Tyw3 (tRNA-yW synthesizing protein 3 homolog) - Rat Genome Database

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Gene: Tyw3 (tRNA-yW synthesizing protein 3 homolog) Rattus norvegicus
Analyze
Symbol: Tyw3
Name: tRNA-yW synthesizing protein 3 homolog
RGD ID: 1559623
Description: Predicted to enable tRNA methyltransferase activity. Predicted to be involved in tRNA methylation and wybutosine biosynthetic process. Predicted to be active in cytoplasm. Orthologous to human TYW3 (tRNA-yW synthesizing protein 3 homolog); INTERACTS WITH bisphenol A; dibutyl phthalate; flutamide.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC499731; RGD1559623; similar to RIKEN cDNA 5230400J09; tRNA wybutosine-synthesizing protein 3 homolog; tRNA-yW synthesizing protein 3 homolog (S. cerevisiae)
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
GRCr82246,189,627 - 246,211,737 (-)NCBIGRCr8
mRatBN7.22243,529,912 - 243,552,043 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2243,529,946 - 243,552,039 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2251,360,240 - 251,382,288 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02249,254,067 - 249,276,115 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02244,153,620 - 244,175,714 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02260,861,825 - 260,884,270 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2260,861,790 - 260,884,449 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02279,523,505 - 279,545,942 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42252,411,091 - 252,433,366 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera2235,453,089 - 235,475,183 (-)NCBICelera
Cytogenetic Map2q45NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cytoplasm  (IBA)

