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 Orthologs
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-Chemical Interaction Annotations     Click to see Annotation Detail View
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:25156364   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:33803269   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

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


Expression

RNA-SEQ Expression


Sequence


Ensembl 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
Ensembl 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
Ensembl 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:
Ensembl Acc Id: ENSMUSP00000032240   ⟸   ENSMUST00000032240
Ensembl 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
  C-type_lectin/snaclec_domain UniProtKB/TrEMBL
  C-type_Lectin_Receptor_IMM 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