Characterization of exon 1B of PAX-5. (A) Heterogeneous transcription initiation. Total RNA (20 μg) isolated from the B-lymphoid BJA-B and KIS-1 cell lines as well as from control HeLa cells was analyzed by S1 nuclease protection assay with a DNA probe labeled at the EagI site in exon 1B. The S1-resistant DNA fragments were separated by electrophoresis together with a G+A sequence ladder obtained by partial depurination of the same end-labeled DNA probe. Arrowheads point to the most abundant transcription start sites. (B) DNA sequence of exon 1B. The most frequently used transcription start sites are denoted by arrows. Exon 1B sequences are shown in capital letters, whereas the flanking promoter and intron sequences are shown in lowercase letters. The numbers to the left refer to the nucleotide position relative to the first prominent transcription start site. The deduced amino acids of exon 1B, the reciprocal breakpoints [der(9) and der(14)] of the MLZ-1 translocation and the restriction sites relevant for probe design are indicated together with a consensus recognition sequence for the transcription factor Sp155 that was shown, by EMSA assay, to bind to this −40 promoter region in B-cell nuclear extract (data not shown). The invariant GT dinucleotide of the 5′ splice junction is underlined.