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Table 3 Expression of ncRNAs in AltDE and AltDE1

From: RNA sequencing provides evidence for functional variability between naturally co-existing Alteromonas macleodii lineages

Strain     AltDE1 (RPKM) AltDE (RPKM)
ncRNA Start* End* Length (bp) RM-13°C RM-25°C MMG-25°C STR-25°C RM-13°C RM-25°C MMG-25°C STR-25°C
TPP riboswitch 152009 152120 111 87.5 35.0 289.9 912.0 100.9 0.0 356.9 461.9
G.II catalytic intron 167749 167819 70 91.0 0.0 114.0 0.0 -- -- -- --
Ribonuclease P 891973 892323 350 39927.4 30365.4 77672.5 925092.0 30718.2 26092.6 98179.9 107875.0
AltRNa1 1066159 1066582 424 20613.4 28361.8 143798.5 90692.6 5133.8 5444.4 61103.3 48553.8
Small SRP 1239467 1239563 96 67.0 80.0 502.0 0.0 63.9 116.4 97.6 0.0
TPP riboswitch 1258919 1259022 103 31.1 0.0 234.1 0.0 123.9 138.8 58.2 235.0
Trp leader 1634441 1634532 91 35.1 42.1 0.0 0.0 0.0 0.0 0.0 0.0
tmRNA 2126827 2127186 359 13072.1 11252.9 56769.8 775951.9 12566.4 10450.9 53778.6 72022.3
His leader 2929451 2929568 117 109.5 0.0 68.8 0.0 6.5 47.5 39.9 80.4
6S RNA 3357865 3358047 182 423.6 529.1 1241.9 558.1 32.9 96.1 161.2 488.1
Thr leader 3471219 3471330 111 64.5 75.2 0.0 0.0 16.1 0.0 0.0 291.4
yybP-ykoY leader 3679956 3680065 109 117.5 70.4 147.6 464.2 -- -- -- --
Alpha RBS 4064601 4064678 77 27744.0 30238.6 5827.2 1964.1 21842.2 19355.7 8201.8 6306.7
AltRNa2 4312594 4312902 309 292.6 1215.7 2206.4 41812.3 949.2 1393.1 1168.1 1047.9
G.II catalytic intron 4420296 4420366 70 45.5 327.3 0.0 0.0 -- -- -- --
G.II catalytic intron D1-D4 4421022 4421188 166 425.5 394.3 291.6 0.0 -- -- -- --
  1. *AltDE1 was used as a reference to the location of the ncRNA. Expression levels are reported here as the normalized RPKM values. RM, nutrient rich marine medium; MMG, minimal medium with 1% glucose; STR, starvation; TPP: thiamine pyrophosphate; SRP: Signal recognition particle; Trp leader: Tryptophan operon leader; tmRNA: Transfer-messenger RNA; His leader: Histidine operon leader; Thr leader: Threonine operon leader; RBS: Ribosome binding site.