Human Gene TGS1 (uc003xsj.4)
  Description: Homo sapiens trimethylguanosine synthase 1 (TGS1), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr8:56,685,791-56,738,005 Size: 52,215 Total Exon Count: 13 Strand: +
Coding Region
   Position: hg19 chr8:56,686,178-56,737,262 Size: 51,085 Coding Exon Count: 13 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr8:56,685,791-56,738,005)mRNA (may differ from genome)Protein (853 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: TGS1_HUMAN
DESCRIPTION: RecName: Full=Trimethylguanosine synthase; EC=2.1.1.-; AltName: Full=CLL-associated antigen KW-2; AltName: Full=Cap-specific guanine-N2 methyltransferase; AltName: Full=Hepatocellular carcinoma-associated antigen 137; AltName: Full=Nuclear receptor coactivator 6-interacting protein; AltName: Full=PRIP-interacting protein with methyltransferase motif; Short=PIMT; Short=PIPMT;
FUNCTION: Catalyzes the 2 serial methylation steps for the conversion of the 7-monomethylguanosine (m(7)G) caps of snRNAs and snoRNAs to a 2,2,7-trimethylguanosine (m(2,2,7)G) cap structure. The enzyme is specific for guanine, and N7 methylation must precede N2 methylation. Hypermethylation of the m7G cap of U snRNAs leads to their concentration in nuclear foci, their colocalization with coilin and the formation of canonical Cajal bodies (CBs). Plays a role in transcriptional regulation.
CATALYTIC ACTIVITY: S-adenosyl-L-methionine + m(7)G(5')pppR-RNA = S-adenosyl-L-homocysteine + m(2,7)G(5')pppR-RNA.
CATALYTIC ACTIVITY: S-adenosyl-L-methionine + m(2,7)G(5')pppR-RNA = S-adenosyl-L-homocysteine + m(2,2,7)G(5')pppR-RNA.
BIOPHYSICOCHEMICAL PROPERTIES: Kinetic parameters: KM=30 uM for m(7)GDP; KM=5 uM for S-adenosyl-L-methionine; pH dependence: Optimum pH is 8.5-9.5;
SUBUNIT: May form homooligomers. Interacts with CREBBP/CBP, EED/WAIT1, EP300/P300, NCOA6/PRIP, PPARBP/PBP and SMN.
SUBCELLULAR LOCATION: Cytoplasm. Nucleus, Cajal body. Note=A 90 kDa isoform is found in the nucleus while a 55 kDa isoform is found in the cytoplasm and colocalizes with the tubulin network.
TISSUE SPECIFICITY: Ubiquitously expressed. High expression in heart, skeletal muscle, kidney, liver and placenta.
SIMILARITY: Belongs to the methyltransferase superfamily. Trimethylguanosine synthase family.
SEQUENCE CAUTION: Sequence=AAH11999.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=BAB15516.1; Type=Erroneous initiation; Note=Translation N-terminally extended;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): TGS1
CDC HuGE Published Literature: TGS1
Positive Disease Associations: height
Related Studies:
  1. height
    Gudbjartsson ,et al. 2008, Many sequence variants affecting diversity of adult human height, Nature genetics 2008 40- 5 : 609-15. [PubMed 18391951]

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 14.30 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 271.20 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -188.31387-0.487 Picture PostScript Text
3' UTR -205.10743-0.276 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR019012 - RNA_cap_Gua-N2-MeTrfase

Pfam Domains:
PF01170 - Putative RNA methylase family UPF0020
PF02475 - Met-10+ like-protein
PF09445 - RNA cap guanine-N2 methyltransferase
PF13649 - Methyltransferase domain

SCOP Domains:
51735 - NAD(P)-binding Rossmann-fold domains
53335 - S-adenosyl-L-methionine-dependent methyltransferases

Protein Data Bank (PDB) 3-D Structure
MuPIT help
3EGI - X-ray MuPIT 3GDH - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q96RS0
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserGenome BrowserGenome BrowserGenome BrowserGenome Browser
Gene DetailsGene Details Gene DetailsGene DetailsGene Details
Gene SorterGene Sorter Gene SorterGene SorterGene Sorter
 RGDEnsemblFlyBaseWormBaseSGD
 Protein SequenceProtein SequenceProtein SequenceProtein SequenceProtein Sequence
 AlignmentAlignmentAlignmentAlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0008168 methyltransferase activity
GO:0008173 RNA methyltransferase activity
GO:0016740 transferase activity
GO:0071164 RNA trimethylguanosine synthase activity

Biological Process:
GO:0000387 spliceosomal snRNP assembly
GO:0001510 RNA methylation
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0009452 7-methylguanosine RNA capping
GO:0019216 regulation of lipid metabolic process
GO:0022613 ribonucleoprotein complex biogenesis
GO:0032259 methylation
GO:0036261 7-methylguanosine cap hypermethylation

Cellular Component:
GO:0005615 extracellular space
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0015030 Cajal body
GO:0030532 small nuclear ribonucleoprotein complex


