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. 2011 May 1;8(3):468–477. doi: 10.4161/rna.8.3.14421

Table 2.

Summary of putative non coding RNAs identified by 454 sequencing

Name Start [nt] Stop [nt] Strand Length [nt] Reference Comments
sRNA, expression verified by northern blot
scr1601 1711967 1712074 c 108
scr2736-2 2982570 2982745 176
scr2952 3208719 3208810 92
scr3202 3510095 3510186 c 92
scr3920 4315358 4315484 127
scr4115 4515318 4515426 109
scr4389 4805579 4805789 c 211
scr4632 5055055 5055172 c 118
scr5676 6176284 6176413 c 130
scr6106 6706584 6706667 84
scr6925 7688336 7688466 131
sRNA, expression not yet verified by northern blot
scr1104 1161587 1161700 c 114
scr2736-1 2982224 2982505 282
scr3580 3958028 3958181 c 154
scr3928 4323842 4324023 182
scr4132 4545730 4545843 114
scr4659 5088759 5088859 101
scr4827 5257254 5257339 86
scr5529 6023430 6023545 116
scr6280 6937783 6937870 88
scr6908 7672451 7672670 220
scr7601 8427312 8427437 c 126
Antisense RNA
as0091 78047 78191 c 145
as0642 682646 682730 85
as2080 2233552 2233634 83
as2247 2416288 2416397 110
as2364 2533451 2533546 c 96
as2780 3034099 3034209 c 111
as3029 3312231 3312325 95
as3111 3412144 3412346 203
as3125 3425777 3425967 c 191
as3287 3636488 3636569 c 82
as3317 3669433 3669657 225
as3321 3673385 3673581 197
as3404 3770178 3770278 101
as3496 3861776 3861898 123
as3680 4064602 4064701 100
as4261 4674583 4674770 188
as4566 4984053 4984157 c 105
as4567 4984635 4984793 c 159
as4672 5104194 5104588 395
as4675 5106760 5106941 182
as4692/3 5119179 5119518 c 340 scO4692/31
as4699 5124039 5124366 c 328
as5028 5464169 5464418 c 250
as5721 6241794 6241937 c 144
as6323 6983615 6983803 189
as6418 7087036 7087162 127
as6721 7476805 7476903 c 99
as7201 8004633 8004746 c 114
Further transcripts
scr0991 1045891 1046090 200 cis encoded, cobRs
scr2076 2226957 2227117 161 cis encoded, t-box
scr4701 5127282 5127536 255 cis encoded, S10
scr3558 3933527 3933668 c 142 15, 16, 19 6C motif
scr3559 3934693 3934927 235 15, 16 6S RNA
scr1821 1950867 1950948 82 16 new ORF2
scr3035 3321216 3321353 c 138 16 new ORF3
scr4164 4580774 4580933 160 16 new ORF4
scr5822 6370296 6370789 c 494 new ORF5
scr1980 2118877 2118959 c 83 16 alternative ORF6
scr3323 3675098 3675329 232 16 alternative ORF7
scr4800 5224234 5224319 c 86 16 alternative ORF8
scr5856 6412335 6412512 c 178 alternative ORF9

References are given for transcripts shown to be expressed in previous studies; c, crick strand; as1234, antisense transcript to the gene SC O1234, cis, transcript verified as cis-encoded RNA (see Supplemental Figure 5); new/alternative ORF, sRNA located within or close to a conserved/alternative but up to now not yet annotated open reading frame.

1

Antisense transcript which overlaps with both SC O4692 and SC O4693

2

A 44 amino acids (aa) long ORF is located close to scr1821 which is conserved in a number of Streptomyces strains. An additional conserved ORF 29 nt downstream of the transcript is also conserved in a large number of bacteria.

3

scr3035 is located sense to a 183 aa long ORF that is annotated as hypothetical protein in several Streptomyces strains.

4

scr4164 overlaps with the 3′end of a 93 aa ORF conserved in several streptomyces species.

5

scr5822 covers a 78 aa ORF conserved in numerous different bacteria. 2–5The location of these new ORFs is displayed in Supplemental Figure 3.

6

There is an alternative ORF to SC O1979 that is 78 aa longer on the 5′end of the gene. This longer fragment is conserved in several Streptomyces strains and covers scr1980.

7

The 5′end of ORF 3323 is annotated at 3675442 nt at NCBI and at 3675181 nt at strepDB. In the latter case, scr3323 represents the 5′UTR of that gene.

8

There is an alternative ORF to SC O4799 that is 23 aa longer on the 5′end of the gene. This longer fragment is conserved in several Streptomyces strains and covers scr4800.

9

There is an alternative ORF to SC O5855 that is 11 aa longer on the 5′ end of the gene. This longer fragment is conserved in several Streptomyces strains. The distance to scr5856 in that case is only 44 nt, so below our threshold. 6,8,9The location of the alternative ORFs is displayed in Supplemental Figure 4.