Table 3. Location of Northern-verified sRNAs expressed in Synechococcus WH7803.
| IGR | Transcript start | Flanking genes | Orientation | Genomic island | Expression | Comparative prediction |
|---|---|---|---|---|---|---|
| i235 | gtcttaagatcagatGAACGACCAA | syn_0290; syn_0291 | ← → → | No | Cold down | a,b,c,d |
| i781 | ./. | syn_0921; syn_0922 | → ← → | 3 | Cold down | a,b,c,d |
| i804 | tggcaagatgttgagGTGAAGCAGC | syn_0948; dcd | → ← → | 3 | Cold up | ./. |
| i824 | cgtgacagtgcatttGTGTGAGGAA | syn_0975; syn_0976 | → ← → | 3 | Cold down | a,b,c,d, yfr2b |
| i1720 | gtgtaagatgttttaTTGGCCTGGC | rpoB; tatD | ←←← | No | Cold down | a,b,c,d |
| i1971 | tcttaagttgcattcGTGTGAGGAG | syn_2370; rplL | → → ← | No | Cold down | a,b,c,d, yfr2a |
| i854 | ./. | syn_1011; syn_1012 | ←← → | 3 | — Fe up | b |
| i855a | tgctctattgagagcCAATCTCAAGT | syn_1012; syn_1013 | → ← → | 3 | — Fe up | d |
| i95a | ./. | syn_0111; syn_0112 | ←←← | No | — P up | ./. |
| i399 | tcatggtccggctcgATTCGCCAGCA | syn_0484; cpeB | ← → → | PBS | High light down | ./. |
| i403 | gctcctaaacttcgt(t)GCGTCAATTC | cpeZ; mpeU | → ←← | PBS | High light up | ./. |
| i405 | ./. | syn_0490; cpeY | → ← → | PBS | High light down | ./. |
| i695 | ./. | syn_0824; syn_0825 | → ← → | No | High light up | ./. |
| i845 | ./. | syn_1000; syn_1001 | ←← → | 3 | High light up | ./. |
| i1692 | ctgagaatcattggtGATCGGCCTC | apcE; apcA | → → → | No | High light down | a,b,c,d |
| i297 | ./. | nctP; psbA | ← → ← | No | — | a,b,c,d |
| i298 | gatagaagtgaaggcCGATGGCGTT | psbA; syn_0367 | ← → → | No | — | a,b,c,d |
| i308 | ./. | fusA; rpsG | ← → ← | No | — | a,b,c,d |
| i357 | ./. | rplC; syn_0435 | ← → → | No | — | a,b,c,d |
| i519a | cgagacagtgatcaaGGTCTAAGAG | rpoD; priA | ← → → | No | — | a,d |
| i583 | ./. | syn_0683; csoS1/ccmK2 | → ← → | No | — | ./. |
| i812 | ggttatctgtgatggAGGGAGCGAA | syn_0956; syn_0957 | → → ← | 3 | — | ./. |
| i834 | cgccagggtgtggggATCCGCGCCA | znuC; syn_0990 | → ← → | 3 | — | ./. |
| i1017 | cctaaattgattgttGAACTACCCC | purK; syn_1207 | → → ← | No | — | b,d, 6SRNA |
| i1255 | ./. | syn_1498; syn_1499 | ←← → | 7 | — | ./. |
| i1331 | ./. | guaB;trxA | → → → | No | — | a,b,c,d, yfr1 |
| i1535 | ./. | syn_1835; gltX | → → → | No | — | b,c,d |
| i1642 | gcgatcgtgagtgctGGACGAGCCA | kaiA; rplU | ← → → | No | — | b,c,d |
| i1684 | ./. | atpA; atpD | ← → ← | No | — | ./. |
| i1720 | ./. | rpoB; tatD | ← → ← | No | — | a,b,c,d |
| i1825a | cctagaacagaatcaCTTCGGCCTT | syn_2189; syn_2190 | → → → | No | — | b,c |
| i1869 | cgttatggttcaagtGTTCAGAGCG | syn_2237; syn_2238 | → ← → | No | — | a,b,c,d |
| i1886 | ./. | syn_2257; syn_2258 | → ←← | No | — | ./. |
| i1908 | ./. | ndhI/frxB; ndhA | ← → ← | No | — | ./. |
| i1973 | atgtaggttgagtggCTGGCGAAAG | rplJ; rplA | ←←← | No | — | a,b,c,d |
| i2037 | ggttaaggtttcggtAGGAGTGATT | syn_2450; syn_2451 | ←←← | No | — | ./. |
Abbreviations: No, location is not in a genomic island; PBS, phycobilisome rod gene cluster.
a
Putative protein-coding function (see also Table 2).
5′ RACE results are shown in 5′ to 3′ direction, with capital letters indicating the first transcribed nucleotide. The classification into genomic islands is based on Dufresne et al. (2008).
The observed regulation of expression is given (—, constitutive under the tested conditions) and the predicted orthologs in closely related marine picocyanobacteria (a=Synechococcus CC9311, b=Synechococcus CC9605, c=Synechococcus WH8102, d=Synechococcus RS9916, /=no orthologs found).