Table 2 Viral gene products and their expression levels.
From: Characterization of viral RNA splicing using whole-transcriptome datasets from host species
Species | Name | Regions | Involved Splicing sites | Nucleotide length (nt) | Effective length | FPKM (RSEM) | Relative expression level (%) | Product characters | NR Best hit overview | Putative Gene products |
|---|---|---|---|---|---|---|---|---|---|---|
AdDNV | AdDNV_NS_ORF1 | 225..866 | none | 642 | 403 | 18362.89 | 5.59 | Known | NS3 (AdDNV) | nonstructural protein NS3 |
AdDNV_NS_ORF1_I2 | join(225..430, 856) | AdDNV_I1 with depth 3 | 207 | 1 | 0 | 0.00 | Truncation (C-terminal) | NS3 (AdDNV) | nonstructural protein | |
AdDNV_NS_ORF2 | 856..2586 | none | 1731 | 1492 | 328484.48 | 100.00 | Known | NS1 (AdDNV) | nonstructural protein NS1 with rolling-circle replication motif, walker/NTPase motif and Parvo_NS1 region | |
AdDNV_NS_ORF3 | 875..1735 | none | 861 | 622 | 0 | 0.00 | Known | NS2 (AdDNV) | nonstructural protein NS2 | |
AdDNV_VP_ORF4 | c(2605..4398) | none | 1794 | 1555 | 65660.96 | 19.99 | Known | NS2 (AdDNV) | structural protein with Denso_VP4 region | |
AdDNV_VP_ORF5 | c(4424..5230) | none | 807 | 568 | 28846.15 | 8.78 | Known | putative structural protein (AdDNV_gp5) | structural protein 2 with Parvo_coat_N and PLA2 motif regions | |
AdDNV_VP_ORF5_I5 | c(join(4398..4402, 4534..5230)) | AdDNV_I5 with depth 18 | 702 | 463 | 8673.58 | 2.64 | Truncation (C-terminal); non-synonymous Mutation (G233V) | putative structural protein (AdDNV_gp5) | structural protein with Parvo_coat_N and PLA2 motif regions | |
AdDNV_VP_ORF6_I4 | c(join(2605..4259, 4435..5230)) | AdDNV_I4 with depth 135 | 2451 | 2212 | 164855.44 | 50.19 | Known; ORF shift (C-terminal); Non-synonymous mutation (E266Q) | structural protein VP1 (AdDNV) | structural protein VP1 with PLA2 motif, Parvo_coat_N and Denso_VP4 regions | |
AdDNV_VP_ORF6_I3 | c(join(2605..4244, 4534..5230)) | AdDNV_I3 with depth 7 | 2337 | 2098 | 7443.55 | 2.27 | Deletion | structural protein VP1 (AdDNV) | structural protein with PLA2 motif, Parvo_coat_N and Denso_VP4 regions | |
PcDNV | PcDNV_NS_ORF1 | 160..873 | none | 714 | 469 | 17344.87 | 6.42 | Known | NS3 (PcDNV) | nonstructural protein NS3 |
PcDNV_NS_ORF2 | 810..2516 | none | 1707 | 1462 | 15339.25 | 5.68 | Known | NS1 (PcDNV) | nonstructural protein NS1 with Parvo_NS1 region | |
PcDNV_NS_ORF2_I8 | join(810..1187, 1300..1701) | PcDNV_I8 with depth 1 | 780 | 535 | 59.63 | 0.02 | ORF shift (C-terminal) | NS1 (PcDNV) | nonstructural protein | |
PcDNV_NS_ORF3 | 880..1701 | none | 822 | 577 | 0 | 0.00 | Novel | Hypothetical protein MPH 12776 | nonstructural protein NS2 | |
PcDNV_NS_ORF6_I1 | join(160..216, 880..1701) | PcDNV_I1 with depth 43 | 879 | 634 | 18452.28 | 6.83 | ORF shift (C-terminal) | putative nonstructural protein (PcDNV, PcdVgp4) | nonstructural protein | |
PcDNV_NS_ORF6_I4 | join(160..303, 880..1701) | PcDNV_I4; splicing reads depth: 20 | 966 | 721 | 814.32 | 0.30 | ORF shift (C-terminal) | putative nonstructural protein (PcDNV, PcdVgp4) | nonstructural protein | |
PcDNV_NS_ORF7_I2 | join(160..220, 880..2516) | PcDNV_I2 with depth 275 | 1698 | 1453 | 182580.84 | 67.63 | Combination | NS1 (PcDNV) | nonstructural protein with Parvo_NS1 region | |
PcDNV_NS_ORF7_I3 | join(160..286, 880..2516) | PcDNV_I3 with depth 1 | 1764 | 1519 | 108.68 | 0.04 | Combination | NS1 (PcDNV) | nonstructural protein with Parvo_NS1 region | |
PcDNV_NS_ORF7_I5 | join(160..688, 880..2516) | PcDNV_I5 with depth 10 | 2166 | 1921 | 729.65 | 0.27 | Combination | NS1 (PcDNV) | nonstructural protein with Parvo_NS1 region | |
PcDNV_NS_ORF7_I6 | join(160..709, 880..2516) | PcDNV_I6 with depth 3 | 2187 | 1942 | 218.03 | 0.08 | Combination | NS1 (PcDNV) | nonstructural protein with Parvo_NS1 region | |
