Clec3b (C-type lectin domain family 3, member B) - Rat Genome Database

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Gene: Clec3b (C-type lectin domain family 3, member B) Rattus norvegicus
Analyze
Symbol: Clec3b
Name: C-type lectin domain family 3, member B
RGD ID: 1311031
Description: Predicted to enable calcium ion binding activity; heparin binding activity; and kringle domain binding activity. Involved in ossification. Predicted to be located in cytoplasm and granular component. Predicted to be active in extracellular space. Human ortholog(s) of this gene implicated in osteoarthritis and retinal macular dystrophy 4. Orthologous to human CLEC3B (C-type lectin domain family 3 member B); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; alpha-Zearalanol; atrazine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC100912012; LOC316099; tetranectin; tetranectin (plasminogen binding protein); tetranectin-like; Tna
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr88131,687,575 - 131,693,292 (+)NCBIGRCr8
mRatBN7.28122,810,120 - 122,815,837 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl8122,810,149 - 122,815,835 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx8128,400,421 - 128,406,145 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.08126,599,361 - 126,605,084 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.08124,427,554 - 124,433,270 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.08132,241,016 - 132,248,066 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8132,241,134 - 132,246,694 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.08131,394,703 - 131,401,659 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera8121,922,992 - 121,930,042 (+)NCBICelera
Cytogenetic Map8q32NCBI
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
cytoplasm  (ISO,ISS)
extracellular space  (IBA,ISO,ISS)
granular component  (ISO,ISS)

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. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
4. Association study of candidate genes for the prevalence and progression of knee osteoarthritis. Valdes AM, etal., Arthritis Rheum. 2004 Aug;50(8):2497-507.
5. A potential role for tetranectin in mineralization during osteogenesis. Wewer UM, etal., J Cell Biol. 1994 Dec;127(6 Pt 1):1767-75.
Additional References at PubMed
PMID:7589422   PMID:9786936   PMID:10727405   PMID:11604516   PMID:12694198   PMID:15632090   PMID:15848710   PMID:15901484   PMID:20106964   PMID:20551380   PMID:23376485   PMID:23533145  
PMID:27068509  


Genomics

Comparative Map Data
Clec3b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr88131,687,575 - 131,693,292 (+)NCBIGRCr8
mRatBN7.28122,810,120 - 122,815,837 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl8122,810,149 - 122,815,835 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx8128,400,421 - 128,406,145 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.08126,599,361 - 126,605,084 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.08124,427,554 - 124,433,270 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.08132,241,016 - 132,248,066 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8132,241,134 - 132,246,694 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.08131,394,703 - 131,401,659 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera8121,922,992 - 121,930,042 (+)NCBICelera
Cytogenetic Map8q32NCBI
CLEC3B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38345,026,303 - 45,036,071 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl345,001,548 - 45,036,071 (+)EnsemblGRCh38hg38GRCh38
GRCh37345,067,795 - 45,077,563 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36345,042,763 - 45,052,567 (+)NCBINCBI36Build 36hg18NCBI36
Celera345,005,711 - 45,015,514 (+)NCBICelera
Cytogenetic Map3p21.31NCBI
HuRef345,111,173 - 45,120,977 (+)NCBIHuRef
CHM1_1345,017,739 - 45,027,543 (+)NCBICHM1_1
T2T-CHM13v2.0345,042,041 - 45,051,809 (+)NCBIT2T-CHM13v2.0
Clec3b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm399122,980,011 - 122,986,497 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl9122,980,011 - 122,986,497 (+)EnsemblGRCm39 Ensembl
GRCm389123,150,946 - 123,157,432 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl9123,150,946 - 123,157,432 (+)EnsemblGRCm38mm10GRCm38
MGSCv379123,060,064 - 123,066,550 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv369122,999,547 - 123,006,125 (+)NCBIMGSCv36mm8
Celera9123,602,080 - 123,608,547 (+)NCBICelera
Cytogenetic Map9F4NCBI
cM Map973.91NCBI
Clec3b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495542026,665,472 - 26,669,474 (-)NCBIChiLan1.0ChiLan1.0
CLEC3B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2244,984,162 - 44,994,010 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1344,989,026 - 44,998,777 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0344,927,098 - 44,936,847 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1346,038,115 - 46,047,927 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl346,038,115 - 46,047,927 (+)Ensemblpanpan1.1panPan2
CLEC3B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12043,319,786 - 43,332,161 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2043,324,231 - 43,332,135 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2043,239,918 - 43,248,089 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02043,808,958 - 43,817,196 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2043,808,965 - 43,817,166 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12043,047,906 - 43,056,075 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02043,455,546 - 43,463,778 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02043,731,532 - 43,739,811 (-)NCBIUU_Cfam_GSD_1.0
Clec3b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118198,378,987 - 198,386,451 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936695730,729 - 738,952 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936695731,184 - 738,752 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CLEC3B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1328,219,500 - 28,229,096 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11328,219,241 - 28,229,113 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21331,096,895 - 31,107,071 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CLEC3B
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1226,501,082 - 6,510,878 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl226,501,102 - 6,512,314 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666041160,658,725 - 160,668,539 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Clec3b
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473075,530,770 - 75,536,248 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473075,531,320 - 75,535,875 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Clec3b
21 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:68
Count of miRNA genes:58
Interacting mature miRNAs:64
Transcripts:ENSRNOT00000006055
Prediction methods:Miranda, Rnahybrid, Targetscan
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
738011Anxrr9Anxiety related response QTL 96.1exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)893535351123900184Rat
1358903Bp252Blood pressure QTL 25270.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)893965141123900184Rat
738014Anxrr15Anxiety related response QTL 153.60.005locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)895718998123900184Rat
2300182Bmd56Bone mineral density QTL 565.4femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)895718998123900184Rat
1554321Bmd3Bone mineral density QTL 37.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)840952565123900184Rat
1358893Bp263Blood pressure QTL 2635.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)893965141123900184Rat
61437Cia6Collagen induced arthritis QTL 6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)882460758122812818Rat

