mutLBSgeneDB

mutLBSgeneDB
mutated Ligand Binding Site gene DataBase

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Gene Summary

Ligand Binding Site Mutation Information

Protein Structure Related Information

Gene Expression and Gene-Gene Network

Phenotype Information

Pharmacological Information

Conservation Information for LBS

Gene summary for TRA2B
Gene summary
Basic gene Info.Gene symbolTRA2B
Gene nametransformer 2 beta homolog (Drosophila)
SynonymsHtra2-beta|PPP1R156|SFRS10|SRFS10|TRA2-BETA|TRAN2B
CytomapUCSC genome browser: 3q26.2-q27
Type of geneprotein-coding
RefGenesNM_001243879.1,
NM_004593.2,
DescriptionTRA-2 betaprotein phosphatase 1, regulatory subunit 156splicing factor, arginine/serine-rich 10 (transformer 2 homolog, Drosophila)transformer-2 protein homolog Btransformer-2 protein homolog beta
Modification date20141207
dbXrefs MIM : 602719
HGNC : HGNC
HPRD : 04097
ProteinUniProt: P62995
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_TRA2B
BioGPS: 6434
PathwayNCI Pathway Interaction Database: TRA2B
KEGG: TRA2B
REACTOME: TRA2B
Pathway Commons: TRA2B
ContextiHOP: TRA2B
ligand binding site mutation search in PubMed: TRA2B
UCL Cancer Institute: TRA2B
Assigned class in mutLBSgeneDBC: This gene just belongs to mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO IDGO TermPubMed ID
GO:0000381regulation of alternative mRNA splicing, via spliceosome12165565
GO:0000398mRNA splicing, via spliceosome9546399
GO:0048026positive regulation of mRNA splicing, via spliceosome15009664


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Ligand binding site mutations for TRA2B
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.

Cancer type specific mutLBS sorted by frequency
LBSAAchange of nsSNVCancer type# samples
R187R187CCOAD2
R111R111LCOAD1
R111R111PHNSC1
R188R188SLUAD1
R159R157CSTAD1
F161F161SSTAD1
R187R187CUCEC1
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 TRA2B
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

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.
LBSAAchange of nsSNVRelative stability change
F161F161S-1.3636754
R187R187C-1.2303642
R159R157C-0.94758487
R111R111P-0.5256912
R188R188S-0.50498258
R111R111L-0.095115897
(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 TRA2B from PDB
PDB IDPDB titlePDB structure
2CQCSolution Structure of the RNA recognition motif in Arginine/serine-rich splicing factor 10

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Differential gene expression and gene-gene network for TRA2B
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)
* Left PPI network was created from samples with mutations in the LBS of TRA2B and the right PPI network was created from samples without mutations in the LBS of TRA2B. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.


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Phenotype information for TRA2B
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type

Mutation level pathogenic information (ClinVar annotation)
Allele IDAA changeClinical significanceOriginPhenotype IDs

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Pharmacological information for TRA2B
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.
Drug information targeting mutLBSgene (Approved drugs only)
Drug statusDrugBank IDNameTypeDrug structure

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of TRA2B go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
NUCNucleic Acids2rraAR111 F161 R187 R188
NUCNucleic Acids2kxnBR111 R159 F161 R187 R188


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Conservation information for LBS of TRA2B
Multiple alignments for P62995 in multiple species
LBSAA sequence# speciesSpecies
D192RRIRVDFSITK4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
F123CCLGVFGLSLY4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
F161RRSRGFAFVYF4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
F163SRGFAFVYFEN4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
F193RIRVDFSITKR4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
G124CLGVFGLSLYT4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
G160SRRSRGFAFVY4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
H24RSGSAHGSGKS4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
I149IADVSIVYDQQ4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
I189LDGRRIRVDFS4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
I195RVDFSITKRPH4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
K197DFSITKRPHTP4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
P199SITKRPHTPTP4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
Q153SIVYDQQSRRS4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
R111RHVGNRANPDP4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
R159QSRRSRGFAFV4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
R187MELDGRRIRVD4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
R188ELDGRRIRVDF4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
R190DGRRIRVDFSI4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
R198FSITKRPHTPT4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
S148PIADVSIVYDQ4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
S194IRVDFSITKRP4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
T196VDFSITKRPHT4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
V150ADVSIVYDQQS4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
Y165GFAFVYFENVD4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus


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