Table 2

Streptomyces sRNAs predicted using an alternative transcription termination.

ID#

Exp.†

Length

Strand*

Genomic coordinates

E-value

5'-flanking gene distance

5' flanking gene termination#

RNAz probability @


60

++

252

← ⇒ →

7243744.. 7243995

2 × 10-74

17

0.99

544, M1 RNA

++

320

← ⇐ ←

2462901..2463220

9 × 10-94

2

C-rich, 2463157.. 2463177

1


† The first symbol stands for detection of expression by microarrays (expressed: '+', not expressed: '-'), the second one for RT-PCR confirmation of the expression (expressed: '+', not expressed: '-'). '0' stands for not applied.

* The double arrows represent sRNA gene, the arrows flanking genes. Right sided arrows show the complementary strand.

# Applicable only if the predicted sRNA and the gene flanking its 5' end are on the same strand. 'C-rich' stands for C-rich stretch of possible Rho-dependent transcrition termination. 'Rho-ind.' stands for a predicted Rho-independent terminator. The number following show the genomic coordinates of the termination factors.

@ In alignments with P < 0.5 a functional RNA is predicted. The higher this value, the more confident is the prediction.

Pánek et al. BMC Genomics 2008 9:217   doi:10.1186/1471-2164-9-217

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