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mutLBSgeneDB |
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| Gene summary for RTF1 |
 Gene summary |
| Basic gene Info. | Gene symbol | RTF1 |
| Gene name | Rtf1, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae) | |
| Synonyms | GTL7|KIAA0252 | |
| Cytomap | UCSC genome browser: 15q15.1 | |
| Type of gene | protein-coding | |
| RefGenes | NM_015138.4, | |
| Description | RNA polymerase-associated protein RTF1 homologortholog of mouse gene trap locus 7 | |
| Modification date | 20141207 | |
| dbXrefs | MIM : 611633 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000137815 | ||
| HPRD : 11071 | ||
| Vega : OTTHUMG00000133744 | ||
| Protein | UniProt: Q92541 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_RTF1 | |
| BioGPS: 23168 | ||
| Pathway | NCI Pathway Interaction Database: RTF1 | |
| KEGG: RTF1 | ||
| REACTOME: RTF1 | ||
| Pathway Commons: RTF1 | ||
| Context | iHOP: RTF1 | |
| ligand binding site mutation search in PubMed: RTF1 | ||
| UCL Cancer Institute: RTF1 | ||
| 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:0019827 | stem cell maintenance | 19345177 | GO:0032968 | positive regulation of transcription elongation from RNA polymerase II promoter | 20178742 | GO:0045944 | positive regulation of transcription from RNA polymerase II promoter | 20178742 |
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| Ligand binding site mutations for RTF1 |
| 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 | Y400 | R401W | BLCA | 1 | Q445 | F447I | SKCM | 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 RTF1 |
| 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 | Y400 | R401W | -0.79523068 | Q445 | F447I | -0.72663386 |
| (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 RTF1 from PDB |
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| Differential gene expression and gene-gene network for RTF1 |
| 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 RTF1 |
| 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 RTF1 |
| 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 RTF1 go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | III | Peptide ligand (GLY,SER,ARG,THR,PRO,MET,TYR,GLY) | 4l1u | B | Y400 Q445 | III | Peptide ligand (SER,GLY,SER,ARG,THR,PRO,MET,TYR,GLY,SER,GLN) | 4l1u | C | Y400 Q445 | III | Peptide ligand (ARG,THR,PRO,MET,TYR) | 4l1u | E | Y400 Q445 | III | Peptide ligand (SER,ARG,THR,PRO,MET) | 4l1u | F | Y400 Q445 |
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| Conservation information for LBS of RTF1 |
| Multiple alignments for Q92541 in multiple species |
| LBS | AA sequence | # species | Species | E440 | RVFRLEFVSNQ | 2 | Homo sapiens, Mus musculus | E440 | RVFRLEFISNQ | 1 | Drosophila melanogaster | F437 | NDQRVFRLEFV | 2 | Homo sapiens, Mus musculus | F437 | TQERVFRLEFI | 1 | Drosophila melanogaster | F441 | VFRLEFVSNQE | 2 | Homo sapiens, Mus musculus | F441 | VFRLEFISNQE | 1 | Drosophila melanogaster | G390 | CFVRIGIGNHN | 2 | Homo sapiens, Mus musculus | G390 | CFVRISIGNNG | 1 | Drosophila melanogaster | G392 | VRIGIGNHNSK | 2 | Homo sapiens, Mus musculus | G392 | VRISIGNNGQK | 1 | Drosophila melanogaster | I391 | FVRIGIGNHNS | 2 | Homo sapiens, Mus musculus | I391 | FVRISIGNNGQ | 1 | Drosophila melanogaster | N393 | RIGIGNHNSKP | 2 | Homo sapiens, Mus musculus | N393 | RISIGNNGQKP | 1 | Drosophila melanogaster | N444 | LEFVSNQEFTE | 2 | Homo sapiens, Mus musculus | N444 | LEFISNQEFTE | 1 | Drosophila melanogaster | P398 | NHNSKPVYRVA | 2 | Homo sapiens, Mus musculus | P398 | NNGQKPVYRVA | 1 | Drosophila melanogaster | Q445 | EFVSNQEFTES | 2 | Homo sapiens, Mus musculus | Q445 | EFISNQEFTEN | 1 | Drosophila melanogaster | R366 | RVRLSRHKLER | 2 | Homo sapiens, Mus musculus | R366 | KLRLSRYKMER | 1 | Drosophila melanogaster | R435 | HGNDQRVFRLE | 2 | Homo sapiens, Mus musculus | R435 | HGTQERVFRLE | 1 | Drosophila melanogaster | S443 | RLEFVSNQEFT | 2 | Homo sapiens, Mus musculus | S443 | RLEFISNQEFT | 1 | Drosophila melanogaster | V399 | HNSKPVYRVAE | 2 | Homo sapiens, Mus musculus | V399 | NGQKPVYRVAE | 1 | Drosophila melanogaster | V442 | FRLEFVSNQEF | 2 | Homo sapiens, Mus musculus | V442 | FRLEFISNQEF | 1 | Drosophila melanogaster | Y400 | NSKPVYRVAEI | 2 | Homo sapiens, Mus musculus | Y400 | GQKPVYRVAEI | 1 | Drosophila melanogaster |
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