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Fusion gene ID: 30169 |
FusionGeneSummary for RAD50_SLC22A4 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: RAD50_SLC22A4 | Fusion gene ID: 30169 | Hgene | Tgene | Gene symbol | RAD50 | SLC22A4 | Gene ID | 10111 | 6583 |
| Gene name | RAD50 double strand break repair protein | solute carrier family 22 member 4 | |
| Synonyms | NBSLD|RAD502|hRad50 | DFNB60|OCTN1 | |
| Cytomap | 5q31.1 | 5q31.1 | |
| Type of gene | protein-coding | protein-coding | |
| Description | DNA repair protein RAD50RAD50 homolog, double strand break repair protein | solute carrier family 22 member 4ET transporterdeafness, autosomal recessive 60ergothioneine transporterintegral membrane transport proteinorganic cation/carnitine transporter 1solute carrier family 22 (organic cation/ergothioneine transporter), mem | |
| Modification date | 20180523 | 20180522 | |
| UniProtAcc | Q92878 | Q9H015 | |
| Ensembl transtripts involved in fusion gene | ENST00000378823, ENST00000265335, ENST00000487596, | ENST00000200652, ENST00000491257, | |
| Fusion gene scores | * DoF score | 5 X 4 X 5=100 | 3 X 2 X 3=18 |
| # samples | 5 | 3 | |
| ** MAII score | log2(5/100*10)=-1 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(3/18*10)=0.736965594166206 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0 | |
| Context | PubMed: RAD50 [Title/Abstract] AND SLC22A4 [Title/Abstract] AND fusion [Title/Abstract] | ||
| Functional or gene categories assigned by FusionGDB annotation | DDR (DNA damage repair) gene involved fusion gene, retained protein feature but frameshift. | ||
| * 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 | RAD50 | GO:0000019 | regulation of mitotic recombination | 8756642 |
| Hgene | RAD50 | GO:0006281 | DNA repair | 9705271 |
| Hgene | RAD50 | GO:0006310 | DNA recombination | 9705271 |
| Hgene | RAD50 | GO:0006974 | cellular response to DNA damage stimulus | 17500065 |
| Hgene | RAD50 | GO:0007004 | telomere maintenance via telomerase | 9705271 |
| Hgene | RAD50 | GO:0031954 | positive regulation of protein autophosphorylation | 15790808 |
| Hgene | RAD50 | GO:0033674 | positive regulation of kinase activity | 15790808 |
| Hgene | RAD50 | GO:1904354 | negative regulation of telomere capping | 17694070 |
| Tgene | SLC22A4 | GO:0015697 | quaternary ammonium group transport | 9426230 |
| Tgene | SLC22A4 | GO:0015879 | carnitine transport | 16729965 |
| 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 | RV | UCEC | TCGA-SL-A6J9-01A | RAD50 | chr5 | 131973915 | + | SLC22A4 | chr5 | 131670411 | + |
| * 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 |
| Frame-shift | ENST00000378823 | ENST00000200652 | RAD50 | chr5 | 131973915 | + | SLC22A4 | chr5 | 131670411 | + |
| 5CDS-intron | ENST00000378823 | ENST00000491257 | RAD50 | chr5 | 131973915 | + | SLC22A4 | chr5 | 131670411 | + |
| Frame-shift | ENST00000265335 | ENST00000200652 | RAD50 | chr5 | 131973915 | + | SLC22A4 | chr5 | 131670411 | + |
| 5CDS-intron | ENST00000265335 | ENST00000491257 | RAD50 | chr5 | 131973915 | + | SLC22A4 | chr5 | 131670411 | + |
| intron-3CDS | ENST00000487596 | ENST00000200652 | RAD50 | chr5 | 131973915 | + | SLC22A4 | chr5 | 131670411 | + |
| intron-intron | ENST00000487596 | ENST00000491257 | RAD50 | chr5 | 131973915 | + | SLC22A4 | chr5 | 131670411 | + |
