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Protein

C-type lectin domain family 9 member A

Gene

Clec9a

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Functions as an endocytic receptor on a small subset of myeloid cells specialized for the uptake and processing of material from dead cells. Recognizes filamentous form of actin in association with particular actin-binding domains of cytoskeletal proteins, including spectrin, exposed when cell membranes are damaged, and mediate the cross-presentation of dead-cell associated antigens in a Syk-dependent manner.4 Publications

GO - Molecular functioni

GO - Biological processi

  • positive regulation of cytokine secretion Source: UniProtKB
  • receptor-mediated endocytosis Source: UniProtKB

Keywordsi

Molecular functionReceptor
LigandLectin

Protein family/group databases

TCDBi1.C.111.1.12 the regiii (regiii) family

Names & Taxonomyi

Protein namesi
Recommended name:
C-type lectin domain family 9 member A
Alternative name(s):
Dendritic cell natural killer lectin group receptor 1
CD_antigen: CD370
Gene namesi
Name:Clec9a
Synonyms:Dngr-1
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 6

Organism-specific databases

MGIiMGI:2444608 Clec9a

Subcellular locationi

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Topological domaini1 – 35CytoplasmicSequence analysisAdd BLAST35
Transmembranei36 – 56Helical; Signal-anchor for type II membrane proteinSequence analysisAdd BLAST21
Topological domaini57 – 238ExtracellularSequence analysisAdd BLAST182

Keywords - Cellular componenti

Membrane

Pathology & Biotechi

Disruption phenotypei

Deficient mice shown no alteration of dendritic cell phenotype and numbers and the response of dendritic cells to innate stimuli is not altered. No alterations are found in leukocyte numbers or frequencies in spleen, lymph node or thymus, and mice appear normal and do not develop any obvious symptoms of autoimmune disease.1 Publication

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi7Y → F: Abolishes the recruitment and activation of the tyrosine kinase Syk. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000466381 – 238C-type lectin domain family 9 member AAdd BLAST238

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Glycosylationi81N-linked (GlcNAc...) asparagineSequence analysis1
Disulfide bondi111 ↔ 122PROSITE-ProRule annotation
Glycosylationi133N-linked (GlcNAc...) asparagineSequence analysis1
Disulfide bondi139 ↔ 229PROSITE-ProRule annotation
Disulfide bondi208 ↔ 221PROSITE-ProRule annotation

Post-translational modificationi

Isoform 1: Not-glycosylated.
Isoform 4: N-glycosylated.

Keywords - PTMi

Disulfide bond, Glycoprotein

Proteomic databases

PRIDEiQ8BRU4

PTM databases

iPTMnetiQ8BRU4
PhosphoSitePlusiQ8BRU4

Expressioni

Tissue specificityi

Isoform 4 expressed at high levels by CD8+ dendritic cells (DCs), and at low levels by plasmacytoid DCs but not by other hematopoietic cells.2 Publications

Gene expression databases

BgeeiENSMUSG00000046080 Expressed in 17 organ(s), highest expression level in lung
CleanExiMM_CLEC9A

Interactioni

Subunit structurei

Isoform 1: Monomer. Isoform 4: Homodimer.2 Publications

Structurei

3D structure databases

ProteinModelPortaliQ8BRU4
SMRiQ8BRU4
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini118 – 230C-type lectinPROSITE-ProRule annotationAdd BLAST113

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi5 – 10ITAM-like6

Keywords - Domaini

Signal-anchor, Transmembrane, Transmembrane helix

Phylogenomic databases

GeneTreeiENSGT00700000104266
HOVERGENiHBG056591
InParanoidiQ8BRU4
KOiK17515
OMAiDNWIQNG
OrthoDBiEOG091G0CXT
TreeFamiTF336674

Family and domain databases

CDDicd03593 CLECT_NK_receptors_like, 1 hit
Gene3Di3.10.100.10, 1 hit
InterProiView protein in InterPro
IPR001304 C-type_lectin-like
IPR016186 C-type_lectin-like/link_sf
IPR018378 C-type_lectin_CS
IPR016187 CTDL_fold
IPR033992 NKR-like_CTLD
PfamiView protein in Pfam
PF00059 Lectin_C, 1 hit
SMARTiView protein in SMART
SM00034 CLECT, 1 hit
SUPFAMiSSF56436 SSF56436, 1 hit
PROSITEiView protein in PROSITE
PS00615 C_TYPE_LECTIN_1, 1 hit
PS50041 C_TYPE_LECTIN_2, 1 hit

Sequences (5)i

Sequence statusi: Complete.

