Tsr3 (TSR3 ribosome maturation factor) - Rat Genome Database

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Gene: Tsr3 (TSR3 ribosome maturation factor) Rattus norvegicus
Analyze
Symbol: Tsr3
Name: TSR3 ribosome maturation factor
RGD ID: 1565744
Description: Predicted to enable rRNA small subunit aminocarboxypropyltransferase activity. Predicted to be involved in enzyme-directed rRNA pseudouridine synthesis and maturation of SSU-rRNA. Predicted to be located in cytoplasm and membrane. Orthologous to human TSR3 (TSR3 ribosome maturation factor); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A; cadmium dichloride.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: 18S rRNA aminocarboxypropyltransferase; hypothetical protein LOC360494; LOC360494; RGD1565744; ribosome biogenesis protein TSR3 homolog; similar to RIKEN cDNA 0610007P22; TSR3, 20S rRNA accumulation; TSR3, acp transferase ribosome maturation factor; uncharacterized protein LOC360494
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
GRCr81014,761,656 - 14,764,061 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1014,761,663 - 14,764,061 (+)EnsemblGRCr8
mRatBN7.21014,257,161 - 14,259,562 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1014,257,171 - 14,259,561 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1018,997,910 - 19,000,305 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01018,486,772 - 18,489,167 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01013,985,987 - 13,988,382 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01014,598,014 - 14,600,576 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1014,598,014 - 14,600,576 (+)Ensemblrn6Rnor6.0
Rnor_5.01014,415,604 - 14,418,166 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41014,487,946 - 14,490,508 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1013,929,574 - 13,932,136 (+)NCBICelera
Cytogenetic Map10q12NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cytoplasm  (IEA)

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. 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
Additional References at PubMed
PMID:12477932   PMID:27084949  


Genomics

Comparative Map Data
Tsr3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81014,761,656 - 14,764,061 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1014,761,663 - 14,764,061 (+)EnsemblGRCr8
mRatBN7.21014,257,161 - 14,259,562 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1014,257,171 - 14,259,561 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1018,997,910 - 19,000,305 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01018,486,772 - 18,489,167 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01013,985,987 - 13,988,382 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01014,598,014 - 14,600,576 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1014,598,014 - 14,600,576 (+)Ensemblrn6Rnor6.0
Rnor_5.01014,415,604 - 14,418,166 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41014,487,946 - 14,490,508 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1013,929,574 - 13,932,136 (+)NCBICelera
Cytogenetic Map10q12NCBI
TSR3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38161,349,240 - 1,351,878 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl161,349,237 - 1,351,878 (-)Ensemblhg38GRCh38
GRCh37161,399,241 - 1,401,879 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36161,339,242 - 1,341,874 (-)NCBIBuild 36Build 36hg18NCBI36
Celera161,613,356 - 1,615,988 (-)NCBICelera
Cytogenetic Map16p13.3NCBI
HuRef161,327,639 - 1,330,271 (-)NCBIHuRef
CHM1_1161,399,182 - 1,401,814 (-)NCBICHM1_1
T2T-CHM13v2.0161,365,417 - 1,368,055 (-)NCBIT2T-CHM13v2.0
Tsr3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391725,459,120 - 25,461,773 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1725,459,141 - 25,461,773 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm381725,240,141 - 25,242,799 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1725,240,170 - 25,242,798 (+)Ensemblmm10GRCm38
MGSCv371725,377,115 - 25,379,744 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361724,967,799 - 24,970,395 (+)NCBIMGSCv36mm8
Celera1722,578,286 - 22,580,908 (+)NCBICelera
Cytogenetic Map17A3.3NCBI
cM Map1712.53NCBI
Tsr3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495544215,881,678 - 15,884,008 (+)Ensembl
ChiLan1.0NW_00495544215,881,663 - 15,884,222 (+)NCBIChiLan1.0ChiLan1.0
TSR3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2181,612,328 - 1,614,973 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1165,399,574 - 5,402,221 (-)NCBINHGRI_mPanPan1
PanPan1.1161,404,730 - 1,406,976 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl161,404,927 - 1,411,747 (-)EnsemblpanPan2panpan1.1
TSR3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1639,418,737 - 39,421,524 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl639,368,492 - 39,421,208 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha640,686,704 - 40,689,223 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0639,764,998 - 39,767,517 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
UMICH_Zoey_3.1639,441,726 - 39,444,245 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0639,414,369 - 39,416,888 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0639,892,678 - 39,895,197 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Tsr3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024409344104,166,797 - 104,169,033 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366942,540,444 - 2,542,666 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049366942,540,446 - 2,542,666 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TSR3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl340,534,222 - 40,536,766 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1340,534,222 - 40,536,773 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2341,986,787 - 41,989,336 (-)NCBISscrofa10.2Sscrofa10.2susScr3
TSR3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.151,237,625 - 1,240,287 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl51,237,821 - 1,240,191 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366606829,843,509 - 29,846,175 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Tsr3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046249132,060,114 - 2,062,308 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046249132,059,904 - 2,062,578 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Tsr3
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v192,506,446 - 2,508,793 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Tsr3
7 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:58
Count of miRNA genes:51
Interacting mature miRNAs:57
Transcripts:ENSRNOT00000068336
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 (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
70223Bp57Blood pressure QTL 575arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)101465354159653541Rat
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
RH135402  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21014,259,449 - 14,259,666 (+)MAPPERmRatBN7.2
Rnor_6.01014,600,314 - 14,600,530NCBIRnor6.0
Rnor_5.01014,417,904 - 14,418,120UniSTSRnor5.0
RGSC_v3.41014,490,246 - 14,490,462UniSTSRGSC3.4
Celera1013,931,874 - 13,932,090UniSTS
RH 3.4 Map10162.6UniSTS
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 67 163 91 90 59 92 59 6 356 192 11 142 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000068336   ⟹   ENSRNOP00000061431
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1014,761,663 - 14,764,061 (+)Ensembl
mRatBN7.2 Ensembl1014,257,171 - 14,259,561 (+)Ensembl
Rnor_6.0 Ensembl1014,598,014 - 14,600,576 (+)Ensembl
RefSeq Acc Id: NM_001108268   ⟹   NP_001101738
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81014,761,666 - 14,764,061 (+)NCBI
mRatBN7.21014,257,167 - 14,259,562 (+)NCBI
Rnor_6.01014,598,014 - 14,600,576 (+)NCBI
Rnor_5.01014,415,604 - 14,418,166 (+)NCBI
RGSC_v3.41014,487,946 - 14,490,508 (+)RGD
Celera1013,929,574 - 13,932,136 (+)RGD
Sequence:
RefSeq Acc Id: NM_001399517   ⟹   NP_001386446
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81014,761,666 - 14,764,061 (+)NCBI
mRatBN7.21014,257,167 - 14,259,562 (+)NCBI
RefSeq Acc Id: NM_001399519   ⟹   NP_001386448
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81014,761,666 - 14,764,061 (+)NCBI
mRatBN7.21014,257,167 - 14,259,562 (+)NCBI
RefSeq Acc Id: XM_039086273   ⟹   XP_038942201
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81014,761,656 - 14,764,061 (+)NCBI
mRatBN7.21014,257,161 - 14,258,764 (+)NCBI
RefSeq Acc Id: NP_001101738   ⟸   NM_001108268
- Peptide Label: isoform 3
- UniProtKB: A6HD11 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000061431   ⟸   ENSRNOT00000068336
RefSeq Acc Id: XP_038942201   ⟸   XM_039086273
- Peptide Label: isoform X1
RefSeq Acc Id: NP_001386448   ⟸   NM_001399519
- Peptide Label: isoform 2
- UniProtKB: D4A6X9 (UniProtKB/TrEMBL),   A6HD10 (UniProtKB/TrEMBL)
RefSeq Acc Id: NP_001386446   ⟸   NM_001399517
- Peptide Label: isoform 1
Protein Domains
16S/18S rRNA aminocarboxypropyltransferase Tsr3 C-   RNase L inhibitor RLI-like possible metal-binding

