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mutLBSgeneDB |
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| Gene summary for YARS |
 Gene summary |
| Basic gene Info. | Gene symbol | YARS |
| Gene name | tyrosyl-tRNA synthetase | |
| Synonyms | CMTDIC|TYRRS|YRS|YTS | |
| Cytomap | UCSC genome browser: 1p35.1 | |
| Type of gene | protein-coding | |
| RefGenes | NM_003680.3, | |
| Description | tyrosine tRNA ligase 1, cytoplasmictyrosine--tRNA ligase, cytoplasmictyrosyl--tRNA ligasetyrosyl-tRNA synthetase, cytoplasmic | |
| Modification date | 20141207 | |
| dbXrefs | MIM : 603623 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000134684 | ||
| HPRD : 09153 | ||
| Vega : OTTHUMG00000003933 | ||
| Protein | UniProt: P54577 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_YARS | |
| BioGPS: 8565 | ||
| Pathway | NCI Pathway Interaction Database: YARS | |
| KEGG: YARS | ||
| REACTOME: YARS | ||
| Pathway Commons: YARS | ||
| Context | iHOP: YARS | |
| ligand binding site mutation search in PubMed: YARS | ||
| UCL Cancer Institute: YARS | ||
| Assigned class in mutLBSgeneDB | C: This gene just belongs to mutLBSgenes. | |
| Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez |
| GO ID | GO Term | PubMed ID |
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| Ligand binding site mutations for YARS |
| Cancer type specific mutLBS sorted by frequency |
| LBS | AAchange of nsSNV | Cancer type | # samples | D173 | E174K | HNSC | 1 | Y39 | I38L | UCEC | 1 |
| cf) Cancer type abbreviation. BLCA: Bladder urothelial carcinoma, BRCA: Breast invasive carcinoma, CESC: Cervical squamous cell carcinoma and endocervical adenocarcinoma, COAD: Colon adenocarcinoma, GBM: Glioblastoma multiforme, LGG: Brain lower grade glioma, HNSC: Head and neck squamous cell carcinoma, KICH: Kidney chromophobe, KIRC: Kidney renal clear cell carcinoma, KIRP: Kidney renal papillary cell carcinoma, LAML: Acute myeloid leukemia, LUAD: Lung adenocarcinoma, LUSC: Lung squamous cell carcinoma, OV: Ovarian serous cystadenocarcinoma, PAAD: Pancreatic adenocarcinoma, PRAD: Prostate adenocarcinoma, SKCM: Skin cutaneous melanoma, STAD: Stomach adenocarcinoma, THCA: Thyroid carcinoma, UCEC: Uterine corpus endometrial carcinoma. |
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| Protein structure related information for YARS |
| Relative protein structure stability change (ΔΔE) using Mupro 1.1 Mupro score denotes assessment of the effect of mutations on thermodynamic stability. (ΔΔE<0: mutation decreases stability, ΔΔE>0: mutation increases stability) |
 : nsSNV at non-LBS : nsSNV at LBS |
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| nsSNVs sorted by the relative stability change of protein structure by each mutation Blue: mutations of positive stability change. and red : the most recurrent mutation for this gene. |
| LBS | AAchange of nsSNV | Relative stability change | Y39 | I38L | -1.2396319 | D173 | E174K | -0.48846126 |
| (MuPro1.1: Jianlin Cheng et al., Prediction of Protein Stability Changes for Single-Site Mutations Using Support Vector Machines, PROTEINS: Structure, Function, and Bioinformatics. 2006, 62:1125-1132) |
| Structure image for YARS from PDB |
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| Differential gene expression and gene-gene network for YARS |
| Differential gene expression between mutated and non-mutated LBS samples in all 16 major cancer types |
| Differential co-expressed gene network based on protein-protein interaction data (CePIN) |
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| Phenotype information for YARS |
| Gene level disease information (DisGeNet) |
| Disease ID | Disease name | # PubMed | Association type |
| umls:C1842237 | Charcot-Marie-Tooth Disease, Dominant Intermediate C | 1 | Biomarker, GeneticVariation |
| Mutation level pathogenic information (ClinVar annotation) |
| Allele ID | AA change | Clinical significance | Origin | Phenotype IDs |
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| Pharmacological information for YARS |
| Gene expression profile of anticancer drug treated cell-lines (CCLE) Heatmap showing the correlation between gene expression and drug response across all the cell-lines. We chose the top 20 among 138 drugs.We used Pearson's correlation coefficient. |
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| Gene-centered drug-gene interaction network |
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| Drug information targeting mutLBSgene (Approved drugs only) |
