Tbl3 (transducin (beta)-like 3) - Rat Genome Database

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Pathways
Gene: Tbl3 (transducin (beta)-like 3) Rattus norvegicus
Analyze
Symbol: Tbl3
Name: transducin (beta)-like 3
RGD ID: 1305142
Description: Predicted to enable U3 snoRNA binding activity. Predicted to be involved in endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) and endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA). Predicted to be located in nucleoplasm. Predicted to be part of 90S preribosome and small-subunit processome. Predicted to be active in nucleolus. Orthologous to human TBL3 (transducin beta like 3); PARTICIPATES IN ribosome biogenesis pathway; INTERACTS WITH (+)-schisandrin B; 2,3,7,8-Tetrachlorodibenzofuran; 2,4-dinitrotoluene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC287120; MGC94510; transducin beta-like 3; transducin beta-like protein 3
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
GRCr81014,230,660 - 14,235,873 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1014,230,661 - 14,235,873 (-)EnsemblGRCr8
mRatBN7.21013,726,127 - 13,731,340 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1013,726,129 - 13,731,372 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1018,472,824 - 18,478,043 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01017,961,677 - 17,966,896 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01013,460,879 - 13,466,098 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01014,066,984 - 14,072,197 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1014,066,948 - 14,072,230 (-)Ensemblrn6Rnor6.0
Rnor_5.01013,883,207 - 13,888,420 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41013,953,946 - 13,959,159 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1013,405,868 - 13,411,081 (-)NCBICelera
RGSC_v3.11013,953,945 - 13,959,159 (-)NCBI
Cytogenetic Map10q12NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
90S preribosome  (IBA)
nucleolus  (IBA,IEA,ISO)
small-subunit processome  (IEA,ISO,ISS)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
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 GOA human gene data--August 2006 GOA data from the GO Consortium
3. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:22658674  


