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Protein

C-type lectin domain family 4 member A

Gene

CLEC4A

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

Functioni

May be involved in regulating immune reactivity. May play a role in modulating dendritic cells (DC) differentiation and/or maturation. May be involved via its ITIM motif (immunoreceptor tyrosine-based inhibitory motifs) in the inhibition of B-cell-receptor-mediated calcium mobilization and protein tyrosine phosphorylation.1 Publication

GO - Molecular functioni

  • carbohydrate binding Source: UniProtKB-KW
  • transmembrane signaling receptor activity Source: ProtInc

GO - Biological processi

  • adaptive immune response Source: UniProtKB-KW
  • cell adhesion Source: ProtInc
  • cell surface receptor signaling pathway Source: ProtInc
  • innate immune response Source: UniProtKB-KW
  • stimulatory C-type lectin receptor signaling pathway Source: Reactome
Complete GO annotation...

Keywords - Biological processi

Adaptive immunity, Immunity, Innate immunity

Keywords - Ligandi

Lectin

Enzyme and pathway databases

ReactomeiR-HSA-5621480. Dectin-2 family.

Names & Taxonomyi

Protein namesi
Recommended name:
C-type lectin domain family 4 member A
Alternative name(s):
C-type lectin DDB27
C-type lectin superfamily member 6
Dendritic cell immunoreceptor
Lectin-like immunoreceptor
Gene namesi
Name:CLEC4A
Synonyms:CLECSF6, DCIR, LLIR
ORF Names:HDCGC13P
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 12

Organism-specific databases

HGNCiHGNC:13257. CLEC4A.

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini1 – 4848CytoplasmicSequence analysisAdd
BLAST
Transmembranei49 – 6921Helical; Signal-anchor for type II membrane proteinSequence analysisAdd
BLAST
Topological domaini70 – 237168ExtracellularSequence analysisAdd
BLAST

GO - Cellular componenti

  • integral component of plasma membrane Source: ProtInc
  • plasma membrane Source: Reactome
Complete GO annotation...

Keywords - Cellular componenti

Membrane

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA26584.

Polymorphism and mutation databases

BioMutaiCLEC4A.
DMDMi59797977.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 237237C-type lectin domain family 4 member APRO_0000046612Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi106 ↔ 117PROSITE-ProRule annotation
Disulfide bondi134 ↔ 230PROSITE-ProRule annotation
Glycosylationi185 – 1851N-linked (GlcNAc...)Sequence analysis
Disulfide bondi203 ↔ 222PROSITE-ProRule annotation

Keywords - PTMi

Disulfide bond, Glycoprotein

Proteomic databases

PaxDbiQ9UMR7.
PeptideAtlasiQ9UMR7.
PRIDEiQ9UMR7.

PTM databases

iPTMnetiQ9UMR7.
PhosphoSiteiQ9UMR7.

Expressioni

Tissue specificityi

Expressed in dendritic cells, myeloid cells, B-cells and HL-60 cells (at protein level). TNF alpha, IL-1 alpha, and LPS, down-regulated expression at the surface of neutrophils (at protein level). Expressed preferentially in hematopoietic tissues. Expressed in peripheral blood leukocytes, neutrophils, moderate quantities in spleen, lymph node, and bone marrow, and at very low levels in thymus. Expressed in Ag-presenting cells (DC, monocytes, macrophages and B-cells), as well as on granulocytes. Expression was decreased in DC by signals inducing its maturation (e.g. CD40 ligand, LPS, and TNF alpha).3 Publications

Inductioni

Isoform 2 mRNA expression is up-regulated by agonists of neutrophils CSF2/GM-CSF, IL3/interleukin-3, IL4/interleukin-4 and IL13/interleukin-13.1 Publication

Gene expression databases

BgeeiENSG00000111729.
CleanExiHS_CLEC4A.
ExpressionAtlasiQ9UMR7. baseline and differential.
GenevisibleiQ9UMR7. HS.

Organism-specific databases

HPAiHPA007842.

Interactioni

Subunit structurei

May interact with PTPN6 via its ITIM motif.

Protein-protein interaction databases

STRINGi9606.ENSP00000229332.

Structurei

Secondary structure

1
237
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi111 – 1133Combined sources
Beta strandi116 – 1205Combined sources
Helixi127 – 13610Combined sources
Helixi147 – 1548Combined sources
Beta strandi163 – 1686Combined sources
Beta strandi172 – 1743Combined sources
Helixi186 – 1883Combined sources
Beta strandi203 – 2097Combined sources
Turni210 – 2134Combined sources
Beta strandi214 – 2207Combined sources
Beta strandi222 – 2243Combined sources
Beta strandi226 – 2338Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
5B1WX-ray3.05A/B/C/D106-237[»]
5B1XX-ray2.90A/B/C/D106-237[»]
ProteinModelPortaliQ9UMR7.
SMRiQ9UMR7. Positions 106-234.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini113 – 231119C-type lectinPROSITE-ProRule annotationAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi5 – 106ITIM motif

Domaini

Sequence similaritiesi

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

Keywords - Domaini

Signal-anchor, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiKOG4297. Eukaryota.
ENOG410XPJ1. LUCA.
GeneTreeiENSGT00760000118924.
HOGENOMiHOG000059556.
HOVERGENiHBG050992.
InParanoidiQ9UMR7.
KOiK10057.
OMAiPNERCVV.
OrthoDBiEOG091G0O28.
PhylomeDBiQ9UMR7.
TreeFamiTF333341.

