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Protein

C-type lectin domain family 4 member F

Gene

CLEC4F

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at transcript leveli

Functioni

Receptor with an affinity for galactose and fucose. Could be involved in endocytosis (By similarity).By similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Receptor

Keywords - Biological processi

Endocytosis

Keywords - Ligandi

Lectin

Names & Taxonomyi

Protein namesi
Recommended name:
C-type lectin domain family 4 member F
Alternative name(s):
C-type lectin superfamily member 13
Short name:
C-type lectin 13
Gene namesi
Name:CLEC4F
Synonyms:CLECSF13
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 2

Organism-specific databases

HGNCiHGNC:25357. CLEC4F.

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini1 – 3939CytoplasmicSequence analysisAdd
BLAST
Transmembranei40 – 6021Helical; Signal-anchor for type II membrane proteinSequence analysisAdd
BLAST
Topological domaini61 – 589529ExtracellularSequence analysisAdd
BLAST

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Membrane

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA134968842.

Polymorphism and mutation databases

BioMutaiCLEC4F.
DMDMi223590178.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 589589C-type lectin domain family 4 member FPRO_0000046622Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Glycosylationi79 – 791N-linked (GlcNAc...)Sequence analysis
Glycosylationi113 – 1131N-linked (GlcNAc...)Sequence analysis
Glycosylationi207 – 2071N-linked (GlcNAc...)Sequence analysis
Glycosylationi230 – 2301N-linked (GlcNAc...)Sequence analysis
Glycosylationi244 – 2441N-linked (GlcNAc...)Sequence analysis
Glycosylationi312 – 3121N-linked (GlcNAc...)Sequence analysis
Glycosylationi385 – 3851N-linked (GlcNAc...)Sequence analysis
Glycosylationi399 – 3991N-linked (GlcNAc...)Sequence analysis

Keywords - PTMi

Glycoprotein

Proteomic databases

EPDiQ8N1N0.
PaxDbiQ8N1N0.
PRIDEiQ8N1N0.

PTM databases

iPTMnetiQ8N1N0.
PhosphoSiteiQ8N1N0.

Expressioni

Gene expression databases

BgeeiQ8N1N0.
CleanExiHS_CLEC4F.
GenevisibleiQ8N1N0. HS.

Organism-specific databases

HPAiHPA030881.

Interactioni

Protein-protein interaction databases

BioGridi127914. 1 interaction.
IntActiQ8N1N0. 2 interactions.
MINTiMINT-2879044.

Structurei

3D structure databases

ProteinModelPortaliQ8N1N0.
SMRiQ8N1N0. Positions 443-581.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini476 – 589114C-type lectinPROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Contains 1 C-type lectin domain.PROSITE-ProRule annotation

Keywords - Domaini

Signal-anchor, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiENOG410IS3X. Eukaryota.
ENOG41123NI. LUCA.
GeneTreeiENSGT00760000118924.
HOGENOMiHOG000264252.
HOVERGENiHBG081248.
InParanoidiQ8N1N0.
KOiK10060.
OMAiGDNITGH.
OrthoDBiEOG7HXCVB.
PhylomeDBiQ8N1N0.
TreeFamiTF333341.

