Clec4m (C-type lectin domain family 4 member M) - Rat Genome Database

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Gene: Clec4m (C-type lectin domain family 4 member M) Rattus norvegicus
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Symbol: Clec4m
Name: C-type lectin domain family 4 member M
RGD ID: 1561466
Description: Predicted to enable several functions, including (1->3)-beta-D-glucan binding activity; D-mannose binding activity; and virus receptor activity. Predicted to be involved in immune response; receptor-mediated virion attachment to host cell; and symbiont entry into host cell. Predicted to act upstream of or within several processes, including detection of other organism; phagocytosis, recognition; and positive regulation of tumor necrosis factor production. Predicted to be located in membrane. Predicted to be active in external side of plasma membrane. Human ortholog(s) of this gene implicated in extrapulmonary tuberculosis; pulmonary tuberculosis; and severe acute respiratory syndrome. Orthologous to human CLEC4M (C-type lectin domain family 4 member M); PARTICIPATES IN measles pathway; phagocytosis pathway; tuberculosis pathway; INTERACTS WITH 1,2-dimethylhydrazine; aflatoxin B1; alpha-Zearalanol.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: Cd209b; CD209b antigen
RGD Orthologs
Human
Mouse
Bonobo
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8126,713,795 - 6,722,414 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl126,713,812 - 6,722,410 (-)EnsemblGRCr8
mRatBN7.2121,915,902 - 1,924,529 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl121,915,919 - 1,924,539 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx122,594,215 - 2,602,852 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0123,217,785 - 3,226,422 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0121,980,552 - 1,989,192 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0122,817,633 - 2,826,303 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl122,816,065 - 2,826,378 (-)Ensemblrn6Rnor6.0
Rnor_5.0124,967,129 - 4,975,729 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4122,256,452 - 2,265,053 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera123,768,182 - 3,776,781 (-)NCBICelera
Cytogenetic Map12p12NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Homozygous L-SIGN (CLEC4M) plays a protective role in SARS coronavirus infection. Chan VS, etal., Nat Genet. 2006 Jan;38(1):38-46. doi: 10.1038/ng1698. Epub 2005 Dec 20.
2. Association of CD209 and CD209L polymorphisms with tuberculosis infection in a Northeastern Brazilian population. da Silva RC, etal., Mol Biol Rep. 2014 Aug;41(8):5449-57. doi: 10.1007/s11033-014-3416-y. Epub 2014 May 30.
3. The allele 4 of neck region liver-lymph node-specific ICAM-3-grabbing integrin variant is associated with spontaneous clearance of hepatitis C virus and decrease of viral loads. Ezzikouri S, etal., Clin Microbiol Infect. 2014 May;20(5):O325-32. doi: 10.1111/1469-0691.12403. Epub 2013 Nov 6.
4. Association of CD209L tandem repeats polymorphism with susceptibility to human immunodeficiency virus-1 infection, disease progression, and treatment outcomes: a Moroccan cohort study. Fayssel N, etal., Clin Microbiol Infect. 2015 May;21(5):513.e1-5. doi: 10.1016/j.cmi.2014.12.012. Epub 2014 Dec 27.
5. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
6. Role of polymorphisms of the inflammatory response genes and DC-SIGNR in genetic susceptibility to SARS and other infections. Khoo US, etal., Hong Kong Med J. 2008 Aug;14 Suppl 4:31-5.
7. Specific ICAM-3 grabbing nonintegrin-related 1 (SIGNR1) expressed by marginal zone macrophages is essential for defense against pulmonary Streptococcus pneumoniae infection. Koppel EA, etal., Eur J Immunol. 2005 Oct;35(10):2962-9. doi: 10.1002/eji.200526216.
8. SIGN-R1 contributes to protection against lethal pneumococcal infection in mice. Lanoue A, etal., J Exp Med. 2004 Dec 6;200(11):1383-93. doi: 10.1084/jem.20040795.
9. Repeat-region polymorphisms in the gene for the dendritic cell-specific intercellular adhesion molecule-3-grabbing nonintegrin-related molecule: effects on HIV-1 susceptibility. Liu H, etal., J Infect Dis. 2006 Mar 1;193(5):698-702. doi: 10.1086/499820. Epub 2006 Jan 27.
10. [Relationship between intrauterine infection and the gene polymorphism of DC-SIGN/DC-SIGNR in the pregnant women of HBV positive]. Liu SR, etal., Zhonghua Shi Yan He Lin Chuang Bing Du Xue Za Zhi. 2011 Oct;25(5):331-3.
11. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
12. GOA pipeline RGD automated data pipeline
13. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
14. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
15. The C-type lectin SIGNR1 binds Schistosoma mansoni antigens in vitro, but SIGNR1-deficient mice have normal responses during schistosome infection. Saunders SP, etal., Infect Immun. 2009 Jan;77(1):399-404. doi: 10.1128/IAI.00762-08. Epub 2008 Nov 3.
16. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
17. Lack of support for an association between CLEC4M homozygosity and protection against SARS coronavirus infection. Tang NL, etal., Nat Genet. 2007 Jun;39(6):691-2; author reply 694-6. doi: 10.1038/ng0607-691.
18. A murine DC-SIGN homologue contributes to early host defense against Mycobacterium tuberculosis. Tanne A, etal., J Exp Med. 2009 Sep 28;206(10):2205-20. doi: 10.1084/jem.20090188. Epub 2009 Sep 21.
19. Mice lacking SIGNR1 have stronger T helper 1 responses to Mycobacterium tuberculosis. Wieland CW, etal., Microbes Infect. 2007 Feb;9(2):134-41. doi: 10.1016/j.micinf.2006.10.018. Epub 2006 Dec 14.
20. The nine-repeat DC-SIGNR isoform is associated with increased HIV-RNA loads and HIV sexual transmission. Xu L, etal., J Clin Immunol. 2010 May;30(3):402-7. doi: 10.1007/s10875-010-9376-7. Epub 2010 Mar 9.
21. Murine SIGNR1 (CD209b) Contributes to the Clearance of Uropathogenic Escherichia coli During Urinary Tract Infections. Zhang Y, etal., Front Cell Infect Microbiol. 2020 Jan 10;9:457. doi: 10.3389/fcimb.2019.00457. eCollection 2019.
22. Lack of support for an association between CLEC4M homozygosity and protection against SARS coronavirus infection. Zhi L, etal., Nat Genet. 2007 Jun;39(6):692-4; author reply 694-6. doi: 10.1038/ng0607-692.
Additional References at PubMed
PMID:12609975   PMID:14707091   PMID:15496474   PMID:16682406   PMID:18697825   PMID:19095040   PMID:20130211   PMID:21810271  


