CLC4F_HUMAN
ID CLC4F_HUMAN Reviewed; 589 AA.
AC Q8N1N0; A4QPA5;
DT 15-FEB-2005, integrated into UniProtKB/Swiss-Prot.
DT 10-FEB-2009, sequence version 2.
DT 03-AUG-2022, entry version 150.
DE RecName: Full=C-type lectin domain family 4 member F;
DE AltName: Full=C-type lectin superfamily member 13;
DE Short=C-type lectin 13;
GN Name=CLEC4F; Synonyms=CLECSF13;
OS Homo sapiens (Human).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC Homo.
OX NCBI_TaxID=9606;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1), AND VARIANT ARG-564.
RC TISSUE=Tongue;
RX PubMed=14702039; DOI=10.1038/ng1285;
RA Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R.,
RA Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H.,
RA Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.,
RA Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K.,
RA Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H.,
RA Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M.,
RA Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K.,
RA Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T.,
RA Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M.,
RA Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S.,
RA Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H.,
RA Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K.,
RA Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N.,
RA Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S.,
RA Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O.,
RA Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H.,
RA Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B.,
RA Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y.,
RA Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K.,
RA Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T.,
RA Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T.,
RA Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y.,
RA Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H.,
RA Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y.,
RA Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H.,
RA Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O.,
RA Isogai T., Sugano S.;
RT "Complete sequencing and characterization of 21,243 full-length human
RT cDNAs.";
RL Nat. Genet. 36:40-45(2004).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX PubMed=15815621; DOI=10.1038/nature03466;
RA Hillier L.W., Graves T.A., Fulton R.S., Fulton L.A., Pepin K.H., Minx P.,
RA Wagner-McPherson C., Layman D., Wylie K., Sekhon M., Becker M.C.,
RA Fewell G.A., Delehaunty K.D., Miner T.L., Nash W.E., Kremitzki C., Oddy L.,
RA Du H., Sun H., Bradshaw-Cordum H., Ali J., Carter J., Cordes M., Harris A.,
RA Isak A., van Brunt A., Nguyen C., Du F., Courtney L., Kalicki J.,
RA Ozersky P., Abbott S., Armstrong J., Belter E.A., Caruso L., Cedroni M.,
RA Cotton M., Davidson T., Desai A., Elliott G., Erb T., Fronick C., Gaige T.,
RA Haakenson W., Haglund K., Holmes A., Harkins R., Kim K., Kruchowski S.S.,
RA Strong C.M., Grewal N., Goyea E., Hou S., Levy A., Martinka S., Mead K.,
RA McLellan M.D., Meyer R., Randall-Maher J., Tomlinson C.,
RA Dauphin-Kohlberg S., Kozlowicz-Reilly A., Shah N., Swearengen-Shahid S.,
RA Snider J., Strong J.T., Thompson J., Yoakum M., Leonard S., Pearman C.,
RA Trani L., Radionenko M., Waligorski J.E., Wang C., Rock S.M.,
RA Tin-Wollam A.-M., Maupin R., Latreille P., Wendl M.C., Yang S.-P., Pohl C.,
RA Wallis J.W., Spieth J., Bieri T.A., Berkowicz N., Nelson J.O., Osborne J.,
RA Ding L., Meyer R., Sabo A., Shotland Y., Sinha P., Wohldmann P.E.,
RA Cook L.L., Hickenbotham M.T., Eldred J., Williams D., Jones T.A., She X.,
RA Ciccarelli F.D., Izaurralde E., Taylor J., Schmutz J., Myers R.M.,
RA Cox D.R., Huang X., McPherson J.D., Mardis E.R., Clifton S.W., Warren W.C.,
RA Chinwalla A.T., Eddy S.R., Marra M.A., Ovcharenko I., Furey T.S.,
RA Miller W., Eichler E.E., Bork P., Suyama M., Torrents D., Waterston R.H.,
RA Wilson R.K.;
RT "Generation and annotation of the DNA sequences of human chromosomes 2 and
RT 4.";
RL Nature 434:724-731(2005).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
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).