Family and domain databases

Gene3Di3.10.100.10. 1 hit.
InterProiIPR001304. C-type_lectin.
IPR016186. C-type_lectin-like.
IPR016187. C-type_lectin_fold.
[Graphical view]
PfamiPF00059. Lectin_C. 1 hit.
[Graphical view]
SMARTiSM00034. CLECT. 1 hit.
[Graphical view]
SUPFAMiSSF56436. SSF56436. 1 hit.
PROSITEiPS50041. C_TYPE_LECTIN_2. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q8N1N0-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MDGEAVRFCT DNQCVSLHPQ EVDSVAMAPA APKIPRLVQA TPAFMAVTLV
60 70 80 90 100
FSLVTLFVVV QQQTRPVPKP VQAVILGDNI TGHLPFEPNN HHHFGREAEM
110 120 130 140 150
RELIQTFKGH MENSSAWVVE IQMLKCRVDN VNSQLQVLGD HLGNTNADIQ
160 170 180 190 200
MVKGVLKDAT TLSLQTQMLR SSLEGTNAEI QRLKEDLEKA DALTFQTLNF
210 220 230 240 250
LKSSLENTSI ELHVLSRGLE NANSEIQMLN ASLETANTQA QLANSSLKNA
260 270 280 290 300
NAEIYVLRGH LDSVNDLRTQ NQVLRNSLEG ANAEIQGLKE NLQNTNALNS
310 320 330 340 350
QTQAFIKSSF DNTSAEIQFL RGHLERAGDE IHVLKRDLKM VTAQTQKANG
360 370 380 390 400
RLDQTDTQIQ VFKSEMENVN TLNAQIQVLN GHMKNASREI QTLKQGMKNA
410 420 430 440 450
SALTSQTQML DSNLQKASAE IQRLRGDLEN TKALTMEIQQ EQSRLKTLHV
460 470 480 490 500
VITSQEQLQR TQSQLLQMVL QGWKFNGGSL YYFSSVKKSW HEAEQFCVSQ
510 520 530 540 550
GAHLASVASK EEQAFLVEFT SKVYYWIGLT DRGTEGSWRW TDGTPFNAAQ
560 570 580
NKAPGSKGSC PLRKYIIVNS GMGACSFIDT PPCPWILSN
Length:589
Mass (Da):65,519
Last modified:February 10, 2009 - v2
Checksum:iACEB27A2B50E80A4
GO
Isoform 2 (identifier: Q8N1N0-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     554-589: PGSKGSCPLRKYIIVNSGMGACSFIDTPPCPWILSN → SHSTRKGCCLHLTV

Note: No experimental confirmation available.
Show »
Length:567
Mass (Da):63,250
Checksum:i70D32AA7B4184B60
GO

Sequence cautioni

The sequence BAC04786.1 differs from that shown. Reason: Erroneous termination at position 540. Translated as Trp.Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti17 – 171L → P in BAC04786 (PubMed:14702039).Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti101 – 1011R → Q.
Corresponds to variant rs2075221 [ dbSNP | Ensembl ].
VAR_054429
Natural varianti351 – 3511R → H.
Corresponds to variant rs722896 [ dbSNP | Ensembl ].
VAR_054430
Natural varianti564 – 5641K → R.1 Publication
Corresponds to variant rs2287101 [ dbSNP | Ensembl ].
VAR_054431

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei554 – 58936PGSKG…WILSN → SHSTRKGCCLHLTV in isoform 2. 1 PublicationVSP_056330Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK096429 mRNA. Translation: BAC04786.1. Sequence problems.
AC007395 Genomic DNA. No translation available.
BC139723 mRNA. Translation: AAI39724.1.
CCDSiCCDS1910.1. [Q8N1N0-1]
RefSeqiNP_775806.2. NM_173535.2. [Q8N1N0-1]
UniGeneiHs.681239.

Genome annotation databases

EnsembliENST00000272367; ENSP00000272367; ENSG00000152672. [Q8N1N0-1]
ENST00000426626; ENSP00000390581; ENSG00000152672. [Q8N1N0-2]
GeneIDi165530.
KEGGihsa:165530.
UCSCiuc002shf.4. human. [Q8N1N0-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Web resourcesi

Functional Glycomics Gateway - Glycan Binding

Kupffer cell receptor

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK096429 mRNA. Translation: BAC04786.1. Sequence problems.
AC007395 Genomic DNA. No translation available.
BC139723 mRNA. Translation: AAI39724.1.
CCDSiCCDS1910.1. [Q8N1N0-1]
RefSeqiNP_775806.2. NM_173535.2. [Q8N1N0-1]
UniGeneiHs.681239.

3D structure databases

ProteinModelPortaliQ8N1N0.
SMRiQ8N1N0. Positions 443-581.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi127914. 1 interaction.
IntActiQ8N1N0. 2 interactions.
MINTiMINT-2879044.

PTM databases

iPTMnetiQ8N1N0.
PhosphoSiteiQ8N1N0.

Polymorphism and mutation databases

BioMutaiCLEC4F.
DMDMi223590178.

