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Protein

C-type lectin domain family 4 member D

Gene

Clec4d

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at transcript leveli

Functioni

Functions as an endocytic receptor. May be involved in antigen uptake at the site of infection, either for clearance of the antigen, or for processing and further presentation to T-cells (By similarity).By similarity

GO - Molecular functioni

  • carbohydrate binding Source: UniProtKB-KW
  • immunoglobulin receptor binding Source: MGI

GO - Biological processi

  • adaptive immune response Source: MGI
  • defense response to bacterium Source: MGI
  • Fc-gamma receptor signaling pathway Source: MGI
  • innate immune response Source: MGI
  • T cell differentiation involved in immune response Source: MGI
Complete GO annotation...

Keywords - Molecular functioni

Receptor

Keywords - Biological processi

Adaptive immunity, Immunity, Innate immunity

Keywords - Ligandi

Lectin

Names & Taxonomyi

Protein namesi
Recommended name:
C-type lectin domain family 4 member D
Alternative name(s):
C-type lectin superfamily member 8
Macrophage-restricted C-type lectin
Gene namesi
Name:Clec4d
Synonyms:Clecsf8, Mcl
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 6

Organism-specific databases

MGIiMGI:1298389. Clec4d.

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini1 – 2020CytoplasmicSequence analysisAdd
BLAST
Transmembranei21 – 4323Helical; Signal-anchor for type II membrane proteinSequence analysisAdd
BLAST
Topological domaini44 – 219176ExtracellularSequence analysisAdd
BLAST

GO - Cellular componenti

  • integral component of membrane Source: UniProtKB-KW
  • plasma membrane Source: MGI
Complete GO annotation...

Keywords - Cellular componenti

Membrane

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 219219C-type lectin domain family 4 member DPRO_0000046617Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi83 ↔ 94PROSITE-ProRule annotation
Glycosylationi101 – 1011N-linked (GlcNAc...)Sequence analysis
Glycosylationi110 – 1101N-linked (GlcNAc...)Sequence analysis
Disulfide bondi111 ↔ 206PROSITE-ProRule annotation
Disulfide bondi181 ↔ 198PROSITE-ProRule annotation

Keywords - PTMi

Disulfide bond, Glycoprotein

Proteomic databases

MaxQBiQ9Z2H6.
PaxDbiQ9Z2H6.
PRIDEiQ9Z2H6.

PTM databases

iPTMnetiQ9Z2H6.
PhosphoSiteiQ9Z2H6.

Expressioni

Tissue specificityi

Expressed in the macrophage populations of bone marrow, spleen, lung and lymph nodes.1 Publication

Gene expression databases

BgeeiQ9Z2H6.
CleanExiMM_CLEC4D.
ExpressionAtlasiQ9Z2H6. baseline and differential.
GenevisibleiQ9Z2H6. MM.

Interactioni

GO - Molecular functioni

  • immunoglobulin receptor binding Source: MGI

Protein-protein interaction databases

MINTiMINT-4998555.
STRINGi10090.ENSMUSP00000032240.

Structurei

3D structure databases

ProteinModelPortaliQ9Z2H6.
SMRiQ9Z2H6. Positions 83-214.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini90 – 207118C-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

eggNOGiKOG4297. Eukaryota.
ENOG410XPJ1. LUCA.
GeneTreeiENSGT00760000118924.
HOGENOMiHOG000059556.
HOVERGENiHBG050992.
InParanoidiQ9Z2H6.
KOiK10058.
OMAiRAFQSNC.
OrthoDBiEOG71ZP2V.
PhylomeDBiQ9Z2H6.
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]

Sequencei

Sequence statusi: Complete.

Q9Z2H6-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MWLEESQMKS KGTRHPQLIP CVFAVVSISF LSACFISTCL VTHHYFLRWT
60 70 80 90 100
RGSVVKLSDY HTRVTCIREE PQPGATGGTW TCCPVSWRAF QSNCYFPLND
110 120 130 140 150
NQTWHESERN CSGMSSHLVT INTEAEQNFV TQLLDKRFSY FLGLADENVE
160 170 180 190 200
GQWQWVDKTP FNPHTVFWEK GESNDFMEED CVVLVHVHEK WVWNDFPCHF
210
EVRRICKLPG ITFNWKPSK
Length:219
Mass (Da):25,619
Last modified:May 1, 1999 - v1
Checksum:i1801A65F4B69BC40
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti70 – 701E → G in BAC40905 (PubMed:16141072).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF061272 mRNA. Translation: AAD05125.1.
AK089500 mRNA. Translation: BAC40905.1.
CCDSiCCDS20513.1.
RefSeqiNP_001156633.1. NM_001163161.1.
NP_034949.3. NM_010819.4.
UniGeneiMm.441101.

Genome annotation databases

EnsembliENSMUST00000032240; ENSMUSP00000032240; ENSMUSG00000030144.
GeneIDi17474.
KEGGimmu:17474.
UCSCiuc009dqg.2. mouse.

Cross-referencesi

Web resourcesi

Functional Glycomics Gateway - Glycan Binding

MCL

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF061272 mRNA. Translation: AAD05125.1.
AK089500 mRNA. Translation: BAC40905.1.
CCDSiCCDS20513.1.
RefSeqiNP_001156633.1. NM_001163161.1.
NP_034949.3. NM_010819.4.
UniGeneiMm.441101.

3D structure databases

ProteinModelPortaliQ9Z2H6.
SMRiQ9Z2H6. Positions 83-214.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

MINTiMINT-4998555.
STRINGi10090.ENSMUSP00000032240.

PTM databases

iPTMnetiQ9Z2H6.
PhosphoSiteiQ9Z2H6.

Proteomic databases

MaxQBiQ9Z2H6.
PaxDbiQ9Z2H6.
PRIDEiQ9Z2H6.

Protocols and materials databases

DNASUi17474.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000032240; ENSMUSP00000032240; ENSMUSG00000030144.
GeneIDi17474.
KEGGimmu:17474.
UCSCiuc009dqg.2. mouse.

Organism-specific databases

CTDi338339.
MGIiMGI:1298389. Clec4d.

Phylogenomic databases

eggNOGiKOG4297. Eukaryota.
ENOG410XPJ1. LUCA.
GeneTreeiENSGT00760000118924.
HOGENOMiHOG000059556.
HOVERGENiHBG050992.
InParanoidiQ9Z2H6.
KOiK10058.
OMAiRAFQSNC.
OrthoDBiEOG71ZP2V.
PhylomeDBiQ9Z2H6.
TreeFamiTF333341.

Miscellaneous databases

PROiQ9Z2H6.
SOURCEiSearch...

Gene expression databases

BgeeiQ9Z2H6.
CleanExiMM_CLEC4D.
ExpressionAtlasiQ9Z2H6. baseline and differential.
GenevisibleiQ9Z2H6. MM.

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

« Hide 'large scale' publications
  1. "Cloning of a novel C-type lectin expressed by murine macrophages."
    Balch S.G., McKnight A.J., Seldin M.F., Gordon S.
    J. Biol. Chem. 273:18656-18664(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], TISSUE SPECIFICITY.
  2. "The transcriptional landscape of the mammalian genome."
    Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.
    , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.
    Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: C57BL/6J.

Entry informationi

Entry nameiCLC4D_MOUSE
AccessioniPrimary (citable) accession number: Q9Z2H6
Secondary accession number(s): Q8C212
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 15, 2005
Last sequence update: May 1, 1999
Last modified: June 8, 2016
This is version 115 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. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. 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.