CC -!- FUNCTION: Receptor with an affinity for galactose and fucose. Could be
CC involved in endocytosis (By similarity). {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: Membrane {ECO:0000250}; Single-pass type II
CC membrane protein {ECO:0000250}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q8N1N0-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q8N1N0-2; Sequence=VSP_056330;
CC -!- SEQUENCE CAUTION:
CC Sequence=BAC04786.1; Type=Erroneous termination; Note=Truncated C-terminus.; Evidence={ECO:0000305};
CC -!- WEB RESOURCE: Name=Functional Glycomics Gateway - Glycan Binding;
CC Note=Kupffer cell receptor;
CC URL="http://www.functionalglycomics.org/glycomics/GBPServlet?&operationType=view&cbpId=cbp_hum_Ctlect_00114";
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DR EMBL; AK096429; BAC04786.1; ALT_SEQ; mRNA.
DR EMBL; AC007395; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; BC139723; AAI39724.1; -; mRNA.
DR CCDS; CCDS1910.1; -. [Q8N1N0-1]
DR CCDS; CCDS82464.1; -. [Q8N1N0-2]
DR RefSeq; NP_001308237.1; NM_001321308.1. [Q8N1N0-2]
DR RefSeq; NP_775806.2; NM_173535.2. [Q8N1N0-1]
DR AlphaFoldDB; Q8N1N0; -.
DR SMR; Q8N1N0; -.
DR BioGRID; 127914; 12.
DR IntAct; Q8N1N0; 2.
DR STRING; 9606.ENSP00000272367; -.
DR GlyGen; Q8N1N0; 8 sites.
DR iPTMnet; Q8N1N0; -.
DR PhosphoSitePlus; Q8N1N0; -.
DR BioMuta; CLEC4F; -.
DR DMDM; 223590178; -.
DR EPD; Q8N1N0; -.
DR jPOST; Q8N1N0; -.
DR PaxDb; Q8N1N0; -.
DR PeptideAtlas; Q8N1N0; -.
DR PRIDE; Q8N1N0; -.
DR Antibodypedia; 31156; 85 antibodies from 22 providers.
DR DNASU; 165530; -.
DR Ensembl; ENST00000272367.7; ENSP00000272367.2; ENSG00000152672.8. [Q8N1N0-1]
DR Ensembl; ENST00000426626.1; ENSP00000390581.1; ENSG00000152672.8. [Q8N1N0-2]
DR GeneID; 165530; -.
DR KEGG; hsa:165530; -.
DR MANE-Select; ENST00000272367.7; ENSP00000272367.2; NM_173535.3; NP_775806.2.
DR UCSC; uc002shf.4; human. [Q8N1N0-1]
DR CTD; 165530; -.
DR DisGeNET; 165530; -.
DR GeneCards; CLEC4F; -.
DR HGNC; HGNC:25357; CLEC4F.
DR HPA; ENSG00000152672; Tissue enhanced (retina).
DR neXtProt; NX_Q8N1N0; -.
DR OpenTargets; ENSG00000152672; -.
DR PharmGKB; PA134968842; -.
DR VEuPathDB; HostDB:ENSG00000152672; -.
DR eggNOG; KOG4297; Eukaryota.
DR GeneTree; ENSGT01030000234575; -.
DR HOGENOM; CLU_030099_1_0_1; -.
DR InParanoid; Q8N1N0; -.
DR OMA; FQYSCYF; -.
DR OrthoDB; 988771at2759; -.
DR PhylomeDB; Q8N1N0; -.
DR TreeFam; TF333341; -.
DR PathwayCommons; Q8N1N0; -.
DR SignaLink; Q8N1N0; -.
DR BioGRID-ORCS; 165530; 17 hits in 1064 CRISPR screens.
DR ChiTaRS; CLEC4F; human.
DR GenomeRNAi; 165530; -.
DR Pharos; Q8N1N0; Tbio.
DR PRO; PR:Q8N1N0; -.
DR Proteomes; UP000005640; Chromosome 2.
DR RNAct; Q8N1N0; protein.
