Alternative 5′ TSS and 3′ PAS identified by GIS-PET analysis. Examples of 5′ and 3′ alternative TSS and PAS found in the ENCODE regions are shown. (A) Three different transcripts encoding PSMB4 were identified by GIS-PET in MCF7 cells. The top one (transcript 2; 152 copies) is the normal transcript identical to the PSMB4 in the known gene track. The 3′ PAS variant (middle transcript 3; three copies) and 5′ TSS variant (bottom transcript 1; two copies) are supported by transfrags detected by tiling array approaches. They are shown within the dotted box. (B) 5′ TSS variants of CTSD defined by three and four copies of PETs are supported by GENCODE reference gene in HCT116 cells. (C) A 3′ PAS variant of BC028568 detected by GIS-PET was confirmed by cDNA PCR and sequencing, shown as forward (F) and reverse (R) read.
