Table 1

S. pyogenes M49 sRNAs, genomic location, Rfam predictions, and conservation across streptococcal genomes
No ID Left nucleotide Right nucleotide Size (nt) Strand Upstream adjacent gene Downstream adjacent gene Rfam and MOSES prediction Previously published Conservation
1 sRNASpy490131 141429 141478 49 - ntpK ntpE a
2 sRNASpy490186c 194707 194791 84 + Spy49_0186c speG SRP_bact [37] c
3 sRNASpy490206 216807d 217021 215 +e fasA rnpA MOSES2 fasX [17] b
4 sRNASpy490229 238850 238899 49 + prgA rpsL b
5 sRNASpy490238 248530 248579 49 + Spy49_0238 bacA a
6 sRNASpy490241 251595 251644 49 + rgpG Spy49_0242 a
7 sRNASpy490305 318826 318910 84 + Spy49_0305 Spy49_0306 23S-methyl b
8 sRNASpy490306 319622 319776 154 + Spy49_0306 Spy49_0307 FMN RNA319780 [20] b
9 sRNASpy490348 362857 362906 49 + Spy49_0348 Spy49_0349c MOSES6 a
10 sRNASpy490366c 373806 373855 49 + Spy49_0366c Spy49_0367c -
11 sRNASpy490370 376843 376892 49 + Spy49_0370 Spy49_0371 a
12 sRNASpy490380c 385431 d 385526 95 + e Spy49_0380c mtsA b
13 sRNASpy490388 393522 393571 49 + rplA pyrH a
14 sRNASpy490434 431752 431836 84 + Spy49_0434 thrS T-box b
15 sRNASpy490483c 476503d 476600 97 + e Spy49_0483c bglG b
16 sRNASpy490493 486133 486182 49 + Spy49_0493 ptsK a
17 sRNASpy490504 495351 495400 49 - Spy49_0504 Spy49_0505c a
18 sRNASpy490592 594852 594936 84 + Spy49_0592 pheS b
19 sRNASpy490727 733841 733890 49 - Spy49_0727 Spy49_0728 a
20 sRNASpy490822 820820 820996 d 176 - e Spy49_0822 Spy49_0823 CRISPR RNA772970 [20] c
21 sRNASpy490827 827456 827785 329 + Spy49_0827 Spy49_0828 CRISPR
MOSES14 a
22 sRNASpy490845c 846977 847061 84 + trmE rplJ L10_leader c
23 sRNASpy490948c 941583 941657 d 74 - Spy49_0948c guaA a
24 sRNASpy490957c 950434 950518 84 - e Spy49_0957c Spy49_0958c SR914400 [20] b
25 sRNASpy491007c 1000709 1000828 119 + pcrA Spy49_1008 Glycine b
26 sRNASpy491023c 1019382 1019746 364 + Spy49_1023c Spy49_1024 tmRNA RNA983400 [20] b
27 sRNASpy491061c 184794 184878 84 + Spy49_1061c Spy49_0176 c
28 sRNASpy491095c 1092894 1092943 49 - ptsH nrdH c
29 sRNASpy491122c 1117169 1117218 49 - sodM holA b
30 sRNASpy491163c 1156488 1156537 49 - Spy49_1163c clpE a
31 sRNASpy491167c 1163270 1163319 49 - ileS divIVA T-box -
32 sRNASpy491206c 1201615 1201734 119 - ccdA Spy49_1207c MOSES16 RNA1239700 [20] a
33 sRNASpy491217c 1214010 1214059 49 - Spy49_1217c Spy49_1218c SR1251900 [20] b
34 sRNASpy491243 1246370 1246419 49 + Spy49_1243 Spy49_1244 a
35 sRNASpy491275c 1282084 1282413 329 - Spy49_1275c Spy49_1276c RNaseP_bact b RNA1320100 [20] c
36 sRNASpy491311c 1321638 1321853d 84 - e glyQ Spy49_1312c b
37 sRNASpy491336c 1341554 1341603 49 + rbfA infB b
38 sRNASpy491340c 1346300 1346349 49 - nusA Spy49_1341c b
39 sRNASpy491354 1357803 1357852 49 - manL manM b
40 sRNASpy491357 1360204 1360323 119 + Spy49_1357 serS T-box RNA1439100 [20] b
41 sRNASpy491409c 1413359 1413408 49 - acpS secA a
42 sRNASpy491489c 1489011 1489060 49 + Spy49_1489c Spy49_1491c b
43 sRNASpy491555c 1528842 1528891 49 - Spy49_1555c Spy49_1556c a
44 sRNASpy491560c 1533843 1533892 49 - Spy49_1560c pyrG a
45 sRNASpy491561c 1535755 1535804 49 - pyrG rpoE c
46 sRNASpy491562c 1536613 1536662 49 - rpoE tig a
47 sRNASpy491591 1571896 1571945 49 - lacR2 Spy49_1592 MOSES18 SR1604140 [20] a
48 sRNASpy491596c 1574723 1574807 84 - rplM 50S Spy49_1597c L13_leader c
49 sRNASpy491671c 1654859 1654908 49 - emm49 Spy49_1672c a
50 sRNASpy491707c 1693440 1693489 49 - Spy49_1707c Spy49_1708 a
51 sRNASpy491713 1698142 1698191 49 + Spy49_1713 Spy49_1714c SR1719800 [20] a
52 sRNASpy491718c 1704471 1704525 54 - ctsR csp a
53 sRNASpy491732c 1724321 1724370 49 + Spy49_1732c rpsB SR1745900 [20] b
54 sRNASpy491738 1733300 1733433d 133 - Spy49_1738 Spy49_1739c SR1754950 [20] b
55 sRNASpy491769c 1763496 1763545 49 + hisS rpmF b

Coordinates and gene designations of adjacent genes are relative to the S. pyogenes NZ131 genome (NCBI accession number: NC_011375).

aStreptococcus pyogenes.

b Beta-haemolytic streptococci.

c Non-beta-haemolytic streptococci.

d Transcriptional start site determined by 5 RACE.

e Strand confirmed by gene specific RT-PCR.

Patenge et al.

Patenge et al. BMC Genomics 2012 13:550   doi:10.1186/1471-2164-13-550

Open Data