Genomics

Comparative Map Data
Clec4m
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8126,713,795 - 6,722,414 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl126,713,812 - 6,722,410 (-)EnsemblGRCr8
mRatBN7.2121,915,902 - 1,924,529 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl121,915,919 - 1,924,539 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx122,594,215 - 2,602,852 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0123,217,785 - 3,226,422 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0121,980,552 - 1,989,192 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0122,817,633 - 2,826,303 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl122,816,065 - 2,826,378 (-)Ensemblrn6Rnor6.0
Rnor_5.0124,967,129 - 4,975,729 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4122,256,452 - 2,265,053 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera123,768,182 - 3,776,781 (-)NCBICelera
Cytogenetic Map12p12NCBI
CLEC4M
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38197,763,243 - 7,769,605 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl197,763,153 - 7,769,606 (+)Ensemblhg38GRCh38
GRCh37197,828,129 - 7,834,491 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36197,734,081 - 7,740,491 (+)NCBIBuild 36Build 36hg18NCBI36
Celera197,699,445 - 7,705,764 (+)NCBICelera
Cytogenetic Map19p13.2NCBI
HuRef197,498,098 - 7,504,416 (+)NCBIHuRef
CHM1_1197,827,770 - 7,834,226 (+)NCBICHM1_1
T2T-CHM13v2.0197,764,262 - 7,770,624 (+)NCBIT2T-CHM13v2.0
Cd209b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3983,967,655 - 3,976,841 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl83,967,655 - 3,976,844 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm3883,917,655 - 3,926,841 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl83,917,655 - 3,926,844 (-)Ensemblmm10GRCm38
MGSCv3783,917,657 - 3,926,814 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv3683,917,657 - 3,926,814 (-)NCBIMGSCv36mm8
Celera83,005,643 - 3,014,800 (-)NCBICelera
Cytogenetic Map8A1.1NCBI
cM Map81.92NCBI
LOC100978434
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22012,444,554 - 12,450,929 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11911,561,684 - 11,568,043 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0197,062,961 - 7,069,381 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1197,916,430 - 7,922,634 (+)NCBIPanPan1.1PanPan1.1panPan2

