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mutLBSgeneDB |
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| Gene summary for RARB |
 Gene summary |
| Basic gene Info. | Gene symbol | RARB |
| Gene name | retinoic acid receptor, beta | |
| Synonyms | HAP|MCOPS12|NR1B2|RRB2 | |
| Cytomap | UCSC genome browser: 3p24.2 | |
| Type of gene | protein-coding | |
| RefGenes | NM_000965.4, NM_001290216.1,NM_001290217.1,NM_001290266.1,NM_001290276.1, NM_001290277.1,NM_001290300.1,NM_016152.3,NR_110892.1, NR_110893.1, | |
| Description | HBV-activated proteinRAR-betaRAR-epsilonhepatitis B virus activated proteinnuclear receptor subfamily 1 group B member 2retinoic acid receptor betaretinoic acid receptor, beta polypeptide | |
| Modification date | 20141207 | |
| dbXrefs | MIM : 180220 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000077092 | ||
| HPRD : 07183 | ||
| Vega : OTTHUMG00000130480 | ||
| Protein | UniProt: P10826 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_RARB | |
| BioGPS: 5915 | ||
| Pathway | NCI Pathway Interaction Database: RARB | |
| KEGG: RARB | ||
| REACTOME: RARB | ||
| Pathway Commons: RARB | ||
| Context | iHOP: RARB | |
| ligand binding site mutation search in PubMed: RARB | ||
| UCL Cancer Institute: RARB | ||
| Assigned class in mutLBSgeneDB | B: This gene belongs to targetable_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 RARB |
| 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 | D127 | K128N | BLCA | 1 | L409 | L409V | BLCA | 1 | R276 | T278A | COAD | 1 | C140 | Q141E | COAD | 1 | E62 | T63A | COAD | 1 | I270 | L271R | HNSC | 1 | P408 | P408H | LUAD | 1 | R394 | R394P | STAD | 1 | F249 | T250A | STAD | 1 | C143 | Y142S | STAD | 1 | I254 | A255T | STAD | 1 | C140 | R139Q | 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 RARB |
| 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 | I254 | A255T | -1.4805283 | D127 | K128N | -1.3523154 | E62 | T63A | -1.3507575 | C140 | Q141E | -1.3198812 | I270 | L271R | -1.3138079 | C140 | R139Q | -1.2275885 | R276 | T278A | -1.1160216 | L409 | L409V | -0.96258638 | P408 | P408H | -0.92037283 | R394 | R394P | -0.77466933 | C143 | Y142S | -0.6667526 | F249 | T250A | -0.23057925 |
| (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 RARB from PDB |
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| Differential gene expression and gene-gene network for RARB |
| 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 RARB |
| Gene level disease information (DisGeNet) |
| Disease ID | Disease name | # PubMed | Association type |
| umls:C0007137 | Carcinoma, Squamous Cell | 13 | AlteredExpression, Biomarker, PostTranslationalModification |
| umls:C1458155 | Breast Neoplasms | 8 | AlteredExpression, Biomarker, PostTranslationalModification, Therapeutic |
| umls:C0024121 | Lung Neoplasms | 6 | AlteredExpression, Biomarker |
| umls:C0018671 | Head and Neck Neoplasms | 2 | Biomarker |
| umls:C0001418 | Adenocarcinoma | 2 | Biomarker |
| umls:C0038356 | Stomach Neoplasms | 2 | Biomarker |
