Clec5a (C-type lectin domain family 5, member a) - Rat Genome Database
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Gene: Clec5a (C-type lectin domain family 5, member a) Mus musculus
Analyze
Symbol: Clec5a
Name: C-type lectin domain family 5, member a
RGD ID: 1620879
MGI Page MGI
Description: Exhibits virus receptor activity. Involved in several processes, including negative regulation of myeloid cell apoptotic process; osteoblast development; and positive regulation of cytokine secretion. Localizes to cell surface. Orthologous to human CLEC5A (C-type lectin domain containing 5A); INTERACTS WITH 1,1-dichloroethene; 2,2',4,4',5,5'-hexachlorobiphenyl; 2,2',5,5'-tetrachlorobiphenyl.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 5; C-type lectin domain family 5 member A; C-type lectin superfamily member 5; Clecs; Clecsf5; Ly10; Ly100; MDL-; MDL-1; Mdl1; MGC129446; MGC129447; myeloid DAP12-associating lectin 1; myeloid DAP12-associating lectin-1; type II transmembrane protein MDL-1
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: GRCm38 - Mouse Genome Assembly GRCm38
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39640,551,832 - 40,562,739 (-)NCBIGRCm39mm39
GRCm38640,574,898 - 40,585,805 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl640,574,894 - 40,585,821 (-)EnsemblGRCm38mm10GRCm38
MGSCv37640,524,897 - 40,535,804 (-)NCBIGRCm37mm9NCBIm37
MGSCv36640,504,505 - 40,515,412 (-)NCBImm8
Celera640,562,066 - 40,572,779 (-)NCBICelera
Cytogenetic Map6B1NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease 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

Mammalian Phenotype
References

References - curated
1. RGD automated import pipeline
2. RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:10349636   PMID:10449773   PMID:11042159   PMID:11076861   PMID:11217851   PMID:11414735   PMID:12466851   PMID:12477932   PMID:14691545   PMID:16141072   PMID:16141073   PMID:18496526  
PMID:19074552   PMID:19120482   PMID:19251634   PMID:20212065   PMID:20637688   PMID:21873635   PMID:22005300   PMID:22536153   PMID:24216483   PMID:26927798   PMID:27033255   PMID:27795434  
PMID:28824166   PMID:29126450   PMID:31160588  


Genomics

Comparative Map Data
Clec5a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39640,551,832 - 40,562,739 (-)NCBIGRCm39mm39
GRCm38640,574,898 - 40,585,805 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl640,574,894 - 40,585,821 (-)EnsemblGRCm38mm10GRCm38
MGSCv37640,524,897 - 40,535,804 (-)NCBIGRCm37mm9NCBIm37
MGSCv36640,504,505 - 40,515,412 (-)NCBImm8
Celera640,562,066 - 40,572,779 (-)NCBICelera
Cytogenetic Map6B1NCBI
CLEC5A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl7141,927,357 - 141,947,007 (-)EnsemblGRCh38hg38GRCh38
GRCh387141,927,356 - 141,947,009 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh377141,627,157 - 141,646,783 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 367141,273,626 - 141,293,252 (-)NCBINCBI36hg18NCBI36
Build 347141,080,340 - 141,099,967NCBI
Celera7136,348,653 - 136,368,271 (-)NCBI
Cytogenetic Map7q34NCBI
HuRef7135,923,563 - 135,943,134 (-)NCBIHuRef
CHM1_17141,561,389 - 141,581,038 (-)NCBICHM1_1
CRA_TCAGchr7v27140,965,368 - 140,984,972 (-)NCBI
Clec5a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.0468,810,330 - 68,819,921 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl468,808,359 - 68,819,928 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04133,597,708 - 133,607,274 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4468,174,953 - 68,183,934 (-)NCBIRGSC3.4rn4RGSC3.4
Celera464,398,299 - 64,407,282 (-)NCBICelera
Cytogenetic Map4q23NCBI
Clec5a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554941,683,956 - 1,693,348 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554941,683,926 - 1,694,914 (+)NCBIChiLan1.0ChiLan1.0
CLEC5A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.17146,320,331 - 146,339,905 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl7146,320,331 - 146,339,905 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v07133,851,242 - 133,870,793 (-)NCBIMhudiblu_PPA_v0panPan3
CLEC5A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl167,243,018 - 7,269,418 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1167,242,424 - 7,269,986 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Clec5a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049365925,733,592 - 5,741,573 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CLEC5A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl188,004,448 - 8,016,318 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1188,004,423 - 8,014,390 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2188,311,180 - 8,313,117 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CLEC5A
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.121110,629,443 - 110,650,350 (-)NCBI
ChlSab1.1 Ensembl21110,632,181 - 110,649,204 (-)Ensembl
Clec5a
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462476521,865,583 - 21,874,985 (-)NCBI