Variants

.
Variants in Clec4m
86 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:28
Count of miRNA genes:27
Interacting mature miRNAs:28
Transcripts:ENSRNOT00000061749
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2312418Kidm41Kidney mass QTL 413.70.0001kidney mass (VT:0002707)single kidney wet weight to body weight ratio (CMO:0000622)12592191825247790Rat
724526Uae3Urinary albumin excretion QTL 34.90.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)12115486827Rat
2306789Ean6Experimental allergic neuritis QTL 64.9nervous system integrity trait (VT:0010566)experimental autoimmune neuritis severity score (CMO:0001528)12129775522Rat
7204484Bp358Blood pressure QTL 3580.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)12124849755Rat
7387292Kidm42Kidney mass QTL 423.030.0004kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)12141361854Rat
1357337Gluco3Glucose level QTL 30.0004adipocyte glucose uptake trait (VT:0004185)absolute change in adipocyte glucose uptake (CMO:0000873)12116966671Rat
5684888Pia42Pristane induced arthritis QTL 42joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)12348941648489416Rat
1331739Hrtrt14Heart rate QTL 143.56232heart pumping trait (VT:2000009)heart rate (CMO:0000002)12138687564Rat
1298081Cia25Collagen induced arthritis QTL 254.7joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)12274769447747694Rat
2303568Bw88Body weight QTL 883body mass (VT:0001259)body weight (CMO:0000012)12128606299Rat
61331Eau2Experimental allergic uveoretinitis QTL 20.0005uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)12133700600Rat
2303575Insul14Insulin level QTL 144blood insulin amount (VT:0001560)blood insulin level (CMO:0000349)12308718048087180Rat
61334Gluco17Glucose level QTL 176.3adipocyte glucose uptake trait (VT:0004185)adipocyte maximal glucose uptake to basal glucose uptake ratio (CMO:0000874)12116966671Rat
2293684Bmd26Bone mineral density QTL 264.40.0002femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)12138635130Rat
6893681Bw109Body weight QTL 1092.30.004body mass (VT:0001259)body weight (CMO:0000012)12128133365Rat
7243862Mcs30Mammary carcinoma susceptibility QTL 308.62mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)12563330650633306Rat
1300174Bw15Body weight QTL 152.93body mass (VT:0001259)body weight loss (CMO:0001399)12128606299Rat
1600391Edcs2Endometrial carcinoma susceptibility QTL23.50.01uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)12111869600Rat
1331787Rf41Renal function QTL 412.998kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)12133700556Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
8 5 7 35 81 83 53 65 53 6 167 90 17 12 33 30

