Cd209d (CD209d molecule) - Rat Genome Database

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Gene: Cd209d (CD209d molecule) Rattus norvegicus
Analyze
Symbol: Cd209d
Name: CD209d molecule
RGD ID: 1561104
Description: Predicted to enable identical protein binding activity; mannose binding activity; and virus receptor activity. Predicted to be involved in several processes, including B cell adhesion; positive regulation of T cell proliferation; and positive regulation of viral life cycle. Predicted to act upstream of or within several processes, including defense response to bacterium; positive regulation of cytokine production; and regulation of T cell proliferation. Predicted to be located in plasma membrane. Predicted to be active in external side of plasma membrane. Human ortholog(s) of this gene implicated in Coronavirus infectious disease; aspergillosis; dengue disease (multiple); human immunodeficiency virus infectious disease (multiple); and tuberculosis (multiple). Orthologous to human CD209 (CD209 molecule); INTERACTS WITH bisphenol A; pravastatin; zaragozic acid A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: C-type lectin domain family 4, member M; Cd209; CD209 molecule; CD209 molecule D; CD209d antigen; Clec4m; DC-SIGN-related protein; Dc-signr; LOC363856; RGD1561104; similar to SIGNR3
RGD Orthologs
Human
Mouse
Bonobo
Dog
Pig
Green Monkey
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8126,689,002 - 6,695,452 (-)NCBIGRCr8
mRatBN7.2121,891,109 - 1,897,559 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl121,891,113 - 1,901,171 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx122,563,742 - 2,570,191 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0123,187,308 - 3,193,757 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0121,950,083 - 1,956,532 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0122,406,879 - 2,413,324 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl122,406,879 - 2,413,324 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0124,560,987 - 4,567,014 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4122,283,730 - 2,290,484 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera123,744,146 - 3,750,549 (-)NCBICelera
Cytogenetic Map12p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. 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.
2. [A variant in the CD209 (DC-SIGN) promoter is associated with severity of dengue disease]. Desprès P, etal., Med Sci (Paris). 2005 Nov;21(11):905-6. doi: 10.1051/medsci/20052111905.
3. 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.
4. DC-SIGN (CD209) gene promoter polymorphisms in a Brazilian population and their association with human T-cell lymphotropic virus type 1 infection. Kashima S, etal., J Gen Virol. 2009 Apr;90(Pt 4):927-934. doi: 10.1099/vir.0.008367-0. Epub 2009 Mar 4.
5. RANTES -28G delays and DC-SIGN - 139C enhances AIDS progression in HIV type 1-infected Japanese hemophiliacs. Koizumi Y, etal., AIDS Res Hum Retroviruses. 2007 May;23(5):713-9. doi: 10.1089/aid.2006.0225.
6. CD209 C-Type Lectins Promote Host Invasion, Dissemination, and Infection of Toxoplasma gondii. Njiri OA, etal., Front Immunol. 2020 Apr 23;11:656. doi: 10.3389/fimmu.2020.00656. eCollection 2020.
7. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
8. [Association between genetic polymorphism in the promotor region of CD209 and propensity to develop invasive pulmonary aspergillosis]. Sainz J, etal., Methods Find Exp Clin Pharmacol. 2010 Dec;32 Suppl A:9-13.
9. Dectin-1 and DC-SIGN polymorphisms associated with invasive pulmonary Aspergillosis infection. Sainz J, etal., PLoS One. 2012;7(2):e32273. doi: 10.1371/journal.pone.0032273. Epub 2012 Feb 27.
10. A variant in the CD209 promoter is associated with severity of dengue disease. Sakuntabhai A, etal., Nat Genet. 2005 May;37(5):507-13. doi: 10.1038/ng1550. Epub 2005 Apr 17.
11. CD209 gene polymorphisms in South Indian HIV and HIV-TB patients. Selvaraj P, etal., Infect Genet Evol. 2009 Mar;9(2):256-62. doi: 10.1016/j.meegid.2008.12.003. Epub 2008 Dec 14.
12. Presence of increased inflammatory infiltrates accompanied by activated dendritic cells in the left atrium in rheumatic heart disease. Shiba M, etal., PLoS One. 2018 Sep 27;13(9):e0203756. doi: 10.1371/journal.pone.0203756. eCollection 2018.
13. DC-SIGN (CD209) Promoter -336 A/G polymorphism is associated with dengue hemorrhagic fever and correlated to DC-SIGN expression and immune augmentation. Wang L, etal., PLoS Negl Trop Dis. 2011 Jan 4;5(1):e934. doi: 10.1371/journal.pntd.0000934.
14. CD209 promoter polymorphisms associate with HCV infection and pegylated-interferon plus ribavirin treatment response. Zupin L, etal., Mol Immunol. 2016 Aug;76:49-54. doi: 10.1016/j.molimm.2016.06.009. Epub 2016 Jun 24.
Additional References at PubMed
PMID:12421943   PMID:12456590   PMID:16621794   PMID:16682406   PMID:18697825   PMID:19770268   PMID:20130211   PMID:24942581  