Family and domain databases

Gene3Di3.10.100.10. 1 hit.
InterProiIPR001304. C-type_lectin.
IPR016186. C-type_lectin-like.
IPR018378. C-type_lectin_CS.
IPR016187. C-type_lectin_fold.
[Graphical view]
PfamiPF00059. Lectin_C. 1 hit.
[Graphical view]
SMARTiSM00034. CLECT. 1 hit.
[Graphical view]
SUPFAMiSSF56436. SSF56436. 1 hit.
PROSITEiPS00615. C_TYPE_LECTIN_1. 1 hit.
PS50041. C_TYPE_LECTIN_2. 1 hit.
[Graphical view]

Sequences (4)i

Sequence statusi: Complete.

This entry describes 4 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q9UMR7-1) [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
MTSEITYAEV RFKNEFKSSG INTASSAASK ERTAPHKSNT GFPKLLCASL
60 70 80 90 100
LIFFLLLAIS FFIAFVIFFQ KYSQLLEKKT TKELVHTTLE CVKKNMPVEE
110 120 130 140 150
TAWSCCPKNW KSFSSNCYFI STESASWQDS EKDCARMEAH LLVINTQEEQ
160 170 180 190 200
DFIFQNLQEE SAYFVGLSDP EGQRHWQWVD QTPYNESSTF WHPREPSDPN
210 220 230
ERCVVLNFRK SPKRWGWNDV NCLGPQRSVC EMMKIHL
Length:237
Mass (Da):27,512
Last modified:May 1, 2000 - v1
Checksum:i1D07003E4C9CF96E
GO
Isoform 2 (identifier: Q9UMR7-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     67-100: IFFQKYSQLLEKKTTKELVHTTLECVKKNMPVEE → K

Show »
Length:204
Mass (Da):23,575
Checksum:i52107ED59D9AEFE0
GO
Isoform 3 (identifier: Q9UMR7-3) [UniParc]FASTAAdd to basket
Also known as: llirV1

The sequence of this isoform differs from the canonical sequence as follows:
     28-67: ASKERTAPHKSNTGFPKLLCASLLIFFLLLAISFFIAFVI → V

Show »
Length:198
Mass (Da):23,203
Checksum:iD165142F9DA7EE85
GO
Isoform 4 (identifier: Q9UMR7-4) [UniParc]FASTAAdd to basket
Also known as: llirV2

The sequence of this isoform differs from the canonical sequence as follows:
     28-99: Missing.

Show »
Length:165
Mass (Da):19,280
Checksum:iE5CB43A6D3437B67
GO

Sequence cautioni

The sequence AAL56016 differs from that shown. Reason: Frameshift at position 229. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti130 – 1301S → C in AAF75560 (PubMed:16541075).Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti36 – 361H → L.3 Publications
Corresponds to variant rs2024301 [ dbSNP | Ensembl ].
VAR_021260

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei28 – 9972Missing in isoform 4. 1 PublicationVSP_012842Add
BLAST
Alternative sequencei28 – 6740ASKER…IAFVI → V in isoform 3. 1 PublicationVSP_041348Add
BLAST
Alternative sequencei67 – 10034IFFQK…MPVEE → K in isoform 2. 1 PublicationVSP_012844Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ133532 mRNA. Translation: CAB54001.1.
AF067800 mRNA. Translation: AAF75560.1.
AF328684 mRNA. Translation: AAL56016.1. Frameshift.
AF109146 mRNA. Translation: AAF14348.1.
AF200738 mRNA. Translation: AAG35593.1.
AC006511 Genomic DNA. No translation available.
AC092111 Genomic DNA. No translation available.
BC074822 mRNA. Translation: AAH74822.1.
BC074874 mRNA. Translation: AAH74874.1.
BC117439 mRNA. Translation: AAI17440.1.
BC117441 mRNA. Translation: AAI17442.1.
CCDSiCCDS41745.1. [Q9UMR7-3]
CCDS8590.1. [Q9UMR7-1]
CCDS8591.1. [Q9UMR7-4]
CCDS8592.1. [Q9UMR7-2]
PIRiJC7608.
RefSeqiNP_057268.1. NM_016184.3. [Q9UMR7-1]
NP_919429.2. NM_194447.2. [Q9UMR7-3]
NP_919430.1. NM_194448.2. [Q9UMR7-4]
NP_919432.1. NM_194450.2. [Q9UMR7-2]
UniGeneiHs.504657.

