Human Gene WARS2 (uc010oxi.2)
  Description: Homo sapiens tryptophanyl tRNA synthetase 2, mitochondrial (WARS2), nuclear gene encoding mitochondrial protein, transcript variant 1, mRNA.
RefSeq Summary (NM_015836): Aminoacyl-tRNA synthetases catalyze the aminoacylation of tRNA by their cognate amino acid. Because of their central role in linking amino acids with nucleotide triplets contained in tRNAs, aminoacyl-tRNA synthetases are thought to be among the first proteins that appeared in evolution. Two forms of tryptophanyl-tRNA synthetase exist, a cytoplasmic form, named WARS, and a mitochondrial form, named WARS2. This gene encodes the mitochondrial tryptophanyl-tRNA synthetase. Two alternative transcripts encoding different isoforms have been described. [provided by RefSeq, Jul 2008].
Transcript (Including UTRs)
   Position: hg19 chr1:119,576,164-119,682,973 Size: 106,810 Total Exon Count: 4 Strand: -
Coding Region
   Position: hg19 chr1:119,576,714-119,619,038 Size: 42,325 Coding Exon Count: 3 

Page IndexSequence and LinksPrimersGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesGeneReviewsModel Information
Methods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:119,576,164-119,682,973)mRNA (may differ from genome)Protein (89 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblExonPrimerGeneCardsGeneNetworkH-INV
HGNCLynxMalacardsMGIPubMedUniProtKB
Wikipedia

-  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): WARS2
CDC HuGE Published Literature: WARS2

-  MalaCards Disease Associations
  MalaCards Gene Search: WARS2
Diseases sorted by gene-association score: autosomal recessive non-syndromic intellectual disability* (60), long qt syndrome 1 (1)
* = Manually curated disease association

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

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 5.81 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 149.51 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 -89.46275-0.325 Picture PostScript Text
3' UTR -119.90550-0.218 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
IPR002305 - aa-tRNA-synth_Ic
IPR014729 - Rossmann-like_a/b/a_fold
IPR002306 - Trp-tRNA-ligase

Pfam Domains:
PF00579 - tRNA synthetases class I (W and Y)

SCOP Domains:
52374 - Nucleotidylyl transferase

ModBase Predicted Comparative 3D Structure on B7Z3L8
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 orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0004812 aminoacyl-tRNA ligase activity
GO:0005524 ATP binding

Biological Process:
GO:0006418 tRNA aminoacylation for protein translation


-  Descriptions from all associated GenBank mRNAs
  BC039889 - Homo sapiens cDNA clone IMAGE:5197934.
BC044575 - Homo sapiens tryptophanyl tRNA synthetase 2, mitochondrial, mRNA (cDNA clone MGC:57158 IMAGE:5287131), complete cds.
AK223197 - Homo sapiens mRNA for mitochondrial tryptophanyl tRNA synthetase 2 isoform 1 precursor variant, clone: REC00846.
AK300295 - Homo sapiens cDNA FLJ53098 complete cds, highly similar to Tryptophanyl-tRNA synthetase, mitochondrial precursor (EC 6.1.1.2).
AK299547 - Homo sapiens cDNA FLJ50844 complete cds, highly similar to Tryptophanyl-tRNA synthetase, mitochondrial precursor (EC 6.1.1.2).
AK296799 - Homo sapiens cDNA FLJ51886 complete cds, highly similar to Tryptophanyl-tRNA synthetase, mitochondrial precursor (EC 6.1.1.2).
AJ242739 - Homo sapiens mRNA for mitochondrial tryptophanyl-tRNA synthetase (WARS2 gene).
BC021722 - Homo sapiens tryptophanyl tRNA synthetase 2 (mitochondrial), mRNA (cDNA clone IMAGE:4819132).
AK313740 - Homo sapiens cDNA, FLJ94340, Homo sapiens tryptophanyl tRNA synthetase 2 (mitochondrial)(WARS2), nuclear gene encoding mitochondrial protein, mRNA.
HQ448484 - Synthetic construct Homo sapiens clone IMAGE:100071916; CCSB010745_01 tryptophanyl tRNA synthetase 2, mitochondrial (WARS2) gene, encodes complete protein.
KJ898196 - Synthetic construct Homo sapiens clone ccsbBroadEn_07590 WARS2 gene, encodes complete protein.
CU692202 - Synthetic construct Homo sapiens gateway clone IMAGE:100020882 5' read WARS2 mRNA.
AK296088 - Homo sapiens cDNA FLJ51977 complete cds, weakly similar to Tryptophanyl-tRNA synthetase, mitochondrial precursor (EC 6.1.1.2).
BC037821 - Homo sapiens cDNA clone IMAGE:4800001.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa00380 - Tryptophan metabolism
hsa00970 - Aminoacyl-tRNA biosynthesis

-  Other Names for This Gene
  Alternate Gene Symbols: AK296088, B7Z3L8, B7Z3L8_HUMAN
UCSC ID: uc010oxi.2
RefSeq Accession: NM_015836
Protein: B7Z3L8

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene WARS2:
wars2-def (WARS2 Deficiency)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: AK296088.1
exon count: 4CDS single in 3' UTR: no RNA size: 1095
ORF size: 270CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 648.00frame 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: 554# 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.