Molecular analysis of the BCOR-RARA fusion transcript. (A) Sequence analysis of the BCOR-RARA transcript at the junction site. The junction of the BCOR and RARA transcripts is indicated by a bold arrowhead. Rearrangement between BCOR exon 12 and RARA exon 3 resulting in an in-frame BCOR-RARA fusion protein. The DNA and amino acid sequences spanning the junction of the BCOR and RARA genes (in bold and normal characters, respectively) are shown below. (B) Schematic diagram of RARA, BCOR, and the BCOR-RARA fusion protein. The break point is indicated by the black line. Primer locations for RT-PCR are shown as arrows. Domains of BCOR-RARA are indicated as follows: BCOR BCL6-binding domain (BBD), ankyrin repeats (AR), DNA-binding domain (DBD), and ligand-binding domain (LBD). (C) RT-PCR analysis of BCOR-RARA fusion transcripts. BCOR-RARA transcripts were detected in cDNA derived from the patient's bone marrow cells on diagnosis, which also contained normal cells with intact BCOR. The control was cDNA derived from EOL1. Primer pairs are shown in the lower lane. A vertical line was inserted to indicate a repositioned gel lane. (D) Long-distance RT-PCR of BCOR-RARA transcripts. No alternative splicing variant was detected.