Clec4d (C-type lectin domain family 4, member d) - Rat Genome Database

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Gene: Clec4d (C-type lectin domain family 4, member d) Mus musculus
Analyze
Symbol: Clec4d
Name: C-type lectin domain family 4, member d
RGD ID: 1553885
MGI Page MGI
Description: Enables immunoglobulin receptor binding activity. Involved in antifungal innate immune response; positive regulation of canonical NF-kappaB signal transduction; and positive regulation of myeloid dendritic cell activation. Acts upstream of or within several processes, including Fc-gamma receptor signaling pathway; T cell differentiation involved in immune response; and defense response to other organism. Located in plasma membrane. Is expressed in several structures, including heart; immune system; intestine; liver; and lung. Orthologous to human CLEC4D (C-type lectin domain family 4 member D).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: C-type (calcium dependent, carbohydrate recognition domain) lectin, superfamily member 8; C-type lectin domain family 4 member D; C-type lectin superfamily member 8; C-type lectin, superfamily member 8; Clecs; Clecsf8; DC-associated C-type lectin 3; dectin-3; dendritic cell-associated C-type lectin 3; macrophage C-type lectin; macrophage-restricted C-type lectin; mc; mcl; MGC117678; mMC; Mp; Mpcl
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Alliance Genes
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm396123,239,066 - 123,252,227 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl6123,239,070 - 123,252,224 (+)EnsemblGRCm39 Ensembl
GRCm386123,262,107 - 123,275,268 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl6123,262,111 - 123,275,265 (+)EnsemblGRCm38mm10GRCm38
MGSCv376123,212,125 - 123,225,286 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv366123,227,736 - 123,240,884 (+)NCBIMGSCv36mm8
Celera6125,059,667 - 125,072,919 (+)NCBICelera
Cytogenetic Map6F2NCBI
cM Map658.33NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. The human C-type lectin CLECSF8 is a novel monocyte/macrophage endocytic receptor. Arce I, etal., Eur J Immunol 2004 Jan;34(1):210-20.
2. Identification of lectin-like receptors expressed by antigen presenting cells and neutrophils and their mapping to a novel gene complex. Flornes LM, etal., Immunogenetics 2004 Oct;56(7):506-17. Epub 2004 Sep 11.
3. MGDs mouse GO annotations MGD data from the GO Consortium
4. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Okazaki Y, etal., Nature. 2002 Dec 5;420(6915):563-73.
5. Mouse MP Annotation Import Pipeline RGD automated import pipeline
6. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
7. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:9660840   PMID:10349636   PMID:11042159   PMID:11076861   PMID:11217851   PMID:11841491   PMID:12477932   PMID:16141072   PMID:16141073   PMID:21308776   PMID:21677750   PMID:21873635  
PMID:23118208   PMID:23602766   PMID:23709686   PMID:23911656   PMID:25068517   PMID:25202022   PMID:25674984   PMID:25888641   PMID:26140582   PMID:26558717   PMID:26667836   PMID:27005451  
PMID:27089465   PMID:27280399   PMID:27432944   PMID:27872290   PMID:28107361   PMID:28988116   PMID:29576482   PMID:32540868   PMID:34480018   PMID:35920835   PMID:36384075   PMID:37799716  
PMID:38170734  