-  Descriptions from all associated GenBank mRNAs
  AF286340 - Homo sapiens hepatocellular carcinoma-associated antigen 137 (HCA137) mRNA, complete cds.
JD195877 - Sequence 176901 from Patent EP1572962.
JD526046 - Sequence 507070 from Patent EP1572962.
JD126470 - Sequence 107494 from Patent EP1572962.
JD037791 - Sequence 18815 from Patent EP1572962.
JD188792 - Sequence 169816 from Patent EP1572962.
JD336713 - Sequence 317737 from Patent EP1572962.
JD144320 - Sequence 125344 from Patent EP1572962.
AY028423 - Homo sapiens PRIP-interacting protein PIPMT mRNA, complete cds.
AK314693 - Homo sapiens cDNA, FLJ95547, highly similar to Homo sapiens nuclear receptor coactivator 6 interacting protein (NCOA6IP), mRNA.
BX648548 - Homo sapiens mRNA; cDNA DKFZp779P029 (from clone DKFZp779P029).
JD255598 - Sequence 236622 from Patent EP1572962.
AF432215 - Homo sapiens CLL-associated antigen KW-2 mRNA, complete cds.
JD218317 - Sequence 199341 from Patent EP1572962.
BC160105 - Synthetic construct Homo sapiens clone IMAGE:100064137, MGC:193220 trimethylguanosine synthase homolog (S. cerevisiae) (TGS1) mRNA, encodes complete protein.
AK054705 - Homo sapiens cDNA FLJ30143 fis, clone BRACE2000229.
AK055178 - Homo sapiens cDNA FLJ30616 fis, clone CTONG2001320, highly similar to RNA methyltransferase NCOA6IP (EC 2.1.1.-).
AY534911 - Homo sapiens hypothetical rhabdomyosarcoma antigen MU-RMS-40.15 (NCOA6IP) mRNA, partial cds.
AL832426 - Homo sapiens mRNA; cDNA DKFZp762A163 (from clone DKFZp762A163).
BC011999 - Homo sapiens trimethylguanosine synthase homolog (S. cerevisiae), mRNA (cDNA clone IMAGE:4513665), complete cds.
AK026648 - Homo sapiens cDNA: FLJ22995 fis, clone KAT11919.
CU680158 - Synthetic construct Homo sapiens gateway clone IMAGE:100017925 5' read TGS1 mRNA.
KJ903616 - Synthetic construct Homo sapiens clone ccsbBroadEn_13010 TGS1 gene, encodes complete protein.
JD327797 - Sequence 308821 from Patent EP1572962.
JD433009 - Sequence 414033 from Patent EP1572962.
JD299408 - Sequence 280432 from Patent EP1572962.
JD285883 - Sequence 266907 from Patent EP1572962.
JD128698 - Sequence 109722 from Patent EP1572962.
JD158264 - Sequence 139288 from Patent EP1572962.
JD541234 - Sequence 522258 from Patent EP1572962.
JD351090 - Sequence 332114 from Patent EP1572962.
JD513041 - Sequence 494065 from Patent EP1572962.
JD098386 - Sequence 79410 from Patent EP1572962.
JD317672 - Sequence 298696 from Patent EP1572962.
JD463292 - Sequence 444316 from Patent EP1572962.
JD422253 - Sequence 403277 from Patent EP1572962.
JD286932 - Sequence 267956 from Patent EP1572962.
JD080252 - Sequence 61276 from Patent EP1572962.
JD295425 - Sequence 276449 from Patent EP1572962.
JD330946 - Sequence 311970 from Patent EP1572962.
JD441630 - Sequence 422654 from Patent EP1572962.
JD329653 - Sequence 310677 from Patent EP1572962.
JD365158 - Sequence 346182 from Patent EP1572962.
JD320452 - Sequence 301476 from Patent EP1572962.
JD119884 - Sequence 100908 from Patent EP1572962.
JD090924 - Sequence 71948 from Patent EP1572962.
JD342476 - Sequence 323500 from Patent EP1572962.
JD480580 - Sequence 461604 from Patent EP1572962.
JD466855 - Sequence 447879 from Patent EP1572962.
JD055526 - Sequence 36550 from Patent EP1572962.
JD506006 - Sequence 487030 from Patent EP1572962.
JD341409 - Sequence 322433 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q96RS0 (Reactome details) participates in the following event(s):

R-HSA-191784 snRNA Cap hypermethylation
R-HSA-400143 Fatty acid ligands activate PPARA
R-HSA-191859 snRNP Assembly
R-HSA-400206 Regulation of lipid metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha)
R-HSA-194441 Metabolism of non-coding RNA
R-HSA-556833 Metabolism of lipids
R-HSA-8953854 Metabolism of RNA
R-HSA-1430728 Metabolism

-  Other Names for This Gene
  Alternate Gene Symbols: A6NJQ5, HCA137, NCOA6IP, NM_024831, NP_079107, PIMT, Q5GH23, Q8TDG9, Q96QU3, Q96RS0, Q9H5V3, TGS1_HUMAN
UCSC ID: uc003xsj.4
RefSeq Accession: NM_024831
Protein: Q96RS0 (aka TGS1_HUMAN)
CCDS: CCDS34894.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_024831.6
exon count: 13CDS single in 3' UTR: no RNA size: 3708
ORF size: 2562CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 5246.00frame shift in genome: no % Coverage: 99.57
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 1
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.