DR Bgee; ENSG00000152672; Expressed in granulocyte and 81 other tissues.
DR Genevisible; Q8N1N0; HS.
DR GO; GO:0009897; C:external side of plasma membrane; IBA:GO_Central.
DR GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
DR GO; GO:0030246; F:carbohydrate binding; IBA:GO_Central.
DR GO; GO:0006897; P:endocytosis; IEA:UniProtKB-KW.
DR CDD; cd03590; CLECT_DC-SIGN_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; IPR033989; CD209-like_CTLD.
DR InterPro; IPR016187; CTDL_fold.
DR Pfam; PF00059; Lectin_C; 1.
DR SMART; SM00034; CLECT; 1.
DR SUPFAM; SSF56436; SSF56436; 1.
DR PROSITE; PS50041; C_TYPE_LECTIN_2; 1.
PE 2: Evidence at transcript level;
KW Alternative splicing; Endocytosis; Glycoprotein; Lectin; Membrane;
KW Receptor; Reference proteome; Signal-anchor; Transmembrane;
KW Transmembrane helix.
FT CHAIN 1..589
FT /note="C-type lectin domain family 4 member F"
FT /id="PRO_0000046622"
FT TOPO_DOM 1..39
FT /note="Cytoplasmic"
FT /evidence="ECO:0000255"
FT TRANSMEM 40..60
FT /note="Helical; Signal-anchor for type II membrane protein"
FT /evidence="ECO:0000255"
FT TOPO_DOM 61..589
FT /note="Extracellular"
FT /evidence="ECO:0000255"
FT DOMAIN 476..589
FT /note="C-type lectin"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00040"
FT CARBOHYD 79
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 113
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 207
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 230
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 244
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 312
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 385
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 399
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT VAR_SEQ 554..589
FT /note="PGSKGSCPLRKYIIVNSGMGACSFIDTPPCPWILSN -> SHSTRKGCCLHL
FT TV (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:15489334"
FT /id="VSP_056330"
FT VARIANT 101
FT /note="R -> Q (in dbSNP:rs2075221)"
FT /id="VAR_054429"
FT VARIANT 351
FT /note="R -> H (in dbSNP:rs722896)"
FT /id="VAR_054430"
FT VARIANT 564
FT /note="K -> R (in dbSNP:rs2287101)"
FT /evidence="ECO:0000269|PubMed:14702039"
FT /id="VAR_054431"
FT CONFLICT 17
FT /note="L -> P (in Ref. 1; BAC04786)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 589 AA; 65519 MW; ACEB27A2B50E80A4 CRC64;
MDGEAVRFCT DNQCVSLHPQ EVDSVAMAPA APKIPRLVQA TPAFMAVTLV FSLVTLFVVV
QQQTRPVPKP VQAVILGDNI TGHLPFEPNN HHHFGREAEM RELIQTFKGH MENSSAWVVE
IQMLKCRVDN VNSQLQVLGD HLGNTNADIQ MVKGVLKDAT TLSLQTQMLR SSLEGTNAEI
QRLKEDLEKA DALTFQTLNF LKSSLENTSI ELHVLSRGLE NANSEIQMLN ASLETANTQA
QLANSSLKNA NAEIYVLRGH LDSVNDLRTQ NQVLRNSLEG ANAEIQGLKE NLQNTNALNS
QTQAFIKSSF DNTSAEIQFL RGHLERAGDE IHVLKRDLKM VTAQTQKANG RLDQTDTQIQ
VFKSEMENVN TLNAQIQVLN GHMKNASREI QTLKQGMKNA SALTSQTQML DSNLQKASAE
IQRLRGDLEN TKALTMEIQQ EQSRLKTLHV VITSQEQLQR TQSQLLQMVL QGWKFNGGSL
YYFSSVKKSW HEAEQFCVSQ GAHLASVASK EEQAFLVEFT SKVYYWIGLT DRGTEGSWRW
TDGTPFNAAQ NKAPGSKGSC PLRKYIIVNS GMGACSFIDT PPCPWILSN