Genomics

Comparative Map Data
Cd209d
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8126,689,002 - 6,695,452 (-)NCBIGRCr8
mRatBN7.2121,891,109 - 1,897,559 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl121,891,113 - 1,901,171 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx122,563,742 - 2,570,191 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0123,187,308 - 3,193,757 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0121,950,083 - 1,956,532 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0122,406,879 - 2,413,324 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl122,406,879 - 2,413,324 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0124,560,987 - 4,567,014 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4122,283,730 - 2,290,484 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera123,744,146 - 3,750,549 (-)NCBICelera
Cytogenetic Map12p12NCBI
CD209
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38197,739,993 - 7,747,534 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl197,739,993 - 7,747,564 (-)EnsemblGRCh38hg38GRCh38
GRCh37197,804,879 - 7,812,420 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36197,710,882 - 7,718,406 (-)NCBINCBI36Build 36hg18NCBI36
Build 34197,710,881 - 7,718,406NCBI
Celera197,676,294 - 7,683,878 (-)NCBICelera
Cytogenetic Map19p13.2NCBI
HuRef197,474,941 - 7,482,525 (-)NCBIHuRef
CHM1_1197,804,605 - 7,812,189 (-)NCBICHM1_1
T2T-CHM13v2.0197,741,021 - 7,748,561 (-)NCBIT2T-CHM13v2.0
Cd209d
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3983,921,824 - 3,928,548 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl83,921,824 - 3,928,555 (-)EnsemblGRCm39 Ensembl
GRCm3883,871,824 - 3,878,548 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl83,871,824 - 3,878,555 (-)EnsemblGRCm38mm10GRCm38
MGSCv3783,871,824 - 3,878,499 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3683,871,824 - 3,878,499 (-)NCBIMGSCv36mm8
Celera84,090,520 - 4,097,195 (-)NCBICelera
Cytogenetic Map8A1.1NCBI
cM Map81.92NCBI
CD209
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22012,421,655 - 12,428,882 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11911,538,933 - 11,546,022 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0197,042,033 - 7,047,350 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1197,884,253 - 7,901,144 (-)NCBIpanpan1.1PanPan1.1panPan2
CD209
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12052,517,759 - 52,542,085 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2052,518,036 - 52,520,942 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2052,321,405 - 52,324,255 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02053,046,667 - 53,049,895 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2053,045,924 - 53,049,856 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12052,250,315 - 52,253,163 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02052,694,052 - 52,696,903 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02052,925,204 - 52,928,055 (-)NCBIUU_Cfam_GSD_1.0
CD209
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl271,394,391 - 71,397,968 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1271,394,414 - 71,397,711 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2271,928,204 - 71,931,502 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CD209
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.167,219,576 - 7,235,755 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl67,228,378 - 7,235,208 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666081610,911 - 626,900 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in Cd209d
16 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:19
Count of miRNA genes:19
Interacting mature miRNAs:19
Transcripts:ENSRNOT00000001344
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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1300174Bw15Body weight QTL 152.93body mass (VT:0001259)body weight loss (CMO:0001399)1219318387Rat
2312418Kidm41Kidney mass QTL 413.70.0001kidney mass (VT:0002707)single kidney wet weight to body weight ratio (CMO:0000622)12119611090Rat
10755457Coatc14Coat color QTL 140.01759coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)12122591684Rat
6893681Bw109Body weight QTL 1092.30.004body mass (VT:0001259)body weight (CMO:0000012)12123297788Rat
1581516Cm56Cardiac mass QTL 564.20.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)12129333307Rat
1598855Bp294Blood pressure QTL 2943.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)12134851688Rat
7411660Foco28Food consumption QTL 2810.90.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12142110980Rat
9590086Insglur6Insulin/glucose ratio QTL 618.970.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)12142110980Rat
8694179Bw150Body weight QTL 1502.90.001body mass (VT:0001259)body weight gain (CMO:0000420)12142110980Rat
7411586Foco5Food consumption QTL 55.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12142110980Rat
7411595Foco9Food consumption QTL 940.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12142110980Rat
7411545Bw128Body weight QTL 1285.20.001body mass (VT:0001259)body weight gain (CMO:0000420)12142110980Rat
9590147Scort7Serum corticosterone level QTL 713.610.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)12142110980Rat
2303575Insul14Insulin level QTL 144blood insulin amount (VT:0001560)blood insulin level (CMO:0000349)12142450532Rat
737979Pia22Pristane induced arthritis QTL 2253.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)12144465750Rat
634351Apr5Acute phase response QTL 56.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)12144503507Rat
2302042Pia38Pristane induced arthritis QTL 383.50.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)12144503507Rat
7243862Mcs30Mammary carcinoma susceptibility QTL 308.62mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)127977298525593Rat
634350Apr4Acute phase response QTL 46orosomucoid 1 amount (VT:0010541)plasma orosomucoid 1 level (CMO:0001467)12117200546172005Rat