Genomics

Comparative Map Data
Clec4d
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm396123,239,066 - 123,252,227 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl6123,239,070 - 123,252,224 (+)EnsemblGRCm39 Ensembl
GRCm386123,262,107 - 123,275,268 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl6123,262,111 - 123,275,265 (+)EnsemblGRCm38mm10GRCm38
MGSCv376123,212,125 - 123,225,286 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv366123,227,736 - 123,240,884 (+)NCBIMGSCv36mm8
Celera6125,059,667 - 125,072,919 (+)NCBICelera
Cytogenetic Map6F2NCBI
cM Map658.33NCBI
CLEC4D
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38128,513,503 - 8,531,696 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl128,509,475 - 8,522,366 (+)EnsemblGRCh38hg38GRCh38
GRCh37128,666,099 - 8,674,962 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36128,557,403 - 8,566,229 (+)NCBINCBI36Build 36hg18NCBI36
Build 34128,557,402 - 8,566,225NCBI
Celera1210,202,132 - 10,210,958 (+)NCBICelera
Cytogenetic Map12p13.31NCBI
HuRef128,448,485 - 8,457,311 (+)NCBIHuRef
CHM1_1128,635,100 - 8,643,926 (+)NCBICHM1_1
T2T-CHM13v2.0128,496,932 - 8,515,063 (+)NCBIT2T-CHM13v2.0
Clec4d
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr84158,275,287 - 158,286,978 (+)NCBIGRCr8
mRatBN7.24156,589,591 - 156,599,279 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl4156,589,792 - 156,598,848 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx4162,841,890 - 162,851,041 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.04158,624,772 - 158,633,925 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.04157,270,184 - 157,279,333 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.04156,253,084 - 156,264,766 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4156,253,079 - 156,264,769 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04223,269,999 - 223,281,665 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44159,883,556 - 159,892,609 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.14160,128,491 - 160,137,545 (+)NCBI
Celera4145,381,212 - 145,388,954 (+)NCBICelera
Cytogenetic Map4q42NCBI
Clec4d
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554135,267,161 - 5,277,090 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554135,267,548 - 5,276,969 (-)NCBIChiLan1.0ChiLan1.0
CLEC4D
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21014,041,441 - 14,050,413 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11214,038,201 - 14,046,060 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0128,599,654 - 8,608,494 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1128,814,680 - 8,823,484 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl128,814,680 - 8,823,484 (+)Ensemblpanpan1.1panPan2
LOC611536
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12737,520,289 - 37,559,920 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2737,551,064 - 37,558,847 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha279,056,404 - 9,095,670 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02737,874,289 - 37,913,533 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2737,860,374 - 37,915,627 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12737,748,924 - 37,788,104 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02737,790,476 - 37,829,811 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0278,543,144 - 8,582,370 (-)NCBIUU_Cfam_GSD_1.0
Clec4d
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494599,887,289 - 99,896,017 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936858303,639 - 312,083 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936858303,639 - 312,092 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LOC110258710
(Sus scrofa - pig)
No map positions available.
CLEC4D
