Genomic cluster at the Sox4 locus. (a) The UCSC genome browser of the over-represented Sox4 genomic locus. SAGE tags were found in both directions within the Sox4 reference gene. (b) The SAGE expression profiles for each tag in the Sox4 locus. (c) The RT-qPCR validations of selected DETs at various loci within the Sox4 canonical gene. (d) The 3' RACE-Southern blotting analysis. The left panel of the figure shows the sizes of the bands and their corresponding tags. (d1-d3) Amplification of Sox4 sense transcripts (ASP); (d4) amplification of Sox4 antisense transcripts (SP). Tags with asterisks are DETs. Both (d5) and (d7) are positive controls exclusively generated from the sense strand of Psmb2 and Hmbs housekeeping genes (ASP), respectively. The corresponding (d6) and (d8) are the antisense expression (negative control) of Psmb2 and Hmbs (SP), respectively. (e) Northern analysis of total RNA isolated from pooled mouse cerebral cortices (N = 7). (f) The regionalized expression of Sox4 sense transcripts determined by ISH. The table consists of SAGE information for related Sox4 sense tags at rostral and caudal regions of the E15.5 cerebral cortex. (f1) and (f2) are sagittal sections obtained from E15.5 and E17.5 mouse brains, respectively. The figures show the expression of the Sox4 sense transcript variants. Arrows show brain regions with greater Sox4 sense expression. C: caudal region of the cerebral cortex; R: rostral region of the cerebral cortex.