QTLs in Region (GRCm38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
25440480Moaq2_mmodifier of alien QTL 2 (mouse)61117500000Mouse
26884414Bzwq12_mbi-zygomatic width QTL 12, 16 week (mouse)63400000139100000Mouse
1300556Cia6_mcollagen induced arthritis QTL 6 (mouse)Not determined6446488487426034Mouse
11353840Bmiq2_mbody mass index QTL 2 (mouse)6450382345314181Mouse
1357481Aaj2_manxiety in A/J 2 (mouse)Not determined6450382348726677Mouse
1357520Axtq2_manxiety QTL 2 (mouse)Not determined6450382348726677Mouse
11353841Bmiq3_mbody mass index QTL 3 (mouse)6450382348726677Mouse
4142126W3q3_mweight 3 weeks QTL 3 (mouse)Not determined450382396656149Mouse
4142361W10q11_mweight 10 weeks QTL 11 (mouse)Not determined450382396656149Mouse
4142271Egq8_mearly growth QTL 8 (mouse)Not determined450382396656149Mouse
4142232W6q4_mweight 6 weeks QTL 4 (mouse)Not determined450382396656149Mouse
26884441Sklq3_mskull length QTL 3, 5 week (mouse)6760000080600000Mouse
1302051Sluc7_msusceptibility to lung cancer 7 (mouse)Not determined6929707543297169Mouse
10043869Cia6a_mcollagen induced arthritis QTL 6a (mouse)Not determined61211797246118070Mouse
1301998Bts2_mbladder tumor susceptibility 2 (mouse)Not determined61275122246751334Mouse
4141749Obrq2_mobesity resistance QTL 2 (mouse)Not determined1275122246751334Mouse
27226726Tibmd7_mtibia midshaft diameter 7, 16 week (mouse)61770000053500000Mouse
1301724Pcd4ts1_mp-glycoprotein positive CD4 T cell subset 1 (mouse)Not determined61773466351734784Mouse
4140989Spqq2_msperm quality QTL 2 (mouse)Not determined1773466351734784Mouse
1301850Fglu_mfasting glucose (mouse)Not determined61773466351734784Mouse
1357442Dbts1_mdiabetes 1 (mouse)Not determined61823414873387692Mouse
12904940Edlmmq5_mextensor digitorum longus muscle mass QTL 5 (mouse)61963941153639411Mouse
12904943Tammq4_mtibialis anterior muscle mass QTL 4 (mouse)61963941153639411Mouse
12904952Gmmq4_mgastrocnemius muscle mass QTL 4 (mouse)61963941153639411Mouse
10412213Sxbq2_mSGC/Knj cross B6 QTL 2 (mouse)Not determined61991268671322775Mouse
10412107Desp4_mdespair 4 (mouse)Not determined62007289554072895Mouse
14700690Ccs6_mcolon cancer susceptibility 6 (mouse)62380000057800000Mouse
13208564Bmiq7_mbody mass index QTL 7 (mouse)62500000080000000Mouse
4141988Obrq3_mobesity resistance QTL 3 (mouse)Not determined2831405962314181Mouse
4141454Obrq4_mobesity resistance QTL 4 (mouse)Not determined3172656565726677Mouse
12880425V25Dq5_mvitamin D inactive form serum level QTL 5 (mouse)63270000066700000Mouse
4141782Mrdq5_mmodifier of retinal degeneration QTL 5 (mouse)Not determined3285065078238974Mouse
1300959Lxw2_mlupus BXSB x NZW 2 (mouse)Not determined63389528167895420Mouse
11252142Mom12_mModifier of Min 12 (mouse)63389528167895420Mouse
1300767Aliq4_macute lung injury QTL 4 (mouse)Not determined63629634770296450Mouse
1357539Bsbob3_mBSB obesity 3 (mouse)Not determined63647147170471591Mouse
4141094Hrtr1_mheart rate 1 (mouse)Not determined3676447870764478Mouse
14746995Manh60_mmandible shape 60 (mouse)63722567771225677Mouse
1558984Cplaq9_mcircadian period of locomotor activity 9 (mouse)Not determined63866962592607450Mouse

