Reviewed, UniProtKB/Swiss-Prot Q9JKF4 (CLC6A_MOUSE)

Names and origin

Protein names

Recommended name:
C-type lectin domain family 6 member A

Alternative name(s):
Dendritic cell-associated C-type lectin 2
Short name=DC-associated C-type lectin 2
Short name=Dectin-2
C-type lectin superfamily member 10

Gene names

Name:	Clec6a
Synonyms:	Clec4n, Clecsf10, Dectin2

Organism

Mus musculus (Mouse)

Taxonomic identifier

10090 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Glires › Rodentia › Sciurognathi › Muroidea › Muridae › Murinae › Mus

Protein attributes

Sequence length	209 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	May be involved in regulating immune reactivity By similarity.
Subcellular location	Membrane; Single-pass type II membrane protein Probable.
Tissue specificity	Expressed by the XS52 DC (dendritic cell) line (at protein level). Expressed constitutively by the epidermis, and skin resident DC appear to be the major source of this expression. Expressed in the spleen and thymus. Expression was undetectable in non-DC lines, including macrophage lines (J774 and Raw), T-cell lines (7-17, HDK-1, and D10), B-cell hybridoma (5C5), a keratinocyte line (Pam 212), and a fibroblast line (NS01). Ref.1
Sequence similarities	Contains 1 C-type lectin domain.

Ontologies

Keywords
Biological process	Immune response
Cellular component	Membrane
Coding sequence diversity	Alternative splicing
Domain	Signal-anchor Transmembrane
Ligand	Lectin
PTM	Disulfide bond Glycoprotein
Gene Ontology (GO)
Biological process	immune response Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	integral to membrane Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	sugar binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Alternative products

This entry describes 3 isoforms produced by alternative splicing. [Align] [Select]

Isoform 1 (identifier: Q9JKF4-1)

Also known as: Alpha;

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.

Isoform 2 (identifier: Q9JKF4-2)

Also known as: Beta;

The sequence of this isoform differs from the canonical sequence as follows:
     39-72: Missing.

Isoform 3 (identifier: Q9JKF4-3)

Also known as: Gamma;

The sequence of this isoform differs from the canonical sequence as follows:
     142-182: Missing.

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 209	209	C-type lectin domain family 6 member A		PRO_0000046636
Regions
	Topological domain	1 – 20	20	Cytoplasmic Potential
	Transmembrane	21 – 43	23	Signal-anchor for type II membrane protein Potential
	Topological domain	44 – 209	166	Extracellular Potential
	Domain	86 – 203	118	C-type lectin
Amino acid modifications
	Glycosylation	131	1	N-linked (GlcNAc...) Potential
	Disulfide bond	79 ↔ 90		By similarity
	Disulfide bond	107 ↔ 202		By similarity
	Disulfide bond	176 ↔ 194		By similarity
Natural variations
	Alternative sequence	39 – 72	34	Missing in isoform 2.		VSP_012846
	Alternative sequence	142 – 182	41	Missing in isoform 3.		VSP_012847

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 (Alpha) [UniParc]. Last modified October 1, 2000. Version 1. Checksum: 7AB8BDC0DB1EA5ED	FASTA	209	24,324
	10 20 30 40 50 60 MVQERQSQGK GVCWTLRLWS AAVISMLLLS TCFIASCVVT YQFIMDQPSR RLYELHTYHS 70 80 90 100 110 120 SLTCFSEGTM VSEKMWGCCP NHWKSFGSSC YLISTKENFW STSEQNCVQM GAHLVVINTE 130 140 150 160 170 180 AEQNFITQQL NESLSYFLGL SDPQGNGKWQ WIDDTPFSQN VRFWHPHEPN LPEERCVSIV 190 200 YWNPSKWGWN DVFCDSKHNS ICEMKKIYL
	Isoform 2 (Beta). Checksum: E1C9632687BF0EA9	FASTA	175	20,313
	10 20 30 40 50 60 MVQERQSQGK GVCWTLRLWS AAVISMLLLS TCFIASCVEK MWGCCPNHWK SFGSSCYLIS 70 80 90 100 110 120 TKENFWSTSE QNCVQMGAHL VVINTEAEQN FITQQLNESL SYFLGLSDPQ GNGKWQWIDD 130 140 150 160 170 TPFSQNVRFW HPHEPNLPEE RCVSIVYWNP SKWGWNDVFC DSKHNSICEM KKIYL
	Isoform 3 (Gamma). Checksum: CF2ADDFE054EB038	FASTA	168	19,332
	10 20 30 40 50 60 MVQERQSQGK GVCWTLRLWS AAVISMLLLS TCFIASCVVT YQFIMDQPSR RLYELHTYHS 70 80 90 100 110 120 SLTCFSEGTM VSEKMWGCCP NHWKSFGSSC YLISTKENFW STSEQNCVQM GAHLVVINTE 130 140 150 160 AEQNFITQQL NESLSYFLGL SNPSKWGWND VFCDSKHNSI CEMKKIYL

