Human Gene WARS1 (ENST00000344102.9_5) from GENCODE V47lift37
  Description: tryptophanyl-tRNA synthetase 1, transcript variant 4 (from RefSeq NM_213646.2)
Gencode Transcript: ENST00000344102.9_5
Gencode Gene: ENSG00000140105.18_14
Transcript (Including UTRs)
   Position: hg19 chr14:100,800,165-100,841,945 Size: 41,781 Total Exon Count: 10 Strand: -
Coding Region
   Position: hg19 chr14:100,801,212-100,828,234 Size: 27,023 Coding Exon Count: 9 

Page IndexSequence and LinksUniProtKB CommentsPrimersGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr14:100,800,165-100,841,945)mRNA (may differ from genome)Protein (430 aa)
Gene SorterGenome BrowserOther Species FASTATable SchemaAlphaFoldBioGPS
EnsemblEntrez GeneExonPrimerGeneCardsMGIOMIM
PubMedReactomeUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SYWC_HUMAN
DESCRIPTION: RecName: Full=Tryptophan--tRNA ligase, cytoplasmic; EC=6.1.1.2; AltName: Full=Interferon-induced protein 53; Short=IFP53; AltName: Full=Tryptophanyl-tRNA synthetase; Short=TrpRS; Short=hWRS; Contains: RecName: Full=T1-TrpRS; Contains: RecName: Full=T2-TrpRS;
FUNCTION: Isoform 1, isoform 2 and T1-TrpRS have aminoacylation activity while T2-TrpRS lacks it. Isoform 2, T1-TrpRS and T2-TrpRS possess angiostatic activity whereas isoform 1 lacks it. T2-TrpRS inhibits fluid shear stress-activated responses of endothelial cells. Regulates ERK, Akt, and eNOS activation pathways that are associated with angiogenesis, cytoskeletal reorganization and shear stress-responsive gene expression.
CATALYTIC ACTIVITY: ATP + L-tryptophan + tRNA(Trp) = AMP + diphosphate + L-tryptophyl-tRNA(Trp).
SUBUNIT: Homodimer. Isoform 1 and isoform 2 interact with an oxidized form of GAPDH. GAPDH stimulates the aminoacylation activity of isoform 2.
SUBCELLULAR LOCATION: Cytoplasm.
INDUCTION: By IFNG/IFN-gamma.
PTM: Proteolytic cleavage generates 2 forms; T1-TrpRS and T2- TrpRS.
SIMILARITY: Belongs to the class-I aminoacyl-tRNA synthetase family.
SIMILARITY: Contains 1 WHEP-TRS domain.
SEQUENCE CAUTION: Sequence=BAF83830.1; Type=Erroneous initiation;

-  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


+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 88.66 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 984.58 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 -108.10350-0.309 Picture PostScript Text
3' UTR -319.101047-0.305 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
IPR001412 - aa-tRNA-synth_I_CS
IPR002305 - aa-tRNA-synth_Ic
IPR014729 - Rossmann-like_a/b/a_fold
IPR009068 - S15_NS1_RNA-bd
IPR002306 - Trp-tRNA-ligase
IPR000738 - WHEP-TRS

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

SCOP Domains:
50729 - PH domain-like
52374 - Nucleotidylyl transferase

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1O5T - X-ray MuPIT 1R6T - X-ray MuPIT 1R6U - X-ray MuPIT 1ULH - X-ray MuPIT 2AKE - X-ray MuPIT 2AZX - X-ray MuPIT 2DR2 - X-ray MuPIT 2QUH - X-ray MuPIT 2QUI - X-ray MuPIT 2QUJ - X-ray MuPIT 2QUK - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P23381
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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 orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0004812 aminoacyl-tRNA ligase activity
GO:0004830 tryptophan-tRNA ligase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016874 ligase activity
GO:0019210 kinase inhibitor activity
GO:0019901 protein kinase binding
GO:0019904 protein domain specific binding
GO:0042803 protein homodimerization activity

Biological Process:
GO:0001525 angiogenesis
GO:0001933 negative regulation of protein phosphorylation
GO:0006412 translation
GO:0006418 tRNA aminoacylation for protein translation
GO:0006436 tryptophanyl-tRNA aminoacylation
GO:0006469 negative regulation of protein kinase activity
GO:0008285 negative regulation of cell proliferation
GO:0010628 positive regulation of gene expression
GO:0010835 regulation of protein ADP-ribosylation
GO:0031334 positive regulation of protein complex assembly
GO:0045765 regulation of angiogenesis

