Tgs1 (trimethylguanosine synthase 1) - Rat Genome Database

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Gene: Tgs1 (trimethylguanosine synthase 1) Rattus norvegicus
Analyze
Symbol: Tgs1
Name: trimethylguanosine synthase 1
RGD ID: 1309953
Description: Predicted to enable RNA cap trimethylguanosine synthase activity. Predicted to be involved in 7-methylguanosine cap hypermethylation. Predicted to be located in cytosol. Predicted to be active in nucleus. Orthologous to human TGS1 (trimethylguanosine synthase 1); PARTICIPATES IN RNA transport pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; acrylamide; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: cap-specific guanine-N(2) methyltransferase; LOC312947; Ncoa6ip; nuclear receptor coactivator 6 interacting protein; nuclear receptor coactivator 6-interacting protein; PIMT; PIPMT; PRIP-interacting protein with methyltransferase motif; trimethylguanosine synthase; trimethylguanosine synthase homolog; trimethylguanosine synthase 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: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8521,322,492 - 21,356,017 (+)NCBIGRCr8
mRatBN7.2516,524,864 - 16,558,399 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl516,524,874 - 16,558,399 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx518,773,465 - 18,806,565 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0520,371,954 - 20,405,057 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0520,123,429 - 20,156,541 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0516,413,356 - 16,446,881 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl516,413,356 - 16,446,881 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0521,194,620 - 21,228,145 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4516,818,391 - 16,851,916 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1516,818,178 - 16,850,318 (+)NCBI
Celera515,891,134 - 15,924,317 (+)NCBICelera
Cytogenetic Map5q12NCBI
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
Cajal body  (IEA)
cytoplasm  (ISO)
cytosol  (IEA,ISO)
nucleolus  (IEA)
nucleus  (IBA,ISO)

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 MGI mouse gene data--August 2006 MGD data from the GO Consortium
3. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
4. GOA pipeline RGD automated data pipeline
5. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12943661   PMID:15057822   PMID:16687569   PMID:22664934   PMID:37175791  


Genomics

Comparative Map Data
Tgs1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8521,322,492 - 21,356,017 (+)NCBIGRCr8
mRatBN7.2516,524,864 - 16,558,399 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl516,524,874 - 16,558,399 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx518,773,465 - 18,806,565 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0520,371,954 - 20,405,057 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0520,123,429 - 20,156,541 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0516,413,356 - 16,446,881 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl516,413,356 - 16,446,881 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0521,194,620 - 21,228,145 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4516,818,391 - 16,851,916 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1516,818,178 - 16,850,318 (+)NCBI
Celera515,891,134 - 15,924,317 (+)NCBICelera
Cytogenetic Map5q12NCBI
TGS1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38855,773,446 - 55,826,445 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl855,773,446 - 55,826,445 (+)EnsemblGRCh38hg38GRCh38
GRCh37856,686,005 - 56,739,004 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36856,848,345 - 56,900,559 (+)NCBINCBI36Build 36hg18NCBI36
Build 34856,848,254 - 56,900,557NCBI
Celera852,677,058 - 52,729,766 (+)NCBICelera
Cytogenetic Map8q12.1NCBI
HuRef852,154,245 - 52,206,403 (+)NCBIHuRef
CHM1_1856,737,385 - 56,789,600 (+)NCBICHM1_1
T2T-CHM13v2.0856,150,498 - 56,203,496 (+)NCBIT2T-CHM13v2.0
Tgs1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3943,574,875 - 3,616,624 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl43,574,875 - 3,616,619 (+)EnsemblGRCm39 Ensembl
GRCm3843,574,841 - 3,616,624 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl43,574,875 - 3,616,619 (+)EnsemblGRCm38mm10GRCm38
MGSCv3743,502,026 - 3,543,771 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3643,502,045 - 3,543,771 (+)NCBIMGSCv36mm8
Celera43,520,719 - 3,562,191 (+)NCBICelera
Cytogenetic Map4A1NCBI
cM Map41.99NCBI
Tgs1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495545414,896,085 - 14,934,414 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495545414,896,085 - 14,937,678 (+)NCBIChiLan1.0ChiLan1.0
TGS1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2771,425,861 - 71,477,581 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1847,150,469 - 47,202,335 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0852,214,283 - 52,266,439 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1849,585,920 - 49,637,832 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl849,585,889 - 49,637,832 (+)Ensemblpanpan1.1panPan2
TGS1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1297,241,050 - 7,281,811 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl297,241,237 - 7,280,500 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha297,553,785 - 7,594,760 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0297,314,445 - 7,355,478 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl297,314,851 - 7,355,474 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1297,328,877 - 7,369,857 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0297,461,655 - 7,502,629 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0297,738,103 - 7,779,317 (+)NCBIUU_Cfam_GSD_1.0
Tgs1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440530372,261,575 - 72,300,775 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364962,484,864 - 2,524,540 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364962,484,700 - 2,524,650 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TGS1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl475,937,129 - 75,969,157 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1475,937,489 - 75,969,152 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2482,879,748 - 82,911,839 (-)NCBISscrofa10.2Sscrofa10.2susScr3
TGS1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1851,819,132 - 51,868,566 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl851,819,572 - 51,856,172 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603989,932,602 - 89,984,290 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Tgs1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462496566,381 - 114,309 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462496590,356 - 114,478 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Tgs1
320 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:440
Count of miRNA genes:223
Interacting mature miRNAs:289
Transcripts:ENSRNOT00000010783
Prediction methods:Microtar, 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
2293666Bmd38Bone mineral density QTL 384.4femur size trait (VT:1000369)femoral neck cortical cross-sectional area (CMO:0001702)5894822853948228Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51131345958Rat
1300117Hrtrt8Heart rate QTL 83.49heart pumping trait (VT:2000009)heart rate (CMO:0000002)5384401847869213Rat
7394712Emca13Estrogen-induced mammary cancer QTL 13mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)5982326699753708Rat
634305Mamtr1Mammary tumor resistance QTL 10.0001mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)512789751113558310Rat
1331771Rf35Renal function QTL 354.36965kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)572947086724018Rat
2312562Pur18Proteinuria QTL 182.60.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)5213896532656739Rat
8662454Vetf3Vascular elastic tissue fragility QTL 327.4artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)5228222669540447Rat
61462Niddm10Non-insulin dependent diabetes mellitus QTL 103.90.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)5511215947171491Rat
1641903Alcrsp3Alcohol response QTL 3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)51268928557689285Rat
1331756Rf34Renal function QTL 344.16275kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5190450412Rat
631827Alc4Alcohol consumption QTL 43.5consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)5818750118616199Rat
2313085Bss59Bone structure and strength QTL 592.90.0001long bone metaphysis morphology trait (VT:0000133)tibia midshaft total cross-sectional area (CMO:0001715)5384401826141981Rat