Genome annotation databases

EnsembliENST00000229332; ENSP00000229332; ENSG00000111729. [Q9UMR7-1]
ENST00000345999; ENSP00000344646; ENSG00000111729. [Q9UMR7-4]
ENST00000352620; ENSP00000247243; ENSG00000111729. [Q9UMR7-2]
ENST00000360500; ENSP00000353690; ENSG00000111729. [Q9UMR7-3]
GeneIDi50856.
KEGGihsa:50856.
UCSCiuc001qtz.1. human. [Q9UMR7-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Web resourcesi

Functional Glycomics Gateway - Glycan Binding

DCIR

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ133532 mRNA. Translation: CAB54001.1.
AF067800 mRNA. Translation: AAF75560.1.
AF328684 mRNA. Translation: AAL56016.1. Frameshift.
AF109146 mRNA. Translation: AAF14348.1.
AF200738 mRNA. Translation: AAG35593.1.
AC006511 Genomic DNA. No translation available.
AC092111 Genomic DNA. No translation available.
BC074822 mRNA. Translation: AAH74822.1.
BC074874 mRNA. Translation: AAH74874.1.
BC117439 mRNA. Translation: AAI17440.1.
BC117441 mRNA. Translation: AAI17442.1.
CCDSiCCDS41745.1. [Q9UMR7-3]
CCDS8590.1. [Q9UMR7-1]
CCDS8591.1. [Q9UMR7-4]
CCDS8592.1. [Q9UMR7-2]
PIRiJC7608.
RefSeqiNP_057268.1. NM_016184.3. [Q9UMR7-1]
NP_919429.2. NM_194447.2. [Q9UMR7-3]
NP_919430.1. NM_194448.2. [Q9UMR7-4]
NP_919432.1. NM_194450.2. [Q9UMR7-2]
UniGeneiHs.504657.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
5B1WX-ray3.05A/B/C/D106-237[»]
5B1XX-ray2.90A/B/C/D106-237[»]
ProteinModelPortaliQ9UMR7.
SMRiQ9UMR7. Positions 106-234.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi9606.ENSP00000229332.

PTM databases

iPTMnetiQ9UMR7.
PhosphoSiteiQ9UMR7.

Polymorphism and mutation databases

BioMutaiCLEC4A.
DMDMi59797977.

Proteomic databases

PaxDbiQ9UMR7.
PeptideAtlasiQ9UMR7.
PRIDEiQ9UMR7.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000229332; ENSP00000229332; ENSG00000111729. [Q9UMR7-1]
ENST00000345999; ENSP00000344646; ENSG00000111729. [Q9UMR7-4]
ENST00000352620; ENSP00000247243; ENSG00000111729. [Q9UMR7-2]
ENST00000360500; ENSP00000353690; ENSG00000111729. [Q9UMR7-3]
GeneIDi50856.
KEGGihsa:50856.
UCSCiuc001qtz.1. human. [Q9UMR7-1]

Organism-specific databases

CTDi50856.
GeneCardsiCLEC4A.
HGNCiHGNC:13257. CLEC4A.
HPAiHPA007842.
MIMi605306. gene.
neXtProtiNX_Q9UMR7.
PharmGKBiPA26584.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG4297. Eukaryota.
ENOG410XPJ1. LUCA.
GeneTreeiENSGT00760000118924.
HOGENOMiHOG000059556.
HOVERGENiHBG050992.
InParanoidiQ9UMR7.
KOiK10057.
OMAiPNERCVV.
OrthoDBiEOG091G0O28.
PhylomeDBiQ9UMR7.
TreeFamiTF333341.

Enzyme and pathway databases

ReactomeiR-HSA-5621480. Dectin-2 family.

Miscellaneous databases

GeneWikiiCLEC4A.
GenomeRNAii50856.
PROiQ9UMR7.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000111729.
CleanExiHS_CLEC4A.
ExpressionAtlasiQ9UMR7. baseline and differential.
GenevisibleiQ9UMR7. HS.

Family and domain databases

Gene3Di3.10.100.10. 1 hit.
InterProiIPR001304. C-type_lectin.
IPR016186. C-type_lectin-like.
IPR018378. C-type_lectin_CS.
IPR016187. C-type_lectin_fold.
[Graphical view]
PfamiPF00059. Lectin_C. 1 hit.
[Graphical view]
SMARTiSM00034. CLECT. 1 hit.
[Graphical view]
SUPFAMiSSF56436. SSF56436. 1 hit.
PROSITEiPS00615. C_TYPE_LECTIN_1. 1 hit.
PS50041. C_TYPE_LECTIN_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiCLC4A_HUMAN
AccessioniPrimary (citable) accession number: Q9UMR7
Secondary accession number(s): Q17R69
, Q8WXW9, Q9H2Z9, Q9NS33, Q9UI34
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 15, 2005
Last sequence update: May 1, 2000
Last modified: September 7, 2016
This is version 132 of the entry and version 1 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

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 12
    Human chromosome 12: 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. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. 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.