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) Mus musculus
Analyze
Symbol: Clec3b
Name: C-type lectin domain family 3, member b
RGD ID: 1553639
MGI Page MGI
Description: Predicted to enable calcium ion binding activity; heparin binding activity; and kringle domain binding activity. Involved in ossification and positive regulation of plasminogen activation. Acts upstream of or within skeletal system development. Located in cytoplasm. Is expressed in several structures, including genitourinary system; gut; integumental system; serum; and skeletal musculature. Used to study Scheuermann's disease. 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).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: plasminogen kringle 4-binding protein; T; tetranectin; tetranectin (plasminogen binding protein); tetranectin (plasminogen-binding protein); TN; Tna
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
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
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

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Genetic mapping of the peripheral sodium channel genes, Scn9a and Scn10a, in the mouse. Kozak CA and Sangameswaran L, Mamm Genome 1996 Oct;7(10):787-8.
2. MGDs mouse GO annotations MGD data from the GO Consortium
3. MGD IEA MGD IEA
4. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Okazaki Y, etal., Nature. 2002 Dec 5;420(6915):563-73.
5. Mouse MP Annotation Import Pipeline RGD automated import pipeline
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
7. Association study of candidate genes for the prevalence and progression of knee osteoarthritis. Valdes AM, etal., Arthritis Rheum. 2004 Aug;50(8):2497-507.
Additional References at PubMed
PMID:7738119   PMID:7798325   PMID:7835708   PMID:8563165   PMID:9154122   PMID:9409787   PMID:9705231   PMID:11604516   PMID:12477932   PMID:12694198   PMID:15848710   PMID:16602821  
PMID:19152657   PMID:21677750   PMID:21873635   PMID:23588617   PMID:24194600   PMID:26597345   PMID:31540696   PMID:32640236   PMID:33451873   PMID:34880220   PMID:38355793  


Genomics

Comparative Map Data
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
(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
(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
(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
206 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:205
Count of miRNA genes:175
Interacting mature miRNAs:187
Transcripts:ENSMUST00000026890
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 (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
18182932Metl3_mmetabolite locus 3, N-acetylglutamate (mouse)989440541123440541Mouse
1301649Psl1_mpromotion susceptibility QTL 1 (mouse)Not determined989289476123289595Mouse
1357648Obq18_mobesity QTL 18 (mouse)Not determined9101829255124359700Mouse
12904961Gmmq7_mgastrocnemius muscle mass QTL 7 (mouse)991560372124359700Mouse
10412242Alpq8_malcohol preference QTL 8 (mouse)Not determined989162124123162124Mouse
1301789Pbwg4_mpostnatal body weight growth 4 (mouse)Not determined9103118511124359700Mouse
14746992Manh67_mmandible shape 67 (mouse)993865836124359700Mouse
10412290Pvacm1l_mplasma vascular cell adhesion molecule 1 levels (mouse)Not determined9103118511124359700Mouse
12879896Berr3_mberghei resistance locus 3 (mouse)9103118511124359700Mouse
1302001Bdln5_mbody length 5 (mouse)Not determined993591658124359700Mouse
1301297Lcho1_mliver cholesterol 1 (mouse)Not determined9100889929124359700Mouse
11537364Cnes5_mC. neoformans susceptibility locus 5 (mouse)996746658124359700Mouse
12904937Edlmmq9_mextensor digitorum longus muscle mass QTL 9 (mouse)991560372124359700Mouse
1357627Tgq2_mtriglyceride QTL 2 (mouse)Not determined9101829255124359700Mouse
12910773Splic3_mspleen iron content 3 (mouse)991291078124359700Mouse
12910772Lvic6_mliver iron content 6 (mouse)991291078124359700Mouse
13463480Mchcq2_mmean corpuscular hemoglobin concentration QTL 2 (mouse)991518283124359700Mouse
12910770Splic1_mspleen iron content 1 (mouse)991291078124359700Mouse
12904947Tammq7_mtibialis anterior muscle mass QTL 7 (mouse)991560372124359700Mouse
1558767Skmw11_mskeletal muscle weight 11 (mouse)Not determined991518283124359700Mouse
13463477Rbc9_mred blood cell count 9 (mouse)991518283124359700Mouse
13463478Mchq18_mmean corpuscular hemoglobin QTL 18 (mouse)991518283124359700Mouse
13463475Hctq7_mhematocrit QTL 7 (mouse)991518283124359700Mouse
1301484Bwq6_mbody weight (mouse)Not determined993591658124359700Mouse
13463474Hbbcq5_mhemoglobin concentration QTL 5 (mouse)991518283124359700Mouse