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1118,294,999 - 8,303,866 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666089393,835 - 402,286 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in Clec4d
346 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:116
Count of miRNA genes:103
Interacting mature miRNAs:106
Transcripts:ENSMUST00000032240
Prediction methods:Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
26884414Bzwq12_mbi-zygomatic width QTL 12, 16 week (mouse)63400000139076998Mouse
10412157Fl1n_mfatty liver 1 in NSY (mouse)Not determined645290993128811995Mouse
4142259Tabw2_mtally ho associated body weight 2 (mouse)Not determined46912919136400690Mouse
25314319Histh6_mhistamine hypersensitivity 6 (mouse)648696934125336963Mouse
25314320Histh5_mhistamine hypersensitivity 5 (mouse)648696934148351498Mouse
1301962Eila2_methanol induced locomotor activity 2 (mouse)Not determined648703490125333748Mouse
13506930Recrq9_mrecombination rate in male meiosis QTL 9 (mouse)673476983134676963Mouse
10043864T2dm4sa_mtype 2 diabetes mellitus 4 in SMXA RI mice (mouse)Not determined683690851146954059Mouse
1301244Ichs_mimmediate cutaneous hypersensitivity QTL (mouse)Not determined690772571124772807Mouse
11353842Bmiq4_mbody mass index QTL 4 (mouse)692584287146330736Mouse
1301292Cfbw2_mcystic fibrosis body weight 2 (mouse)Not determined694981612128981699Mouse
11040599Lmr4b_mleishmaniasis resistance 4b (mouse)696324286130324483Mouse
1300704Cia3_mcollagen induced arthritis QTL 3 (mouse)Not determined696324286130324483Mouse
4141940W6q5_mweight 6 weeks QTL 5 (mouse)Not determined96632912146535124Mouse
4142416Egq11_mearly growth QTL 11 (mouse)Not determined96632912146535124Mouse
1357555Tesq2_mtestis weight QTL 2 (mouse)Not determined696632912146535124Mouse
10043923Bhr7_mbronchial hyperresponsiveness 7 (mouse)Not determined698219814132219938Mouse
1301518Bbaa5_mB.burgdorferi-associated arthritis 5 (mouse)Not determined698483798145881170Mouse
1301923Lith6_mlithogenic gene 6 (mouse)Not determined698694477132694676Mouse
1301915Chab3_mcholesterol absorption 3 (mouse)Not determined698908709132916997Mouse
1302131Bmd8_mbone mineral density 8 (mouse)Not determined699132089133132228Mouse
1300887Pabr1_mplasma apolipoprotein B (human) regulator 1 (mouse)Not determined6103754405136400690Mouse
1301509Sluc3_msusceptibility to lung cancer 3 (mouse)Not determined6104480321127019938Mouse
1357806Aaj3_manxiety in A/J 3 (mouse)Not determined6104480321136400690Mouse
10412207Cypr5_mcytokine production 5 (mouse)Not determined6110815180144815323Mouse
13463481Mcvq14_mmean corpuscular volume QTL 14 (mouse)6111142448145142541Mouse
10043891Tilss4_mTNF-induced lethal shock susceptibility 3 (mouse)Not determined6112246918125333748Mouse
11252138Clas1_mcarcinogen-induced lung adenoma susceptibility 1 (mouse)6112246918146954059Mouse
4140980Mvwf2_mmodifier of von Willebrand factor 2 (mouse)Not determined114345693145601739Mouse
1301658Radpf3_mradiation pulmonary fibrosis 3 (mouse)Not determined6115219814146330736Mouse
4141889Qui_mquinine sensitivity, taste (mouse)Not determined115546805149549364Mouse
4141194Cyx_mcycloheximide tasting (mouse)Not determined115546805149549364Mouse
4141295Rua_mraffinose acetate tasting (mouse)Not determined115546805149549364Mouse
1301927Etohcta6_methanol conditioned taste aversion 6 (mouse)Not determined6115578005149578150Mouse
1301083Bhr5_mbronchial hyperresponsiveness 5 (mouse)Not determined6115694477132578150Mouse
4141064Ath37_matherosclerosis 37 (mouse)Not determined6116641858128495988Mouse
4142079Skmw15_mskeletal muscle weight 15 (mouse)Not determined6116829851149588044Mouse
1301152Athsq2_matherosclerosis susceptibility QTL 2 (mouse)Not determined6117059949149588044Mouse
1301804Bulb2_mbulb size 2 (mouse)Not determined6120416806149588044Mouse


