Clec2d2l3 (C-type lectin domain family 2 member D2 like 3) - Rat Genome Database

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Gene: Clec2d2l3 (C-type lectin domain family 2 member D2 like 3) Rattus norvegicus
Analyze
No known orthologs.
Symbol: Clec2d2l3 (Ensembl: LOC500331)
Name: C-type lectin domain family 2 member D2 like 3 (Ensembl:similar to osteoclast inhibitory lectin)
RGD ID: 1564464
Description: Predicted to enable natural killer cell lectin-like receptor binding activity. Predicted to be active in external side of plasma membrane. Orthologous to human CLEC2D (C-type lectin domain family 2 member D).
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: C-type lectin domain family 2 member D-related protein; C-type lectin domain family 2 member D-related protein-like; LOC100910725; LOC500331; similar to osteoclast inhibitory lectin
RGD Orthologs
Alliance Genes
More Info homologs ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr84163,695,931 - 163,710,700 (+)NCBIGRCr8
mRatBN7.24162,009,857 - 162,024,626 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl4162,009,857 - 162,024,625 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx4168,244,716 - 168,259,485 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.04164,027,656 - 164,042,425 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.04162,661,704 - 162,676,473 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.04162,073,423 - 162,088,240 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4162,077,188 - 162,168,221 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04227,273,528 - 227,288,297 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44165,760,258 - 165,775,027 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera4150,711,001 - 150,725,770 (+)NCBICelera
Cytogenetic Map4q42NCBI
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. 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. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
5. 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.

Genomics

Variants

.
Variants in Clec2d2l3
315 total Variants

QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)411320076180699135Rat
1576316Ept5Estrogen-induced pituitary tumorigenesis QTL 53.8pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)483428419177635233Rat
1358202Gluco11Glucose level QTL 112.40.02adipocyte glucose uptake trait (VT:0004185)absolute change in adipocyte glucose uptake (CMO:0000873)485379421167139601Rat
634335Anxrr16Anxiety related response QTL 167.22locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)493308457167139447Rat
737821Hcar9Hepatocarcinoma resistance QTL 93.7liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)4109866907167139601Rat
1331759Hrtrt13Heart rate QTL 133.54628heart pumping trait (VT:2000009)heart rate (CMO:0000002)4110275411168266883Rat
724535Cm18Cardiac mass QTL 182.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)4118856416163856416Rat
634347Hcar8Hepatocarcinoma resistance QTL 85.8liver integrity trait (VT:0010547)liver tumorous lesion area to total liver area ratio (CMO:0001075)4123143783168143783Rat
631683Bp116Blood pressure QTL 1160.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4124303370169303370Rat
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)4124778595169778595Rat
7411558Bw133Body weight QTL 13313.840.001body mass (VT:0001259)body weight gain (CMO:0000420)4125590636170590636Rat
61451Ciaa4CIA Autoantibody QTL 43.1blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)4126395976167139601Rat
737978Pia23Pristane induced arthritis QTL 235.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4131730738167139601Rat
631511Pia7Pristane induced arthritis QTL 74.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4131730738167139601Rat
1549827Scl46Serum cholesterol level QTL 463.5blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)4132396220177396220Rat
724558Plsm2Polydactyly-luxate syndrome (PLS) morphotypes QTL 20.0003hindlimb integrity trait (VT:0010563)hind foot phalanges count (CMO:0001949)4132422778177422778Rat
61422Cia13Collagen induced arthritis QTL 134.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4132642577167139601Rat
2303623Vencon2Ventilatory control QTL 23.8respiration trait (VT:0001943)minute ventilation (CMO:0000132)4135204660180204660Rat
1578674Bmd12Bone mineral density QTL 123.8femur mineral mass (VT:0010011)compact volumetric bone mineral density (CMO:0001730)4135699135180699135Rat
2293659Bmd35Bone mineral density QTL 354.50.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)4137755016181392681Rat
61362Oia2Oil induced arthritis QTL 20.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4138503169173369699Rat
1298524Oia8Oil induced arthritis QTL 8joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4138503169173369699Rat
1331738Bp209Blood pressure QTL 2092.979arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)4138503169179293946Rat
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)4144639524182687754Rat
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)4144639524182687754Rat
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)4144639524182687754Rat
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)4144639524182687754Rat
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)4144639524182687754Rat
10401796Kidm48Kidney mass QTL 48kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)4145568712182687754Rat
634342Cia24Collagen induced arthritis QTL 244.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4146565735175236377Rat
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)4147278504167139601Rat
1582237Kidm34Kidney mass QTL 3440.0001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)4148090542168069246Rat
10053718Scort25Serum corticosterone level QTL 252.150.0097blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)4155561574182687754Rat
1300109Rf13Renal function QTL 133.91renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)4157710145182687754Rat


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 integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 9 6 2
Low 3 11 27 11 19 11 8 11 6 11 18 9 8
Below cutoff 2 41 18 15

