ID   CLC9A_RAT               Reviewed;         241 AA.
AC   D4AD02; D9Z4I7;
DT   28-JUN-2011, integrated into UniProtKB/Swiss-Prot.
DT   20-APR-2010, sequence version 1.
DT   03-AUG-2022, entry version 67.
DE   RecName: Full=C-type lectin domain family 9 member A;
DE   AltName: CD_antigen=CD370;
GN   Name=Clec9a;
OS   Rattus norvegicus (Rat).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC   Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC   Murinae; Rattus.
OX   NCBI_TaxID=10116;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [MRNA], AND TISSUE SPECIFICITY.
RC   STRAIN=PVG;
RX   PubMed=20544345; DOI=10.1007/s00251-010-0455-y;
RA   Flornes L.M., Nylenna O., Saether P.C., Daws M.R., Dissen E., Fossum S.;
RT   "The complete inventory of receptors encoded by the rat natural killer cell
RT   gene complex.";
RL   Immunogenetics 62:521-530(2010).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=Brown Norway;
RX   PubMed=15057822; DOI=10.1038/nature02426;
RA   Gibbs R.A., Weinstock G.M., Metzker M.L., Muzny D.M., Sodergren E.J.,
RA   Scherer S., Scott G., Steffen D., Worley K.C., Burch P.E., Okwuonu G.,
RA   Hines S., Lewis L., Deramo C., Delgado O., Dugan-Rocha S., Miner G.,
RA   Morgan M., Hawes A., Gill R., Holt R.A., Adams M.D., Amanatides P.G.,
RA   Baden-Tillson H., Barnstead M., Chin S., Evans C.A., Ferriera S.,
RA   Fosler C., Glodek A., Gu Z., Jennings D., Kraft C.L., Nguyen T.,
RA   Pfannkoch C.M., Sitter C., Sutton G.G., Venter J.C., Woodage T., Smith D.,
RA   Lee H.-M., Gustafson E., Cahill P., Kana A., Doucette-Stamm L.,
RA   Weinstock K., Fechtel K., Weiss R.B., Dunn D.M., Green E.D.,
RA   Blakesley R.W., Bouffard G.G., De Jong P.J., Osoegawa K., Zhu B., Marra M.,
RA   Schein J., Bosdet I., Fjell C., Jones S., Krzywinski M., Mathewson C.,
RA   Siddiqui A., Wye N., McPherson J., Zhao S., Fraser C.M., Shetty J.,
RA   Shatsman S., Geer K., Chen Y., Abramzon S., Nierman W.C., Havlak P.H.,
RA   Chen R., Durbin K.J., Egan A., Ren Y., Song X.-Z., Li B., Liu Y., Qin X.,
RA   Cawley S., Cooney A.J., D'Souza L.M., Martin K., Wu J.Q.,
RA   Gonzalez-Garay M.L., Jackson A.R., Kalafus K.J., McLeod M.P.,
RA   Milosavljevic A., Virk D., Volkov A., Wheeler D.A., Zhang Z., Bailey J.A.,
RA   Eichler E.E., Tuzun E., Birney E., Mongin E., Ureta-Vidal A., Woodwark C.,
RA   Zdobnov E., Bork P., Suyama M., Torrents D., Alexandersson M., Trask B.J.,
RA   Young J.M., Huang H., Wang H., Xing H., Daniels S., Gietzen D., Schmidt J.,
RA   Stevens K., Vitt U., Wingrove J., Camara F., Mar Alba M., Abril J.F.,
RA   Guigo R., Smit A., Dubchak I., Rubin E.M., Couronne O., Poliakov A.,
RA   Huebner N., Ganten D., Goesele C., Hummel O., Kreitler T., Lee Y.-A.,
RA   Monti J., Schulz H., Zimdahl H., Himmelbauer H., Lehrach H., Jacob H.J.,
RA   Bromberg S., Gullings-Handley J., Jensen-Seaman M.I., Kwitek A.E.,
RA   Lazar J., Pasko D., Tonellato P.J., Twigger S., Ponting C.P., Duarte J.M.,
RA   Rice S., Goodstadt L., Beatson S.A., Emes R.D., Winter E.E., Webber C.,
RA   Brandt P., Nyakatura G., Adetobi M., Chiaromonte F., Elnitski L.,
RA   Eswara P., Hardison R.C., Hou M., Kolbe D., Makova K., Miller W.,
RA   Nekrutenko A., Riemer C., Schwartz S., Taylor J., Yang S., Zhang Y.,
RA   Lindpaintner K., Andrews T.D., Caccamo M., Clamp M., Clarke L., Curwen V.,
RA   Durbin R.M., Eyras E., Searle S.M., Cooper G.M., Batzoglou S., Brudno M.,
RA   Sidow A., Stone E.A., Payseur B.A., Bourque G., Lopez-Otin C., Puente X.S.,
RA   Chakrabarti K., Chatterji S., Dewey C., Pachter L., Bray N., Yap V.B.,
RA   Caspi A., Tesler G., Pevzner P.A., Haussler D., Roskin K.M., Baertsch R.,
RA   Clawson H., Furey T.S., Hinrichs A.S., Karolchik D., Kent W.J.,
RA   Rosenbloom K.R., Trumbower H., Weirauch M., Cooper D.N., Stenson P.D.,
RA   Ma B., Brent M., Arumugam M., Shteynberg D., Copley R.R., Taylor M.S.,
RA   Riethman H., Mudunuri U., Peterson J., Guyer M., Felsenfeld A., Old S.,
RA   Mockrin S., Collins F.S.;
RT   "Genome sequence of the Brown Norway rat yields insights into mammalian
RT   evolution.";
RL   Nature 428:493-521(2004).