Expression


Sequence


RefSeq Acc Id: ENSMUST00000032240   ⟹   ENSMUSP00000032240
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl6123,239,076 - 123,252,224 (+)Ensembl
GRCm38.p6 Ensembl6123,262,117 - 123,275,265 (+)Ensembl
RefSeq Acc Id: ENSMUST00000203421
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl6123,244,681 - 123,251,671 (+)Ensembl
GRCm38.p6 Ensembl6123,267,722 - 123,274,712 (+)Ensembl
RefSeq Acc Id: ENSMUST00000204826   ⟹   ENSMUSP00000145134
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl6123,239,070 - 123,251,882 (+)Ensembl
GRCm38.p6 Ensembl6123,262,111 - 123,274,923 (+)Ensembl
RefSeq Acc Id: NM_001163161   ⟹   NP_001156633
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm396123,239,066 - 123,252,227 (+)NCBI
GRCm386123,262,107 - 123,275,268 (+)ENTREZGENE
MGSCv376123,212,125 - 123,225,286 (+)RGD
Celera6125,059,667 - 125,072,919 (+)RGD
cM Map6 ENTREZGENE
Sequence:
RefSeq Acc Id: NM_010819   ⟹   NP_034949
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm396123,239,066 - 123,252,227 (+)NCBI
GRCm386123,262,107 - 123,275,268 (+)ENTREZGENE
MGSCv376123,212,125 - 123,225,286 (+)RGD
Celera6125,059,667 - 125,072,919 (+)RGD
cM Map6 ENTREZGENE
Sequence:
RefSeq Acc Id: NP_034949   ⟸   NM_010819
- Peptide Label: isoform 1
- UniProtKB: Q8C212 (UniProtKB/Swiss-Prot),   Q9Z2H6 (UniProtKB/Swiss-Prot),   Q4KL29 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001156633   ⟸   NM_001163161
- Peptide Label: isoform 2
- UniProtKB: Q3UBK0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSMUSP00000032240   ⟸   ENSMUST00000032240
RefSeq Acc Id: ENSMUSP00000145134   ⟸   ENSMUST00000204826
Protein Domains
C-type lectin

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q9Z2H6-F1-model_v2 AlphaFold Q9Z2H6 1-219 view protein structure

Promoters
RGD ID:6839115
Promoter ID:MM_KWN:47507
Type:Non-CpG
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:BoneMarrow_0Hour,   BoneMarrow_2Hour,   BoneMarrow_4Hour
Transcripts:NM_001163161,   NM_010819,   UC009DQH.1,   UC009DQI.1
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv366123,211,556 - 123,212,622 (+)MPROMDB
RGD ID:6847982
Promoter ID:MM_ACW:42679
Type:Non-CpG
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:BoneMarrow_0Hour,   BoneMarrow_2Hour,   BoneMarrow_4Hour
Transcripts:CLEC4D.JSEP07
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv366123,216,989 - 123,217,489 (+)MPROMDB
RGD ID:6890946
Promoter ID:EPDNEW_M8924
Type:initiation region
Name:Clec4d_1
Description:Mus musculus C-type lectin domain family 4, member d , transcriptvariant 2, mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm386123,262,170 - 123,262,230EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:1298389 AgrOrtholog
Ensembl Genes ENSMUSG00000030144 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Transcript ENSMUST00000032240 ENTREZGENE
  ENSMUST00000032240.4 UniProtKB/Swiss-Prot
  ENSMUST00000204826.3 UniProtKB/TrEMBL
Gene3D-CATH 3.10.100.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro C-type_lectin-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  C-type_lectin-like/link_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CD209-like_CTLD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CTDL_fold UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report mmu:17474 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGD MGI:1298389 ENTREZGENE
NCBI Gene 17474 ENTREZGENE
PANTHER C-TYPE LECTIN DOMAIN FAMILY 19 MEMBER A-RELATED UniProtKB/TrEMBL
  CD209 ANTIGEN-LIKE PROTEIN C-LIKE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  KILLER CELL LECTIN-LIKE RECEPTOR SUBFAMILY F MEMBER 2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MANNOSE, PHOSPHOLIPASE, LECTIN RECEPTOR RELATED UniProtKB/TrEMBL
Pfam Lectin_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Clec4d PhenoGen
PROSITE C_TYPE_LECTIN_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART CLECT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF56436 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0N4SVJ7_MOUSE UniProtKB/TrEMBL
  CLC4D_MOUSE UniProtKB/Swiss-Prot
  Q3UBK0 ENTREZGENE, UniProtKB/TrEMBL
  Q4KL29 ENTREZGENE, UniProtKB/TrEMBL
  Q8C212 ENTREZGENE
  Q9Z2H6 ENTREZGENE
UniProt Secondary Q8C212 UniProtKB/Swiss-Prot