Clec2m (C-type lectin domain family 2, member m) - Rat Genome Database

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Gene: Clec2m (C-type lectin domain family 2, member m) Mus musculus
Analyze
Symbol: Clec2m
Name: C-type lectin domain family 2, member m
RGD ID: 1557648
MGI Page MGI
Description: ENCODES a protein that exhibits signaling receptor activity (ortholog); INVOLVED IN natural killer cell mediated cytotoxicity (ortholog); negative regulation of GTPase activity (ortholog); negative regulation of natural killer cell chemotaxis (ortholog); FOUND IN cell surface (ortholog); plasma membrane (ortholog); INTERACTS WITH sodium arsenite; bisphenol A (ortholog); DDT (ortholog)
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: 4922502D21Rik; C-type lectin-like receptor 2m; Gm1074; hypothetical protein LOC381816; MGC107125; RIKEN cDNA 4922502D21 gene; SPATA78
RGD Orthologs
Human
Rat
Chinchilla
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
GRCm396129,299,128 - 129,308,770 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl6129,299,127 - 129,308,759 (-)EnsemblGRCm39 Ensembl
GRCm386129,322,165 - 129,331,807 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl6129,322,164 - 129,331,796 (-)EnsemblGRCm38mm10GRCm38
MGSCv376129,272,183 - 129,281,799 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv366129,287,857 - 129,297,446 (-)NCBIMGSCv36mm8
Celera6131,044,514 - 131,054,123 (-)NCBICelera
Cytogenetic Map6F3NCBI
cM Map663.25NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


1 to 9 of 9 rows

  
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Clec2mMousebisphenol A increases methylationISOClec2m (Rattus norvegicus)6480464bisphenol A results in increased methylation of CLEC2M geneCTDPMID:28505145
Clec2mMousebisphenol A decreases expressionISOKLRC4-KLRK1 (Homo sapiens)6480464bisphenol A results in decreased expression of KLRC4-KLRK1 mRNACTDPMID:36232920
Clec2mMouseDDT increases methylationISOClec2m (Rattus norvegicus)6480464DDT results in increased methylation of CLEC2M geneCTDPMID:31682807
Clec2mMouselipopolysaccharide multiple interactionsISOKLRC4-KLRK1 (Homo sapiens)6480464[S-(1 more ...CTDPMID:35811015
Clec2mMouselipopolysaccharide decreases expressionISOKLRC4-KLRK1 (Homo sapiens)6480464Lipopolysaccharides results in decreased expression of KLRC4-KLRK1 mRNACTDPMID:35811015
Clec2mMouseS-(1,2-dichlorovinyl)-L-cysteine multiple interactionsISOKLRC4-KLRK1 (Homo sapiens)6480464[S-(1 more ...CTDPMID:35811015
Clec2mMousesodium arsenite decreases expressionEXP 6480464sodium arsenite results in decreased expression of CLEC2M mRNACTDPMID:37682722
Clec2mMousetriphenyl phosphate affects expressionISOKLRC4-KLRK1 (Homo sapiens)6480464triphenyl phosphate affects the expression of KLRC4-KLRK1 mRNACTDPMID:37042841
Clec2mMousevinclozolin increases methylationISOClec2m (Rattus norvegicus)6480464vinclozolin results in increased methylation of CLEC2M geneCTDPMID:31682807

1 to 9 of 9 rows

Biological Process

  

Cellular Component

  
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Clec2mMousecell surface located_inISOKLRC4-KLRK1 (Homo sapiens)9068941 PMID:10426994 and PMID:15294961UniProtPMID:10426994 and PMID:15294961
Clec2mMousecellular_component is_active_inND 2290270 MGIGO_REF:0000015
Clec2mMouseplasma membrane located_inISOKLRC4-KLRK1 (Homo sapiens)9068941 PMID:17562706UniProtGO_REF:0000052 and PMID:17562706

