Clec4a2 (C-type lectin domain family 4, member A2) - Rat Genome Database

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Gene: Clec4a2 (C-type lectin domain family 4, member A2) Rattus norvegicus
Analyze
No known orthologs.
Symbol: Clec4a2
Name: C-type lectin domain family 4, member A2
RGD ID: 1359163
Description: Predicted to enable carbohydrate binding activity and pattern recognition receptor activity. Predicted to be involved in antifungal innate immune response. Predicted to be located in plasma membrane. Predicted to be active in external side of plasma membrane. Orthologous to human CLEC4A (C-type lectin domain family 4 member A); INTERACTS WITH 17beta-estradiol; 17beta-estradiol 3-benzoate; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: Dcir2; dendritic cell inhibitory receptor 2; immunoreceptor
RGD Orthologs
Alliance Orthologs
More Info homologs ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr84157,934,342 - 157,993,595 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl4157,934,357 - 157,993,588 (+)EnsemblGRCr8
mRatBN7.24156,262,438 - 156,321,695 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl4156,262,692 - 156,321,392 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx4162,546,464 - 162,609,257 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.04158,329,685 - 158,392,478 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.04156,974,769 - 157,037,562 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.04155,793,059 - 155,867,731 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4155,792,761 - 155,867,708 (-)Ensemblrn6Rnor6.0
Rnor_5.04222,810,975 - 222,885,994 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.44159,513,951 - 159,573,152 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera4145,081,095 - 145,139,321 (+)NCBICelera
RGSC_v3.14159,758,886 - 159,818,088 (+)NCBI
Cytogenetic Map4q42NCBI
JBrowse:




Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Identification of lectin-like receptors expressed by antigen presenting cells and neutrophils and their mapping to a novel gene complex. Flornes LM, etal., Immunogenetics 2004 Oct;56(7):506-17. Epub 2004 Sep 11.
2. 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.
3. GOA pipeline RGD automated data pipeline
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Variants

