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mutLBSgeneDB |
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| Gene summary for TYW5 |
 Gene summary |
| Basic gene Info. | Gene symbol | TYW5 |
| Gene name | tRNA-yW synthesizing protein 5 | |
| Synonyms | C2orf60|hTYW5 | |
| Cytomap | UCSC genome browser: 2q33.1 | |
| Type of gene | protein-coding | |
| RefGenes | NM_152382.1, NM_001039693.2,NR_004862.1,NR_109905.1,NR_109906.1, NR_109907.1, | |
| Description | jmjC domain-containing protein C2orf60tRNA wybutosine-synthesizing protein 5tRNA yW-synthesizing enzyme 5tRNA(Phe) (7-(3-amino-3-carboxypropyl)wyosine(37)-C(2))-hydroxylase | |
| Modification date | 20141207 | |
| dbXrefs | HGNC : HGNC | |
| Ensembl : ENSG00000162971 | ||
| HPRD : 08232 | ||
| Vega : OTTHUMG00000132770 | ||
| Protein | UniProt: A2RUC4 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_TYW5 | |
| BioGPS: 129450 | ||
| Pathway | NCI Pathway Interaction Database: TYW5 | |
| KEGG: TYW5 | ||
| REACTOME: TYW5 | ||
| Pathway Commons: TYW5 | ||
| Context | iHOP: TYW5 | |
| ligand binding site mutation search in PubMed: TYW5 | ||
| UCL Cancer Institute: TYW5 | ||
| 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 | GO:0031591 | wybutosine biosynthetic process | 20739293 |
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| Ligand binding site mutations for TYW5 |
| Lollipop-style diagram of mutations at LBS in amino-acid sequence. We represented ligand binding site mutations only. (You can see big image via clicking.)  : non-synonymous mutation on LBS, Circle size denotes number of samples. |
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| Cancer type specific mutLBS sorted by frequency |
| LBS | AAchange of nsSNV | Cancer type | # samples | Y106 | R108W | COAD | 2 | H235 | W233R | COAD | 1 | Y106 | R108Q | STAD | 1 | K175 | K174Q | 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 TYW5 |
| 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 | K175 | K174Q | -1.0146778 | Y106 | R108Q | -0.62046034 | H235 | W233R | -0.52277253 | Y106 | R108W | -0.34728902 |
| (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 TYW5 from PDB |
| PDB ID | PDB title | PDB structure | 3AL5 | Crystal structure of Human TYW5 |  |
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| Differential gene expression and gene-gene network for TYW5 |
| 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 TYW5 |
| Gene level disease information (DisGeNet) |
| Disease ID | Disease name | # PubMed | Association type |
| Mutation level pathogenic information (ClinVar annotation) |
| Allele ID | AA change | Clinical significance | Origin | Phenotype IDs |
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| Pharmacological information for TYW5 |
| Drug information targeting mutLBSgene (Approved drugs only) |
| Drug status | DrugBank ID | Name | Type | Drug structure |
| Gene-centered ligand-gene interaction network |
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| Ligands binding to mutated ligand binding site of TYW5 go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | MG | MAGNESIUM(2+) | 3al5 | B | H235 | MG | MAGNESIUM(2+) | 3al5 | D | H235 | AKG | 2-OXOGLUTARIC ACID | 3al6 | B | Y106 K175 H235 | AKG | 2-OXOGLUTARIC ACID | 3al6 | D | Y106 K175 H235 |
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| Conservation information for LBS of TYW5 |
| Multiple alignments for A2RUC4 in multiple species |
| LBS | AA sequence | # species | Species | D162 | LWTHYDVMDNL | 2 | Homo sapiens, Danio rerio | D162 | LWTHYDVMDNF | 1 | Mus musculus | F249 | VGVNIFWKHLP | 2 | Homo sapiens, Mus musculus | F249 | VGVNVFWRHLP | 1 | Danio rerio | H160 | LQLWTHYDVMD | 3 | Homo sapiens, Danio rerio, Mus musculus | H235 | PALWFHNVISE | 1 | Homo sapiens | H235 | PALWFHNTLAL | 1 | Danio rerio | H235 | PALWFHNVVSE | 1 | Mus musculus | K175 | QVTGKKRVVLF | 1 | Homo sapiens | K175 | QVTGKKRVVLY | 1 | Danio rerio | K175 | QVTGKKRITLF | 1 | Mus musculus | L157 | SPGLQLWTHYD | 3 | Homo sapiens, Danio rerio, Mus musculus | L168 | VMDNLLIQVTG | 1 | Homo sapiens | L168 | VMDNLLAQVTG | 1 | Danio rerio | L168 | VMDNFLIQVTG | 1 | Mus musculus | N166 | YDVMDNLLIQV | 1 | Homo sapiens | N166 | YDVMDNLLAQV | 1 | Danio rerio | N166 | YDVMDNFLIQV | 1 | Mus musculus | N247 | FGVGVNIFWKH | 2 | Homo sapiens, Mus musculus | N247 | FGVGVNVFWRH | 1 | Danio rerio | R149 | FSSVFRISSPG | 3 | Homo sapiens, Danio rerio, Mus musculus | V237 | LWFHNVISEEF | 1 | Homo sapiens | V237 | LWFHNTLALQF | 1 | Danio rerio | V237 | LWFHNVVSEEF | 1 | Mus musculus | Y106 | EDEKYYLRSLG | 2 | Homo sapiens, Mus musculus | Y106 | EDESYYLRSLG | 1 | Danio rerio |
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