Molecular Function
1 to 14 of 14 rows

  
1 to 14 of 14 rows


#
Reference Title
Reference Citation
1. MGDs mouse GO annotations MGD data from the GO Consortium
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
PMID:10349636   PMID:11042159   PMID:11076861   PMID:11217851   PMID:12466851   PMID:12477932   PMID:15613475   PMID:16141072   PMID:16141073   PMID:20544345   PMID:21677750   PMID:21873635  



Clec2m
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm396129,299,128 - 129,308,770 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl6129,299,127 - 129,308,759 (-)EnsemblGRCm39 Ensembl
GRCm386129,322,165 - 129,331,807 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl6129,322,164 - 129,331,796 (-)EnsemblGRCm38mm10GRCm38
MGSCv376129,272,183 - 129,281,799 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv366129,287,857 - 129,297,446 (-)NCBIMGSCv36mm8
Celera6131,044,514 - 131,054,123 (-)NCBICelera
Cytogenetic Map6F3NCBI
cM Map663.25NCBI
KLRC4-KLRK1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381210,372,353 - 10,410,146 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1210,372,353 - 10,391,874 (-)EnsemblGRCh38hg38GRCh38
GRCh38.p14 Ensembl1210,372,353 - 10,410,146 (-)EnsemblGRCh38hg38GRCh38
GRCh371210,524,952 - 10,562,745 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map12p13.2NCBI
HuRef1210,267,379 - 10,305,170 (-)NCBIHuRef
CHM1_11210,494,385 - 10,532,177 (-)NCBICHM1_1
T2T-CHM13v2.01210,259,174 - 10,296,963 (-)NCBIT2T-CHM13v2.0
Clec2m
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr84164,455,031 - 164,465,936 (-)NCBIGRCr8
mRatBN7.24162,768,988 - 162,779,951 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl4162,768,994 - 162,779,899 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx4169,004,613 - 169,014,521 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.04164,787,558 - 164,797,469 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.04163,421,609 - 163,431,518 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.04163,085,480 - 163,095,387 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4163,084,689 - 163,095,614 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04211,729,448 - 211,739,355 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44166,571,242 - 166,582,151 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera4151,457,726 - 151,467,634 (-)NCBICelera
Cytogenetic Map4q42NCBI
LOC102005691
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554137,489,127 - 7,504,956 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554137,489,158 - 7,503,014 (+)NCBIChiLan1.0ChiLan1.0
LOC100687968
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12736,059,707 - 36,068,092 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2710,555,689 - 10,564,069 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02736,406,096 - 36,414,471 (+)NCBIROS_Cfam_1.0
UMICH_Zoey_3.12736,293,162 - 36,301,539 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02736,316,965 - 36,325,348 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02710,077,763 - 10,086,143 (-)NCBIUU_Cfam_GSD_1.0
LOC101976242
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494597,084,874 - 97,099,433 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936902216,495 - 229,141 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936902216,495 - 229,150 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LOC100519314
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1561,724,744 - 61,736,667 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2564,653,296 - 64,665,221 (+)NCBISscrofa10.2Sscrofa10.2susScr3
KLRK1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11110,207,066 - 10,223,922 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1110,207,211 - 10,223,899 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660892,283,754 - 2,301,143 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0

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Variants in Clec2m
585 total Variants

Predicted Target Of
Summary Value
Count of predictions:264
Count of miRNA genes:210
Interacting mature miRNAs:232
Transcripts:ENSMUST00000051283
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.


1 to 10 of 41 rows
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD ID
Symbol
Name
LOD
P Value
Trait
Sub Trait
Chr
Start
Stop
Species
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
10449437Pas15_mpulmonary adenoma susceptibility 15 (mouse)6128180868149588044Mouse
10449436Pas17_mpulmonary adenoma susceptibility 17 (mouse)6124334273145601739Mouse
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