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A6X9-F1-model_v2 AlphaFold D4A6X9 1-263 view protein structure

Transcriptome

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

Promoters
RGD ID:13697046
Promoter ID:EPDNEW_R7571
Type:initiation region
Name:Tsr3_1
Description:TSR3, acp transferase ribosome maturation factor
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_6.01014,598,046 - 14,598,106EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1565744 AgrOrtholog
BioCyc Gene G2FUF-25796 BioCyc
Ensembl Genes ENSRNOG00000017858 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000068336 ENTREZGENE
  ENSRNOT00000068336.3 UniProtKB/TrEMBL
InterPro DUF367 UniProtKB/TrEMBL
  Rbsm_biogenesis UniProtKB/TrEMBL
  RNaseL-inhib_metal-bd_dom UniProtKB/TrEMBL
KEGG Report rno:360494 UniProtKB/TrEMBL
NCBI Gene 360494 ENTREZGENE
PANTHER 18S RRNA AMINOCARBOXYPROPYLTRANSFERASE UniProtKB/TrEMBL
  PTHR20426 UniProtKB/TrEMBL
Pfam DUF367 UniProtKB/TrEMBL
  RLI UniProtKB/TrEMBL
PhenoGen Tsr3 PhenoGen
RatGTEx ENSRNOG00000017858 RatGTEx
UniProt A6HD10 ENTREZGENE, UniProtKB/TrEMBL
  A6HD11 ENTREZGENE, UniProtKB/TrEMBL
  A6HD12_RAT UniProtKB/TrEMBL
  D4A6X9 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-04-02 Tsr3  TSR3 ribosome maturation factor  Tsr3  TSR3, acp transferase ribosome maturation factor  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2017-03-21 Tsr3  TSR3, acp transferase ribosome maturation factor  Tsr3  TSR3, 20S rRNA accumulation  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-10-12 Tsr3  TSR3, 20S rRNA accumulation  RGD1565744  similar to RIKEN cDNA 0610007P22  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1565744  similar to RIKEN cDNA 0610007P22   RGD1565744_predicted  similar to RIKEN cDNA 0610007P22 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-07 RGD1565744_predicted  similar to RIKEN cDNA 0610007P22 (predicted)  LOC360494  similar to RIKEN cDNA 0610007P22  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC360494  similar to RIKEN cDNA 0610007P22      Symbol and Name status set to provisional 70820 PROVISIONAL