Characterization of HOXD-AS1 transcript. (A) Positions of different primer pairs targeting different annotated transcripts in the intergenic locus between HOXD1 and HOXD3 genes (Locus primers track, green) mapped in UCSC browser relative to HOXD-AS1 RefSeq NR_1104661.1 (orange) and UCSC Genes track LOC401022 transcripts (blue). (B) SH-SY5Y cells were induced to differentiate with RA and total RNA was extracted at the time-points of 0 hours (uninduced), 6, 24 and 120 hours. The relative levels of the different transcripts amplified by the indicated primer pairs were measured by qRT-PCR and expressed as fold change relative to the uninduced (0 h) time-point. (C) The relative expression levels of the indicated target transcripts in uninduced SH-SY5Y cells were measured by qRT-PCR. (D) Effect of siRNA#1 and siRNA#2 (see Materials and Methods) on the relative levels of various parts of HOXD-AS1 transcript as determined by qRT-PCR.