Clec2dl1 (C-type lectin domain family 2 member D-like 1) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Behavioral & Substance Use Disorder Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Advanced Search (OLGA)
Gene: Clec2dl1 (C-type lectin domain family 2 member D-like 1) Rattus norvegicus
Analyze
No known orthologs.
Symbol: Clec2dl1
Name: C-type lectin domain family 2 member D-like 1
RGD ID: 1588698
Description: Predicted to enable natural killer cell lectin-like receptor binding activity. Predicted to be located in plasma membrane. Predicted to be active in external side of plasma membrane. Orthologous to human CLEC2D (C-type lectin domain family 2 member D); INTERACTS WITH 6-propyl-2-thiouracil; acrylamide; bromobenzene.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: C-type lectin domain family 2 member D6; C-type lectin-like; Clec2d6; LOC689790; similar to osteoclast inhibitory lectin
RGD Orthologs
Alliance Orthologs
More Info homologs ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr84163,949,688 - 163,960,935 (+)NCBIGRCr8GRCr8GRCr8
mRatBN7.24162,263,635 - 162,274,882 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl4162,263,639 - 162,274,880 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx4168,500,022 - 168,507,400 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.04164,282,968 - 164,290,348 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.04162,917,017 - 162,924,395 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.04162,391,309 - 162,402,569 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4162,281,574 - 162,402,635 (+)Ensemblrn6Rnor6.0
Rnor_5.04227,591,450 - 227,602,644 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.44166,034,747 - 166,042,125 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera4150,963,522 - 150,970,900 (+)NCBICelera
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. 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.
2. GOA pipeline RGD automated data pipeline
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:17462921   PMID:19130483  


Genomics

Variants

.
Variants in Clec2dl1
825 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:131
Count of miRNA genes:102
Interacting mature miRNAs:108
Transcripts:ENSRNOT00000038801, ENSRNOT00000047790, ENSRNOT00000072064
Prediction methods:Microtar, 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
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
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
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
2293659Bmd35Bone mineral density QTL 354.50.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)4160623982184426481Rat
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
D3Got77  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24162,271,408 - 162,271,538 (+)MAPPERmRatBN7.2
mRatBN7.24162,062,467 - 162,062,601 (-)MAPPERmRatBN7.2
Rnor_6.04162,444,005 - 162,444,138NCBIRnor6.0
Rnor_6.04162,399,096 - 162,399,225NCBIRnor6.0
Rnor_5.04227,643,117 - 227,643,250UniSTSRnor5.0
Rnor_5.04227,599,171 - 227,599,300UniSTSRnor5.0
RGSC_v3.44165,813,461 - 165,813,594UniSTSRGSC3.4
RGSC_v3.44166,040,974 - 166,041,103UniSTSRGSC3.4
Celera4150,969,749 - 150,969,878UniSTS
Celera4150,763,180 - 150,763,314UniSTS
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 4 23 88 83 86 55 67 55 6 245 116 11 66 55 88 31 3 3

Sequence


Ensembl Acc Id: ENSRNOT00000047790   ⟹   ENSRNOP00000048461
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4162,263,639 - 162,274,880 (+)Ensembl
Rnor_6.0 Ensembl4162,392,869 - 162,400,247 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000087850   ⟹   ENSRNOP00000069949
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl4162,281,574 - 162,402,635 (+)Ensembl
RefSeq Acc Id: NM_001085404   ⟹   NP_001078873
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr84163,949,688 - 163,960,935 (+)NCBI
mRatBN7.24162,263,635 - 162,274,882 (+)NCBI
Rnor_6.04162,392,869 - 162,400,247 (+)NCBI
Rnor_5.04227,591,450 - 227,602,644 (+)NCBI
RGSC_v3.44166,034,747 - 166,042,125 (+)RGD
Celera4150,963,522 - 150,970,900 (+)RGD
Sequence:
RefSeq Acc Id: XM_008763333   ⟹   XP_008761555
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr84163,955,337 - 163,960,935 (+)NCBI
mRatBN7.24162,267,995 - 162,274,882 (+)NCBI
Rnor_6.04162,396,792 - 162,402,569 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001078873 (Get FASTA)   NCBI Sequence Viewer  
  XP_008761555 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein A4KWA8 (Get FASTA)   NCBI Sequence Viewer  
  ABO15829 (Get FASTA)   NCBI Sequence Viewer  
  ACJ23590 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000048461
  ENSRNOP00000048461.2
  ENSRNOP00000103094
RefSeq Acc Id: NP_001078873   ⟸   NM_001085404
- UniProtKB: A4KWA8 (UniProtKB/Swiss-Prot),   B7TXW3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008761555   ⟸   XM_008763333
- Peptide Label: isoform X1
- Sequence:
Ensembl Acc Id: ENSRNOP00000048461   ⟸   ENSRNOT00000047790
Ensembl Acc Id: ENSRNOP00000069949   ⟸   ENSRNOT00000087850
Protein Domains
C-type lectin

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A4KWA8-F1-model_v2 AlphaFold A4KWA8 1-233 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:1588698 AgrOrtholog
BioCyc Gene G2FUF-42817 BioCyc
Ensembl Genes ENSRNOG00000007866 Ensembl, UniProtKB/Swiss-Prot
  ENSRNOG00000072423 ENTREZGENE
Ensembl Transcript ENSRNOT00000047790 ENTREZGENE
  ENSRNOT00000047790.3 UniProtKB/Swiss-Prot
  ENSRNOT00000159982 ENTREZGENE
Gene3D-CATH 3.10.100.10 UniProtKB/Swiss-Prot
InterPro C-type_lectin-like UniProtKB/Swiss-Prot
  C-type_lectin-like/link_sf UniProtKB/Swiss-Prot
  C-type_lectin/matrix_domain UniProtKB/Swiss-Prot
  CTDL_fold UniProtKB/Swiss-Prot
  NKR-like_CTLD UniProtKB/Swiss-Prot
KEGG Report rno:689790 UniProtKB/Swiss-Prot
NCBI Gene 689790 ENTREZGENE
PANTHER C-TYPE LECTIN DOMAIN FAMILY 2 MEMBER D-RELATED UniProtKB/Swiss-Prot
  C-TYPE LECTIN DOMAIN-CONTAINING PROTEIN 180 UniProtKB/Swiss-Prot
Pfam Lectin_C UniProtKB/Swiss-Prot
PhenoGen Clec2dl1 PhenoGen
PROSITE C_TYPE_LECTIN_2 UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000007866 RatGTEx
  ENSRNOG00000072423 RatGTEx
SMART CLECT UniProtKB/Swiss-Prot
Superfamily-SCOP SSF56436 UniProtKB/Swiss-Prot
UniProt A0ABK0LCM5_RAT UniProtKB/TrEMBL
  A0ABK0LU60_RAT UniProtKB/TrEMBL
  A4KWA8 ENTREZGENE
  B7TXW3 ENTREZGENE, UniProtKB/TrEMBL
  CL2D6_RAT UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2011-06-08 Clec2dl1  C-type lectin domain family 2 member D-like 1  Clec2dl1  C-type lectin domain family 2 member d-like 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-12-01 Clec2dl1  C-type lectin domain family 2 member d-like 1  LOC689790  similar to osteoclast inhibitory lectin  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-19 LOC689790  similar to osteoclast inhibitory lectin      Symbol and Name status set to provisional 70820 PROVISIONAL