Clec3a (C-type lectin domain family 3, member A) - Rat Genome Database

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Gene: Clec3a (C-type lectin domain family 3, member A) Rattus norvegicus
Analyze
Symbol: Clec3a
Name: C-type lectin domain family 3, member A
RGD ID: 1306295
Description: Predicted to be involved in ossification. Predicted to be active in extracellular space. Orthologous to human CLEC3A (C-type lectin domain family 3 member A); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; 3,4-methylenedioxymethamphetamine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 1 (cartilage-derived); C-type lectin domain family 3 member A; Clecsf1; LOC365009
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81959,313,746 - 59,321,126 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1959,313,570 - 59,321,126 (+)EnsemblGRCr8
mRatBN7.21942,404,628 - 42,412,008 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1942,404,628 - 42,412,008 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1949,228,860 - 49,236,240 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01949,882,060 - 49,889,440 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01952,125,051 - 52,132,449 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01946,733,668 - 46,741,245 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1946,733,633 - 46,743,013 (+)Ensemblrn6Rnor6.0
Rnor_5.01957,554,455 - 57,562,032 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41944,488,787 - 44,496,167 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1941,713,152 - 41,720,459 (+)NCBICelera
RGSC_v3.11944,493,667 - 44,501,016 (+)NCBI
Cytogenetic Map19q12NCBI
JBrowse:




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

Biological Process
ossification  (IBA)

Cellular Component

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. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data
Clec3a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81959,313,746 - 59,321,126 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1959,313,570 - 59,321,126 (+)EnsemblGRCr8
mRatBN7.21942,404,628 - 42,412,008 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1942,404,628 - 42,412,008 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1949,228,860 - 49,236,240 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01949,882,060 - 49,889,440 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01952,125,051 - 52,132,449 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01946,733,668 - 46,741,245 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1946,733,633 - 46,743,013 (+)Ensemblrn6Rnor6.0
Rnor_5.01957,554,455 - 57,562,032 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41944,488,787 - 44,496,167 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1941,713,152 - 41,720,459 (+)NCBICelera
RGSC_v3.11944,493,667 - 44,501,016 (+)NCBI
Cytogenetic Map19q12NCBI
CLEC3A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381678,022,548 - 78,032,101 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1678,022,515 - 78,066,761 (+)Ensemblhg38GRCh38
GRCh371678,056,445 - 78,065,998 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361676,613,944 - 76,623,499 (+)NCBIBuild 36Build 36hg18NCBI36
Celera1662,354,541 - 62,364,097 (+)NCBICelera
Cytogenetic Map16q23.1NCBI
HuRef1663,813,062 - 63,822,623 (+)NCBIHuRef
CHM1_11679,467,866 - 79,477,427 (+)NCBICHM1_1
T2T-CHM13v2.01684,078,524 - 84,088,079 (+)NCBIT2T-CHM13v2.0
Clec3a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm398115,144,744 - 115,154,871 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl8115,144,826 - 115,152,586 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm388114,418,034 - 114,428,133 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl8114,418,086 - 114,425,846 (+)Ensemblmm10GRCm38
MGSCv378116,941,986 - 116,949,746 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv368117,304,063 - 117,311,823 (+)NCBIMGSCv36mm8
Celera8118,628,412 - 118,636,085 (+)NCBICelera
Cytogenetic Map8E1NCBI
cM Map860.96NCBI
Clec3a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555221,203,559 - 1,211,562 (+)Ensembl
ChiLan1.0NW_0049555221,203,559 - 1,211,562 (+)NCBIChiLan1.0ChiLan1.0
CLEC3A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21887,757,784 - 87,767,257 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11693,677,082 - 93,686,553 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01658,613,482 - 58,623,026 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11678,048,940 - 78,058,454 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1678,048,940 - 78,058,445 (+)EnsemblpanPan2panpan1.1
CLEC3A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1573,291,210 - 73,299,593 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl573,292,422 - 73,299,492 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha573,239,164 - 73,247,570 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0573,598,432 - 73,606,832 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl573,598,908 - 73,606,800 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1573,538,305 - 73,546,689 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0573,373,745 - 73,382,141 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0573,857,661 - 73,866,061 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Clec3a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934933,284,402 - 33,291,463 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647526,297,621 - 26,305,731 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_00493647526,297,679 - 26,304,707 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CLEC3A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl69,907,682 - 9,915,384 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.169,907,145 - 9,915,384 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.269,640,139 - 9,648,381 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CLEC3A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1563,502,003 - 63,510,612 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl563,502,738 - 63,510,552 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366604712,529,367 - 12,543,085 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Clec3a
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247468,983,844 - 8,992,735 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046247468,983,946 - 8,993,894 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Clec3a
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11734,055,508 - 34,065,070 (+)NCBIRrattus_CSIRO_v1

miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:70
Count of miRNA genes:63
Interacting mature miRNAs:65
Transcripts:ENSRNOT00000016307
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
61447Tcas1Tongue tumor susceptibility QTL 16.08tongue integrity trait (VT:0010553)squamous cell carcinoma of the tongue maximum tumor diameter (CMO:0001875)191922068964220689Rat
631840Niddm38Non-insulin dependent diabetes mellitus QTL 383.86blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)191032907674246245Rat
724546Kidm3Kidney mass QTL 33.1kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)194622677874246245Rat
7411549Bw130Body weight QTL 13050.001body mass (VT:0001259)body weight gain (CMO:0000420)193236531174246245Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)193628974246245Rat
724518Uae19Urinary albumin excretion QTL 195.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)192409397369093973Rat
61423Cia14Collagen induced arthritis QTL 143joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)191083361874246245Rat
2303628Vencon9Ventilatory control QTL 90.005respiration trait (VT:0001943)minute ventilation (CMO:0000132)192318858668188586Rat
2313395Anxrr26Anxiety related response QTL 26aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)194438513474246245Rat
1578764Stresp19Stress response QTL 193.60.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)193253961574246245Rat
1331788Rf45Renal function QTL 452.818kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)193177788874246245Rat
1554318Bmd5Bone mineral density QTL 512.10.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)192318858668188586Rat
2317848Alcrsp21Alcohol response QTL 211.8999999761581420.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)192010930665109306Rat
7247442Uae39Urinary albumin excretion QTL 39urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19219431774246245Rat
1549835Tcas7Tongue tumor susceptibility QTL 70.001tongue integrity trait (VT:0010553)squamous cell carcinoma of the head and neck tumor number (CMO:0001876)194172254674246245Rat
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19219431774246245Rat


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
9 10 60 88 57 55 25 24 25 6 168 113 9 59 13 47 30

Sequence


Ensembl Acc Id: ENSRNOT00000016307   ⟹   ENSRNOP00000016307
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1946,733,633 - 46,743,013 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000099875   ⟹   ENSRNOP00000090689
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1959,313,570 - 59,321,126 (+)Ensembl
mRatBN7.2 Ensembl1942,404,628 - 42,412,008 (+)Ensembl
RefSeq Acc Id: NM_001108899   ⟹   NP_001102369
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81959,313,746 - 59,321,126 (+)NCBI
mRatBN7.21942,404,628 - 42,412,008 (+)NCBI
Rnor_6.01946,733,668 - 46,741,245 (+)NCBI
Rnor_5.01957,554,455 - 57,562,032 (+)NCBI
RGSC_v3.41944,488,787 - 44,496,167 (+)RGD
Celera1941,713,152 - 41,720,459 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001102369 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL92622 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000090689
  ENSRNOP00000090689.1
RefSeq Acc Id: NP_001102369   ⟸   NM_001108899
- Peptide Label: precursor
- UniProtKB: D4A0E3 (UniProtKB/TrEMBL),   A6IZE4 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000016307   ⟸   ENSRNOT00000016307
Ensembl Acc Id: ENSRNOP00000090689   ⟸   ENSRNOT00000099875
Protein Domains
C-type lectin

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A0E3-F1-model_v2 AlphaFold D4A0E3 1-196 view protein structure

Transcriptome

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

Promoters
RGD ID:13701163
Promoter ID:EPDNEW_R11686
Type:single initiation site
Name:Clec3a_1
Description:C-type lectin domain family 3, member A
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01946,733,586 - 46,733,646EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1306295 AgrOrtholog
BioCyc Gene G2FUF-5597 BioCyc
Ensembl Genes ENSRNOG00000012238 Ensembl
  ENSRNOG00000070954 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000099875 ENTREZGENE
  ENSRNOT00000099875.2 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
  CLec_Tetranectin-domain UniProtKB/TrEMBL
KEGG Report rno:365009 UniProtKB/TrEMBL
NCBI Gene 365009 ENTREZGENE
PANTHER C-TYPE LECTIN DOMAIN FAMILY 3 MEMBER A UniProtKB/TrEMBL
  TETRANECTIN-RELATED UniProtKB/TrEMBL
Pfam Lectin_C UniProtKB/TrEMBL
PhenoGen Clec3a PhenoGen
PROSITE C_TYPE_LECTIN_1 UniProtKB/TrEMBL
  C_TYPE_LECTIN_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000012238 RatGTEx
  ENSRNOG00000070954 RatGTEx
SMART CLECT UniProtKB/TrEMBL
Superfamily-SCOP C-type_lectin_fold UniProtKB/TrEMBL
UniProt A6IZE4 ENTREZGENE, UniProtKB/TrEMBL
  D4A0E3 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2011-06-08 Clec3a  C-type lectin domain family 3, member A  Clec3a  C-type lectin domain family 3, member a  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-03 Clec3a  C-type lectin domain family 3, member a  Clecsf1_predicted  C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 1 (cartilage-derived) (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-12 Clecsf1_predicted  C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 1 (cartilage-derived) (predicted)      Symbol and Name status set to approved 70820 APPROVED