Table 2.
Verification of new junctions in conflict with known junctions
| Gene name | PlasmoDBv6.3 description | Score | Validated | Type | Frame-shift? | Isoform difference in bp (aa) | R | T | LT/ES | S |
|---|---|---|---|---|---|---|---|---|---|---|
| PFL1810w | Conserved Plasmodium protein | 1544.2 | Yes | 5′ss | Yes | 131 | 11 | 8 | 11 | 5 |
| 1283.2 | Yes | 5′ss | Yes | 218 | 3 | 0 | 3 | 1 | ||
| PFE0390w | Conserved Plasmodium protein | 1422.1 | Yes | 5′ss | Yes | 65 | 13 | 10 | 8 | 3 |
| PF13_0138 | MSF-1 like protein | 1372 | Yes | 5′ss | Yes | 55 | 7 | 5 | 3 | 7 |
| PFI0400c | Conserved Plasmodium membrane protein | 1369.8 | Yes | Exon skip | No | 126 (42) | 2 | 1 | 19 | 1 |
| PFF0290w | Long chain polyunsaturated fatty acid elongation enzyme | 1291.8 | Yes | Antisense | – | N/A | 9 | 6 | 14 | 5 |
| MAL13P1.225 | Thioredoxin | 1277.3 | Yes | Exon skip | Yes | 34 | 2 | 6 | 0 | 0 |
| PFE0055c | Heat shock protein | 1275.4 | Yes | 5′ss | No | 36 (12) | 54 | 14 | 3 | 8 |
| MAL8P1.126 | Serine protease | 1257.4 | Yes | 5′ss | Yes | 109 | 1 | 1 | 11 | 8 |
| PF10_0025 | PF70 protein | 1256.8 | Yes | 5′ss | Yes | 74 | 18 | 2 | 0 | 0 |
| PFD1050w | Alpha-tubulin II | 1243.2 | – | Antisense | – | N/A | 1 | 0 | 5 | 1 |
| MAL13P1.159a | Thioredoxin | 1239.9 | Yes | Exon skip | No | 33 (11) | 0 | 1 | 0 | 3 |
| PFC0780w | Cleavage and polyadenylation specific factor | 1231.7 | – | Antisense | – | N/A | 2 | 6 | 27 | 8 |
| PFD0775c | RNA binding protein | 1228.4 | Yes | Antisense | – | N/A | 1 | 6 | 8 | 0 |
| PF10_0194 | NoOP12-like protein | 1219.4 | Yes | Exon skip | Yes | 41 | 1 | 0 | 0 | 1 |
| PFL1440c | Conserved Plasmodium protein | 1217.6 | Yes | Exon skip | No | 57 (19) | 0 | 2 | 0 | 1 |
| PF11_0291 | Conserved Plasmodium protein | 1203.5 | Yes | 5′ss | No | 39 (13) | 1 | 0 | 0 | 5 |
| PFC0360w | Activator of HSP90 ATPase homolog 1-like protein | 1200.5 | Yes | Exon skip | Yes | 223 | 1 | 1 | 3 | 0 |
| PFC0495w | Plasmepsin VI | 1192.6 | Yes | Antisense | – | N/A | 0 | 0 | 8 | 3 |
| PF14_0394 | Conserved Plasmodium protein | 1190 | Yes | 5′ss | Yes | 98 | 2 | 4 | 5 | 0 |
| MAL13P1.146 | AMP deaminase | 1189.3 | Yes | antisense | – | N/A | 1 | 1 | 0 | 0 |
| PF11_0379 | Conserved Plasmodium protein | 1050.5 | Yes | Exon skip | No | 60 (20) | 1 | 0 | 0 | 1 |
| PFL1445w | Conserved Plasmodium protein | 1041.3 | Yes | Exon skip | Yes | 85 | 0 | 6 | 0 | 0 |
| MAL13P1.16 | SNARE protein | 1034.7 | Yes | Exon skip | No | 108 (36) | 0 | 0 | 0 | 4 |
| MAL13P1.277 | DNAJ-like protein | 1034.2 | Yes | Exon skip | Yes | 146 | 2 | 0 | 3 | 0 |
| PFF1210w | Phosphatidic acid phosphatase | 1032.4 | Yes | 5′ss | No | 66 (22) | 2 | 0 | 3 | 5 |
| PFB0600c | Conserved Plasmodium protein | 1026.1 | Yes | Antisense | – | N/A | 1 | 1 | 3 | 0 |
| PF14_0128 | Ubiquitin conjugating enzyme | 1018.5 | Yes | Exon skip | Yes | 104 | 0 | 1 | 3 | 0 |
| PF14_0316 | DNA topoisomerase II | 1011.4 | – | 5′ss | No | 459 (153) | 0 | 0 | 3 | 1 |
| PFB0279wa | Conserved Plasmodium protein | 1010.9 | Yes | 3′ss | Yes | 97 | 1 | 4 | 3 | 0 |
| PFL1465c | Heat shock protein hslv | 1004.5 | – | Exon skip | Yes | 40 | 0 | 2 | 0 | 4 |
| PF10_0372 | Antigen UB05 | 1004.4 | – | antisense | – | N/A | 0 | 1 | 0 | 1 |
| PF11_0182 | Conserved Plasmodium protein | 1004.1 | Yes | Exon skip | Yes | 56 | 0 | 0 | 5 | 0 |
| PFF0365c | G-protein associated signal transduction protein | 996.3 | – | Exon skip | Yes | 163 | 2 | 0 | 0 | 0 |
| PFB0445c | DEAD box helicase, UAP56 | 995.9 | – | 3′ss | Yes | 74 | 1 | 0 | 0 | 0 |
| PFD0895c | Bet3 transport protein | 991 | – | Antisense | – | N/A | 0 | 0 | 2 | 0 |
| PF10_0116 | Conserved Plasmodium protein | 989.9 | Yes | 5′ss | Yes | 74 | 0 | 0 | 2 | 0 |
| PF14_0604 | Conserved Plasmodium protein | 988.1 | Yes | Exon skip | Yes | 344 | 1 | 0 | 0 | 0 |
| PFI0560c | Conserved Plasmodium protein | 987.7 | Yes | Exon skip | Yes | 40 | 1 | 0 | 0 | 2 |
| PFB0550w | Peptide chain release factor subunit 1 | 985.5 | – | Exon skip | Yes | 155 | 0 | 0 | 2 | 0 |
| PF11_0355 | Conserved Plasmodium protein | 984.6 | Yes | Antisense | – | N/A | 1 | 1 | 0 | 0 |
Conflicts are ranked by lowest HMMSplicer score within the pair, and the black line denotes the operating HMMSplicer threshold of 1075.
aValidations shown in more detail in Figure 2. For all conflict types except antisense, the new junction was evaluated for maintenance of the ORF—nucleotide and amino acid (if applicable) differences between new and known isoforms are listed. Read counts for new junctions (normalized by the number of reads mapped by Bowtie for each timepoint) are listed for ring [R, (TP1, TP0, TP8)], troph [T, (TP2, TP16, TP24)], late troph/early schizont [LT/ES, (TP3, TP32)] and schizont [S, (TP4, TP40, TP48)] timepoints.