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FusionProtFeatures for RAD50_SLC22A4 |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| RAD50 | SLC22A4 |
| Component of the MRN complex, which plays a central rolein double-strand break (DSB) repair, DNA recombination,maintenance of telomere integrity and meiosis. The complexpossesses single-strand endonuclease activity and double-strand-specific 3'-5' exonuclease activity, which are provided by MRE11.RAD50 may be required to bind DNA ends and hold them in closeproximity. This could facilitate searches for short or longregions of sequence homology in the recombining DNA templates, andmay also stimulate the activity of DNA ligases and/or restrict thenuclease activity of MRE11 to prevent nucleolytic degradation pasta given point (PubMed:11741547, PubMed:9590181, PubMed:9705271,PubMed:9651580). The complex may also be required for DNA damagesignaling via activation of the ATM kinase (PubMed:15064416). Intelomeres the MRN complex may modulate t-loop formation(PubMed:10888888). {ECO:0000269|PubMed:10888888,ECO:0000269|PubMed:11741547, ECO:0000269|PubMed:15064416,ECO:0000269|PubMed:9590181, ECO:0000269|PubMed:9651580,ECO:0000269|PubMed:9705271}. | Sodium-ion dependent, low affinity carnitinetransporter. Probably transports one sodium ion with one moleculeof carnitine. Also transports organic cations such astetraethylammonium (TEA) without the involvement of sodium.Relative uptake activity ratio of carnitine to TEA is 1.78. A keysubstrate of this transporter seems to be ergothioneine (ET).{ECO:0000269|PubMed:10215651, ECO:0000269|PubMed:15795384}. |
| 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 RAD50_SLC22A4 |
| 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 RAD50_SLC22A4 |
| 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 |
| RAD50 | HNF4A, H2AFX, BLM, BRCA1, MRE11A, NBN, ATM, MLH1, MSH2, MSH6, RFC1, TERF2, TERF2IP, MDC1, RINT1, CHEK2, RECQL5, USP11, USP42, USP53, DDX1, PHF1, PAXIP1, GEMIN2, DCLRE1B, KAT5, TERF1, HDAC5, EP300, BARD1, RBBP8, SMARCAD1, SKP2, SIRT7, HNRNPA1, MDM2, TFAP4, DCLRE1C, NOP56, NCSTN, HNRNPR, RBL2, RNF8, PAN2, FBXO6, RPA1, RPA2, RPA3, PASK, ATRX, CUL7, OBSL1, EED, RNF2, SUMO2, SIRT6, ILF2, ILF3, MCM5, ZNF511, MAF1, ZFAND2B, CELA2B, LRRC39, FAM219A, MDM4, CHAMP1, SMC5, NTRK1, SCARNA22, MED23, OFD1, FGFR1OP, CEP128, RPGRIP1L, HIST1H3E, HSF2, SLC33A1, TMEM132A, GLI1, FOXL1, USP4, ESR1, SNW1, CDC5L, RNF126, NFATC2, HIST3H3, DUSP23, DUSP28, RGS20, BMP1, ATG14, RAB39B, HS1BP3, FAM196A, RAD50, C15orf26, CCDC150, BRIP1, SPTA1, DLST, HDAC6, MCM9, MCM8 | SLC22A4 | PDZK1 |
| - 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 RAD50_SLC22A4 |
| 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 |
| Tgene | SLC22A4 | Q9H015 | DB00583 | L-Carnitine | Solute carrier family 22 member 4 | small molecule | approved|investigational |
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RelatedDiseases for RAD50_SLC22A4 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Hgene | RAD50 | C0004096 | Asthma | 1 | CTD_human |
| Tgene | SLC22A4 | C0010246 | Coxsackievirus Infections | 1 | CTD_human |
| Tgene | SLC22A4 | C0014378 | Enterovirus Infections | 1 | CTD_human |
| Tgene | SLC22A4 | C0027059 | Myocarditis | 1 | CTD_human |
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