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system nervous system renal system reproductive system respiratory system
High
Medium 1
Low 1 3 13 2 2 2
Below cutoff 1 2 15 6 5 6 7 6 9 9

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000001344   ⟹   ENSRNOP00000001344
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl121,891,113 - 1,901,171 (-)Ensembl
Rnor_6.0 Ensembl122,406,879 - 2,413,324 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000108377   ⟹   ENSRNOP00000081859
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl121,891,113 - 1,901,171 (-)Ensembl
RefSeq Acc Id: NM_001108849   ⟹   NP_001102319
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8126,689,002 - 6,695,452 (-)NCBI
mRatBN7.2121,891,109 - 1,897,559 (-)NCBI
Rnor_6.0122,406,879 - 2,413,324 (-)NCBI
Rnor_5.0124,560,987 - 4,567,014 (-)NCBI
RGSC_v3.4122,283,730 - 2,290,484 (+)RGD
Celera123,744,146 - 3,750,549 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001102319 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL74968 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000001344.3
  ENSRNOP00000081859
  ENSRNOP00000081859.1
Reference Protein Sequences
RefSeq Acc Id: NP_001102319   ⟸   NM_001108849
- UniProtKB: A6KQ43 (UniProtKB/TrEMBL),   A0A8I5ZTZ4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000001344   ⟸   ENSRNOT00000001344
RefSeq Acc Id: ENSRNOP00000081859   ⟸   ENSRNOT00000108377
Protein Domains
C-type lectin

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZXN3-F1-model_v2 AlphaFold D3ZXN3 1-237 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1561104 AgrOrtholog
BioCyc Gene G2FUF-20377 BioCyc
Ensembl Genes ENSRNOG00000001017 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000001344.4 UniProtKB/TrEMBL
  ENSRNOT00000108377 ENTREZGENE
  ENSRNOT00000108377.1 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_CS UniProtKB/TrEMBL
  C-type_lectin_fold UniProtKB/TrEMBL
  CD209-like_CTLD UniProtKB/TrEMBL
KEGG Report rno:363856 UniProtKB/TrEMBL
NCBI Gene 363856 ENTREZGENE
PANTHER C-TYPE LECTIN DOMAIN FAMILY 4 MEMBER M UniProtKB/TrEMBL
  C-TYPE LECTIN SUPERFAMILY MEMBER UniProtKB/TrEMBL
Pfam Lectin_C UniProtKB/TrEMBL
PhenoGen Cd209d PhenoGen
PROSITE C_TYPE_LECTIN_1 UniProtKB/TrEMBL
  C_TYPE_LECTIN_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000001017 RatGTEx
SMART CLECT UniProtKB/TrEMBL
Superfamily-SCOP C-type_lectin_fold UniProtKB/TrEMBL
UniProt A0A8I5ZTZ4 ENTREZGENE, UniProtKB/TrEMBL
  A6KQ43 ENTREZGENE, UniProtKB/TrEMBL
  D3ZXN3_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2022-03-07 Cd209d  CD209d molecule  Cd209d  CD209 molecule D  Name changed 629549 APPROVED
2022-03-07 Cd209d  CD209 molecule D  Cd209  CD209 molecule  Name and Symbol changed 629549 APPROVED
2018-01-15 Cd209  CD209 molecule  Cd209d  CD209d antigen  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2015-10-27 Cd209d  CD209d antigen  Clec4m  C-type lectin domain family 4, member M  Name and Symbol changed 629549 APPROVED
2013-02-22 Clec4m  C-type lectin domain family 4, member M  Cd209d  CD209d antigen  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-07-16 Cd209d  CD209d antigen  Clec4m  C-type lectin domain family 4, member M  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-04-20 Clec4m  C-type lectin domain family 4, member M  Cd209d  CD209d antigen  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-28 Cd209d  CD209d antigen  RGD1561104_predicted  similar to SIGNR3 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1561104_predicted  similar to SIGNR3 (predicted)  LOC363856  similar to SIGNR3  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC363856  similar to SIGNR3      Symbol and Name status set to provisional 70820 PROVISIONAL