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Fusion gene ID: 32334 |
FusionGeneSummary for RTF1_SNX24 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: RTF1_SNX24 | Fusion gene ID: 32334 | Hgene | Tgene | Gene symbol | RTF1 | SNX24 | Gene ID | 23168 | 28966 |
| Gene name | RTF1 homolog, Paf1/RNA polymerase II complex component | sorting nexin 24 | |
| Synonyms | GTL7|KIAA0252 | PRO1284|SBBI31 | |
| Cytomap | 15q15.1 | 5q23.2 | |
| Type of gene | protein-coding | protein-coding | |
| Description | RNA polymerase-associated protein RTF1 homologRtf1, Paf1/RNA polymerase II complex component, homologortholog of mouse gene trap locus 7 | sorting nexin-24sorting nexing 24 | |
| Modification date | 20180523 | 20180519 | |
| UniProtAcc | Q92541 | Q9Y343 | |
| Ensembl transtripts involved in fusion gene | ENST00000389629, ENST00000462276, | ENST00000511211, ENST00000261369, ENST00000513881, ENST00000395451, ENST00000506996, | |
| Fusion gene scores | * DoF score | 7 X 7 X 6=294 | 1 X 1 X 1=1 |
| # samples | 9 | 1 | |
| ** MAII score | log2(9/294*10)=-1.70781924850669 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(1/1*10)=3.32192809488736 | |
| Context | PubMed: RTF1 [Title/Abstract] AND SNX24 [Title/Abstract] AND fusion [Title/Abstract] | ||
| Functional or gene categories assigned by FusionGDB annotation | |||
| * DoF score (Degree of Frequency) = # partners X # break points X # cancer types ** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10) |
| Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Partner | Gene | GO ID | GO term | PubMed ID |
| Hgene | RTF1 | GO:0019827 | stem cell population maintenance | 19345177 |
| Hgene | RTF1 | GO:0032968 | positive regulation of transcription elongation from RNA polymerase II promoter | 20178742 |
| Hgene | RTF1 | GO:0045944 | positive regulation of transcription by RNA polymerase II | 20178742 |
| Fusion gene information from three resources (ChiTars (NAR, 2018), tumorfusions (NAR, 2018), Gao et al. (Cell, 2018)) * All genome coordinats were lifted-over on hg19. * Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser. |
| Data type | Source | Cancer type | Sample | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand |
| TCGA | LD | BRCA | TCGA-OL-A5D6-01A | RTF1 | chr15 | 41709511 | + | SNX24 | chr5 | 122272429 | + |
| * LD: Li Ding group's fusion gene list RV: Roel Verhaak group's fusion gene list ChiTaRs fusion database |
| Open reading frame (ORF) analsis of fusion genes based on Ensembl gene isoform structure. * Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser. |
| ORF | Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand |
| 5CDS-3UTR | ENST00000389629 | ENST00000511211 | RTF1 | chr15 | 41709511 | + | SNX24 | chr5 | 122272429 | + |
| 5CDS-3UTR | ENST00000389629 | ENST00000261369 | RTF1 | chr15 | 41709511 | + | SNX24 | chr5 | 122272429 | + |
| 5CDS-3UTR | ENST00000389629 | ENST00000513881 | RTF1 | chr15 | 41709511 | + | SNX24 | chr5 | 122272429 | + |
| 5CDS-3UTR | ENST00000389629 | ENST00000395451 | RTF1 | chr15 | 41709511 | + | SNX24 | chr5 | 122272429 | + |
| 5CDS-3UTR | ENST00000389629 | ENST00000506996 | RTF1 | chr15 | 41709511 | + | SNX24 | chr5 | 122272429 | + |
| 3UTR-3UTR | ENST00000462276 | ENST00000511211 | RTF1 | chr15 | 41709511 | + | SNX24 | chr5 | 122272429 | + |
| 3UTR-3UTR | ENST00000462276 | ENST00000261369 | RTF1 | chr15 | 41709511 | + | SNX24 | chr5 | 122272429 | + |
| 3UTR-3UTR | ENST00000462276 | ENST00000513881 | RTF1 | chr15 | 41709511 | + | SNX24 | chr5 | 122272429 | + |
| 3UTR-3UTR | ENST00000462276 | ENST00000395451 | RTF1 | chr15 | 41709511 | + | SNX24 | chr5 | 122272429 | + |
| 3UTR-3UTR | ENST00000462276 | ENST00000506996 | RTF1 | chr15 | 41709511 | + | SNX24 | chr5 | 122272429 | + |
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FusionProtFeatures for RTF1_SNX24 |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| RTF1 | SNX24 |
