Table 2 RNA-seq based predicted gene models
Description | Cuffcompare Code | U. maydis a | U. maydis a with FPKM >1 | U. hordei a | U. hordei a with FPKM >1 | S. reilianum a | S. reilianum a with FPKM >1 |
|---|---|---|---|---|---|---|---|
MIPS genes and genetic elements | Â | 6902 | Â | 7218 | Â | 6779 | Â |
PASA 5' UTR predictions (contain intron) | Â | 6016 (371) | Â | 5701 (262) | Â | 5971 (239) | Â |
PASA 3' UTR predictions (contain intron) | Â | 6064 (146) | Â | 5749 (133) | Â | 6051 (76) | Â |
PASA predicted transcript isoforms b | Â | 763 | Â | 681 | Â | 466 | Â |
Protein-coding genes and genetic elements | Â | 7665 | 7080 (6394) | 7899 | 6555 (5943) | 7245 | 6585 (6184) |
Single exon transfrag overlapping a reference exon and at least 10Â bp of a reference intron, indicating a possible pre-mRNA fragment | e | 1593 (1423) | 330 (298) | 1327 (1192) | 193 (181) | 1003 (910) | 183 (172) |
A transfrag falling entirely within a reference intron | i | 101 (88) | 39 (37) | 131 (96) | 9 (9) | 128 (90) | 29 (25) |
Potentially novel isoform (fragment): at least one splice junction is shared with a reference transcript | j | 659 (327) | 386 (242) | 407 (280) | 249 (191) | 337 (246) | 196 (157) |
Generic exonic overlap with a reference transcript | o | 227 (202) | 115 (107) | 164 (152) | 81 (78) | 133 (130) | 64 (62) |
Possible polymerase run-on fragment (within 2Kbases of a reference transcript) | p | 1875 (1287) | 755 (650) | 1413 (1055) | 473 (423) | 1435 (1026) | 554 (490) |
Exonic overlap with reference on the opposite strand | x | 8173 (3469) | 4500 (2624) | 5847 (2640) | 2332 (1606) | 6842 (3083) | 2768 (1949) |
Unknown, intergenic transcript | u | 3853 (3853) | 1832 (1832) | 2313 (2313) | 898 (898) | 2888 (2888) | 1331 (1331) |
Total Transcripts | Â | 24146 | 15,037 (12184) | 19501 | 10790 (9329) | 20011 | 11710 (10370) |