Markers in Region
D10Chm27  
Rat AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map5q12UniSTS
D5Got321  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2516,540,236 - 16,540,387 (+)MAPPERmRatBN7.2
Rnor_6.0516,428,719 - 16,428,869NCBIRnor6.0
Rnor_5.0521,209,983 - 21,210,133UniSTSRnor5.0
RGSC_v3.4516,833,754 - 16,833,904UniSTSRGSC3.4
Celera515,906,513 - 15,906,663UniSTS
Cytogenetic Map5q12UniSTS
RH138074  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2516,558,237 - 16,558,374 (+)MAPPERmRatBN7.2
Rnor_6.0516,446,720 - 16,446,856NCBIRnor6.0
Rnor_5.0521,227,984 - 21,228,120UniSTSRnor5.0
RGSC_v3.4516,851,755 - 16,851,891UniSTSRGSC3.4
Celera515,924,156 - 15,924,292UniSTS
RH 3.4 Map590.3UniSTS
Cytogenetic Map5q12UniSTS


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: ENSRNOT00000010783   ⟹   ENSRNOP00000010783
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl516,524,874 - 16,558,399 (+)Ensembl
Rnor_6.0 Ensembl516,413,356 - 16,446,881 (+)Ensembl
RefSeq Acc Id: NM_001107904   ⟹   NP_001101374
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8521,322,492 - 21,356,017 (+)NCBI
mRatBN7.2516,524,874 - 16,558,399 (+)NCBI
Rnor_6.0516,413,356 - 16,446,881 (+)NCBI
Rnor_5.0521,194,620 - 21,228,145 (+)NCBI
RGSC_v3.4516,818,391 - 16,851,916 (+)RGD
Celera515,891,134 - 15,924,317 (+)RGD
Sequence:
RefSeq Acc Id: XM_039109760   ⟹   XP_038965688
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8521,322,616 - 21,356,007 (+)NCBI
mRatBN7.2516,524,864 - 16,558,391 (+)NCBI
RefSeq Acc Id: XM_063287525   ⟹   XP_063143595
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8521,325,002 - 21,356,007 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001101374 (Get FASTA)   NCBI Sequence Viewer  
  XP_038965688 (Get FASTA)   NCBI Sequence Viewer  
  XP_063143595 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM11602 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000010783.5
GenBank Protein P85107 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_001101374   ⟸   NM_001107904
- UniProtKB: P85107 (UniProtKB/Swiss-Prot),   A6JFK6 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000010783   ⟸   ENSRNOT00000010783
RefSeq Acc Id: XP_038965688   ⟸   XM_039109760
- Peptide Label: isoform X1
RefSeq Acc Id: XP_063143595   ⟸   XM_063287525
- Peptide Label: isoform X2

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P85107-F1-model_v2 AlphaFold P85107 1-850 view protein structure

Transcriptome

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

Promoters
RGD ID:13693548
Promoter ID:EPDNEW_R4073
Type:initiation region
Name:Tgs1_1
Description:trimethylguanosine synthase 1
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_6.0516,413,360 - 16,413,420EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1309953 AgrOrtholog
BioCyc Gene G2FUF-42126 BioCyc
Ensembl Genes ENSRNOG00000008156 Ensembl, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000010783.6 UniProtKB/Swiss-Prot
Gene3D-CATH 3.40.50.150 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro RNA_cap_Gua-N2-MeTrfase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SAM-dependent_MTases UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:312947 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 312947 ENTREZGENE
PANTHER S-ADENOSYLMETHIONINE-DEPENDENT METHYLTRANSFERASE RELATED UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TRIMETHYLGUANOSINE SYNTHASE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Methyltransf_15 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Tgs1 PhenoGen
RatGTEx ENSRNOG00000008156 RatGTEx
Superfamily-SCOP S-adenosyl-L-methionine-dependent methyltransferases UniProtKB/TrEMBL, UniProtKB/Swiss-Prot
UniProt A6JFK6 ENTREZGENE, UniProtKB/TrEMBL
  P85107 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-10-16 Tgs1  trimethylguanosine synthase 1  Tgs1  trimethylguanosine synthase homolog (S. cerevisiae)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-04 Tgs1  trimethylguanosine synthase homolog (S. cerevisiae)  Ncoa6ip_predicted  nuclear receptor coactivator 6 interacting protein (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-12 Ncoa6ip_predicted  nuclear receptor coactivator 6 interacting protein (predicted)      Symbol and Name status set to approved 70820 APPROVED