Genomics

Comparative Map Data
Tbl3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81014,230,660 - 14,235,873 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1014,230,661 - 14,235,873 (-)EnsemblGRCr8
mRatBN7.21013,726,127 - 13,731,340 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1013,726,129 - 13,731,372 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1018,472,824 - 18,478,043 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01017,961,677 - 17,966,896 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01013,460,879 - 13,466,098 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01014,066,984 - 14,072,197 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1014,066,948 - 14,072,230 (-)Ensemblrn6Rnor6.0
Rnor_5.01013,883,207 - 13,888,420 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41013,953,946 - 13,959,159 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1013,405,868 - 13,411,081 (-)NCBICelera
RGSC_v3.11013,953,945 - 13,959,159 (-)NCBI
Cytogenetic Map10q12NCBI
TBL3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38161,972,053 - 1,982,929 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl161,972,050 - 1,982,929 (+)Ensemblhg38GRCh38
GRCh37162,022,054 - 2,032,930 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36161,962,065 - 1,968,752 (+)NCBIBuild 36Build 36hg18NCBI36
Build 34161,962,064 - 1,968,752NCBI
Celera162,234,243 - 2,240,930 (+)NCBICelera
Cytogenetic Map16p13.3NCBI
HuRef161,946,130 - 1,952,817 (+)NCBIHuRef
CHM1_1162,021,993 - 2,028,680 (+)NCBICHM1_1
T2T-CHM13v2.0161,992,012 - 2,002,867 (+)NCBIT2T-CHM13v2.0
Tbl3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391724,919,627 - 24,926,627 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1724,916,923 - 24,926,634 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm381724,700,653 - 24,707,653 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1724,697,949 - 24,707,660 (-)Ensemblmm10GRCm38
MGSCv371724,837,598 - 24,844,598 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361724,428,253 - 24,435,253 (-)NCBIMGSCv36mm8
Celera1725,223,575 - 25,230,579 (-)NCBICelera
Cytogenetic Map17A3.3NCBI
cM Map1712.49NCBI
Tbl3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495544215,290,759 - 15,297,442 (-)Ensembl
ChiLan1.0NW_00495544215,290,759 - 15,297,070 (-)NCBIChiLan1.0ChiLan1.0
TBL3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2182,365,658 - 2,377,209 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1166,150,383 - 6,159,150 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v016725,629 - 732,350 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1162,061,074 - 2,067,974 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl162,061,199 - 2,067,715 (+)EnsemblpanPan2panpan1.1
TBL3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1638,956,227 - 38,962,189 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl638,788,454 - 38,962,167 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha640,195,917 - 40,201,875 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0639,273,245 - 39,279,203 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl639,273,245 - 39,279,193 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1638,950,022 - 38,955,978 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0638,922,328 - 38,928,286 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0639,401,215 - 39,407,173 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Tbl3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024409344104,642,890 - 104,649,243 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366942,060,220 - 2,066,575 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049366942,060,218 - 2,066,525 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TBL3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl339,989,740 - 39,995,123 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1339,989,739 - 39,996,138 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
TBL3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.151,867,943 - 1,874,640 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl51,867,917 - 1,875,236 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366606829,193,058 - 29,199,944 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Tbl3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624913282,887 - 289,407 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_004624913282,883 - 289,523 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Tbl3
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v191,984,631 - 1,989,924 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Tbl3
37 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:36
Count of miRNA genes:35
Interacting mature miRNAs:36
Transcripts:ENSRNOT00000018405
Prediction methods: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
2313095Bss62Bone structure and strength QTL 621.50.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)10589381150893811Rat
631660Hcar1Hepatocarcinoma resistance QTL 13.40.0001liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)10666111835509383Rat
8662860Vetf10Vascular elastic tissue fragility QTL 10artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)10666092373950353Rat
2313066Bss63Bone structure and strength QTL 631.40.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)10589381150893811Rat
631554Bp133Blood pressure QTL 1330.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)10125055464349221Rat
2313064Bmd71Bone mineral density QTL 710.90.0001tibia mineral mass (VT:1000283)compact volumetric bone mineral density (CMO:0001730)10589381150893811Rat
1578761Stresp21Stress response QTL 213.3thymus mass (VT:0004954)thymus wet weight (CMO:0000855)10687714251877142Rat
2293680Bss40Bone structure and strength QTL 405.660.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)10135730538Rat
7387235Uae41Urinary albumin excretion QTL 415.260.1874urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)10130004247Rat
2313104Bss61Bone structure and strength QTL 610.90.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)10589381150893811Rat
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10686461896620484Rat
10401803Kidm50Kidney mass QTL 50kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1092219745922197Rat
2317754Glom25Glomerulus QTL 253.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)10210370847103708Rat
2313081Bss64Bone structure and strength QTL 641.30.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)10589381150893811Rat
631828Alc5Alcohol consumption QTL 52.4consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)10117749933Rat
634327Hc4Hypercalciuria QTL 42.4urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)10138832698Rat

Markers in Region
RH135372  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21013,725,784 - 13,725,983 (+)MAPPERmRatBN7.2
Rnor_6.01014,066,642 - 14,066,840NCBIRnor6.0
Rnor_5.01013,882,865 - 13,883,063UniSTSRnor5.0
RGSC_v3.41013,953,604 - 13,953,802UniSTSRGSC3.4
Celera1013,405,526 - 13,405,724UniSTS
RH 3.4 Map10173.1UniSTS
Cytogenetic Map10q12UniSTS
AU049127  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21013,733,462 - 13,733,715 (+)MAPPERmRatBN7.2
Rnor_6.01014,074,322 - 14,074,574NCBIRnor6.0
Rnor_5.01013,889,995 - 13,890,247UniSTSRnor5.0
RGSC_v3.41013,960,934 - 13,961,186UniSTSRGSC3.4
Celera1013,413,172 - 13,413,424UniSTS
Cytogenetic Map10q12UniSTS


