The GABAB1 gene length based on the UCSC genome browser database was longer than the gene length found from the gene specific library due to two rare splicing junctions. The two rare junctions are the 3’ end junction (left end arrow in Figure S1 in Supplement 1) and the 5’ end junction (right end arrow in Figure S1 in Supplement 1). The junction area must have low expression because there is no identical junction finding. TopHat junction identification requires enough read depth to form coverage islands (http://tophat.cbcb.umd.edu/manual.html). Therefore, it is hard to find splice junctions from the less expressed area. Because reverse transcription using gene specific primer starts from the 3’ UTR to the 5’ end, it is also difficult to identify the 3’ end junction.