| Drug status | DrugBank ID | Name | Type | Drug structure |
| Approved|nutraceutical | DB00135 | L-Tyrosine | Small molecule |  |
| Experimental | DB01766 | Beta-(2-Naphthyl)-Alanine | Small molecule |  |
| Experimental | DB03978 | Tyrosinal | Small molecule |  |
| Experimental | DB07205 | N6-ISOPENTENYL-ADENOSINE-5'-MONOPHOSPHATE | Small molecule |  |
| Experimental | DB08371 | PARA-(BENZOYL)-PHENYLALANINE | Small molecule |  |
| Experimental | DB08617 | 4-(2,2,2-TRIFLUOROETHYL)-L-PHENYLALANINE | Small molecule |  |
| Gene-centered ligand-gene interaction network |
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| Ligands binding to mutated ligand binding site of YARS go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | TYE | TYROSINOL | 1q11 | A | Y39 D173 | STL | RESVERATROL | 4q93 | A | Y39 D173 | TYR | L-TYROSINE | 4qbt | A | Y39 D173 |
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| Conservation information for LBS of YARS |
| Multiple alignments for P54577 in multiple species |
| LBS | AA sequence | # species | Species | A74 | VTILFADLHAY | 7 | Homo sapiens, Danio rerio, Xenopus tropicalis, Gallus gallus, Bos taurus, Mus musculus, Rattus norvegicus | A74 | VTVLLADLHAF | 1 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | A74 | VTVLLADVHAF | 1 | Schizosaccharomyces pombe (strain 972 / ATCC 24843) | D173 | GLQALDEEYLK | 7 | Homo sapiens, Danio rerio, Xenopus tropicalis, Gallus gallus, Bos taurus, Mus musculus, Rattus norvegicus | D173 | LMQALDEQFLD | 1 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | D173 | GMQALDEQYLG | 1 | Schizosaccharomyces pombe (strain 972 / ATCC 24843) | G41 | LKVYWGTATTG | 4 | Danio rerio, Bos taurus, Mus musculus, Rattus norvegicus | G41 | LKIYWGTATTG | 1 | Homo sapiens | G41 | LRIYWGTATTG | 1 | Xenopus tropicalis | G41 | VKIYWGTATTG | 1 | Gallus gallus | G41 | LKLYWGTAPTG | 1 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | G41 | ISLYWGSAPTG | 1 | Schizosaccharomyces pombe (strain 972 / ATCC 24843) | H77 | LFADLHAYLDN | 7 | Homo sapiens, Danio rerio, Xenopus tropicalis, Gallus gallus, Bos taurus, Mus musculus, Rattus norvegicus | H77 | LLADLHAFLDN | 1 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | H77 | LLADVHAFLDN | 1 | Schizosaccharomyces pombe (strain 972 / ATCC 24843) | L72 | CEVTILFADLH | 7 | Homo sapiens, Danio rerio, Xenopus tropicalis, Gallus gallus, Bos taurus, Mus musculus, Rattus norvegicus | L72 | CEVTVLLADLH | 1 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | L72 | VHVTVLLADVH | 1 | Schizosaccharomyces pombe (strain 972 / ATCC 24843) | Q170 | LYPGLQALDEE | 7 | Homo sapiens, Danio rerio, Xenopus tropicalis, Gallus gallus, Bos taurus, Mus musculus, Rattus norvegicus | Q170 | IYPLMQALDEQ | 1 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | Q170 | IYPGMQALDEQ | 1 | Schizosaccharomyces pombe (strain 972 / ATCC 24843) | Q182 | LKVDAQFGGVD | 5 | Danio rerio, Xenopus tropicalis, Gallus gallus, Bos taurus, Mus musculus | Q182 | LKVDAQFGGID | 2 | Homo sapiens, Rattus norvegicus | Q182 | LDVDCQFGGVD | 1 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | Q182 | LGVDVQFGGVD | 1 | Schizosaccharomyces pombe (strain 972 / ATCC 24843) | Q188 | FGGVDQRKIFT | 5 | Danio rerio, Xenopus tropicalis, Gallus gallus, Bos taurus, Mus musculus | Q188 | FGGIDQRKIFT | 2 | Homo sapiens, Rattus norvegicus | Q188 | FGGVDQRKIFV | 2 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Schizosaccharomyces pombe (strain 972 / ATCC 24843) | V152 | KAGAEVVKQVE | 7 | Homo sapiens, Danio rerio, Xenopus tropicalis, Gallus gallus, Bos taurus, Mus musculus, Rattus norvegicus | V152 | RAGADVVKQVA | 1 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | V152 | RAGAEVVKQVA | 1 | Schizosaccharomyces pombe (strain 972 / ATCC 24843) | Y166 | LSGLLYPGLQA | 7 | Homo sapiens, Danio rerio, Xenopus tropicalis, Gallus gallus, Bos taurus, Mus musculus, Rattus norvegicus | Y166 | LSGLIYPLMQA | 1 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | Y166 | LSSLIYPGMQA | 1 | Schizosaccharomyces pombe (strain 972 / ATCC 24843) | Y39 | RELKVYWGTAT | 4 | Danio rerio, Bos taurus, Mus musculus, Rattus norvegicus | Y39 | RELKIYWGTAT | 1 | Homo sapiens | Y39 | RPLRIYWGTAT | 1 | Xenopus tropicalis | Y39 | REVKIYWGTAT | 1 | Gallus gallus | Y39 | RHLKLYWGTAP | 1 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | Y39 | RDISLYWGSAP | 1 | Schizosaccharomyces pombe (strain 972 / ATCC 24843) |
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