Proteomic databases

EPDiQ8N1N0.
PaxDbiQ8N1N0.
PRIDEiQ8N1N0.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000272367; ENSP00000272367; ENSG00000152672. [Q8N1N0-1]
ENST00000426626; ENSP00000390581; ENSG00000152672. [Q8N1N0-2]
GeneIDi165530.
KEGGihsa:165530.
UCSCiuc002shf.4. human. [Q8N1N0-1]

Organism-specific databases

CTDi165530.
GeneCardsiCLEC4F.
HGNCiHGNC:25357. CLEC4F.
HPAiHPA030881.
neXtProtiNX_Q8N1N0.
PharmGKBiPA134968842.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiENOG410IS3X. Eukaryota.
ENOG41123NI. LUCA.
GeneTreeiENSGT00760000118924.
HOGENOMiHOG000264252.
HOVERGENiHBG081248.
InParanoidiQ8N1N0.
KOiK10060.
OMAiGDNITGH.
OrthoDBiEOG7HXCVB.
PhylomeDBiQ8N1N0.
TreeFamiTF333341.

Miscellaneous databases

GenomeRNAii165530.
PROiQ8N1N0.

Gene expression databases

BgeeiQ8N1N0.
CleanExiHS_CLEC4F.
GenevisibleiQ8N1N0. HS.

Family and domain databases

Gene3Di3.10.100.10. 1 hit.
InterProiIPR001304. C-type_lectin.
IPR016186. C-type_lectin-like.
IPR016187. C-type_lectin_fold.
[Graphical view]
PfamiPF00059. Lectin_C. 1 hit.
[Graphical view]
SMARTiSM00034. CLECT. 1 hit.
[Graphical view]
SUPFAMiSSF56436. SSF56436. 1 hit.
PROSITEiPS50041. C_TYPE_LECTIN_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
    Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
    , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
    Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1), VARIANT ARG-564.
    Tissue: Tongue.
  2. "Generation and annotation of the DNA sequences of human chromosomes 2 and 4."
    Hillier L.W., Graves T.A., Fulton R.S., Fulton L.A., Pepin K.H., Minx P., Wagner-McPherson C., Layman D., Wylie K., Sekhon M., Becker M.C., Fewell G.A., Delehaunty K.D., Miner T.L., Nash W.E., Kremitzki C., Oddy L., Du H.
    , Sun H., Bradshaw-Cordum H., Ali J., Carter J., Cordes M., Harris A., Isak A., van Brunt A., Nguyen C., Du F., Courtney L., Kalicki J., Ozersky P., Abbott S., Armstrong J., Belter E.A., Caruso L., Cedroni M., Cotton M., Davidson T., Desai A., Elliott G., Erb T., Fronick C., Gaige T., Haakenson W., Haglund K., Holmes A., Harkins R., Kim K., Kruchowski S.S., Strong C.M., Grewal N., Goyea E., Hou S., Levy A., Martinka S., Mead K., McLellan M.D., Meyer R., Randall-Maher J., Tomlinson C., Dauphin-Kohlberg S., Kozlowicz-Reilly A., Shah N., Swearengen-Shahid S., Snider J., Strong J.T., Thompson J., Yoakum M., Leonard S., Pearman C., Trani L., Radionenko M., Waligorski J.E., Wang C., Rock S.M., Tin-Wollam A.-M., Maupin R., Latreille P., Wendl M.C., Yang S.-P., Pohl C., Wallis J.W., Spieth J., Bieri T.A., Berkowicz N., Nelson J.O., Osborne J., Ding L., Meyer R., Sabo A., Shotland Y., Sinha P., Wohldmann P.E., Cook L.L., Hickenbotham M.T., Eldred J., Williams D., Jones T.A., She X., Ciccarelli F.D., Izaurralde E., Taylor J., Schmutz J., Myers R.M., Cox D.R., Huang X., McPherson J.D., Mardis E.R., Clifton S.W., Warren W.C., Chinwalla A.T., Eddy S.R., Marra M.A., Ovcharenko I., Furey T.S., Miller W., Eichler E.E., Bork P., Suyama M., Torrents D., Waterston R.H., Wilson R.K.
    Nature 434:724-731(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  3. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).

Entry informationi

Entry nameiCLC4F_HUMAN
AccessioniPrimary (citable) accession number: Q8N1N0
Secondary accession number(s): A4QPA5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 15, 2005
Last sequence update: February 10, 2009
Last modified: June 8, 2016
This is version 112 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human chromosome 2
    Human chromosome 2: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.