Provided herein are systems and methods for analyzing biomolecules (e.g.,
nucleic acid molecules, proteins). A method of
nucleic acid analysis can comprise: (a) providing a sample comprising a
cell comprising a target
polynucleotide comprising a first
exon segment and a second
exon segment, wherein the first
exon segment and the second exon segment flank opposite ends of a splice junction site of the target
polynucleotide. The method can further comprise (b) contacting the
cell with: (i) a first probe, wherein the first probe hybridizes to a first target sequence of the first exon segment, and (ii) a second probe, wherein the second probe hybridizes to a second target sequence of the second exon segment. The method can further comprise (c) linking the first probe and the second probe together, thereby generating a probe-linked
nucleic acid molecule comprising the first probe and the second probe. The method can further comprise (d) identifying a sequence of the probe-linked
nucleic acid molecule or derivative thereof, thereby locating the splice junction site of the target
polynucleotide.