full-length transcript reads of mouse hippocampus

Alternative splicing expands the functional repertoire of synaptic molecules and adds a layer of regulatory control and splicing factors are important for all aspects of neural development including neuronal health and accurate neuronal wiring. Kirrel3 is a single pass transmembrane protein in the immunoglobulin (Ig) superfamily mediating cell-adhesion and synapse formation via trans-cellular, homophilic interactions and is essential for normal brain connectivity in mice. The Kirrel3 gene is composed of many small exons predicted to undergo alternative splicing. In this project, we generated full-length transcript reads for the wildtype mouse hippocampus. We enriched the sequence collection for Kirrel3 transcripts by amplifying hippocampal cDNA in a mild stringency PCR using a target specific forward primer matching exon 2 of mouse Kirrel3 and a universal cDNA-reverse primer. Though Kirrel3 remains a small part of the total data set (~1%), we estimate that Kirrel3 transcripts were enriched at least 1000-fold compared to whole-transcriptome libraries for brain tissue.