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mutLBSgeneDB |
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| Gene summary for RPAP3 |
 Gene summary |
| Basic gene Info. | Gene symbol | RPAP3 |
| Gene name | RNA polymerase II associated protein 3 | |
| Synonyms | - | |
| Cytomap | UCSC genome browser: 12q13.11 | |
| Type of gene | protein-coding | |
| RefGenes | NM_001146075.1, NM_001146076.1,NM_024604.2, | |
| Description | RNA polymerase II-associated protein 3 | |
| Modification date | 20141207 | |
| dbXrefs | MIM : 611477 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000005175 | ||
| HPRD : 07970 | ||
| Vega : OTTHUMG00000169668 | ||
| Protein | UniProt: Q9H6T3 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_RPAP3 | |
| BioGPS: 79657 | ||
| Pathway | NCI Pathway Interaction Database: RPAP3 | |
| KEGG: RPAP3 | ||
| REACTOME: RPAP3 | ||
| Pathway Commons: RPAP3 | ||
| Context | iHOP: RPAP3 | |
| ligand binding site mutation search in PubMed: RPAP3 | ||
| UCL Cancer Institute: RPAP3 | ||
| 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 |
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| 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. |
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| Cancer type specific mutLBS sorted by frequency |
| LBS | AAchange of nsSNV | Cancer type | # samples | Y156 | D154Y | UCEC | 2 | R206 | R207Q | LUSC | 1 | V168 | N166T | LUSC | 1 | N141,K137 | K139N | UCEC | 1 | V168 | V168M | 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 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 |
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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 | N141 | K139N | -1.0844961 | K137 | K139N | -1.0844961 | V168 | V168M | -1.0644812 | R206 | R207Q | -0.83229948 | V168 | N166T | -0.78821124 | Y156 | D154Y | -0.29750084 |
| (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 ID | PDB title | PDB structure | 2Z6K | Crystal structure of full-length human RPA14/32 heterodimer |  |
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| 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) |
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| Phenotype information for RPAP3 |
| 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 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. |
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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 RPAP3 go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | III | Peptide ligand (SER,ARG,MET,GLU,GLU,VAL,ASP) | 4cgv | C | K137 N141 V168 R206 | III | Peptide ligand (GLU,GLU,VAL,ASP) | 4cgv | B | K137 N141 Y156 V168 R206 |
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| Conservation information for LBS of RPAP3 |
| Multiple alignments for Q9H6T3 in multiple species |
| LBS | AA sequence | # species | Species | A354 | YSKAFARRGTA | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | A354 | YCKAFARRGTA | 1 | Xenopus tropicalis | A354 | YSKAFARRGAA | 1 | Gallus gallus | F144 | KGNKYFKQGKY | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | F144 | KGNNYFKSGQY | 1 | Xenopus tropicalis | F144 | KGNKYFKQGNF | 1 | Gallus gallus | F293 | LGNGFFKEGKY | 2 | Mus musculus, Rattus norvegicus | F293 | RGNGFFKEGKY | 1 | Homo sapiens | F293 | LGNAYFKEGKY | 1 | Xenopus tropicalis | F293 | LGNGYFKEGKY | 1 | Gallus gallus | K137 | KALVLKEKGNK | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | K137 | KALLEKEKGNN | 1 | Xenopus tropicalis | K137 | KALAEKEKGNK | 1 | Gallus gallus | K202 | NRSYTKAYSRR | 1 | Homo sapiens | K202 | NHNYAKAYARR | 1 | Xenopus tropicalis | K202 | DKNYTKAYARR | 1 | Gallus gallus | K202 | SRTYTKAYARR | 1 | Mus musculus | K202 | SRSYTKAYARR | 1 | Rattus norvegicus | K286 | KAIAEKDLGNG | 2 | Mus musculus, Rattus norvegicus | K286 | QAISEKDRGNG | 1 | Homo sapiens | K286 | QAIMQKDLGNA | 1 | Xenopus tropicalis | K286 | KAVTEKDLGNG | 1 | Gallus gallus | K328 | AMAYLKIQKYE | 2 | Homo sapiens, Gallus gallus | K328 | AMAYLKIQKYK | 1 | Xenopus tropicalis | K328 | AMAYLKIQRYE | 1 | Mus musculus | K328 | AMAYLKVQKYE | 1 | Rattus norvegicus | K351 | DGSYSKAFARR | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | K351 | DASYCKAFARR | 1 | Xenopus tropicalis | K351 | DASYSKAFARR | 1 | Gallus gallus | L317 | DGANALLPANR | 1 | Homo sapiens | L317 | DTTNALLPANR | 1 | Xenopus tropicalis | L317 | DGTNALLPANR | 1 | Gallus gallus | L317 | DRTNALLPANR | 1 | Mus musculus | L317 | DSTNALLPANR | 1 | Rattus norvegicus | M324 | PANRAMAYLKI | 4 | Homo sapiens, Xenopus tropicalis, Gallus gallus, Mus musculus | M324 | PANRAMAYLKV | 1 | Rattus norvegicus | N141 | LKEKGNKYFKQ | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | N141 | EKEKGNNYFKS | 1 | Xenopus tropicalis | N141 | EKEKGNKYFKQ | 1 | Gallus gallus | N172 | PVLPTNRASAY | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | N172 | AVLPTNRASAF | 1 | Xenopus tropicalis | N172 | PVLPTNRASAF | 1 | Gallus gallus | N290 | EKDLGNGFFKE | 2 | Mus musculus, Rattus norvegicus | N290 | EKDRGNGFFKE | 1 | Homo sapiens | N290 | QKDLGNAYFKE | 1 | Xenopus tropicalis | N290 | EKDLGNGYFKE | 1 | Gallus gallus | N321 | ALLPANRAMAY | 5 | Homo sapiens, Xenopus tropicalis, Gallus gallus, Mus musculus, Rattus norvegicus | R179 | ASAYFRLKKFA | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | R179 | ASAFFRLKKYA | 1 | Xenopus tropicalis | R179 | ASAFYRMKKFS | 1 | Gallus gallus | R206 | TKAYARRGAAR | 3 | Gallus gallus, Mus musculus, Rattus norvegicus | R206 | TKAYSRRGAAR | 1 | Homo sapiens | R206 | AKAYARRGAAR | 1 | Xenopus tropicalis | R355 | SKAFARRGTAR | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | R355 | CKAFARRGTAR | 1 | Xenopus tropicalis | R355 | SKAFARRGAAR | 1 | Gallus gallus | S175 | PTNRASAYFRL | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | S175 | PTNRASAFFRL | 1 | Xenopus tropicalis | S175 | PTNRASAFYRM | 1 | Gallus gallus | V168 | DPYNPVLPTNR | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | V168 | DPYNAVLPTNR | 1 | Xenopus tropicalis | V168 | DPFNPVLPTNR | 1 | Gallus gallus | Y156 | EAIECYTKGMD | 2 | Mus musculus, Rattus norvegicus | Y156 | EAIDCYTKGMD | 1 | Homo sapiens | Y156 | EAIECYTRGMD | 1 | Xenopus tropicalis | Y156 | EAIKCYTRGMH | 1 | Gallus gallus | Y200 | ALNRSYTKAYS | 1 | Homo sapiens | Y200 | ALNHNYAKAYA | 1 | Xenopus tropicalis | Y200 | ALDKNYTKAYA | 1 | Gallus gallus | Y200 | ALSRTYTKAYA | 1 | Mus musculus | Y200 | ALSRSYTKAYA | 1 | Rattus norvegicus | Y349 | LLDGSYSKAFA | 2 | Homo sapiens, Rattus norvegicus | Y349 | SLDASYCKAFA | 1 | Xenopus tropicalis | Y349 | LLDASYSKAFA | 1 | Gallus gallus | Y349 | VLDGSYSKAFA | 1 | Mus musculus |
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