Table 3. Upregulation of transcript abundance by CTR9 RNAi.
| geneID | rpkm | CTR9/WT | features | |
| Procyclin locus | ||||
| Tb927.6.520 | EP3-2 procyclin | 36.4 | 17 | pol I |
| Tb927.6.510 | GPEET2 procyclin | 31.3 | 14 | pol I |
| Tb927.10.10240 | PAG1 | 2.5 | 48 | pol I |
| Tb927.10.10220 | PAG2 | 1.9 | 57 | pol I |
| Tb927.6.530 | PAG3 | 12.2 | 11 | pol I |
| Tb927.10.10210 | PAG4 | 2.6 | 31 | pol I |
| Tb927.10.10230 | PAG5 | 2.3 | 37 | pol I |
| Near rRNA locus | ||||
| Tb09.v2.0450 | Unlikely ORF | 2.0 | 17.0 | rRNA locus |
| Tb927.2.1470 | hypothetical conserved | 3.6 | 10.0 | 0 kb, rRNA |
| Tb927.1.3750 | hypothetical conserved | 8.7 | 7.7 | 0 kb, rRNA |
| Tb927.3.3430 | hypothetical conserved | 7.4 | 7.6 | 0 kb, rRNA |
| Other | ||||
| Tb927.5.4020 | hypothetical | 4.0 | 13** | 3 kb |
| Tb927.8.6570 | hypothetical conserved | 3.4 | 10 | 0 kb |
| Tb927.8.510 | hypothetical | 1.1 | 21* | 6 kb |
| Tb927.10.4390 | hypothetical | 3.6 | 7.8 | 3 kb |
| Tb927.10.4380 | hypothetical | 0.8 | 39* | 2 kb, ESAG |
| Tb927.10.12270 | hypothetical conserved | 4.1 | 14* | 1 kb |
| Tb927.10.1760 | hypothetical | 1.7 | 20* | 0 kb |
| Tb927.11.9380 | hypothetical | 1.1 | 14* | 0 kb |
| Tb927.1.2020 | hypothetical | 3.3 | 11 | 0 kb |
| Tb927.11.11990 | hypothetical | 1.3 | 11 | 0 kb |
| Tb927.8.480 | phosphatase | 26.6 | 9.8 | 0 kb |
| Tb927.2.3330 | hypothetical | 5.3 | 8.7 | 0 kb |
| Tb927.7.310 | hypothetical conserved | 8.9 | 8.1 | 0 kb |
| Tb927.10.9550 | hypothetical | 0.6 | 8.4 | 6 kb |
| Tb927.8.5930 | hypothetical | 0.3 | 9.4 | stop/start |
| Tb927.3.650 | hypothetical conserved | 25.8 | 8.1 | 11 kb |
| Tb927.7.2430 | Long poly(AT) tracts | 0.2 | 16.9* | repetitive |
| Tb927.11.4600 | hypothetical | 1.0 | 18.5 | None |
| Tb927.10.10040 | hypothetical | 4.1 | 13.3 | None |
| Tb927.3.2880 | hypothetical conserved | 7.6 | 11.7 | None |
| Tb927.10.9030 | hypothetical conserved | 10.7 | 9.7 | None |
| Tb927.3.3570 | hypothetical conserved | 10.8 | 9.1 | None |
| Tb927.11.7260 | hypothetical conserved | 7.8 | 8.7 | None |
| Tb927.6.4790 | hypothetical conserved | 33.9 | 8.2 | None |
| Tb11.v4.0003 | hypothetical | 2.3 | 8.2 | None |
| Tb07.26A24.210 | hypothetical | 4.7 | 7.8 | None |
| Tb927.3.2370 | hypothetical conserved | 36.0 | 7.8 | None |
| Tb927.10.260 | hypothetical conserved | 29.4 | 7.7 | None |
| Tb927.10.7720 | hypothetical conserved | 35.7 | 7.6 | None |
| Tb927.11.12330 | hypothetical conserved | 24.5 | 7.5 | None |
| Tb927.2.2070 | hypothetical | 3.5 | 8.6 | |
| Tb927.6.4570 | hypothetical conserved | 13.8 | 8.6 | start |
One representative of each of the procyclin locus ORFs is shown, along with the 36 other ORFs showing the greatest increases in RNA after CTR9 RNAi. “rpkm” is the reads per kilobase per million reads seen in poly(A)+RNA from normal (wild-type) cells, taken from [30]; the median for all ORFs is 30.6. “CTR9/WT” shows the fold change in rpkm after RNAi (2 significant figures); **no signal was seen on a Northern blot using an ORF probe; *no RNA detected by reverse transcription and PCR targeting the ORF. “Features” indicates transcription by polymerase I (pol I), and the distance of the 3′ end of the locus mRNA from a convergent transcription stop area – “0 kb” indicates that this is the last ORF in a transcription unit. “0 kb, rRNA” indicats that the ORF is the last on a pol II transcription unit, next to an rRNA locus read in the opposite direction. “2 kb, ESAG” is a gene upstream of an ESAG. An rpkm of 20 corresponds to 1 mRNA per cell, which is difficult to detect by Northern blotting.