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. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data
Tyw3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82246,189,627 - 246,211,737 (-)NCBIGRCr8
mRatBN7.22243,529,912 - 243,552,043 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2243,529,946 - 243,552,039 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2251,360,240 - 251,382,288 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02249,254,067 - 249,276,115 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02244,153,620 - 244,175,714 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02260,861,825 - 260,884,270 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2260,861,790 - 260,884,449 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02279,523,505 - 279,545,942 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42252,411,091 - 252,433,366 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera2235,453,089 - 235,475,183 (-)NCBICelera
Cytogenetic Map2q45NCBI
TYW3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38174,733,152 - 74,766,677 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl174,733,152 - 74,766,678 (+)EnsemblGRCh38hg38GRCh38
GRCh37175,198,836 - 75,232,361 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36174,971,428 - 75,003,896 (+)NCBINCBI36Build 36hg18NCBI36
Celera173,444,068 - 73,477,631 (+)NCBICelera
Cytogenetic Map1p31.1NCBI
HuRef173,333,242 - 73,366,956 (+)NCBIHuRef
CHM1_1175,314,278 - 75,347,771 (+)NCBICHM1_1
T2T-CHM13v2.0174,574,793 - 74,608,590 (+)NCBIT2T-CHM13v2.0
Tyw3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm393154,282,157 - 154,302,750 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl3154,282,068 - 154,302,741 (-)EnsemblGRCm39 Ensembl
GRCm383154,576,520 - 154,597,113 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl3154,576,431 - 154,597,104 (-)EnsemblGRCm38mm10GRCm38
MGSCv373154,239,484 - 154,260,062 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv363154,514,379 - 154,532,376 (-)NCBIMGSCv36mm8
Celera3161,035,779 - 161,056,260 (-)NCBICelera
Cytogenetic Map3H4NCBI
cM Map379.24NCBI
Tyw3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542317,931,947 - 17,952,669 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495542317,932,008 - 17,952,681 (-)NCBIChiLan1.0ChiLan1.0
TYW3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21152,113,760 - 152,146,531 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11151,274,227 - 151,306,846 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0173,961,851 - 73,994,638 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1175,935,862 - 75,968,593 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl175,935,862 - 75,968,593 (+)Ensemblpanpan1.1panPan2
TYW3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1671,634,368 - 71,648,762 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl671,634,654 - 71,646,894 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha674,296,693 - 74,313,123 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0672,226,759 - 72,243,184 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl672,227,550 - 72,244,264 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1671,721,248 - 71,736,925 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0671,667,024 - 71,683,390 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0672,161,727 - 72,177,928 (-)NCBIUU_Cfam_GSD_1.0
Tyw3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505886,523,141 - 86,540,486 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365712,033,438 - 2,050,844 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365712,033,463 - 2,050,838 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TYW3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl6138,418,658 - 138,435,300 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.16138,418,652 - 138,435,300 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.26128,285,939 - 128,301,886 (-)NCBISscrofa10.2Sscrofa10.2susScr3
TYW3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12058,394,130 - 58,427,503 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2058,394,070 - 58,428,119 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603359,027,708 - 59,061,378 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Tyw3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474221,933,635 - 21,951,571 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474221,933,631 - 21,952,183 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Tyw3
70 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:38
Count of miRNA genes:36
Interacting mature miRNAs:38
Transcripts:ENSRNOT00000032874
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
631563Hcuc3Hepatic copper content QTL 33.87liver copper amount (VT:0003065)liver copper weight to liver dry weight ratio (CMO:0001512)2229059610249053267Rat
1298075Scl17Serum cholesterol level QTL 173.4blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)2211744537249053267Rat
2293833Kiddil8Kidney dilation QTL 82.9kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)2219753301247136170Rat
1598835Anxrr18Anxiety related response QTL 182.98body movement coordination trait (VT:0005424)number of rearing movements in an experimental apparatus (CMO:0001752)2200990457245990457Rat
1300126Bp175Blood pressure QTL 1753.46arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2214226044247136170Rat
7207490Bss111Bone structure and strength QTL 1116.4femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)2211744537249053267Rat
7207484Bss108Bone structure and strength QTL 1085.3femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)2211744537249053267Rat
7411555Bw132Body weight QTL 1320.001body mass (VT:0001259)body weight gain (CMO:0000420)2223389739249053267Rat
9587428Epfw6Epididymal fat weight QTL 67.470.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)2223389739249053267Rat
7207482Bss107Bone structure and strength QTL 1077femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)2211744537249053267Rat
2293844Kiddil7Kidney dilation QTL 73.5kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)2219753301247136170Rat
1641891Alcrsp17Alcohol response QTL 17response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2149559561249053267Rat
2317752Glom23Glomerulus QTL 233.6urine protein amount (VT:0005160)urine protein level (CMO:0000591)2193452645245889826Rat
1549836Bss2Bone structure and strength QTL 27.5femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)2211744537249053267Rat
724534Uae6Urinary albumin excretion QTL 610urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)278665619249053267Rat
2317885Alcrsp28Alcohol response QTL 282.10.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2212828222249053267Rat

Markers in Region
BE114677  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22243,529,983 - 243,530,084 (+)MAPPERmRatBN7.2
Rnor_6.02260,861,888 - 260,861,988NCBIRnor6.0
Rnor_5.02279,523,568 - 279,523,668UniSTSRnor5.0
RGSC_v3.42252,411,154 - 252,411,254UniSTSRGSC3.4
Celera2235,453,152 - 235,453,252UniSTS
RH 3.4 Map21630.2UniSTS
Cytogenetic Map2q45UniSTS


