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 RPAP3
Gene summary
Basic gene Info.Gene symbolRPAP3
Gene nameRNA polymerase II associated protein 3
CytomapUCSC genome browser: 12q13.11
Type of geneprotein-coding
DescriptionRNA polymerase II-associated protein 3
Modification date20141207
dbXrefs MIM : 611477
Ensembl : ENSG00000005175
HPRD : 07970
Vega : OTTHUMG00000169668
ProteinUniProt: Q9H6T3
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RPAP3
BioGPS: 79657
PathwayNCI Pathway Interaction Database: RPAP3
Pathway Commons: RPAP3
ContextiHOP: RPAP3
ligand binding site mutation search in PubMed: RPAP3
UCL Cancer Institute: RPAP3
Assigned class in mutLBSgeneDBC: This gene just belongs to mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez

Ligand binding site mutations for RPAP3
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
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.

Protein structure related information for RPAP3
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
(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 RPAP3 from PDB
PDB IDPDB titlePDB structure
2Z6KCrystal structure of full-length human RPA14/32 heterodimer

Differential gene expression and gene-gene network for RPAP3
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 RPAP3 and the right PPI network was created from samples without mutations in the LBS of RPAP3. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.


Phenotype information for RPAP3
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type

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

Pharmacological information for RPAP3
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 RPAP3 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
IIIPeptide ligand (SER,ARG,MET,GLU,GLU,VAL,ASP)4cgvCK137 N141 V168 R206
IIIPeptide ligand (GLU,GLU,VAL,ASP)4cgvBK137 N141 Y156 V168 R206

Conservation information for LBS of RPAP3
Multiple alignments for Q9H6T3 in multiple species
LBSAA sequence# speciesSpecies
A354YSKAFARRGTA3Homo sapiens, Mus musculus, Rattus norvegicus
A354YCKAFARRGTA1Xenopus tropicalis
A354YSKAFARRGAA1Gallus gallus
F144KGNKYFKQGKY3Homo sapiens, Mus musculus, Rattus norvegicus
F144KGNNYFKSGQY1Xenopus tropicalis
F144KGNKYFKQGNF1Gallus gallus
F293LGNGFFKEGKY2Mus musculus, Rattus norvegicus
F293RGNGFFKEGKY1Homo sapiens
F293LGNAYFKEGKY1Xenopus tropicalis
F293LGNGYFKEGKY1Gallus gallus
K137KALVLKEKGNK3Homo sapiens, Mus musculus, Rattus norvegicus
K137KALLEKEKGNN1Xenopus tropicalis
K137KALAEKEKGNK1Gallus gallus
K202NRSYTKAYSRR1Homo sapiens
K202NHNYAKAYARR1Xenopus tropicalis
K202DKNYTKAYARR1Gallus gallus
K202SRTYTKAYARR1Mus musculus
K202SRSYTKAYARR1Rattus norvegicus
K286KAIAEKDLGNG2Mus musculus, Rattus norvegicus
K286QAISEKDRGNG1Homo sapiens
K286QAIMQKDLGNA1Xenopus tropicalis
K286KAVTEKDLGNG1Gallus gallus
K328AMAYLKIQKYE2Homo sapiens, Gallus gallus
K328AMAYLKIQKYK1Xenopus tropicalis
K328AMAYLKIQRYE1Mus musculus
K328AMAYLKVQKYE1Rattus norvegicus
K351DGSYSKAFARR3Homo sapiens, Mus musculus, Rattus norvegicus
K351DASYCKAFARR1Xenopus tropicalis
K351DASYSKAFARR1Gallus gallus
L317DGANALLPANR1Homo sapiens
L317DTTNALLPANR1Xenopus tropicalis
L317DGTNALLPANR1Gallus gallus
L317DRTNALLPANR1Mus musculus
L317DSTNALLPANR1Rattus norvegicus
M324PANRAMAYLKI4Homo sapiens, Xenopus tropicalis, Gallus gallus, Mus musculus
M324PANRAMAYLKV1Rattus norvegicus
N141LKEKGNKYFKQ3Homo sapiens, Mus musculus, Rattus norvegicus
N141EKEKGNNYFKS1Xenopus tropicalis
N141EKEKGNKYFKQ1Gallus gallus
N172PVLPTNRASAY3Homo sapiens, Mus musculus, Rattus norvegicus
N172AVLPTNRASAF1Xenopus tropicalis
N172PVLPTNRASAF1Gallus gallus
N290EKDLGNGFFKE2Mus musculus, Rattus norvegicus
N290EKDRGNGFFKE1Homo sapiens
N290QKDLGNAYFKE1Xenopus tropicalis
N290EKDLGNGYFKE1Gallus gallus
N321ALLPANRAMAY5Homo sapiens, Xenopus tropicalis, Gallus gallus, Mus musculus, Rattus norvegicus
R179ASAYFRLKKFA3Homo sapiens, Mus musculus, Rattus norvegicus
R179ASAFFRLKKYA1Xenopus tropicalis
R179ASAFYRMKKFS1Gallus gallus
R206TKAYARRGAAR3Gallus gallus, Mus musculus, Rattus norvegicus
R206TKAYSRRGAAR1Homo sapiens
R206AKAYARRGAAR1Xenopus tropicalis
R355SKAFARRGTAR3Homo sapiens, Mus musculus, Rattus norvegicus
R355CKAFARRGTAR1Xenopus tropicalis
R355SKAFARRGAAR1Gallus gallus
S175PTNRASAYFRL3Homo sapiens, Mus musculus, Rattus norvegicus
S175PTNRASAFFRL1Xenopus tropicalis
S175PTNRASAFYRM1Gallus gallus
V168DPYNPVLPTNR3Homo sapiens, Mus musculus, Rattus norvegicus
V168DPYNAVLPTNR1Xenopus tropicalis
V168DPFNPVLPTNR1Gallus gallus
Y156EAIECYTKGMD2Mus musculus, Rattus norvegicus
Y156EAIDCYTKGMD1Homo sapiens
Y156EAIECYTRGMD1Xenopus tropicalis
Y156EAIKCYTRGMH1Gallus gallus
Y200ALNRSYTKAYS1Homo sapiens
Y200ALNHNYAKAYA1Xenopus tropicalis
Y200ALDKNYTKAYA1Gallus gallus
Y200ALSRTYTKAYA1Mus musculus
Y200ALSRSYTKAYA1Rattus norvegicus
Y349LLDGSYSKAFA2Homo sapiens, Rattus norvegicus
Y349SLDASYCKAFA1Xenopus tropicalis
Y349LLDASYSKAFA1Gallus gallus
Y349VLDGSYSKAFA1Mus musculus

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