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1142
Count of miRNA genes:580
Interacting mature miRNAs:704
Transcripts:ENSMUST00000031975, ENSMUST00000101491, ENSMUST00000129948, ENSMUST00000177178
Prediction methods:Miranda, Rnahybrid, Targetscan
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.


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSMUST00000031975
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl640,576,717 - 40,585,821 (-)Ensembl
RefSeq Acc Id: ENSMUST00000101491   ⟹   ENSMUSP00000099030
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl640,574,894 - 40,585,803 (-)Ensembl
RefSeq Acc Id: ENSMUST00000129948   ⟹   ENSMUSP00000121848
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl640,577,850 - 40,585,795 (-)Ensembl
RefSeq Acc Id: ENSMUST00000177178   ⟹   ENSMUSP00000135240
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl640,577,960 - 40,585,790 (-)Ensembl
RefSeq Acc Id: NM_001038604   ⟹   NP_001033693
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39640,551,832 - 40,562,739 (-)NCBI
GRCm38640,574,898 - 40,585,805 (-)ENTREZGENE
MGSCv37640,524,897 - 40,535,804 (-)RGD
Celera640,562,066 - 40,572,779 (-)RGD
cM Map6 ENTREZGENE
Sequence:
RefSeq Acc Id: NM_021364   ⟹   NP_067339
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39640,551,832 - 40,562,739 (-)NCBI
GRCm38640,574,898 - 40,585,805 (-)ENTREZGENE
MGSCv37640,524,897 - 40,535,804 (-)RGD
Celera640,562,066 - 40,572,779 (-)RGD
cM Map6 ENTREZGENE
Sequence:
Reference Sequences
RefSeq Acc Id: NP_067339   ⟸   NM_021364
- Peptide Label: isoform 2
- UniProtKB: Q9R007 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001033693   ⟸   NM_001038604
- Peptide Label: isoform 1
- UniProtKB: Q9R007 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSMUSP00000135240   ⟸   ENSMUST00000177178
RefSeq Acc Id: ENSMUSP00000099030   ⟸   ENSMUST00000101491
RefSeq Acc Id: ENSMUSP00000121848   ⟸   ENSMUST00000129948
Protein Domains
C-type lectin

Promoters
RGD ID:6839624
Promoter ID:MM_KWN:45691
Type:Non-CpG
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:BoneMarrow_0Hour,   BoneMarrow_4Hour
Transcripts:NM_001038604,   NM_021364,   UC009BNC.1,   UC009BND.1
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv36640,535,469 - 40,535,969 (-)MPROMDB
RGD ID:6889438
Promoter ID:EPDNEW_M8164
Type:initiation region
Name:Clec5a_1
Description:Mus musculus C-type lectin domain family 5, member a , 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
GRCm38640,585,802 - 40,585,862EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:1345151 AgrOrtholog
Ensembl Genes ENSMUSG00000029915 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSMUSP00000099030 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSMUSP00000121848 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSMUSP00000135240 UniProtKB/TrEMBL
Ensembl Transcript ENSMUST00000101491 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSMUST00000129948 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSMUST00000177178 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
  CTDL_fold UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NKR-like_CTLD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report mmu:23845 UniProtKB/Swiss-Prot
MGD MGI:1345151 ENTREZGENE
NCBI Gene 23845 ENTREZGENE
Pfam Lectin_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Clec5a 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
UniGene Mm.103765 ENTREZGENE
UniProt A0A0R4J269_MOUSE UniProtKB/TrEMBL
  CLC5A_MOUSE UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q3SXC9 UniProtKB/Swiss-Prot
  Q3UV97 UniProtKB/Swiss-Prot
  Q8BL24 UniProtKB/Swiss-Prot