1 to 10 of 41 rows






Ensembl Acc Id: ENSMUST00000051283   ⟹   ENSMUSP00000062024
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl6129,299,127 - 129,308,759 (-)Ensembl
GRCm38.p6 Ensembl6129,322,164 - 129,331,796 (-)Ensembl
Ensembl Acc Id: ENSMUST00000203159   ⟹   ENSMUSP00000145310
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl6129,299,810 - 129,303,659 (-)Ensembl
GRCm38.p6 Ensembl6129,322,847 - 129,326,696 (-)Ensembl
RefSeq Acc Id: NM_199034   ⟹   NP_950199
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm396129,299,128 - 129,308,744 (-)NCBI
GRCm386129,322,165 - 129,331,781 (-)NCBI
MGSCv376129,272,183 - 129,281,799 (-)RGD
Celera6131,044,514 - 131,054,123 (-)RGD
cM Map6 ENTREZGENE
Sequence:
RefSeq Acc Id: XM_006506353   ⟹   XP_006506416
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm396129,299,128 - 129,308,770 (-)NCBI
GRCm386129,322,165 - 129,331,807 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006506354   ⟹   XP_006506417
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm396129,299,128 - 129,308,769 (-)NCBI
GRCm386129,322,165 - 129,331,806 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006506355   ⟹   XP_006506418
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm396129,299,810 - 129,308,769 (-)NCBI
GRCm386129,322,165 - 129,331,806 (-)NCBI
Sequence:
RefSeq Acc Id: NP_950199   ⟸   NM_199034
- UniProtKB: Q8C634 (UniProtKB/TrEMBL),   A0A0S2SPY8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006506418   ⟸   XM_006506355
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_006506416   ⟸   XM_006506353
- Peptide Label: isoform X1
- UniProtKB: A0A0S2SPY8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006506417   ⟸   XM_006506354
- Peptide Label: isoform X2
- Sequence:
Ensembl Acc Id: ENSMUSP00000145310   ⟸   ENSMUST00000203159
C-type lectin

Name Modeler Protein Id AA Range Protein Structure
AF-Q8C634-F1-model_v2 AlphaFold Q8C634 1-189 view protein structure

RGD ID:6891190
Promoter ID:EPDNEW_M9046
Type:initiation region
Name:4922502D21Rik_1
Description:Mus musculus RIKEN cDNA 4922502D21 gene , 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
GRCm386129,331,765 - 129,331,825EPDNEW


1 to 24 of 24 rows
Database
Acc Id
Source(s)
Ensembl Genes ENSMUSG00000047720 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSMUST00000051283 ENTREZGENE
  ENSMUST00000051283.8 UniProtKB/TrEMBL
  ENSMUST00000203159.2 UniProtKB/TrEMBL
Gene3D-CATH 3.10.100.10 UniProtKB/TrEMBL
InterPro C-type_lectin UniProtKB/TrEMBL
  C-type_lectin-like UniProtKB/TrEMBL
  C-type_lectin_fold UniProtKB/TrEMBL
  KLR_subfamily_B UniProtKB/TrEMBL
  NKR-like_CTLD UniProtKB/TrEMBL
KEGG Report mmu:381816 UniProtKB/TrEMBL
MGD MGI:2685920 ENTREZGENE
NCBI Gene 381816 ENTREZGENE
PANTHER KILLER CELL LECTIN-LIKE RECEPTOR SUBFAMILY B MEMBER 1 UniProtKB/TrEMBL
  KILLER CELL LECTIN-LIKE RECEPTOR SUBFAMILY B MEMBER 1 UniProtKB/TrEMBL
Pfam Lectin_C UniProtKB/TrEMBL
PhenoGen Clec2m PhenoGen
PROSITE C_TYPE_LECTIN_2 UniProtKB/TrEMBL
SMART CLECT UniProtKB/TrEMBL
Superfamily-SCOP C-type_lectin_fold UniProtKB/TrEMBL
UniProt A0A0N4SVZ3_MOUSE UniProtKB/TrEMBL
  A0A0S2SPY8 ENTREZGENE, UniProtKB/TrEMBL
  Q3V138_MOUSE UniProtKB/TrEMBL
  Q8C634 ENTREZGENE, UniProtKB/TrEMBL
1 to 24 of 24 rows


Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-08-20 Clec2m  C-type lectin domain family 2, member m  4922502D21Rik  RIKEN cDNA 4922502D21 gene  Symbol and/or name change 5135510 APPROVED