This entry describes 5 isoformsi produced by alternative splicing. AlignAdd to basket
Isoform 1 (identifier: Q8BRU4-1) [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
MHAEEIYTSL QWDIPTSEAS QKCQSPSKCS GAWCVVTMIS CVVCMGLLAT
60 70 80 90 100
SIFLGIKFFQ VSSLVLEQQE RLIQQDTALV NLTQWQRKYT LEYCQALLQR
110 120 130 140 150
SLHSGSDCSP CPHNWIQNGK SCYYVFERWE MWNISKKSCL KEGASLFQID
160 170 180 190 200
SKEEMEFISS IGKLKGGNKY WVGVFQDGIS GSWFWEDGSS PLSDLLPAER
210 220 230
QRSAGQICGY LKDSTLISDK CDSWKYFICE KKAFGSCI
Length:238
Mass (Da):27,014
Last modified:March 1, 2003 - v1
Checksum:i07368A0380B95EA1
GO
Isoform 2 (identifier: Q8BRU4-2) [UniParc]FASTAAdd to basket
Also known as: Gamma

The sequence of this isoform differs from the canonical sequence as follows:
     31-58: GAWCVVTMISCVVCMGLLATSIFLGIKF → V
     105-105: G → GTDASTGPVLLTSPQMVPQTLDSKETG

Show »
Length:237
Mass (Da):26,823
Checksum:i1F479949C214578A
GO
Isoform 3 (identifier: Q8BRU4-3) [UniParc]FASTAAdd to basket
Also known as: Delta

The sequence of this isoform differs from the canonical sequence as follows:
     156-173: EFISSIGKLKGGNKYWVG → SRWNQWILVLGRWLFSSL
     174-238: Missing.

Show »
Length:173
Mass (Da):20,038
Checksum:iE4B644B997ECFFB2
GO
Isoform 4 (identifier: Q8BRU4-4) [UniParc]FASTAAdd to basket
Also known as: Beta

The sequence of this isoform differs from the canonical sequence as follows:
     105-105: G → GTDASTGPVLLTSPQMVPQTLDSKETG

Show »
Length:264
Mass (Da):29,670
Checksum:i69F90C10F2F06B94
GO
Isoform 5 (identifier: Q8BRU4-5) [UniParc]FASTAAdd to basket
Also known as: Epsilon

The sequence of this isoform differs from the canonical sequence as follows:
     106-147: SDCSPCPHNW...SCLKEGASLF → CQQKDSDQPA...VRRRHLDPAS
     148-238: Missing.

Show »
Length:148
Mass (Da):16,523
Checksum:iEE35B2F1890FB4FD
GO

Sequence cautioni

The sequence BAC29411 differs from that shown. Reason: Frameshift at position 234.Curated

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_04150031 – 58GAWCV…LGIKF → V in isoform 2. 1 PublicationAdd BLAST28
Alternative sequenceiVSP_041501105G → GTDASTGPVLLTSPQMVPQT LDSKETG in isoform 2 and isoform 4. 2 Publications1
Alternative sequenceiVSP_041502106 – 147SDCSP…GASLF → CQQKDSDQPARSVDTSKILL SSQISAIAGNILSVRRRHLD PAS in isoform 5. 1 PublicationAdd BLAST42
Alternative sequenceiVSP_041503148 – 238Missing in isoform 5. 1 PublicationAdd BLAST91
Alternative sequenceiVSP_041504156 – 173EFISS…KYWVG → SRWNQWILVLGRWLFSSL in isoform 3. 1 PublicationAdd BLAST18
Alternative sequenceiVSP_041505174 – 238Missing in isoform 3. 1 PublicationAdd BLAST65

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
EU339277 mRNA Translation: ABZ04558.1
EU339278 mRNA Translation: ABZ04559.1
EU339279 mRNA Translation: ABZ04560.1
EU339280 mRNA Translation: ABZ04561.1
EU339281 mRNA Translation: ABZ04562.1
AK036399 mRNA Translation: BAC29411.1 Frameshift.
AK041288 mRNA Translation: BAC30890.1
CH466523 Genomic DNA Translation: EDK99924.1
BC087955 mRNA Translation: AAH87955.1
CCDSiCCDS39658.1 [Q8BRU4-1]
CCDS57454.1 [Q8BRU4-4]
CCDS57455.1 [Q8BRU4-2]
RefSeqiNP_001192292.1, NM_001205363.1 [Q8BRU4-4]
NP_001192293.1, NM_001205364.1 [Q8BRU4-2]
NP_001192294.1, NM_001205365.1
NP_766320.2, NM_172732.3 [Q8BRU4-1]
UniGeneiMm.391518

