Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

C-type lectin domain family 9 member A

Gene

Clec9a

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at transcript 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 (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 9 member A
Gene namesi
Name:Clec9a
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Chromosome 4

Organism-specific databases

RGDi1562513. Clec9a.

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini1 – 3434CytoplasmicSequence analysisAdd
BLAST
Transmembranei35 – 5521Helical; Signal-anchor for type II membrane proteinSequence analysisAdd
BLAST
Topological domaini56 – 241186ExtracellularSequence analysisAdd
BLAST

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Membrane

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 241241C-type lectin domain family 9 member APRO_0000410724Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Glycosylationi81 – 811N-linked (GlcNAc...)Sequence analysis
Glycosylationi88 – 881N-linked (GlcNAc...)Sequence analysis
Disulfide bondi113 ↔ 124PROSITE-ProRule annotation
Glycosylationi135 – 1351N-linked (GlcNAc...)Sequence analysis
Disulfide bondi141 ↔ 232PROSITE-ProRule annotation
Glycosylationi161 – 1611N-linked (GlcNAc...)Sequence analysis
Disulfide bondi211 ↔ 224PROSITE-ProRule annotation
Glycosylationi223 – 2231N-linked (GlcNAc...)Sequence analysis

Post-translational modificationi

N-glycosylated.By similarity

Keywords - PTMi

Disulfide bond, Glycoprotein

Proteomic databases

PaxDbiD4AD02.

Expressioni

Tissue specificityi

High expression in the spleen, moderate to low levels in several other tissues and cell types, but no detectable expression in skin dendritic cells or CD4+ T-cells.1 Publication

Gene expression databases

GenevisibleiD4AD02. RN.

Interactioni

Subunit structurei

Homodimer.By similarity

Protein-protein interaction databases

STRINGi10116.ENSRNOP00000052698.

Structurei

3D structure databases

ProteinModelPortaliD4AD02.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini120 – 233114C-type lectinPROSITE-ProRule annotationAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi5 – 106ITAM-like

Sequence similaritiesi

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

Keywords - Domaini

Signal-anchor, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiKOG4297. Eukaryota.
ENOG410XPJ1. LUCA.
GeneTreeiENSGT00700000104266.
InParanoidiD4AD02.
KOiK17515.
OMAiDYWVGLS.
OrthoDBiEOG7T1RCH.
PhylomeDBiD4AD02.
TreeFamiTF336674.

Family and domain databases

Gene3Di3.10.100.10. 2 hits.
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.
PROSITEiPS00615. C_TYPE_LECTIN_1. 1 hit.
PS50041. C_TYPE_LECTIN_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

D4AD02-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MHEEEIYTSL QWDIPTSEAS QKCPSLSKCP GTWCIVTVIS CVVCVGLLAA
60 70 80 90 100
SIFLGIKFSQ VSSLVMEQRE RLIRQDTALL NLTEWQRNHT LQLKSCQASL
110 120 130 140 150
QRSLRSGSNC NPCPPNWIQN GKSCYYAFDR WETWNNSKKS CLKEGDSLLQ
160 170 180 190 200
IDSKEEMEFI NLSIWKLKGG YEYWVGVFQD GPSGSWFWED GSSPLSDLLP
210 220 230 240
TDRQLSASQI CGYLKDHTLI SDNCSNWKYF ICEKKAFGSC I
Length:241
Mass (Da):27,429
Last modified:April 20, 2010 - v1
Checksum:i6BC68486AFC2DD5F
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti158 – 1581Missing in ADK94896 (PubMed:20544345).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
GU357486 mRNA. Translation: ADK94896.1.
AABR03033287 Genomic DNA. No translation available.
CH473964 Genomic DNA. Translation: EDM01742.1.
RefSeqiNP_001102824.1. NM_001109354.1.
UniGeneiRn.14822.

Genome annotation databases

EnsembliENSRNOT00000088108; ENSRNOP00000071858; ENSRNOG00000051690.
GeneIDi502901.
KEGGirno:502901.
UCSCiRGD:1562513. rat.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
GU357486 mRNA. Translation: ADK94896.1.
AABR03033287 Genomic DNA. No translation available.
CH473964 Genomic DNA. Translation: EDM01742.1.
RefSeqiNP_001102824.1. NM_001109354.1.
UniGeneiRn.14822.

3D structure databases

ProteinModelPortaliD4AD02.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi10116.ENSRNOP00000052698.

Proteomic databases

PaxDbiD4AD02.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSRNOT00000088108; ENSRNOP00000071858; ENSRNOG00000051690.
GeneIDi502901.
KEGGirno:502901.
UCSCiRGD:1562513. rat.

Organism-specific databases

CTDi283420.
RGDi1562513. Clec9a.

Phylogenomic databases

eggNOGiKOG4297. Eukaryota.
ENOG410XPJ1. LUCA.
GeneTreeiENSGT00700000104266.
InParanoidiD4AD02.
KOiK17515.
OMAiDYWVGLS.
OrthoDBiEOG7T1RCH.
PhylomeDBiD4AD02.
TreeFamiTF336674.