.
Variants in Clec4a2
229 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:17
Count of miRNA genes:17
Interacting mature miRNAs:17
Transcripts:ENSRNOT00000051525
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
6478754Anxrr43Anxiety related response QTL 430.14035locomotor behavior trait (VT:0001392)distance moved per unit of time into, out of or within a discrete space in an experimental apparatus (CMO:0001493)4146370897184426481Rat
724558Plsm2Polydactyly-luxate syndrome (PLS) morphotypes QTL 20.0003hindlimb integrity trait (VT:0010563)hind foot phalanges count (CMO:0001949)4134095016179095016Rat
1582237Kidm34Kidney mass QTL 3440.0001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)4149763204169799698Rat
61446Coreg2Compensatory renal growth QTL 23.5kidney mass (VT:0002707)compensatory renal growth score (CMO:0001894)4150095743159267220Rat
6478693Anxrr32Anxiety related response QTL 320.00092locomotor behavior trait (VT:0001392)measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)4146370897184426481Rat
6478757Anxrr44Anxiety related response QTL 440.01087locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4155834926184426481Rat
1358364Sradr4Stress Responsive Adrenal Weight QTL 44.92adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)4131384565176384565Rat
10755501Bp390Blood pressure QTL 3902.5arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)427730518170099664Rat
61451Ciaa4CIA Autoantibody QTL 43.1blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)4123870974168870974Rat
1331802Srn5Serum renin concentration QTL 53.045renin activity (VT:0005581)plasma renin activity level (CMO:0000116)4117559384162559384Rat
1331738Bp209Blood pressure QTL 2092.979arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)4140059299181024663Rat
6478700Anxrr33Anxiety related response QTL 330.00896locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4146370897184426481Rat
1298524Oia8Oil induced arthritis QTL 8joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4140059299184426481Rat
10053718Scort25Serum corticosterone level QTL 252.150.0097blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)4157292416184426481Rat
738009Sach4Saccharine consumption QTL 44.90.000016consumption behavior trait (VT:0002069)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)460916264184426481Rat
634335Anxrr16Anxiety related response QTL 167.22locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)494638356168870820Rat
737821Hcar9Hepatocarcinoma resistance QTL 93.7liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)4106848959168870974Rat
7411558Bw133Body weight QTL 13313.840.001body mass (VT:0001259)body weight gain (CMO:0000420)4127263297172263297Rat
6478778Anxrr51Anxiety related response QTL 510.25384locomotor behavior trait (VT:0001392)measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)4126334185171334185Rat
10401796Kidm48Kidney mass QTL 48kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)4147299608184426481Rat
6478718Anxrr34Anxiety related response QTL 340.00896locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4146370897184426481Rat
6478782Anxrr52Anxiety related response QTL 520.02091locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4155834926184426481Rat
631511Pia7Pristane induced arthritis QTL 74.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4123870974168870974Rat
634347Hcar8Hepatocarcinoma resistance QTL 85.8liver integrity trait (VT:0010547)liver tumorous lesion area to total liver area ratio (CMO:0001075)4124700988169700988Rat
6478720Alc23Alcohol consumption QTL 230.00509drinking behavior trait (VT:0001422)ethanol drink intake rate to body weight ratio (CMO:0001616)4155834926184426481Rat
6478785Anxrr53Anxiety related response QTL 530.01397locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4155834926184426481Rat
738031Alc14Alcohol consumption QTL 147.60.00003consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)460916264174095838Rat
1576316Ept5Estrogen-induced pituitary tumorigenesis QTL 53.8pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)4100752691179366077Rat
1581566Eae21Experimental allergic encephalomyelitis QTL 216.2body mass (VT:0001259)maximum body weight loss to initial body weight ratio (CMO:0001400)4137447185182447185Rat
1578674Bmd12Bone mineral density QTL 123.8femur mineral mass (VT:0010011)compact volumetric bone mineral density (CMO:0001730)4137430611182430611Rat
6478728Anxrr36Anxiety related response QTL 360.01061locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4155834926184426481Rat
738016Alc16Alcohol consumption QTL 163.60.00015consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)460916264184426481Rat
1358202Gluco11Glucose level QTL 112.40.02adipocyte glucose uptake trait (VT:0004185)absolute change in adipocyte glucose uptake (CMO:0000873)486709649168870974Rat
61422Cia13Collagen induced arthritis QTL 134.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4134199006168870974Rat
634342Cia24Collagen induced arthritis QTL 244.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4148121375176967367Rat
6478733Anxrr37Anxiety related response QTL 370.00095locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4155834926184426481Rat
737978Pia23Pristane induced arthritis QTL 235.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4123870974168870974Rat
61362Oia2Oil induced arthritis QTL 20.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4140059299184426481Rat
631674Iddm14Insulin dependent diabetes mellitus QTL 14blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)465495851159259805Rat
6478737Anxrr38Anxiety related response QTL 380.00159locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4155834926184426481Rat
12798519Anxrr54Anxiety related response QTL 542.540.05locomotor behavior trait (VT:0001392)distance moved per unit of time into, out of or within a discrete space in an experimental apparatus (CMO:0001493)4116184844161184844Rat
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)412212457182430611Rat
6478748Anxrr42Anxiety related response QTL 420.28008locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4146370897184426481Rat
12798525Anxrr57Anxiety related response QTL 573.210.05locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4148834094168870974Rat

Markers in Region
D4Got294  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24156,226,387 - 156,226,550 (+)MAPPERmRatBN7.2
mRatBN7.24156,226,387 - 156,226,550 (-)MAPPERmRatBN7.2
Rnor_6.04155,911,274 - 155,911,436NCBIRnor6.0
Rnor_6.04155,797,708 - 155,797,870NCBIRnor6.0
Rnor_5.04222,931,414 - 222,931,576UniSTSRnor5.0
Rnor_5.04222,815,624 - 222,815,786UniSTSRnor5.0
RGSC_v3.44159,475,954 - 159,476,116UniSTSRGSC3.4
Celera4145,043,483 - 145,043,659UniSTS
Cytogenetic Map4q42UniSTS