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
sensory system
visual system
16 12 67 161 91 90 59 92 59 6 356 192 11 140 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000018405   ⟹   ENSRNOP00000018405
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1014,230,661 - 14,235,873 (-)Ensembl
mRatBN7.2 Ensembl1013,726,129 - 13,731,372 (-)Ensembl
Rnor_6.0 Ensembl1014,066,948 - 14,072,230 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000118653   ⟹   ENSRNOP00000083634
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1014,230,661 - 14,235,873 (-)Ensembl
mRatBN7.2 Ensembl1013,726,129 - 13,731,372 (-)Ensembl
RefSeq Acc Id: NM_001008277   ⟹   NP_001008278
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81014,230,660 - 14,235,873 (-)NCBI
mRatBN7.21013,726,127 - 13,731,340 (-)NCBI
Rnor_6.01014,066,984 - 14,072,197 (-)NCBI
Rnor_5.01013,883,207 - 13,888,420 (-)NCBI
RGSC_v3.41013,953,946 - 13,959,159 (-)RGD
Celera1013,405,868 - 13,411,081 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001008278 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH85837 (Get FASTA)   NCBI Sequence Viewer  
  EDM03861 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000018405
  ENSRNOP00000018405.4
GenBank Protein Q5U2W5 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_001008278   ⟸   NM_001008277
- UniProtKB: Q5U2W5 (UniProtKB/Swiss-Prot),   A6HCV6 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000018405   ⟸   ENSRNOT00000018405
Ensembl Acc Id: ENSRNOP00000083634   ⟸   ENSRNOT00000118653
Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5U2W5-F1-model_v2 AlphaFold Q5U2W5 1-800 view protein structure

Transcriptome

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

Promoters
RGD ID:13697023
Promoter ID:EPDNEW_R7548
Type:initiation region
Name:Tbl3_1
Description:transducin -like 3
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_6.01014,072,213 - 14,072,273EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1305142 AgrOrtholog
BioCyc Gene G2FUF-25833 BioCyc
Ensembl Genes ENSRNOG00000013429 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000018405 ENTREZGENE
  ENSRNOT00000018405.6 UniProtKB/Swiss-Prot
Gene3D-CATH 2.130.10.10 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7135552 IMAGE-MGC_LOAD
InterPro G-protein_beta_WD-40_rep UniProtKB/Swiss-Prot
  Quinoprotein_ADH-like_supfam UniProtKB/Swiss-Prot
  SSU_processome_Utp13 UniProtKB/Swiss-Prot
  WD40/YVTN_repeat-like_dom_sf UniProtKB/Swiss-Prot
  WD40_repeat UniProtKB/Swiss-Prot
  WD40_repeat_CS UniProtKB/Swiss-Prot
  WD40_repeat_dom_sf UniProtKB/Swiss-Prot
KEGG Report rno:287120 UniProtKB/Swiss-Prot
MGC_CLONE MGC:94510 IMAGE-MGC_LOAD
NCBI Gene 287120 ENTREZGENE
PANTHER TRANSDUCIN BETA-LIKE 3 UniProtKB/Swiss-Prot
  TRANSDUCIN BETA-LIKE PROTEIN 3 UniProtKB/Swiss-Prot
Pfam Utp13 UniProtKB/Swiss-Prot
  WD40 UniProtKB/Swiss-Prot
PhenoGen Tbl3 PhenoGen
PRINTS GPROTEINBRPT UniProtKB/Swiss-Prot
PROSITE WD_REPEATS_1 UniProtKB/Swiss-Prot
  WD_REPEATS_2 UniProtKB/Swiss-Prot
  WD_REPEATS_REGION UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000013429 RatGTEx
SMART WD40 UniProtKB/Swiss-Prot
Superfamily-SCOP SSF50978 UniProtKB/Swiss-Prot
  SSF50998 UniProtKB/Swiss-Prot
UniProt A0A8I6G9A5_RAT UniProtKB/TrEMBL
  A6HCV6 ENTREZGENE, UniProtKB/TrEMBL
  Q5U2W5 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-12-06 Tbl3  transducin (beta)-like 3  Tbl3_predicted  transducin (beta)-like 3 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Tbl3_predicted  transducin (beta)-like 3 (predicted)      Symbol and Name status set to approved 70820 APPROVED