Human Gene TYW1 (uc003tvn.4) Description and Page Index
  Description: Homo sapiens tRNA-yW synthesizing protein 1 homolog (S. cerevisiae) (TYW1), mRNA.
RefSeq Summary (NM_018264): Wybutosine (yW) is a hypermodified guanosine found in phenylalanine tRNA adjacent to the anticodon that stabilizes codon-anticodon interactions in the ribosome. In yeast, the homolog of this gene is essential for the synthesis of wybutosine. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2015].
Transcript (Including UTRs)
   Position: hg19 chr7:66,461,792-66,704,507 Size: 242,716 Total Exon Count: 16 Strand: +
Coding Region
   Position: hg19 chr7:66,461,966-66,703,516 Size: 241,551 Coding Exon Count: 16 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-15

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr7:66,461,792-66,704,507)mRNA (may differ from genome)Protein (732 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCHPRDLynxMGIneXtProt
OMIMPubMedReactomeStanford SOURCEUniProtKB

-  Comments and Description Text from UniProtKB
  ID: TYW1_HUMAN
DESCRIPTION: RecName: Full=tRNA wybutosine-synthesizing protein 1 homolog; AltName: Full=Radical S-adenosyl methionine and flavodoxin domain-containing protein 1; AltName: Full=tRNA-yW-synthesizing protein;
FUNCTION: Probable 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).
COFACTOR: Binds 1 4Fe-4S cluster. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine (By similarity).
PATHWAY: tRNA modification; wybutosine-tRNA(Phe) biosynthesis.
SIMILARITY: Belongs to the TYW1 family.
SIMILARITY: Contains 1 flavodoxin-like domain.
SEQUENCE CAUTION: Sequence=AAH15591.1; Type=Frameshift; Positions=663; Sequence=BAB14307.1; Type=Erroneous initiation;

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): TYW1
CDC HuGE Published Literature: TYW1

-  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: 13.35 RPKM in Cervix - Ectocervix
Total median expression: 287.02 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 -81.80174-0.470 Picture PostScript Text
3' UTR -282.91991-0.285 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
IPR001094 - Flavdoxin
IPR008254 - Flavodoxin/NO_synth
IPR007197 - rSAM
IPR013917 - tRNA_wybutosine-synth

Pfam Domains:
PF00258 - Flavodoxin
PF04055 - Radical SAM superfamily
PF08608 - Wyosine base formation

SCOP Domains:
102114 - Radical SAM enzymes
52218 - Flavoproteins

ModBase Predicted Comparative 3D Structure on Q9NV66
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 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:0000166 nucleotide binding
GO:0003824 catalytic activity
GO:0010181 FMN binding
GO:0016829 lyase activity
GO:0046872 metal ion binding
GO:0051536 iron-sulfur cluster binding
GO:0051539 4 iron, 4 sulfur cluster binding

Biological Process:
GO:0008033 tRNA processing
GO:0055114 oxidation-reduction process


-  Descriptions from all associated GenBank mRNAs
  AK001762 - Homo sapiens cDNA FLJ10900 fis, clone NT2RP5003522, weakly similar to NADPH-CYTOCHROME P450 REDUCTASE (EC 1.6.2.4).
BC015591 - Homo sapiens tRNA-yW synthesizing protein 1 homolog (S. cerevisiae), mRNA (cDNA clone MGC:23001 IMAGE:4644035), complete cds.
BC051888 - Homo sapiens tRNA-yW synthesizing protein 1 homolog (S. cerevisiae), mRNA (cDNA clone MGC:60291 IMAGE:6173301), complete cds.
AK022917 - Homo sapiens cDNA FLJ12855 fis, clone NT2RP2003506, weakly similar to NADPH-CYTOCHROME P450 REDUCTASE (EC 1.6.2.4).
AK301330 - Homo sapiens cDNA FLJ57623 complete cds, highly similar to Homo sapiens radical S-adenosyl methionine and flavodoxin domains 1 (RSAFD1), mRNA.
BC042156 - Homo sapiens tRNA-yW synthesizing protein 1 homolog (S. cerevisiae), mRNA (cDNA clone IMAGE:4541379), partial cds.
JD048323 - Sequence 29347 from Patent EP1572962.
JD267444 - Sequence 248468 from Patent EP1572962.
JD229520 - Sequence 210544 from Patent EP1572962.
JD348130 - Sequence 329154 from Patent EP1572962.
JD373718 - Sequence 354742 from Patent EP1572962.
JD287590 - Sequence 268614 from Patent EP1572962.
JD040552 - Sequence 21576 from Patent EP1572962.
JD302081 - Sequence 283105 from Patent EP1572962.
JD372495 - Sequence 353519 from Patent EP1572962.
JD358294 - Sequence 339318 from Patent EP1572962.
JD224876 - Sequence 205900 from Patent EP1572962.
JD539783 - Sequence 520807 from Patent EP1572962.
JD301965 - Sequence 282989 from Patent EP1572962.
JD432195 - Sequence 413219 from Patent EP1572962.
JD501017 - Sequence 482041 from Patent EP1572962.
JD430074 - Sequence 411098 from Patent EP1572962.
JD197358 - Sequence 178382 from Patent EP1572962.
JD079733 - Sequence 60757 from Patent EP1572962.
JD297283 - Sequence 278307 from Patent EP1572962.
JD494259 - Sequence 475283 from Patent EP1572962.
JD196664 - Sequence 177688 from Patent EP1572962.
JD128518 - Sequence 109542 from Patent EP1572962.
JD453757 - Sequence 434781 from Patent EP1572962.
JD224494 - Sequence 205518 from Patent EP1572962.
JD533483 - Sequence 514507 from Patent EP1572962.
JD263206 - Sequence 244230 from Patent EP1572962.
JD264235 - Sequence 245259 from Patent EP1572962.
JD137687 - Sequence 118711 from Patent EP1572962.
JD488089 - Sequence 469113 from Patent EP1572962.
JD488090 - Sequence 469114 from Patent EP1572962.
JD166681 - Sequence 147705 from Patent EP1572962.
JD276336 - Sequence 257360 from Patent EP1572962.
JD428129 - Sequence 409153 from Patent EP1572962.

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

Protein Q9NV66 (Reactome details) participates in the following event(s):

R-HSA-6782895 TYW1:FMN:4Fe-4S transforms 1-methylguanosine yielding yW-187 (4-demethylwyosine) 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_018264, NP_060734, Q6PJG8, Q75MG8, Q75MN3, Q86V12, Q8IVS7, Q9H9C4, Q9NV66, RSAFD1, TYW1_HUMAN, uc003tvn.3
UCSC ID: uc003tvn.4
RefSeq Accession: NM_018264
Protein: Q9NV66 (aka TYW1_HUMAN)
CCDS: CCDS5538.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_018264.3
exon count: 16CDS single in 3' UTR: no RNA size: 3364
ORF size: 2199CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 4421.00frame shift in genome: no % Coverage: 100.00
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.