| Component of the PAF1 complex (PAF1C) which has multiplefunctions during transcription by RNA polymerase II and isimplicated in regulation of development and maintenance ofembryonic stem cell pluripotency. PAF1C associates with RNApolymerase II through interaction with POLR2A CTD non-phosphorylated and 'Ser-2'- and 'Ser-5'-phosphorylated forms andis involved in transcriptional elongation, acting bothindepentently and synergistically with TCEA1 and in cooperationwith the DSIF complex and HTATSF1. PAF1C is required fortranscription of Hox and Wnt target genes. PAF1C is involved inhematopoiesis and stimulates transcriptional activity ofKMT2A/MLL1; it promotes leukemogenesis through association withKMT2A/MLL1-rearranged oncoproteins, such as KMT2A/MLL1-MLLT3/AF9and KMT2A/MLL1-MLLT1/ENL. PAF1C is involved in histonemodifications such as ubiquitination of histone H2B andmethylation on histone H3 'Lys-4' (H3K4me3). PAF1C recruits theRNF20/40 E3 ubiquitin-protein ligase complex and the E2 enzymeUBE2A or UBE2B to chromatin which mediate monoubiquitination of'Lys-120' of histone H2B (H2BK120ub1); UB2A/B-mediated H2Bubiquitination is proposed to be coupled to transcription. PAF1Cis involved in mRNA 3' end formation probably through associationwith cleavage and poly(A) factors. In case of infection byinfluenza A strain H3N2, PAF1C associates with viral NS1 protein,thereby regulating gene transcription. Binds single-stranded DNA.Required for maximal induction of heat-shock genes. Required forthe trimethylation of histone H3 'Lys-4' (H3K4me3) on genesinvolved in stem cell pluripotency; this function is synergisticwith CXXC1 indicative for an involvement of a SET1 complex (Bysimilarity). {ECO:0000250, ECO:0000269|PubMed:19345177,ECO:0000269|PubMed:20178742}. | May be involved in several stages of intracellulartrafficking. {ECO:0000250}. |
| Retention analysis result of each fusion partner protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at . * Minus value of BPloci means that the break pointn is located before the CDS. |
| - In-frame and retained protein feature among the 13 regional features. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Protein feature | Protein feature note |
| - In-frame and not-retained protein feature among the 13 regional features. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Protein feature | Protein feature note |
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FusionGeneSequence for RTF1_SNX24 |
| For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. (nt: nucleotides, aa: amino acids) |
| * Fusion amino acid sequences. |
| * Fusion transcript sequences (only coding sequence (CDS) region). |
| * Fusion transcript sequences (Full-length transcript). |
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FusionGenePPI for RTF1_SNX24 |
| Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in . |
| Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160) |
| Hgene | Hgene's interactors | Tgene | Tgene's interactors |
| RTF1 | ARRB1, PAF1, CTR9, LEO1, TCEA1, CDC73, WDR61, NEDD4, HADHA, HADHB, PTPN11, APP, SUPT16H, CSNK2A1, SSRP1, TRPM8, CD81, DNMT3B, DNMT3A, SRPK2, ETF1, GSPT1, SNX6, YAP1, STAT1, DENND2D, CHD1, RPL37, BRD4, NUMA1, RPL35A, UBTF, ZC3H18, SRRM2, SUPT5H, NTRK1, PIP4K2A, ARRB2 | SNX24 | YWHAZ, SEPT2, CSNK1A1, CSNK1E, TSSK1B, C1orf111, FLNC, KPTN, ITFG2, UGP2, RAP1GDS1, XPO1, GAPVD1, LONRF2, FGFR2, SNX22, CSNK1D, PACS1, MLLT3, FNBP1L, MOB4, HINT1, STRN, YWHAG |
| - Retained PPIs in in-frame fusion. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Still interaction with |
| - Lost PPIs in in-frame fusion. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Interaction lost with |
| - Retained PPIs, but lost function due to frame-shift fusion. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Interaction lost with |
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RelatedDrugs for RTF1_SNX24 |
| Drugs targeting genes involved in this fusion gene. (DrugBank Version 5.1.0 2018-04-02) |
| Partner | Gene | UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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RelatedDiseases for RTF1_SNX24 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
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