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Fig. 6 | BMC Genomics

Fig. 6

From: ChimPipe: accurate detection of fusion genes and transcription-induced chimeras from RNA-seq data

Fig. 6

UBA2-WTIP chimeric transcript isoforms. a Experimentally validated UBA2-WTIP chimeric transcript isoforms. (Top) UBA2 and WTIP parent transcripts according to RefSeq version 74. Coding and UTR exonic sequences are displayed as thick and thin boxes, respectively, and introns as lines. The genomic strand of the transcripts is represented as an arrow on the 5’ end (Bottom) Chimeric RNAs with chimeric splice junctions are depicted as yellow dashed lines. On the left, list of cancer cell lines where each isoform was validated b UBA2-WTIP chimeric splice junction validation (Left) Primer design for validating the chimeric junction through RT-PCR plus Sanger sequencing. (Right) Chimeric junction validation in 4 different cell lines. The 72 bp amplicons proving the expression of the chimeric RNAs are highlighted in red. c UBA2-WTIP Q1 isoform protein coding potential. (Top) UBA2 and WTIP annotated start and stop codons represented over the transcript sequence. (Bottom) ORFs in the six possible frames. The selected ORF from the UBA2 annotated start codon to the WTIP annotated stop codon is highlighted in dark yellow. d Putative chimeric protein encoded by the UBA2-WTIP Q1 isoform. (Top) UBA2 and WTIP wild-type proteins. The exact position of the two protein breakpoints is indicated by yellow stars. Protein domains are depicted as boxes and triangles over the protein sequences. Thin boxes on the WTIP protein sequence correspond to low complexity regions. The x axis shows the amino acid position along the protein sequence. (Bottom) Putative UBA2-WTIP chimeric protein. Full-length domains are represented over the protein sequence. e The predicted 3D structure of the UBA2-WTIP chimeric protein as modelled by Phyre2 [51]. The chimeric protein part derived from UBA2 is depicted in blue and the one derived from WTIP in red

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