Markers in Region
D8Rat71  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.28122,812,566 - 122,812,818 (+)MAPPERmRatBN7.2
Rnor_6.08132,243,591 - 132,243,842NCBIRnor6.0
Rnor_5.08131,397,184 - 131,397,435UniSTSRnor5.0
RGSC_v3.48127,907,014 - 127,907,265UniSTSRGSC3.4
RGSC_v3.48127,906,996 - 127,907,359RGDRGSC3.4
RGSC_v3.18127,926,751 - 127,927,002RGD
Celera8121,925,567 - 121,925,818UniSTS
RH 3.4 Map81259.4RGD
RH 3.4 Map81259.4UniSTS
SHRSP x BN Map885.2699UniSTS
SHRSP x BN Map885.2699RGD
Cytogenetic Map8q32UniSTS
RH143893  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.28122,815,422 - 122,815,566 (+)MAPPERmRatBN7.2
Rnor_6.08132,246,447 - 132,246,590NCBIRnor6.0
Rnor_5.08131,400,040 - 131,400,183UniSTSRnor5.0
RGSC_v3.48127,909,870 - 127,910,013UniSTSRGSC3.4
Celera8121,928,423 - 121,928,566UniSTS
RH 3.4 Map81275.9UniSTS
Cytogenetic Map8q32UniSTS
AU049759  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.28122,812,682 - 122,812,869 (+)MAPPERmRatBN7.2
Rnor_6.08132,243,707 - 132,243,893NCBIRnor6.0
Rnor_5.08131,397,300 - 131,397,486UniSTSRnor5.0
RGSC_v3.48127,907,130 - 127,907,316UniSTSRGSC3.4
Celera8121,925,683 - 121,925,869UniSTS


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
nervous system
renal system
reproductive system
respiratory system
9 11 49 113 89 88 57 25 57 6 216 97 93 45 59 31

Sequence


Ensembl Acc Id: ENSRNOT00000006055   ⟹   ENSRNOP00000006055
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl8122,810,149 - 122,815,835 (+)Ensembl
Rnor_6.0 Ensembl8132,241,134 - 132,246,694 (+)Ensembl
RefSeq Acc Id: NM_001398638   ⟹   NP_001385567
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88131,687,575 - 131,693,292 (+)NCBI
mRatBN7.28122,810,120 - 122,815,837 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001385567 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL76764 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000006055.4
Ensembl Acc Id: ENSRNOP00000006055   ⟸   ENSRNOT00000006055
RefSeq Acc Id: NP_001385567   ⟸   NM_001398638
- Peptide Label: precursor
- UniProtKB: A6I4B3 (UniProtKB/TrEMBL),   D3ZUU6 (UniProtKB/TrEMBL)
Protein Domains
C-type lectin

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZUU6-F1-model_v2 AlphaFold D3ZUU6 1-202 view protein structure

Transcriptome

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

Promoters
RGD ID:13696417
Promoter ID:EPDNEW_R6930
Type:initiation region
Name:Clec3b_1
Description:C-type lectin domain family 3, member B
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_6.08132,241,201 - 132,241,261EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1311031 AgrOrtholog
BioCyc Gene G2FUF-28620 BioCyc
Ensembl Genes ENSRNOG00000004540 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000006055.8 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
NCBI Gene Clec3b ENTREZGENE
PANTHER TETRANECTIN UniProtKB/TrEMBL
  TETRANECTIN-RELATED UniProtKB/TrEMBL
Pfam Lectin_C UniProtKB/TrEMBL
PhenoGen Clec3b PhenoGen
PRINTS PNCREATITSAP UniProtKB/TrEMBL
PROSITE C_TYPE_LECTIN_1 UniProtKB/TrEMBL
  C_TYPE_LECTIN_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000004540 RatGTEx
SMART CLECT UniProtKB/TrEMBL
Superfamily-SCOP C-type_lectin_fold UniProtKB/TrEMBL
  Triple coiled coil domain of C-type lectins UniProtKB/TrEMBL
UniProt A6I4B3 ENTREZGENE, UniProtKB/TrEMBL
  D3ZUU6 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-11-30 Clec3b  C-type lectin domain family 3, member B  LOC100912012  tetranectin-like  Data merged from RGD:6489383 737654 APPROVED
2015-11-30 Clec3b  C-type lectin domain family 3, member B  Clec3b  C-type lectin domain family 3, member B  Type changed (type changed from [miscrna] to [protein-coding]) 629549 APPROVED
2012-07-05 LOC100912012  tetranectin-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2011-06-08 Clec3b  C-type lectin domain family 3, member B  Clec3b  C-type lectin domain family 3, member b  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Clec3b  C-type lectin domain family 3, member b   Clec3b_predicted  C-type lectin domain family 3, member b (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Clec3b_predicted  C-type lectin domain family 3, member b (predicted)  Tna_predicted  tetranectin (plasminogen binding protein) (predicted)  Symbol and Name updated 1299863 APPROVED
2005-01-12 Tna_predicted  tetranectin (plasminogen binding protein) (predicted)      Symbol and Name status set to approved 70820 APPROVED