Markers in Region
Clec3b  
Mouse AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map9F1-F3UniSTS
cM Map971.0UniSTS


Expression

RNA-SEQ Expression


Sequence


Ensembl Acc Id: ENSMUST00000026890   ⟹   ENSMUSP00000026890
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl9122,980,011 - 122,986,497 (+)Ensembl
GRCm38.p6 Ensembl9123,150,946 - 123,157,432 (+)Ensembl
RefSeq Acc Id: NM_011606   ⟹   NP_035736
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm399122,980,011 - 122,986,497 (+)NCBI
GRCm389123,150,946 - 123,157,432 (+)ENTREZGENE
MGSCv379123,060,064 - 123,066,550 (+)RGD
Celera9123,602,080 - 123,608,547 (+)RGD
cM Map9 ENTREZGENE
Sequence:
Protein Sequences
Protein RefSeqs NP_035736 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA96811 (Get FASTA)   NCBI Sequence Viewer  
  AAH35043 (Get FASTA)   NCBI Sequence Viewer  
  CAA55791 (Get FASTA)   NCBI Sequence Viewer  
  CAA66804 (Get FASTA)   NCBI Sequence Viewer  
  EDL09070 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSMUSP00000026890
  ENSMUSP00000026890.5
GenBank Protein P43025 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_035736   ⟸   NM_011606
- Peptide Label: precursor
- UniProtKB: P43025 (UniProtKB/Swiss-Prot),   Q8CFZ6 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSMUSP00000026890   ⟸   ENSMUST00000026890
Protein Domains
C-type lectin

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P43025-F1-model_v2 AlphaFold P43025 1-202 view protein structure

Promoters
RGD ID:6844330
Promoter ID:MM_KWN:59263
Type:Non-CpG
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:Lung
Transcripts:UC009SFW.1
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv369123,060,001 - 123,060,501 (+)MPROMDB
RGD ID:6849265
Promoter ID:MM_XEF:7730
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:Lung
Transcripts:NM_001011424
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv369123,065,601 - 123,066,101 (+)MPROMDB
RGD ID:8671332
Promoter ID:EPDNEW_M13696
Type:initiation region
Name:Clec3b_1
Description:Mus musculus C-type lectin domain family 3, member b , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm389123,151,013 - 123,151,073EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:104540 AgrOrtholog
Ensembl Genes ENSMUSG00000025784 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSMUST00000026890 ENTREZGENE
  ENSMUST00000026890.6 UniProtKB/TrEMBL
Gene3D-CATH 3.10.100.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro C-type_lectin-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  C-type_lectin-like/link_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  C-type_lectin_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CLec_Tetranectin-domain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CTDL_fold UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report mmu:21922 UniProtKB/TrEMBL
MGD MGI:104540 ENTREZGENE
NCBI Gene 21922 ENTREZGENE
PANTHER TETRANECTIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TETRANECTIN-RELATED UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Lectin_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Clec3b PhenoGen
PRINTS PNCREATITSAP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE C_TYPE_LECTIN_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  C_TYPE_LECTIN_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART CLECT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF56436 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Triple coiled coil domain of C-type lectins UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt P43025 ENTREZGENE
  Q8CFZ6 ENTREZGENE, UniProtKB/TrEMBL
  TETN_MOUSE UniProtKB/Swiss-Prot