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mutLBSgeneDB |
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| Gene summary for JMJD6 |
 Gene summary |
| Basic gene Info. | Gene symbol | JMJD6 |
| Gene name | jumonji domain containing 6 | |
| Synonyms | PSR|PTDSR|PTDSR1 | |
| Cytomap | UCSC genome browser: 17q25 | |
| Type of gene | protein-coding | |
| RefGenes | NM_001081461.1, NM_015167.2, | |
| Description | bifunctional arginine demethylase and lysyl-hydroxylase JMJD6histone arginine demethylase JMJD6jmjC domain-containing protein 6jumonji domain-containing protein 6lysyl-hydroxylase JMJD6peptide-lysine 5-dioxygenase JMJD6phosphatidylserine receptor | |
| Modification date | 20141207 | |
| dbXrefs | MIM : 604914 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000070495 | ||
| HPRD : 05371 | ||
| Vega : OTTHUMG00000169267 | ||
| Protein | UniProt: Q6NYC1 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_JMJD6 | |
| BioGPS: 23210 | ||
| Pathway | NCI Pathway Interaction Database: JMJD6 | |
| KEGG: JMJD6 | ||
| REACTOME: JMJD6 | ||
| Pathway Commons: JMJD6 | ||
| Context | iHOP: JMJD6 | |
| ligand binding site mutation search in PubMed: JMJD6 | ||
| UCL Cancer Institute: JMJD6 | ||
| 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:0018395 | peptidyl-lysine hydroxylation to 5-hydroxy-L-lysine | 19574390 | GO:0070078 | histone H3-R2 demethylation | 17947579 | GO:0070079 | histone H4-R3 demethylation | 17947579 |
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| Ligand binding site mutations for JMJD6 |
| 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 | H187 | H187N | KIRC | 1 | H273 | W271C | LUSC | 1 | D189 | L191M | SKCM | 1 | W174 | R173M | UCEC | 1 | N197 | W196C | UCEC | 1 | T184 | G183E | 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 JMJD6 |
| 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 | W174 | R173M | -1.2188492 | N197 | W196C | -1.1387977 | D189 | L191M | -1.0569189 | H273 | W271C | -0.91630934 | H187 | H187N | -0.60064509 | T184 | G183E | -0.49638965 |
| (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 JMJD6 from PDB |
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| Differential gene expression and gene-gene network for JMJD6 |
| 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 JMJD6 |
| 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 JMJD6 |
| 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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| 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 JMJD6 go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | FE | IRON(3+) | 3ld8 | A | H187 D189 H273 | FE | IRON(3+) | 3ldb | A | H187 D189 H273 | AKG | 2-OXOGLUTARIC ACID | 3ldb | A | W174 T184 N197 |
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| Conservation information for LBS of JMJD6 |
| Multiple alignments for Q6NYC1 in multiple species |
| LBS | AA sequence | # species | Species | D189 | TGIHIDPLGTS | 6 | Homo sapiens, Danio rerio, Gallus gallus, Bos taurus, Mus musculus, Rattus norvegicus | D189 | TAIHIDPLGTS | 1 | Caenorhabditis elegans | H187 | SGTGIHIDPLG | 6 | Homo sapiens, Danio rerio, Gallus gallus, Bos taurus, Mus musculus, Rattus norvegicus | H187 | SGTAIHIDPLG | 1 | Caenorhabditis elegans | H273 | PGGWWHVVLNL | 6 | Homo sapiens, Danio rerio, Gallus gallus, Bos taurus, Mus musculus, Rattus norvegicus | H273 | PSGWWHVVINE | 1 | Caenorhabditis elegans | K204 | LVQGHKRWCLF | 6 | Homo sapiens, Danio rerio, Gallus gallus, Bos taurus, Mus musculus, Rattus norvegicus | K204 | LLQGHKRWVLI | 1 | Caenorhabditis elegans | N197 | GTSAWNALVQG | 6 | Homo sapiens, Danio rerio, Gallus gallus, Bos taurus, Mus musculus, Rattus norvegicus | N197 | GTSAWNSLLQG | 1 | Caenorhabditis elegans | T184 | PPRSGTGIHID | 5 | Homo sapiens, Gallus gallus, Bos taurus, Mus musculus, Rattus norvegicus | T184 | PARSGTAIHID | 1 | Caenorhabditis elegans | T184 | PARSGTGIHID | 1 | Danio rerio | T285 | TTIAITQNFAS | 5 | Homo sapiens, Gallus gallus, Bos taurus, Mus musculus, Rattus norvegicus | T285 | YTIAVTHNYCS | 1 | Caenorhabditis elegans | T285 | TTIAVTQNFAS | 1 | Danio rerio | W174 | RPPYRWFVMGP | 6 | Homo sapiens, Danio rerio, Gallus gallus, Bos taurus, Mus musculus, Rattus norvegicus | W174 | RPPHRWFVMGP | 1 | Caenorhabditis elegans |
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