Cellular Component:
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0032991 macromolecular complex
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  KJ892380 - Synthetic construct Homo sapiens clone ccsbBroadEn_01774 WARS gene, encodes complete protein.
AK130698 - Homo sapiens cDNA FLJ27188 fis, clone SYN02464, highly similar to Tryptophanyl-tRNA synthetase (EC 6.1.1.2).
LF384888 - JP 2014500723-A/192391: Polycomb-Associated Non-Coding RNAs.
AK124668 - Homo sapiens cDNA FLJ42677 fis, clone BRAMY2037971, weakly similar to Homo sapiens tryptophanyl-tRNA synthetase (WARS).
AK025487 - Homo sapiens cDNA: FLJ21834 fis, clone HEP01596, highly similar to HSIFP53 Homo sapiens mRNA for IFP53.
X59892 - H.sapiens mRNA for IFN-inducible gamma2 protein.
BC017489 - Homo sapiens tryptophanyl-tRNA synthetase, mRNA (cDNA clone MGC:15973 IMAGE:3542671), complete cds.
GQ891525 - Homo sapiens clone HEL-S-246 epididymis secretory sperm binding protein mRNA, complete cds.
X62570 - H.sapiens mRNA for IFP53.
JD527173 - Sequence 508197 from Patent EP1572962.
JD268123 - Sequence 249147 from Patent EP1572962.
BX248006 - human full-length cDNA clone CS0DM004YH09 of Fetal liver of Homo sapiens (human).
JD179651 - Sequence 160675 from Patent EP1572962.
JD068344 - Sequence 49368 from Patent EP1572962.
JD427728 - Sequence 408752 from Patent EP1572962.
JD316932 - Sequence 297956 from Patent EP1572962.
JD248517 - Sequence 229541 from Patent EP1572962.
JD046560 - Sequence 27584 from Patent EP1572962.
JD156493 - Sequence 137517 from Patent EP1572962.
JD332938 - Sequence 313962 from Patent EP1572962.
JD290163 - Sequence 271187 from Patent EP1572962.
JD403258 - Sequence 384282 from Patent EP1572962.
JD554292 - Sequence 535316 from Patent EP1572962.
JD294652 - Sequence 275676 from Patent EP1572962.
JD358772 - Sequence 339796 from Patent EP1572962.
JD046185 - Sequence 27209 from Patent EP1572962.
JD297081 - Sequence 278105 from Patent EP1572962.
JD248736 - Sequence 229760 from Patent EP1572962.
JD026191 - Sequence 7215 from Patent EP1572962.
AK291141 - Homo sapiens cDNA FLJ75448 complete cds, highly similar to Homo sapiens tryptophanyl-tRNA synthetase (WARS), transcript variant 4, mRNA.
JD027832 - Sequence 8856 from Patent EP1572962.
M77804 - Human tryptophanyl tRNA synthetase (IFNWRS) mRNA, complete cds.
BC095453 - Homo sapiens tryptophanyl-tRNA synthetase, mRNA (cDNA clone MGC:111225 IMAGE:30418785), complete cds.
M61715 - Human tryptophanyl-tRNA synthetase (WRS) mRNA, complete cds.
JD137080 - Sequence 118104 from Patent EP1572962.
JD525406 - Sequence 506430 from Patent EP1572962.
JD062839 - Sequence 43863 from Patent EP1572962.
JD136690 - Sequence 117714 from Patent EP1572962.
AK056100 - Homo sapiens cDNA FLJ31538 fis, clone NT2RI2000727, highly similar to TRYPTOPHANYL-TRNA SYNTHETASE (EC 6.1.1.2).
JD193440 - Sequence 174464 from Patent EP1572962.
JD089931 - Sequence 70955 from Patent EP1572962.
AB529126 - Synthetic construct DNA, clone: pF1KB4987, Homo sapiens WARS gene for tryptophanyl-tRNA synthetase, without stop codon, in Flexi system.
LF330443 - JP 2014500723-A/137946: Polycomb-Associated Non-Coding RNAs.
LF330444 - JP 2014500723-A/137947: Polycomb-Associated Non-Coding RNAs.
LF330446 - JP 2014500723-A/137949: Polycomb-Associated Non-Coding RNAs.
JD019156 - Sequence 180 from Patent EP1572962.
JD035914 - Sequence 16938 from Patent EP1572962.
AK300255 - Homo sapiens cDNA FLJ58878 complete cds, highly similar to Tryptophanyl-tRNA synthetase (EC 6.1.1.2).
JD024723 - Sequence 5747 from Patent EP1572962.
JD029989 - Sequence 11013 from Patent EP1572962.
JD474114 - Sequence 455138 from Patent EP1572962.
JD480254 - Sequence 461278 from Patent EP1572962.
JD284126 - Sequence 265150 from Patent EP1572962.
JD244339 - Sequence 225363 from Patent EP1572962.
JD034990 - Sequence 16014 from Patent EP1572962.
MA620465 - JP 2018138019-A/192391: Polycomb-Associated Non-Coding RNAs.
MA566020 - JP 2018138019-A/137946: Polycomb-Associated Non-Coding RNAs.
MA566021 - JP 2018138019-A/137947: Polycomb-Associated Non-Coding RNAs.
MA566023 - JP 2018138019-A/137949: Polycomb-Associated Non-Coding RNAs.

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

Protein P23381 (Reactome details) participates in the following event(s):

R-HSA-379977 tryptophan + tRNA(Trp) + ATP => Trp-tRNA(Trp) + AMP + pyrophosphate
R-HSA-379716 Cytosolic tRNA aminoacylation
R-HSA-379724 tRNA Aminoacylation
R-HSA-72766 Translation
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: A6NGN1, A6NID3, ENST00000344102.1, ENST00000344102.2, ENST00000344102.3, ENST00000344102.4, ENST00000344102.5, ENST00000344102.6, ENST00000344102.7, ENST00000344102.8, IFI53, NM_213646, P23381, P78535, Q502Y0, Q53XB6, Q9UDI5, Q9UDL3, SYWC_HUMAN, uc317wvn.1, uc317wvn.2, WARS, WARS1 , WRS
UCSC ID: ENST00000344102.9_5
RefSeq Accession: NM_213646.2
Protein: P23381 (aka SYWC_HUMAN)

-  Gene Model Information
  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.