 and
FT isoform 4)"
FT /evidence="ECO:0000303|PubMed:16141072,
FT ECO:0000303|PubMed:18408006"
FT /id="VSP_041501"
FT VAR_SEQ 106..147
FT /note="SDCSPCPHNWIQNGKSCYYVFERWEMWNISKKSCLKEGASLF -> CQQKDS
FT DQPARSVDTSKILLSSQISAIAGNILSVRRRHLDPAS (in isoform 5)"
FT /evidence="ECO:0000303|PubMed:18408006"
FT /id="VSP_041502"
FT VAR_SEQ 148..238
FT /note="Missing (in isoform 5)"
FT /evidence="ECO:0000303|PubMed:18408006"
FT /id="VSP_041503"
FT VAR_SEQ 156..173
FT /note="EFISSIGKLKGGNKYWVG -> SRWNQWILVLGRWLFSSL (in isoform
FT 3)"
FT /evidence="ECO:0000303|PubMed:18408006"
FT /id="VSP_041504"
FT VAR_SEQ 174..238
FT /note="Missing (in isoform 3)"
FT /evidence="ECO:0000303|PubMed:18408006"
FT /id="VSP_041505"
FT MUTAGEN 7
FT /note="Y->F: Abolishes the recruitment and activation of
FT the tyrosine kinase Syk."
FT /evidence="ECO:0000269|PubMed:19219027"
SQ SEQUENCE 238 AA; 27014 MW; 07368A0380B95EA1 CRC64;
MHAEEIYTSL QWDIPTSEAS QKCQSPSKCS GAWCVVTMIS CVVCMGLLAT SIFLGIKFFQ
VSSLVLEQQE RLIQQDTALV NLTQWQRKYT LEYCQALLQR SLHSGSDCSP CPHNWIQNGK
SCYYVFERWE MWNISKKSCL KEGASLFQID SKEEMEFISS IGKLKGGNKY WVGVFQDGIS
GSWFWEDGSS PLSDLLPAER QRSAGQICGY LKDSTLISDK CDSWKYFICE KKAFGSCI