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
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 7 48 94 85 84 53 91 53 6 308 167 11 69 66 71 31 9 9

Sequence


Ensembl Acc Id: ENSRNOT00000051525   ⟹   ENSRNOP00000048802
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl4157,934,357 - 157,993,588 (+)Ensembl
mRatBN7.2 Ensembl4156,262,692 - 156,321,392 (+)Ensembl
Rnor_6.0 Ensembl4155,792,761 - 155,867,708 (-)Ensembl
RefSeq Acc Id: NM_001005880   ⟹   NP_001005880
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr84157,934,596 - 157,993,293 (+)NCBI
mRatBN7.24156,262,693 - 156,321,393 (+)NCBI
Rnor_6.04155,793,059 - 155,867,512 (-)NCBI
Rnor_5.04222,810,975 - 222,885,994 (-)NCBI
RGSC_v3.44159,513,951 - 159,573,152 (+)RGD
Celera4145,081,095 - 145,139,321 (+)RGD
Sequence:
RefSeq Acc Id: XM_017592587   ⟹   XP_017448076
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr84157,934,342 - 157,993,595 (+)NCBI
mRatBN7.24156,262,438 - 156,321,695 (+)NCBI
Rnor_6.04155,793,105 - 155,867,731 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001005880 (Get FASTA)   NCBI Sequence Viewer  
  XP_017448076 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAR31146 (Get FASTA)   NCBI Sequence Viewer  
  AAS76657 (Get FASTA)   NCBI Sequence Viewer  
  AAT92028 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000048802
  ENSRNOP00000048802.2
RefSeq Acc Id: NP_001005880   ⟸   NM_001005880
- UniProtKB: Q5YIS1 (UniProtKB/TrEMBL),   Q2TUM0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017448076   ⟸   XM_017592587
- Peptide Label: isoform X1
- UniProtKB: A6ILG5 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000048802   ⟸   ENSRNOT00000051525
Protein Domains
C-type lectin

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q2TUM0-F1-model_v2 AlphaFold Q2TUM0 1-235 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:1359163 AgrOrtholog
BioCyc Gene G2FUF-43134 BioCyc
Ensembl Genes ENSRNOG00000030012 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000051525 ENTREZGENE
  ENSRNOT00000051525.5 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/snaclec_domain UniProtKB/TrEMBL
  C-type_lectin_CS UniProtKB/TrEMBL
  C-type_lectin_fold UniProtKB/TrEMBL
  C-type_Lectin_Receptor_IMM UniProtKB/TrEMBL
  CD209-like_CTLD UniProtKB/TrEMBL
KEGG Report rno:297584 UniProtKB/TrEMBL
NCBI Gene 297584 ENTREZGENE
PANTHER CD209 ANTIGEN-LIKE PROTEIN C-LIKE UniProtKB/TrEMBL
  KILLER CELL LECTIN-LIKE RECEPTOR SUBFAMILY F MEMBER 2 UniProtKB/TrEMBL
  MANNOSE, PHOSPHOLIPASE, LECTIN RECEPTOR RELATED UniProtKB/TrEMBL
Pfam Lectin_C UniProtKB/TrEMBL
PhenoGen Clec4a2 PhenoGen
PROSITE C_TYPE_LECTIN_1 UniProtKB/TrEMBL
  C_TYPE_LECTIN_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000030012 RatGTEx
SMART CLECT UniProtKB/TrEMBL
Superfamily-SCOP C-type_lectin_fold UniProtKB/TrEMBL
UniProt A6ILG5 ENTREZGENE, UniProtKB/TrEMBL
  Q2TUM0 ENTREZGENE, UniProtKB/TrEMBL
  Q5YIS1 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2011-06-08 Clec4a2  C-type lectin domain family 4, member A2  Clec4a2  C-type lectin domain family 4, member a2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-04-20 Clec4a2  C-type lectin domain family 4, member a2  Dcir2  dendritic cell inhibitory receptor 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-07-29 Dcir2  dendritic cell inhibitory receptor 2      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in NK cells as well as dendritic cells, macrophages, B cells and neutrophils 1359744