RN   [3]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=Brown Norway;
RA   Mural R.J., Adams M.D., Myers E.W., Smith H.O., Venter J.C.;
RL   Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases.
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 (By similarity). {ECO:0000250}.
CC   -!- SUBUNIT: Homodimer. {ECO:0000250}.
CC   -!- SUBCELLULAR LOCATION: Membrane {ECO:0000250}; Single-pass type II
CC       membrane protein {ECO:0000250}.
CC   -!- TISSUE SPECIFICITY: High expression in the spleen, moderate to low
CC       levels in several other tissues and cell types, but no detectable
CC       expression in skin dendritic cells or CD4(+) T-cells.
CC       {ECO:0000269|PubMed:20544345}.
CC   -!- PTM: N-glycosylated. {ECO:0000250}.
CC   ---------------------------------------------------------------------------
CC   Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC   Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC   ---------------------------------------------------------------------------
DR   EMBL; GU357486; ADK94896.1; -; mRNA.
DR   EMBL; AABR03033287; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR   EMBL; CH473964; EDM01742.1; -; Genomic_DNA.
DR   RefSeq; NP_001102824.1; NM_001109354.1.
DR   AlphaFoldDB; D4AD02; -.
DR   SMR; D4AD02; -.
DR   STRING; 10116.ENSRNOP00000052698; -.
DR   GlyGen; D4AD02; 5 sites.
DR   PaxDb; D4AD02; -.
DR   PRIDE; D4AD02; -.
DR   Ensembl; ENSRNOT00000088108; ENSRNOP00000071858; ENSRNOG00000051690.
DR   GeneID; 502901; -.
DR   KEGG; rno:502901; -.
DR   UCSC; RGD:1562513; rat.
DR   CTD; 283420; -.
DR   RGD; 1562513; Clec9a.
DR   eggNOG; KOG4297; Eukaryota.
DR   GeneTree; ENSGT00940000161796; -.
DR   HOGENOM; CLU_049894_9_0_1; -.
DR   InParanoid; D4AD02; -.
DR   OMA; SCIFCMG; -.
DR   OrthoDB; 1201127at2759; -.
DR   PhylomeDB; D4AD02; -.
DR   TreeFam; TF336674; -.
DR   PRO; PR:D4AD02; -.
DR   Proteomes; UP000002494; Chromosome 4.
DR   Proteomes; UP000234681; Chromosome 4.
DR   Bgee; ENSRNOG00000051690; Expressed in spleen and 16 other tissues.
DR   Genevisible; D4AD02; RN.
DR   GO; GO:0009986; C:cell surface; ISS: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; ISS: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; 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   2: Evidence at transcript level;
KW   Disulfide bond; Endocytosis; Glycoprotein; Lectin; Membrane; Receptor;
KW   Reference proteome; Signal-anchor; Transmembrane; Transmembrane helix.
FT   CHAIN           1..241
FT                   /note="C-type lectin domain family 9 member A"
FT                   /id="PRO_0000410724"
FT   TOPO_DOM        1..34
FT                   /note="Cytoplasmic"
FT                   /evidence="ECO:0000255"
FT   TRANSMEM        35..55
FT                   /note="Helical; Signal-anchor for type II membrane protein"
FT                   /evidence="ECO:0000255"
FT   TOPO_DOM        56..241
FT                   /note="Extracellular"
FT                   /evidence="ECO:0000255"
FT   DOMAIN          120..233
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        88
FT                   /note="N-linked (GlcNAc...) asparagine"
FT                   /evidence="ECO:0000255"
FT   CARBOHYD        135
FT                   /note="N-linked (GlcNAc...) asparagine"
FT                   /evidence="ECO:0000255"
FT   CARBOHYD        161
FT                   /note="N-linked (GlcNAc...) asparagine"
FT                   /evidence="ECO:0000255"
FT   CARBOHYD        223
FT                   /note="N-linked (GlcNAc...) asparagine"
FT                   /evidence="ECO:0000255"
FT   DISULFID        113..124
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00040"
FT   DISULFID        141..232
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00040"
FT   DISULFID        211..224
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00040"
FT   CONFLICT        158
FT                   /note="Missing (in Ref. 1; ADK94896)"
FT                   /evidence="ECO:0000305"
SQ   SEQUENCE   241 AA;  27429 MW;  6BC68486AFC2DD5F CRC64;
     MHEEEIYTSL QWDIPTSEAS QKCPSLSKCP GTWCIVTVIS CVVCVGLLAA SIFLGIKFSQ
     VSSLVMEQRE RLIRQDTALL NLTEWQRNHT LQLKSCQASL QRSLRSGSNC NPCPPNWIQN
     GKSCYYAFDR WETWNNSKKS CLKEGDSLLQ IDSKEEMEFI NLSIWKLKGG YEYWVGVFQD
     GPSGSWFWED GSSPLSDLLP TDRQLSASQI CGYLKDHTLI SDNCSNWKYF ICEKKAFGSC
     I