Cd209c (CD209c molecule) - Rat Genome Database

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Gene: Cd209c (CD209c molecule) Rattus norvegicus
Analyze
No known orthologs.
Symbol: Cd209c
Name: CD209c molecule
RGD ID: 1582956
Description: 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); PARTICIPATES IN measles pathway; phagocytosis pathway; tuberculosis pathway; .
Type: protein-coding
RefSeq Status: MODEL
Previously known as: Cd209; CD209 antigen-like protein C; CD209c antigen; LOC683037; LOC688951; similar to CD209c antigen
RGD Orthologs
Alliance Orthologs
More Info homologs ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8126,732,890 - 6,741,757 (-)NCBIGRCr8
mRatBN7.2121,936,233 - 1,943,841 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl121,936,396 - 1,942,040 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.0122,837,991 - 2,846,709 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl122,838,128 - 2,843,772 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0124,987,480 - 4,995,158 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4122,236,285 - 2,244,559 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera123,788,537 - 3,797,099 (-)NCBICelera
Cytogenetic Map12p12NCBI
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

Biological Process

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Paradoxical role of CD16+CCR2+CCR5+ monocytes in tuberculosis: efficient APC in pleural effusion but also mark disease severity in blood. Balboa L, etal., J Leukoc Biol. 2011 Mar 31.
2. Association of a single nucleotide polymorphism in the CD209 (DC-SIGN) promoter with SARS severity. Chan KY, etal., Hong Kong Med J. 2010;16(5 Suppl 4):37-42.
3. Pulmonary dendritic cells in lungs of preterm infants: neglected participants in bronchopulmonary dysplasia? De Paepe ME, etal., Pediatr Dev Pathol. 2011 Jan-Feb;14(1):20-7. Epub 2010 Jan 5.
4. 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.
5. Mite allergen decreases DC-SIGN expression and modulates human dendritic cell differentiation and function in allergic asthma. Huang HJ, etal., Mucosal Immunol. 2011 Apr 6.
6. N-linked glycosylation facilitates sialic acid-independent attachment and entry of influenza A viruses into cells expressing DC-SIGN or L-SIGN. Londrigan SL, etal., J Virol. 2011 Mar;85(6):2990-3000. Epub 2010 Dec 29.
7. Dendritic cell recruitment in lesions of human and experimental pulmonary hypertension. Perros F, etal., Eur Respir J. 2007 Mar;29(3):462-8. Epub 2006 Nov 15.
8. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
9. GOA pipeline RGD automated data pipeline
10. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
11. [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.
12. CD209 genetic polymorphism and tuberculosis disease. Vannberg FO, etal., PLoS One. 2008 Jan 2;3(1):e1388.

Genomics

Variants

.
Variants in Cd209c
9 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:34
Count of miRNA genes:33
Interacting mature miRNAs:34
Transcripts:ENSRNOT00000061750
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 endocrine system exocrine system hemolymphoid system hepatobiliary system nervous system reproductive system respiratory system
High
Medium
Low 1 5 15
Below cutoff 1 4 1 4 1 2 4 5

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000061750   ⟹   ENSRNOP00000058463
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl121,936,396 - 1,942,040 (-)Ensembl
Rnor_6.0 Ensembl122,838,128 - 2,843,772 (-)Ensembl
RefSeq Acc Id: XM_006248792   ⟹   XP_006248854
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8126,732,890 - 6,741,757 (-)NCBI
mRatBN7.2121,936,233 - 1,943,841 (-)NCBI
Rnor_6.0122,837,991 - 2,846,709 (-)NCBI
Rnor_5.0124,987,480 - 4,995,158 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs XP_006248854 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000058463.2
Reference Protein Sequences
RefSeq Acc Id: XP_006248854   ⟸   XM_006248792
- Sequence:
RefSeq Acc Id: ENSRNOP00000058463   ⟸   ENSRNOT00000061750
Protein Domains
C-type lectin

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1LXR5-F1-model_v2 AlphaFold F1LXR5 1-177 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:1582956 AgrOrtholog
BioCyc Gene G2FUF-20375 BioCyc
Ensembl Genes ENSRNOG00000042807 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000061750.2 UniProtKB/TrEMBL
Gene3D-CATH 3.10.100.10 UniProtKB/TrEMBL
InterPro C-type_lectin-like UniProtKB/TrEMBL
  C-type_lectin-like/link_sf UniProtKB/TrEMBL
  C-type_lectin_CS UniProtKB/TrEMBL
  CD209-like_CTLD UniProtKB/TrEMBL
  CTDL_fold UniProtKB/TrEMBL
NCBI Gene 688951 ENTREZGENE
PANTHER CD209 ANTIGEN-LIKE PROTEIN C-LIKE UniProtKB/TrEMBL
  KILLER CELL LECTIN-LIKE RECEPTOR SUBFAMILY F MEMBER 2 UniProtKB/TrEMBL
Pfam Lectin_C UniProtKB/TrEMBL
PhenoGen Cd209c PhenoGen
PROSITE C_TYPE_LECTIN_1 UniProtKB/TrEMBL
  C_TYPE_LECTIN_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000042807 RatGTEx
SMART CLECT UniProtKB/TrEMBL
Superfamily-SCOP SSF56436 UniProtKB/TrEMBL
UniProt F1LXR5_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2011-09-08 Cd209c  CD209c molecule  LOC683037  similar to CD209c antigen  Data merged from RGD:1591571 737654 APPROVED
2008-06-27 Cd209c  CD209c molecule  Cd209c  CD209c antigen  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-06 Cd209c  CD209c antigen  LOC688951  similar to CD209c antigen  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 LOC683037  similar to CD209c antigen      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-19 LOC688951  similar to CD209c antigen      Symbol and Name status set to provisional 70820 PROVISIONAL