PcDNV_NS_ORF7_I7 | join(160..769, 880..2516) | PcDNV_I7 with depth 4 | 2247 | 2002 | 177.05 | 0.07 | Combination; Mutation (D204Y) | NS1 (PcDNV) | nonstructural protein with Parvo_NS1 region | |
PcDNV_VP_ORF4 | c(2531..4402) | none | 1872 | 1627 | 107736.5 | 39.91 | Known | putative structural protein (PcDNV, PcdVgp2) | structural protein with Denso_VP4 region | |
PcDNV_VP_ORF4_I9 | c(join(2602..2720, 2821..4402)) | PcDNV_I9 with depth 3 | 1701 | 1456 | 212.52 | 0.08 | ORF shift (C-terminal) | putative structural protein (PcDNV, PcdVgp2) | structural protein | |
PcDNV | PcDNV_VP_ORF4_I10 | c(join(2531..2739, 2821..4402)) | PcDNV_I10 with depth 2 | 1791 | 1546 | 0 | 0.00 | Deletion | putative structural protein (PcDNV, PcdVgp2) | structural protein |
PcDNV_VP_ORF4_I11 | c(join(2531..3720, 3907..4402)) | PcDNV_I11 with depth 1 | 1686 | 1441 | 3190.9 | 1.18 | Deletion | putative structural protein (PcDNV, PcdVgp2) | structural protein | |
PcDNV_VP_ORF4_I12 | c(join(3789..3823, 3898..4402)) | PcDNV_I12 with depth 291 | 540 | 295 | 319.37 | 0.12 | ORF shift (C-terminal) | putative structural protein (PcDNV, PcdVgp2) | structural protein | |
PcDNV_VP_ORF4_I13 | c(join(3789..3823, 3907..4402)) | PcDNV_I13 with depth 44 | 531 | 286 | 210.38 | 0.08 | ORF shift (C-terminal) | putative structural protein (PcDNV, PcdVgp2) | structural protein | |
PcDNV_VP_ORF4_I15 | c(join(4206..4248, 4341..4402)) | PcDNV_I15 with depth 1 | 105 | 0 | 0 | 0.00 | ORF shift (C-terminal) | putative structural protein (PcDNV, PcdVgp2) | structural protein | |
PcDNV_VP_ORF5 | c(4392..5222) | none | 831 | 586 | 0 | 0.00 | Known | putative structural protein (PcDNV, PcdVgp1) | structural protein with PLA2 motif and Parvo_coat_N regions | |
PcDNV_VP_ORF5_I19 | c(join(4336..4340, 4424..5222)) | PcDNV_I19 with depth 1 | 804 | 559 | 0 | 0.00 | Truncation (C-terminal) | putative structural protein (PcDNV, PcdVgp1) | structural protein with PLA2 motif and Parvo_coat_N regions | |
PcDNV_VP_ORF5_I20(MI1) | c(join(4392..4402, 4481..5222)) | PcDNV_I20 with depth 429; or PcDNV_MI2 with depth 3 | 753 | 508 | 1659.65 | 0.61 | Deletion | putative structural protein (PcDNV, PcdVgp1) | structural protein with PLA2 motif and Parvo_coat_N regions | |
PcDNV_VP_ORF5_I21 | c(join(4392..4774, 4853..5222)) | PcDNV_I21 with depth 2 | 753 | 508 | 119.93 | 0.04 | Deletion | putative structural protein (PcDNV, PcdVgp1) | structural protein with PLA2 motif and Parvo_coat_N regions | |
PcDNV_VP_ORF8_I14 | c(join(2531..4197, 4481..5222)) | PcDNV_I14 with depth 3 | 2409 | 2164 | 614.74 | 0.23 | Combination | putative structural protein (PcDNV, PcdVgp2) | structural protein with PLA2 motif, Parvo_coat_N and Denso_VP4 regions | |
PcDNV_VP_ORF8_I16 | c(join(2531..4248, 4424..5222)) | PcDNV_I16 with depth 1994 | 2517 | 2272 | 185726.27 | 68.79 | Combination; Mutation (E267K) | putative structural protein (PcDNV, PcdVgp2) | structural protein with PLA2 motif, Parvo_coat_N and Denso_VP4 regions | |
PcDNV_VP_ORF8_I17 | c(join(2531..4248, 4481..5222)) | PcDNV_I17 with depth 7 | 2460 | 2215 | 166.07 | 0.06 | Combination | putative structural protein (PcDNV, PcdVgp2) | structural protein with PLA2 motif, Parvo_coat_N and Denso_VP4 regions | |
PcDNV_VP_ORF9_I18 | c(join(4177..4280, 4424..5222)) | PcDNV_I18 with depth 3 | 903 | 658 | 103.55 | 0.04 | ORF shift (C-terminal) | putative structural protein (PcDNV, PcdVgp1) | structural protein with PLA2 motif and Parvo_coat_N regions | |
PcDNV_VP_ORF10_I22 | c(join(4481..4774, 4899..5222)) | PcDNV_I22 with depth 6 | 618 | 373 | 203.45 | 0.08 | ORF shift (C-terminal) | putative structural protein (PcDNV, PcdVgp1) | structural protein | |
PcDNV_VP_ORF10_I23 | c(join(4481..4774, 4959..5222)) | PcDNV_I23 with depth 1699 | 558 | 313 | 269981.32 | 100.00 | ORF shift (C-terminal) | putative structural protein (PcDNV, PcdVgp1) | structural protein |
