Human Gene TYW3 (uc001dgn.3) Description and Page Index
  Description: Homo sapiens tRNA-yW synthesizing protein 3 homolog (S. cerevisiae) (TYW3), transcript variant 1, mRNA.
RefSeq Summary (NM_138467): 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. TYW3 is the human homolog of a yeast gene essential for yW synthesis (Noma and Suzuki, 2006).[supplied by OMIM, Mar 2008].
Transcript (Including UTRs)
   Position: hg19 chr1:75,198,836-75,232,360 Size: 33,525 Total Exon Count: 6 Strand: +
Coding Region
   Position: hg19 chr1:75,198,929-75,229,797 Size: 30,869 Coding Exon Count: 6 

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 (chr1:75,198,836-75,232,360)mRNA (may differ from genome)Protein (259 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
neXtProtOMIMPubMedReactomeStanford SOURCETreefam

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=tRNA wybutosine-synthesizing protein 3 homolog; EC=2.1.1.-; AltName: Full=tRNA-yW-synthesizing protein 3;
FUNCTION: Probable S-adenosyl-L-methionine-dependent methyltransferase 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 TYW3 family.
SEQUENCE CAUTION: Sequence=CAI46106.1; Type=Erroneous initiation;

-  MalaCards Disease Associations
  MalaCards Gene Search: TYW3
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: 14.56 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 295.45 RPKM

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

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -27.6093-0.297 Picture PostScript Text
3' UTR -675.512563-0.264 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
IPR003827 - tRNA_yW-synthesising

Pfam Domains:
PF02676 - Methyltransferase TYW3

SCOP Domains:
111278 - SSo0622-like (Pfam 02676)

ModBase Predicted Comparative 3D Structure on Q6IPR3
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 orthologNo orthologGenome BrowserNo orthologNo orthologGenome Browser
Gene Details    Gene Details
Gene Sorter    Gene Sorter
  Ensembl  SGD
  Protein Sequence  Protein Sequence
  Alignment  Alignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0008168 methyltransferase activity
GO:0016740 transferase activity

Biological Process:
GO:0008033 tRNA processing
GO:0032259 methylation

-  Descriptions from all associated GenBank mRNAs
  LF383841 - JP 2014500723-A/191344: Polycomb-Associated Non-Coding RNAs.
BC071765 - Homo sapiens tRNA-yW synthesizing protein 3 homolog (S. cerevisiae), mRNA (cDNA clone MGC:88405 IMAGE:3931600), complete cds.
AK098237 - Homo sapiens cDNA FLJ40918 fis, clone UTERU2005593.
AK294264 - Homo sapiens cDNA FLJ50478 complete cds.
AK299849 - Homo sapiens cDNA FLJ51960 complete cds.
BC009514 - Homo sapiens tRNA-yW synthesizing protein 3 homolog (S. cerevisiae), mRNA (cDNA clone IMAGE:3542597), partial cds.
AK311272 - Homo sapiens cDNA, FLJ18314.
AB590606 - Synthetic construct DNA, clone: pFN21AE2228, Homo sapiens TYW3 gene for tRNA-yW synthesizing protein 3 homolog, without stop codon, in Flexi system.
KJ900112 - Synthetic construct Homo sapiens clone ccsbBroadEn_09506 TYW3 gene, encodes complete protein.
LF353681 - JP 2014500723-A/161184: Polycomb-Associated Non-Coding RNAs.
JD232108 - Sequence 213132 from Patent EP1572962.
JD184125 - Sequence 165149 from Patent EP1572962.
BX647591 - Homo sapiens mRNA; cDNA DKFZp313J0833 (from clone DKFZp313J0833).
JD301914 - Sequence 282938 from Patent EP1572962.
BC032341 - Homo sapiens chromosome 1 open reading frame 171, mRNA (cDNA clone IMAGE:5194639).
JD327783 - Sequence 308807 from Patent EP1572962.
JD432930 - Sequence 413954 from Patent EP1572962.
JD550260 - Sequence 531284 from Patent EP1572962.
JD234097 - Sequence 215121 from Patent EP1572962.
JD415482 - Sequence 396506 from Patent EP1572962.
JD553815 - Sequence 534839 from Patent EP1572962.
JD269770 - Sequence 250794 from Patent EP1572962.
JD091927 - Sequence 72951 from Patent EP1572962.
JD469786 - Sequence 450810 from Patent EP1572962.
JD354415 - Sequence 335439 from Patent EP1572962.
JD446230 - Sequence 427254 from Patent EP1572962.
JD321374 - Sequence 302398 from Patent EP1572962.
JD040854 - Sequence 21878 from Patent EP1572962.
JD279629 - Sequence 260653 from Patent EP1572962.
JD500825 - Sequence 481849 from Patent EP1572962.
JD502196 - Sequence 483220 from Patent EP1572962.
LF353679 - JP 2014500723-A/161182: Polycomb-Associated Non-Coding RNAs.
JD039908 - Sequence 20932 from Patent EP1572962.
JD077816 - Sequence 58840 from Patent EP1572962.
JD219431 - Sequence 200455 from Patent EP1572962.
JD327474 - Sequence 308498 from Patent EP1572962.
JD079934 - Sequence 60958 from Patent EP1572962.
LF353678 - JP 2014500723-A/161181: Polycomb-Associated Non-Coding RNAs.
JD451352 - Sequence 432376 from Patent EP1572962.
JD083504 - Sequence 64528 from Patent EP1572962.
JD168545 - Sequence 149569 from Patent EP1572962.
JD171902 - Sequence 152926 from Patent EP1572962.
JD087440 - Sequence 68464 from Patent EP1572962.
JD263640 - Sequence 244664 from Patent EP1572962.
BC015841 - Homo sapiens cDNA clone IMAGE:4332919.
BC020995 - Homo sapiens cDNA clone IMAGE:4332605, with apparent retained intron.
BC009532 - Homo sapiens cDNA clone IMAGE:3891356, with apparent retained intron.
MA619418 - JP 2018138019-A/191344: Polycomb-Associated Non-Coding RNAs.
MA589258 - JP 2018138019-A/161184: Polycomb-Associated Non-Coding RNAs.
MA589256 - JP 2018138019-A/161182: Polycomb-Associated Non-Coding RNAs.
MA589255 - JP 2018138019-A/161181: Polycomb-Associated Non-Coding RNAs.

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

Protein Q6IPR3 (Reactome details) participates in the following event(s):

R-HSA-6782879 TYW3 methylates yW-86 yielding yW-72 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: B4DSP9, C1orf171, E9PGR7, NM_138467, NP_612476, Q5HYJ0, Q6IPR3, Q8N7L1, TYW3_HUMAN
UCSC ID: uc001dgn.3
RefSeq Accession: NM_138467
Protein: Q6IPR3 (aka TYW3_HUMAN)

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: NM_138467.2
exon count: 6CDS single in 3' UTR: no RNA size: 3448
ORF size: 780CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1689.00frame shift in genome: no % Coverage: 99.54
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.