Genome annotation databases

EnsembliENSMUST00000058352; ENSMUSP00000056625; ENSMUSG00000046080 [Q8BRU4-4]
ENSMUST00000088075; ENSMUSP00000085394; ENSMUSG00000046080 [Q8BRU4-1]
ENSMUST00000164513; ENSMUSP00000128622; ENSMUSG00000046080 [Q8BRU4-2]
ENSMUST00000204860; ENSMUSP00000144990; ENSMUSG00000046080 [Q8BRU4-5]
GeneIDi232414
KEGGimmu:232414
UCSCiuc009efr.2 mouse [Q8BRU4-1]
uc009efs.2 mouse [Q8BRU4-4]
uc012etj.2 mouse [Q8BRU4-2]
uc012etk.2 mouse [Q8BRU4-5]

Keywords - Coding sequence diversityi

Alternative splicing

Similar proteinsi

Cross-referencesi

Web resourcesi

Functional Glycomics Gateway - Glycan Binding

mCLEC9

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
EU339277 mRNA Translation: ABZ04558.1
EU339278 mRNA Translation: ABZ04559.1
EU339279 mRNA Translation: ABZ04560.1
EU339280 mRNA Translation: ABZ04561.1
EU339281 mRNA Translation: ABZ04562.1
AK036399 mRNA Translation: BAC29411.1 Frameshift.
AK041288 mRNA Translation: BAC30890.1
CH466523 Genomic DNA Translation: EDK99924.1
BC087955 mRNA Translation: AAH87955.1
CCDSiCCDS39658.1 [Q8BRU4-1]
CCDS57454.1 [Q8BRU4-4]
CCDS57455.1 [Q8BRU4-2]
RefSeqiNP_001192292.1, NM_001205363.1 [Q8BRU4-4]
NP_001192293.1, NM_001205364.1 [Q8BRU4-2]
NP_001192294.1, NM_001205365.1
NP_766320.2, NM_172732.3 [Q8BRU4-1]
UniGeneiMm.391518

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3J82electron microscopy7.70A108-238[»]
ProteinModelPortaliQ8BRU4
SMRiQ8BRU4
ModBaseiSearch...
MobiDBiSearch...

Protein family/group databases

TCDBi1.C.111.1.12 the regiii (regiii) family

PTM databases

iPTMnetiQ8BRU4
PhosphoSitePlusiQ8BRU4

Proteomic databases

PRIDEiQ8BRU4

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000058352; ENSMUSP00000056625; ENSMUSG00000046080 [Q8BRU4-4]
ENSMUST00000088075; ENSMUSP00000085394; ENSMUSG00000046080 [Q8BRU4-1]
ENSMUST00000164513; ENSMUSP00000128622; ENSMUSG00000046080 [Q8BRU4-2]
ENSMUST00000204860; ENSMUSP00000144990; ENSMUSG00000046080 [Q8BRU4-5]
GeneIDi232414
KEGGimmu:232414
UCSCiuc009efr.2 mouse [Q8BRU4-1]
uc009efs.2 mouse [Q8BRU4-4]
uc012etj.2 mouse [Q8BRU4-2]
uc012etk.2 mouse [Q8BRU4-5]

Organism-specific databases

CTDi283420
MGIiMGI:2444608 Clec9a

Phylogenomic databases

GeneTreeiENSGT00700000104266
HOVERGENiHBG056591
InParanoidiQ8BRU4
KOiK17515
OMAiDNWIQNG
OrthoDBiEOG091G0CXT
TreeFamiTF336674

Miscellaneous databases

PROiPR:Q8BRU4
SOURCEiSearch...

Gene expression databases

BgeeiENSMUSG00000046080 Expressed in 17 organ(s), highest expression level in lung
CleanExiMM_CLEC9A

Family and domain databases

CDDicd03593 CLECT_NK_receptors_like, 1 hit
Gene3Di3.10.100.10, 1 hit
InterProiView protein in InterPro
IPR001304 C-type_lectin-like
IPR016186 C-type_lectin-like/link_sf
IPR018378 C-type_lectin_CS
IPR016187 CTDL_fold
IPR033992 NKR-like_CTLD
PfamiView protein in Pfam
PF00059 Lectin_C, 1 hit
SMARTiView protein in SMART
SM00034 CLECT, 1 hit
SUPFAMiSSF56436 SSF56436, 1 hit
PROSITEiView protein in PROSITE
PS00615 C_TYPE_LECTIN_1, 1 hit
PS50041 C_TYPE_LECTIN_2, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiCLC9A_MOUSE
AccessioniPrimary (citable) accession number: Q8BRU4
Secondary accession number(s): B0ZBM3
, B0ZBM5, B0ZBM6, B0ZBM7, Q5M8M6, Q8CBB4
Entry historyiIntegrated into UniProtKB/Swiss-Prot: August 30, 2005
Last sequence update: March 1, 2003
Last modified: November 7, 2018
This is version 112 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
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Main funding by: National Institutes of Health

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