Miscellaneous databases

NextBioi712735.
PROiD4AD02.

Gene expression databases

GenevisibleiD4AD02. RN.

Family and domain databases

Gene3Di3.10.100.10. 2 hits.
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.
PROSITEiPS00615. C_TYPE_LECTIN_1. 1 hit.
PS50041. C_TYPE_LECTIN_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The complete inventory of receptors encoded by the rat natural killer cell gene complex."
    Flornes L.M., Nylenna O., Saether P.C., Daws M.R., Dissen E., Fossum S.
    Immunogenetics 62:521-530(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], TISSUE SPECIFICITY.
    Strain: PVG.
  2. "Genome sequence of the Brown Norway rat yields insights into mammalian evolution."
    Gibbs R.A., Weinstock G.M., Metzker M.L., Muzny D.M., Sodergren E.J., Scherer S., Scott G., Steffen D., Worley K.C., Burch P.E., Okwuonu G., Hines S., Lewis L., Deramo C., Delgado O., Dugan-Rocha S., Miner G., Morgan M.
    , Hawes A., Gill R., Holt R.A., Adams M.D., Amanatides P.G., Baden-Tillson H., Barnstead M., Chin S., Evans C.A., Ferriera S., Fosler C., Glodek A., Gu Z., Jennings D., Kraft C.L., Nguyen T., Pfannkoch C.M., Sitter C., Sutton G.G., Venter J.C., Woodage T., Smith D., Lee H.-M., Gustafson E., Cahill P., Kana A., Doucette-Stamm L., Weinstock K., Fechtel K., Weiss R.B., Dunn D.M., Green E.D., Blakesley R.W., Bouffard G.G., De Jong P.J., Osoegawa K., Zhu B., Marra M., Schein J., Bosdet I., Fjell C., Jones S., Krzywinski M., Mathewson C., Siddiqui A., Wye N., McPherson J., Zhao S., Fraser C.M., Shetty J., Shatsman S., Geer K., Chen Y., Abramzon S., Nierman W.C., Havlak P.H., Chen R., Durbin K.J., Egan A., Ren Y., Song X.-Z., Li B., Liu Y., Qin X., Cawley S., Cooney A.J., D'Souza L.M., Martin K., Wu J.Q., Gonzalez-Garay M.L., Jackson A.R., Kalafus K.J., McLeod M.P., Milosavljevic A., Virk D., Volkov A., Wheeler D.A., Zhang Z., Bailey J.A., Eichler E.E., Tuzun E., Birney E., Mongin E., Ureta-Vidal A., Woodwark C., Zdobnov E., Bork P., Suyama M., Torrents D., Alexandersson M., Trask B.J., Young J.M., Huang H., Wang H., Xing H., Daniels S., Gietzen D., Schmidt J., Stevens K., Vitt U., Wingrove J., Camara F., Mar Alba M., Abril J.F., Guigo R., Smit A., Dubchak I., Rubin E.M., Couronne O., Poliakov A., Huebner N., Ganten D., Goesele C., Hummel O., Kreitler T., Lee Y.-A., Monti J., Schulz H., Zimdahl H., Himmelbauer H., Lehrach H., Jacob H.J., Bromberg S., Gullings-Handley J., Jensen-Seaman M.I., Kwitek A.E., Lazar J., Pasko D., Tonellato P.J., Twigger S., Ponting C.P., Duarte J.M., Rice S., Goodstadt L., Beatson S.A., Emes R.D., Winter E.E., Webber C., Brandt P., Nyakatura G., Adetobi M., Chiaromonte F., Elnitski L., Eswara P., Hardison R.C., Hou M., Kolbe D., Makova K., Miller W., Nekrutenko A., Riemer C., Schwartz S., Taylor J., Yang S., Zhang Y., Lindpaintner K., Andrews T.D., Caccamo M., Clamp M., Clarke L., Curwen V., Durbin R.M., Eyras E., Searle S.M., Cooper G.M., Batzoglou S., Brudno M., Sidow A., Stone E.A., Payseur B.A., Bourque G., Lopez-Otin C., Puente X.S., Chakrabarti K., Chatterji S., Dewey C., Pachter L., Bray N., Yap V.B., Caspi A., Tesler G., Pevzner P.A., Haussler D., Roskin K.M., Baertsch R., Clawson H., Furey T.S., Hinrichs A.S., Karolchik D., Kent W.J., Rosenbloom K.R., Trumbower H., Weirauch M., Cooper D.N., Stenson P.D., Ma B., Brent M., Arumugam M., Shteynberg D., Copley R.R., Taylor M.S., Riethman H., Mudunuri U., Peterson J., Guyer M., Felsenfeld A., Old S., Mockrin S., Collins F.S.
    Nature 428:493-521(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Brown Norway.
  3. Mural R.J., Adams M.D., Myers E.W., Smith H.O., Venter J.C.
    Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Brown Norway.

Entry informationi

Entry nameiCLC9A_RAT
AccessioniPrimary (citable) accession number: D4AD02
Secondary accession number(s): D9Z4I7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 28, 2011
Last sequence update: April 20, 2010
Last modified: November 11, 2015
This is version 40 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. 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.