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000043078   ⟹   ENSRNOP00000050011
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4162,009,857 - 162,024,625 (+)Ensembl
Rnor_6.0 Ensembl4162,151,904 - 162,168,177 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000049620   ⟹   ENSRNOP00000042979
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl4162,078,905 - 162,087,997 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000090431   ⟹   ENSRNOP00000071394
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl4162,077,188 - 162,168,221 (+)Ensembl
RefSeq Acc Id: NM_001024337   ⟹   NP_001019508
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr84163,695,931 - 163,710,700 (+)NCBI
mRatBN7.24162,009,857 - 162,024,626 (+)NCBI
Rnor_6.04162,073,423 - 162,088,192 (+)NCBI
Rnor_5.04227,273,528 - 227,288,297 (+)NCBI
RGSC_v3.44165,760,258 - 165,775,027 (+)RGD
Celera4150,711,001 - 150,725,770 (+)RGD
Sequence:
RefSeq Acc Id: XM_039108213   ⟹   XP_038964141
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr84163,696,261 - 163,710,700 (+)NCBI
mRatBN7.24162,010,257 - 162,024,624 (+)NCBI
RefSeq Acc Id: XM_039108214   ⟹   XP_038964142
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr84163,696,094 - 163,710,700 (+)NCBI
mRatBN7.24162,010,015 - 162,024,624 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001019508 (Get FASTA)   NCBI Sequence Viewer  
  XP_038964141 (Get FASTA)   NCBI Sequence Viewer  
  XP_038964142 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH86997 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000050011
  ENSRNOP00000050011.3
  ENSRNOP00055015315
  ENSRNOP00060027080
  ENSRNOP00065047715
GenBank Protein Q5M9I1 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: NP_001019508   ⟸   NM_001024337
- UniProtKB: Q5M9I1 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000050011   ⟸   ENSRNOT00000043078
RefSeq Acc Id: ENSRNOP00000071394   ⟸   ENSRNOT00000090431
RefSeq Acc Id: ENSRNOP00000042979   ⟸   ENSRNOT00000049620
RefSeq Acc Id: XP_038964142   ⟸   XM_039108214
- Peptide Label: isoform X1
- UniProtKB: Q5M9I1 (UniProtKB/Swiss-Prot)
RefSeq Acc Id: XP_038964141   ⟸   XM_039108213
- Peptide Label: isoform X1
- UniProtKB: Q5M9I1 (UniProtKB/Swiss-Prot)
Protein Domains
C-type lectin

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5M9I1-F1-model_v2 AlphaFold Q5M9I1 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:1564464 AgrOrtholog
BioCyc Gene G2FUF-42834 BioCyc
Ensembl Genes ENSRNOG00000030522 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOG00055011181 UniProtKB/Swiss-Prot
  ENSRNOG00060019119 UniProtKB/Swiss-Prot
  ENSRNOG00065033736 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000043078 ENTREZGENE
  ENSRNOT00000043078.4 UniProtKB/Swiss-Prot
  ENSRNOT00055018979 UniProtKB/Swiss-Prot
  ENSRNOT00060033090 UniProtKB/Swiss-Prot
  ENSRNOT00065057949 UniProtKB/Swiss-Prot
Gene3D-CATH 3.10.100.10 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7131139 IMAGE-MGC_LOAD
InterPro C-type_lectin-like UniProtKB/Swiss-Prot
  C-type_lectin-like/link_sf UniProtKB/Swiss-Prot
  CTDL_fold UniProtKB/Swiss-Prot
  NKR-like_CTLD UniProtKB/Swiss-Prot
KEGG Report rno:500331 UniProtKB/Swiss-Prot
MGC_CLONE MGC:93238 IMAGE-MGC_LOAD
NCBI Gene 500331 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 Clec2d2l3 PhenoGen
PROSITE C_TYPE_LECTIN_2 UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000030522 RatGTEx
  ENSRNOG00055011181 RatGTEx
  ENSRNOG00060019119 RatGTEx
  ENSRNOG00065033736 RatGTEx
SMART CLECT UniProtKB/Swiss-Prot
Superfamily-SCOP SSF56436 UniProtKB/Swiss-Prot
UniProt CL2DR_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2023-09-19 Clec2d2l3  C-type lectin domain family 2 member D2 like 3  LOC500331  similar to osteoclast inhibitory lectin  Symbol and Name Changed 1299863 APPROVED
2021-03-09 LOC500331  similar to osteoclast inhibitory lectin  LOC100910725  C-type lectin domain family 2 member D-related protein-like  Data merged from RGD:6497009 737654 PROVISIONAL
2012-07-05 LOC100910725  C-type lectin domain family 2 member D-related protein-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-02-09 LOC500331  similar to osteoclast inhibitory lectin      Symbol and Name status set to provisional 70820 PROVISIONAL