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 91 90 59 25 59 6 218 97 93 45 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000032874   ⟹   ENSRNOP00000037831
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2243,529,946 - 243,552,039 (-)Ensembl
Rnor_6.0 Ensembl2260,861,790 - 260,884,449 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000096868   ⟹   ENSRNOP00000078566
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2243,529,946 - 243,552,039 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000105899   ⟹   ENSRNOP00000082080
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2243,530,367 - 243,551,969 (-)Ensembl
RefSeq Acc Id: NM_001399415   ⟹   NP_001386344
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82246,189,627 - 246,211,669 (-)NCBI
mRatBN7.22243,529,912 - 243,551,955 (-)NCBI
RefSeq Acc Id: NM_001399416   ⟹   NP_001386345
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82246,189,627 - 246,211,669 (-)NCBI
mRatBN7.22243,529,912 - 243,551,955 (-)NCBI
RefSeq Acc Id: XM_039103890   ⟹   XP_038959818
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82246,189,655 - 246,211,737 (-)NCBI
mRatBN7.22243,529,921 - 243,552,043 (-)NCBI
Ensembl Acc Id: ENSRNOP00000037831   ⟸   ENSRNOT00000032874
RefSeq Acc Id: XP_038959818   ⟸   XM_039103890
- Peptide Label: isoform X1
- UniProtKB: A0A8I5ZL47 (UniProtKB/TrEMBL),   D3ZHR8 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000078566   ⟸   ENSRNOT00000096868
Ensembl Acc Id: ENSRNOP00000082080   ⟸   ENSRNOT00000105899
RefSeq Acc Id: NP_001386345   ⟸   NM_001399416
- Peptide Label: isoform 2
- UniProtKB: A0A8I5ZSZ8 (UniProtKB/TrEMBL),   A6HWQ2 (UniProtKB/TrEMBL)
RefSeq Acc Id: NP_001386344   ⟸   NM_001399415
- Peptide Label: isoform 1
- UniProtKB: A6HWQ1 (UniProtKB/TrEMBL),   A6HWQ0 (UniProtKB/TrEMBL)
Protein Domains
tRNA wybutosine-synthesizing protein

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZHR8-F1-model_v2 AlphaFold D3ZHR8 1-293 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1559623 AgrOrtholog
BioCyc Gene G2FUF-50757 BioCyc
BioCyc Pathway PWY-7286 [7-(3-amino-3-carboxypropyl)-wyosine biosynthesis] BioCyc
BioCyc Pathway Image PWY-7286 BioCyc
Ensembl Genes ENSRNOG00000028328 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000032874.7 UniProtKB/TrEMBL
  ENSRNOT00000096868.1 UniProtKB/TrEMBL
  ENSRNOT00000105899.1 UniProtKB/TrEMBL
Gene3D-CATH 3.30.1960.10 UniProtKB/TrEMBL
InterPro tRNA_yW-synthesising UniProtKB/TrEMBL
  tRNA_yW-synthesising-like_sf UniProtKB/TrEMBL
  TYW3 UniProtKB/TrEMBL
NCBI Gene 499731 ENTREZGENE
PANTHER TRNA WYBUTOSINE-SYNTHESIZING PROTEIN 3 UniProtKB/TrEMBL
  TRNA WYBUTOSINE-SYNTHESIZING PROTEIN 3 UniProtKB/TrEMBL
Pfam TYW3 UniProtKB/TrEMBL
PhenoGen Tyw3 PhenoGen
RatGTEx ENSRNOG00000028328 RatGTEx
Superfamily-SCOP DUF207 UniProtKB/TrEMBL
UniProt A0A8I5ZL47 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I5ZSZ8 ENTREZGENE, UniProtKB/TrEMBL
  A6HWQ0 ENTREZGENE, UniProtKB/TrEMBL
  A6HWQ1 ENTREZGENE, UniProtKB/TrEMBL
  A6HWQ2 ENTREZGENE, UniProtKB/TrEMBL
  D3ZHR8 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-11-25 Tyw3  tRNA-yW synthesizing protein 3 homolog  Tyw3  tRNA-yW synthesizing protein 3 homolog (S. cerevisiae)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-06 Tyw3  tRNA-yW synthesizing protein 3 homolog (S. cerevisiae)  RGD1559623_predicted  similar to RIKEN cDNA 5230400J09 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1559623_predicted  similar to RIKEN cDNA 5230400J09 (predicted)  LOC499731  similar to RIKEN cDNA 5230400J09  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC499731  similar to RIKEN cDNA 5230400J09      Symbol and Name status set to provisional 70820 PROVISIONAL