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Cloning of a second dendritic cell-associated C-type lectin (dectin-2) and its alternatively spliced isoforms." Ariizumi K., Shen G.-L., Shikano S., Ritter R. III, Zukas P., Edelbaum D., Morita A., Takashima A. J. Biol. Chem. 275:11957-11963(2000) [PubMed: 10766825] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1; 2 AND 3), TISSUE SPECIFICITY. Strain: BALB/c.
[2]	"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: 15489334] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1). Strain: FVB/N-3. Tissue: Mammary tumor.
+	Additional computationally mapped references.

Web resources

Functional Glycomics Gateway - Glycan Binding

Dectin-2

Cross-references

Sequence databases
EMBL GenBank DDBJ	AF240357 mRNA. Translation: AAF67177.1. AF240358 mRNA. Translation: AAF67178.1. AF240359 mRNA. Translation: AAF67179.1. BC023008 mRNA. Translation: AAH23008.1.
IPI	IPI00122937. IPI00122939. IPI00459254.
RefSeq	NP_064385.1.
UniGene	Mm.271782
3D structure databases
SMR	Q9JKF4. Positions 72-206.
ModBase	Search...
Protein-protein interaction databases
STRING	Q9JKF4.
Proteomic databases
PRIDE	Q9JKF4.
Genome annotation databases
Ensembl	ENSMUST00000024118; ENSMUSP00000024118; ENSMUSG00000023349; Mus musculus. [Genome view] ENSMUST00000112554; ENSMUSP00000108173; ENSMUSG00000023349; Mus musculus. [Genome view]
GeneID	56620.
KEGG	mmu:56620.
UCSC	uc009dqe.1. mouse. uc009dqf.1. mouse.
Organism-specific databases
CTD	56620.
MGI	MGI:1861231. Clec4n.
Phylogenomic databases
HOGENOM	HBG283199.
HOVERGEN	HBG050992.
InParanoid	Q9JKF4.
OMA	NDVFCDS.
PhylomeDB	Q9JKF4.
Gene expression databases
ArrayExpress	Q9JKF4.
Bgee	Q9JKF4.
CleanEx	MM_CLEC4N.
Genevestigator	Q9JKF4.
GermOnline	ENSMUSG00000023349. Mus musculus.
Family and domain databases
InterPro	IPR002353. AntifreezeII. IPR001304. C-type_lectin. IPR016186. C-type_lectin-like. IPR018378. C-type_lectin_CS. IPR016187. C-type_lectin_fold. [Graphical view]
Gene3D	G3DSA:3.10.100.10. C-type_lectin-like. 1 hit.
Pfam	PF00059. Lectin_C. 1 hit. [Graphical view]
PRINTS	PR00356. ANTIFREEZEII.
SMART	SM00034. CLECT. 1 hit. [Graphical view]
SUPFAM	SSF56436. C-type_lectin_fold. 1 hit.
PROSITE	PS00615. C_TYPE_LECTIN_1. 1 hit. PS50041. C_TYPE_LECTIN_2. 1 hit. [Graphical view]
ProtoNet	Search...
Other Resources
NextBio	313047.
SOURCE	Search...

Entry information

Entry name

CLC6A_MOUSE

Accession

Primary (citable) accession number: Q9JKF4
Secondary accession number(s): Q9JKF2, Q9JKF3

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 15, 2005
Last sequence update:	October 1, 2000
Last modified:	March 2, 2010
This is version 71 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HPI (Human Proteome Initiative)