Human Gene TRMT12 (uc003yra.4) Description and Page Index
  Description: Homo sapiens tRNA methyltransferase 12 homolog (S. cerevisiae) (TRMT12), mRNA.
RefSeq Summary (NM_017956): Wybutosine (yW) is a hypermodified guanosine at the 3-prime position adjacent to the anticodon of phenylalanine tRNA that stabilizes codon-anticodon interactions during decoding on the ribosome. TRMT12 is the human homolog of a yeast gene essential for yW synthesis (Noma and Suzuki, 2006).[supplied by OMIM, Mar 2008]. ##Evidence-Data-START## Transcript is intronless :: AK225083.1, SRR1660803.138373.1 [ECO:0000345] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000328599.4/ ENSP00000329858.3 RefSeq Select criteria :: based on single protein-coding transcript ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr8:125,463,048-125,465,266 Size: 2,219 Total Exon Count: 1 Strand: +
Coding Region
   Position: hg19 chr8:125,463,169-125,464,515 Size: 1,347 Coding Exon Count: 1 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr8:125,463,048-125,465,266)mRNA (may differ from genome)Protein (448 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCHPRDLynxMGIneXtProt
OMIMPubMedReactomeStanford SOURCETreefamUniProtKB
Wikipedia

-  Comments and Description Text from UniProtKB
  ID: TYW2_HUMAN
DESCRIPTION: RecName: Full=tRNA wybutosine-synthesizing protein 2 homolog; Short=tRNA-yW-synthesizing protein 2; AltName: Full=Alpha-amino-alpha-carboxypropyl transferase TYW2; EC=2.5.1.-;
FUNCTION: Probable S-adenosyl-L-methionine-dependent transferase that acts as a component of the wybutosine biosynthesis pathway. Wybutosine is a hyper modified guanosine with a tricyclic base found at the 3'-position adjacent to the anticodon of eukaryotic phenylalanine tRNA (By similarity).
PATHWAY: tRNA modification; wybutosine-tRNA(Phe) biosynthesis.
SIMILARITY: Belongs to the TRM5 / TYW2 family.
SEQUENCE CAUTION: Sequence=AAH03057.2; Type=Erroneous initiation; Note=Translation N-terminally shortened; Sequence=AAH03057.2; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence starting in position 371;

-  MalaCards Disease Associations
  MalaCards Gene Search: TRMT12
Diseases sorted by gene-association score: noma (3)

-  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: 7.03 RPKM in Testis
Total median expression: 187.03 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 -39.60121-0.327 Picture PostScript Text
3' UTR -200.53751-0.267 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
IPR003402 - tRNA_Trfase_Trm5/Tyw2

Pfam Domains:
PF02475 - Met-10+ like-protein

SCOP Domains:
53335 - S-adenosyl-L-methionine-dependent methyltransferases

ModBase Predicted Comparative 3D Structure on Q53H54
FrontTopSide
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 BrowserNo orthologGenome BrowserGenome Browser
Gene DetailsGene Details  Gene DetailsGene Details
Gene SorterGene Sorter  Gene SorterGene Sorter
 RGDEnsembl WormBaseSGD
 Protein SequenceProtein Sequence Protein SequenceProtein Sequence
 AlignmentAlignment AlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0016740 transferase activity
GO:0102522 tRNA 4-demethylwyosine alpha-amino-alpha-carboxypropyltransferase activity

Biological Process:
GO:0008033 tRNA processing


-  Descriptions from all associated GenBank mRNAs
  AK225083 - Homo sapiens mRNA for homolog of yeast tRNA methyltransferase variant, clone: CAS01869.
AK222727 - Homo sapiens mRNA for hypothetical protein FLJ20772 variant, clone: COL09944.
AK000779 - Homo sapiens cDNA FLJ20772 fis, clone COL06053.
BC011713 - Homo sapiens tRNA methyltransferase 12 homolog (S. cerevisiae), mRNA (cDNA clone MGC:19516 IMAGE:3929724), complete cds.
BC003057 - Homo sapiens tRNA methyltransferase 12 homolog (S. cerevisiae), mRNA (cDNA clone IMAGE:3050210), partial cds.
KJ899068 - Synthetic construct Homo sapiens clone ccsbBroadEn_08462 TRMT12 gene, encodes complete protein.
JD136546 - Sequence 117570 from Patent EP1572962.
JD363549 - Sequence 344573 from Patent EP1572962.
JD061096 - Sequence 42120 from Patent EP1572962.
JD509474 - Sequence 490498 from Patent EP1572962.
JD091783 - Sequence 72807 from Patent EP1572962.
JD434279 - Sequence 415303 from Patent EP1572962.
JD488290 - Sequence 469314 from Patent EP1572962.
JD223316 - Sequence 204340 from Patent EP1572962.

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

Protein Q53H54 (Reactome details) participates in the following event(s):

R-HSA-6782893 TRMT12 transforms yW-187 yielding yW-86 at nucleotide 37 of tRNA(Phe)
R-HSA-6782861 Synthesis of wybutosine at G37 of tRNA(Phe)
R-HSA-6782315 tRNA modification in the nucleus and cytosol
R-HSA-72306 tRNA processing
R-HSA-8953854 Metabolism of RNA

-  Other Names for This Gene
  Alternate Gene Symbols: NM_017956, NP_060426, Q53H54, Q6PKB9, Q96F21, Q9NWK6, TRM12, TYW2, TYW2_HUMAN
UCSC ID: uc003yra.4
RefSeq Accession: NM_017956
Protein: Q53H54 (aka TYW2_HUMAN)
CCDS: CCDS6349.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_017956.3
exon count: 1CDS single in 3' UTR: no RNA size: 2232
ORF size: 1347CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2858.00frame shift in genome: no % Coverage: 99.42
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
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.