Sequence


Ensembl Acc Id: ENSRNOT00000061749   ⟹   ENSRNOP00000058462
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl126,713,812 - 6,722,410 (-)Ensembl
mRatBN7.2 Ensembl121,915,919 - 1,924,539 (-)Ensembl
Rnor_6.0 Ensembl122,816,065 - 2,826,378 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000109537   ⟹   ENSRNOP00000095311
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl126,713,812 - 6,722,398 (-)Ensembl
mRatBN7.2 Ensembl121,915,919 - 1,924,505 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000112550   ⟹   ENSRNOP00000097292
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl126,714,002 - 6,722,398 (-)Ensembl
mRatBN7.2 Ensembl121,915,919 - 1,924,539 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000113925   ⟹   ENSRNOP00000079214
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl126,714,002 - 6,722,398 (-)Ensembl
mRatBN7.2 Ensembl121,916,109 - 1,924,505 (-)Ensembl
RefSeq Acc Id: NM_001170397   ⟹   NP_001163868
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8126,713,795 - 6,722,395 (-)NCBI
mRatBN7.2121,915,902 - 1,924,502 (-)NCBI
Rnor_6.0122,817,633 - 2,826,233 (-)NCBI
Rnor_5.0124,967,129 - 4,975,729 (-)NCBI
RGSC_v3.4122,256,452 - 2,265,053 (+)RGD
Celera123,768,182 - 3,776,781 (-)RGD
Sequence:
RefSeq Acc Id: XM_039089146   ⟹   XP_038945074
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8126,713,854 - 6,722,414 (-)NCBI
mRatBN7.2121,915,961 - 1,924,529 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001163868 (Get FASTA)   NCBI Sequence Viewer  
  XP_038945074 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH91252 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000058462
  ENSRNOP00000058462.4
  ENSRNOP00000079214.1
  ENSRNOP00000095311.1
  ENSRNOP00000097292.2
RefSeq Acc Id: NP_001163868   ⟸   NM_001170397
- UniProtKB: F1LM87 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000058462   ⟸   ENSRNOT00000061749
RefSeq Acc Id: XP_038945074   ⟸   XM_039089146
- Peptide Label: isoform X1
- UniProtKB: A0A8I6ANB8 (UniProtKB/TrEMBL),   F1LM87 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000079214   ⟸   ENSRNOT00000113925
Ensembl Acc Id: ENSRNOP00000097292   ⟸   ENSRNOT00000112550
Ensembl Acc Id: ENSRNOP00000095311   ⟸   ENSRNOT00000109537
Protein Domains
C-type lectin

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1LM87-F1-model_v2 AlphaFold F1LM87 1-319 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13698386
Promoter ID:EPDNEW_R8910
Type:single initiation site
Name:Clec4m_1
Description:C-type lectin domain family 4 member M
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0122,826,236 - 2,826,296EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1561466 AgrOrtholog
BioCyc Gene G2FUF-20376 BioCyc
Ensembl Genes ENSRNOG00000029881 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000061749 ENTREZGENE
  ENSRNOT00000061749.6 UniProtKB/TrEMBL
  ENSRNOT00000109537.2 UniProtKB/TrEMBL
  ENSRNOT00000112550.2 UniProtKB/TrEMBL
  ENSRNOT00000113925.2 UniProtKB/TrEMBL
Gene3D-CATH 3.10.100.10 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7373942 IMAGE-MGC_LOAD
InterPro C-type_lectin UniProtKB/TrEMBL
  C-type_lectin-like UniProtKB/TrEMBL
  C-type_lectin/snaclec_domain UniProtKB/TrEMBL
  C-type_lectin_fold UniProtKB/TrEMBL
  CD209-like_CTLD UniProtKB/TrEMBL
KEGG Report rno:288378 UniProtKB/TrEMBL
MGC_CLONE MGC:109062 IMAGE-MGC_LOAD
NCBI Gene 288378 ENTREZGENE
PANTHER MANNOSE, PHOSPHOLIPASE, LECTIN RECEPTOR RELATED UniProtKB/TrEMBL
Pfam Lectin_C UniProtKB/TrEMBL
PhenoGen Clec4m PhenoGen
PROSITE C_TYPE_LECTIN_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000029881 RatGTEx
SMART CLECT UniProtKB/TrEMBL
Superfamily-SCOP C-type_lectin_fold UniProtKB/TrEMBL
UniProt A0A8I6AN71_RAT UniProtKB/TrEMBL
  A0A8I6ANB8 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6G4Z8_RAT UniProtKB/TrEMBL
  F1LM87 ENTREZGENE, UniProtKB/TrEMBL
  Q5BK08_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-11-02 Clec4m  C-type lectin domain family 4 member M  Cd209b  CD209b antigen  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-02-09 Cd209b  CD209b antigen      Symbol and Name status set to provisional 70820 PROVISIONAL