| umls:C3809803 | MICROPHTHALMIA, SYNDROMIC 12 | 1 | GeneticVariation |
| umls:C0014175 | Endometriosis | 1 | Biomarker |
| umls:C0149940 | Sciatic Neuropathy | 1 | Biomarker |
| umls:C0007873 | Uterine Cervical Neoplasms | 1 | Biomarker |
| Mutation level pathogenic information (ClinVar annotation) |
| Allele ID | AA change | Clinical significance | Origin | Phenotype IDs |
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| Pharmacological information for RARB |
| 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 | DB00210 | Adapalene | Small molecule |  |
| Approved | DB00459 | Acitretin | Small molecule |  |
| Approved|investigational | DB00523 | Alitretinoin | Small molecule |  |
| Approved|investigational | DB00799 | Tazarotene | Small molecule |  |
| Withdrawn | DB00926 | Etretinate | Small molecule |  |
| Experimental | DB02877 | TTNPB | Small molecule |  |
| Approved|investigational | DB04942 | Tamibarotene | Small molecule |  |
| Investigational | DB05785 | LGD-1550 | Small molecule |  |
| Gene-centered ligand-gene interaction network |
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| Ligands binding to mutated ligand binding site of RARB go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS |
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| Conservation information for LBS of RARB |
| Multiple alignments for P10826 in multiple species |
| LBS | AA sequence | # species | Species | A232 | KFSELATKCII | 3 | Homo sapiens, Gallus gallus, Mus musculus | A232 | KFSELSTKCII | 1 | Danio rerio | C124 | NMIYTCHRDKN | 2 | Homo sapiens, Mus musculus | C124 | NMVYTCHRDKN | 2 | Danio rerio, Gallus gallus | C130 | HRDKNCVINKV | 3 | Homo sapiens, Gallus gallus, Mus musculus | C130 | HRDKNCQINKV | 1 | Danio rerio | C140 | VTRNRCQYCRL | 4 | Homo sapiens, Danio rerio, Gallus gallus, Mus musculus | C143 | NRCQYCRLQKC | 4 | Homo sapiens, Danio rerio, Gallus gallus, Mus musculus | C235 | ELATKCIIKIV | 3 | Homo sapiens, Gallus gallus, Mus musculus | C235 | ELSTKCIIKIV | 1 | Danio rerio | D127 | YTCHRDKNCVI | 3 | Homo sapiens, Gallus gallus, Mus musculus | D127 | YTCHRDKNCQI | 1 | Danio rerio | E412 | PPLIQEMLENS | 3 | Homo sapiens, Gallus gallus, Mus musculus | E412 | PPLIREMLENP | 1 | Danio rerio | E415 | IQEMLENSEGH | 3 | Homo sapiens, Gallus gallus, Mus musculus | E415 | IREMLENPEAF | 1 | Danio rerio | E62 | ----VETQSTS | 2 | Danio rerio, Gallus gallus | E62 | ----IETQSTS | 1 | Homo sapiens | E62 | LNAAIETQSTS | 1 | Mus musculus | F199 | AHQETFPSLCQ | 4 | Homo sapiens, Danio rerio, Gallus gallus, Mus musculus | F228 | GLWDKFSELAT | 3 | Homo sapiens, Gallus gallus, Mus musculus | F228 | GLWDKFSELST | 1 | Danio rerio | F249 | KRLPGFTGLTI | 2 | Homo sapiens, Mus musculus | F249 | KRLPGFTTLTI | 1 | Danio rerio | F249 | KRLPGFTSLTI | 1 | Gallus gallus | F286 | QDTMTFSDGLT | 4 | Homo sapiens, Danio rerio, Gallus gallus, Mus musculus | F302 | MHNAGFGPLTD | 4 | Homo sapiens, Danio rerio, Gallus gallus, Mus musculus | G301 | QMHNAGFGPLT | 4 | Homo sapiens, Danio rerio, Gallus gallus, Mus musculus | G391 | SISAKGAERVI | 3 | Homo sapiens, Gallus gallus, Mus musculus | G391 | GISTKGAERAI | 1 | Danio rerio | I254 | FTGLTIADQIT | 2 | Homo sapiens, Mus musculus | I254 | FTTLTIADQIT | 1 | Danio rerio | I254 | FTSLTIADQIT | 1 | Gallus gallus | I258 | TIADQITLLKA | 3 | Homo sapiens, Gallus gallus, Mus musculus | I258 | TIADQITLLKS | 1 | Danio rerio | I270 | CLDILILRICT | 3 | Homo sapiens, Gallus gallus, Mus musculus | I270 | CLDILMLRICT | 1 | Danio rerio | I273 | ILILRICTRYT | 3 | Homo sapiens, Gallus gallus, Mus musculus | I273 | ILMLRICTRYT | 1 | Danio rerio | I410 | SMPPLIQEMLE | 3 | Homo sapiens, Gallus gallus, Mus musculus | I410 | PMPPLIREMLE | 1 | Danio rerio | K244 | IVEFAKRLPGF | 4 | Homo sapiens, Danio rerio, Gallus gallus, Mus musculus | K262 | QITLLKAACLD | 3 | Homo sapiens, Gallus gallus, Mus musculus | K262 | QITLLKSACLD | 1 | Danio rerio | L231 | DKFSELATKCI | 3 | Homo sapiens, Gallus gallus, Mus musculus | L231 | DKFSELSTKCI | 1 | Danio rerio | L261 | DQITLLKAACL | 3 | Homo sapiens, Gallus gallus, Mus musculus | L261 | DQITLLKSACL | 1 | Danio rerio | L266 | LKAACLDILIL | 3 | Homo sapiens, Gallus gallus, Mus musculus | L266 | LKSACLDILML | 1 | Danio rerio | L269 | ACLDILILRIC | 3 | Homo sapiens, Gallus gallus, Mus musculus | L269 | ACLDILMLRIC | 1 | Danio rerio | L305 | AGFGPLTDLVF | 4 | Homo sapiens, Danio rerio, Gallus gallus, Mus musculus | L319 | NQLLPLEMDDT | 3 | Homo sapiens, Gallus gallus, Mus musculus | L319 | GQLLPLEMDDT | 1 | Danio rerio | L398 | ERVITLKMEIP | 3 | Homo sapiens, Gallus gallus, Mus musculus | L398 | ERAITLKMEIP | 1 | Danio rerio | L409 | GSMPPLIQEML | 3 | Homo sapiens, Gallus gallus, Mus musculus | L409 | GPMPPLIREML | 1 | Danio rerio | L414 | LIQEMLENSEG | 3 | Homo sapiens, Gallus gallus, Mus musculus | L414 | LIREMLENPEA | 1 | Danio rerio | M413 | PLIQEMLENSE | 3 | Homo sapiens, Gallus gallus, Mus musculus | M413 | PLIREMLENPE | 1 | Danio rerio | P408 | PGSMPPLIQEM | 3 | Homo sapiens, Gallus gallus, Mus musculus | P408 | PGPMPPLIREM | 1 | Danio rerio | Q257 | LTIADQITLLK | 4 | Homo sapiens, Danio rerio, Gallus gallus, Mus musculus | Q411 | MPPLIQEMLEN | 3 | Homo sapiens, Gallus gallus, Mus musculus | Q411 | MPPLIREMLEN | 1 | Danio rerio | R126 | IYTCHRDKNCV | 2 | Homo sapiens, Mus musculus | R126 | VYTCHRDKNCQ | 1 | Danio rerio | R126 | VYTCHRDKNCV | 1 | Gallus gallus | R276 | LRICTRYTPEQ | 4 | Homo sapiens, Danio rerio, Gallus gallus, Mus musculus | R394 | AKGAERVITLK | 3 | Homo sapiens, Gallus gallus, Mus musculus | R394 | TKGAERAITLK | 1 | Danio rerio | S287 | DTMTFSDGLTL | 4 | Homo sapiens, Danio rerio, Gallus gallus, Mus musculus | V240 | CIIKIVEFAKR | 4 | Homo sapiens, Danio rerio, Gallus gallus, Mus musculus | V309 | PLTDLVFTFAN | 3 | Homo sapiens, Gallus gallus, Mus musculus | V309 | PLTDLVFAFAG | 1 | Danio rerio | V395 | KGAERVITLKM | 3 | Homo sapiens, Gallus gallus, Mus musculus | V395 | KGAERAITLKM | 1 | Danio rerio | W225 | LDLGLWDKFSE | 4 | Homo sapiens, Danio rerio, Gallus gallus, Mus musculus |
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