Clec3b (C-type lectin domain family 3, member B) - Rat Genome Database
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
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 have calcium ion binding activity; heparin binding activity; and kringle domain binding activity. Involved in ossification. Predicted to localize to cytoplasm; extracellular space; and granular component. Human ortholog(s) of this gene implicated in osteoarthritis. Orthologous to human CLEC3B (C-type lectin domain family 3 member B); INTERACTS WITH endosulfan; 17beta-estradiol (ortholog); 2,3,7,8-tetrachlorodibenzodioxine (ortholog).
Type: protein-coding
RefSeq Status: MODEL
Also 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 Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.28122,810,091 - 122,817,039 (+)NCBI
Rnor_6.0 Ensembl8132,241,134 - 132,246,694 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.08132,241,016 - 132,248,066 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
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

Cellular Component
cytoplasm  (ISO,ISS)
extracellular space  (IBA,ISO,ISS)
granular component  (ISO,ISS)

Molecular Function

References

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
mRatBN7.28122,810,091 - 122,817,039 (+)NCBI
Rnor_6.0 Ensembl8132,241,134 - 132,246,694 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.08132,241,016 - 132,248,066 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
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
GRCh38.p13 Ensembl345,001,548 - 45,036,071 (+)EnsemblGRCh38hg38GRCh38
GRCh38345,026,207 - 45,036,071 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37345,067,795 - 45,077,563 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36345,042,763 - 45,052,567 (+)NCBINCBI36hg18NCBI36
Celera345,005,711 - 45,015,514 (+)NCBI
Cytogenetic Map3p21.31NCBI
HuRef345,111,173 - 45,120,977 (+)NCBIHuRef
CHM1_1345,017,739 - 45,027,545 (+)NCBICHM1_1
Clec3b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm399122,980,011 - 122,986,497 (+)NCBIGRCm39mm39
GRCm39 Ensembl9122,980,011 - 122,986,497 (+)Ensembl
GRCm389123,150,946 - 123,157,432 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl9123,150,946 - 123,157,432 (+)EnsemblGRCm38mm10GRCm38
MGSCv379123,060,064 - 123,066,550 (+)NCBIGRCm37mm9NCBIm37
MGSCv369122,999,547 - 123,006,125 (+)NCBImm8
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
PanPan1.1346,038,115 - 46,047,927 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl346,038,115 - 46,047,927 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0344,927,098 - 44,936,847 (+)NCBIMhudiblu_PPA_v0panPan3
CLEC3B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl2043,324,231 - 43,332,135 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.12043,319,786 - 43,332,161 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Clec3b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_004936695731,184 - 738,752 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CLEC3B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1328,176,793 - 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 - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1226,501,082 - 6,510,878 (+)NCBI
ChlSab1.1 Ensembl226,501,102 - 6,512,314 (+)Ensembl
Clec3b
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473075,531,320 - 75,535,875 (-)NCBI

Position Markers
D8Rat71  
Rat AssemblyChrPosition (strand)SourceJBrowse
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
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
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


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61437Cia6Collagen induced arthritis QTL 6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)889058229132243842Rat
1358893Bp263Blood pressure QTL 2635.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)8100873811133307652Rat
1358903Bp252Blood pressure QTL 25270.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)8100873811133307652Rat
738011Anxrr9Anxiety related response QTL 96.1exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)8102051964133307652Rat
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)8104682575133307652Rat
2300182Bmd56Bone mineral density QTL 565.4femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)8104682575133307652Rat

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.


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 3 26 4 13 5 8 22 19 24 11 5
Low 11 33 21 6 21 3 3 42 14 10 3
Below cutoff 6 18 18 18 10 2 6

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000006055   ⟹   ENSRNOP00000006055
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl8132,241,134 - 132,246,694 (+)Ensembl
RefSeq Acc Id: XM_003750609   ⟹   XP_003750657
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28122,810,091 - 122,817,039 (+)NCBI
Rnor_6.08132,241,016 - 132,248,066 (+)NCBI
Sequence:
RefSeq Acc Id: XM_003754467   ⟹   XP_003754515
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera8121,922,992 - 121,930,042 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs XP_003750657 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL76764 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: XP_003754515   ⟸   XM_003754467
- Sequence:
RefSeq Acc Id: XP_003750657   ⟸   XM_003750609
- UniProtKB: D3ZUU6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000006055   ⟸   ENSRNOT00000006055
Protein Domains
C-type lectin

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

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1311031 AgrOrtholog
Ensembl Genes ENSRNOG00000004540 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000006055 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000006055 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
KEGG Report rno:100912012 UniProtKB/TrEMBL
NCBI Gene Clec3b ENTREZGENE
Pfam Lectin_C UniProtKB/TrEMBL
PhenoGen Clec3b PhenoGen
PROSITE C_TYPE_LECTIN_1 UniProtKB/TrEMBL
  C_TYPE_LECTIN_2 UniProtKB/TrEMBL
SMART CLECT UniProtKB/TrEMBL
Superfamily-SCOP C-type_lectin_fold UniProtKB/TrEMBL
UniProt 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 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