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sRNA Annotations

2nd structure
(RNAfold)
sRNAG0057Get Sequence
Gene Name sokB
Synonyms ECK1414;b4429;
Position 1490143.....1490198
Length 56 bp
Strand forward
Gene Class antisense RNA blocking mokB and hokB translation
Species Escherichia coli K12 MG1655
Evidence Inferred from direct assay;Human inference of function from sequence;
Source regulonDB

Genome position Promoter site

Structural RNA alignment
(RNALogo)
Get alignment sequences

Descriptions


            " sokB appears to be an antisense RNA that regulates the translation of MokB and HokB. The highly similar hokC locus codes for a hok/sok toxin/antitoxin system (Pedersen K,1999). In the plasmid R1 hok/sok system, sok antisense RNA binds with hok mRNA, allowing cleavage by RNase III (Franch T,1999. Gerdes K,1992). Both the hokC and sokC RNAs are processed at their 3' ends (Pedersen K,1999)."
 

References

Pedersen K, and Gerdes K (1999) "Multiple hok genes on the chromosome of Escherichia coli." Mol Microbiol 32 (5)  PubMed
Franch T, Thisted T, and Gerdes K (1999) "Ribonuclease III processing of coaxially stacked RNA helices." J Biol Chem 274 (37)  PubMed
Gerdes K, Nielsen A, Thorsted P, and Wagner EG (1992) "Mechanism of killer gene activation. Antisense RNA-dependent RNase III cleavage ensures rapid turn-over of the stable hok, srnB and pndA effector messenger RNAs." J Mol Biol 226 (3)  PubMed

Comparative Genomics by UCSC Genome Browser

Network Visualization

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sRNAs/Targets


sRNA Expression Profiles

TitleF plasmid induced changes in expression levels in E. coli
Citation(s)16432259;16981998;SeriesGSE1154
Samples
1:MG1655_replicate12:MG1655_replicate23:MG1655F_replicate1
4:MG1655F_replicate25:DH5alpha_replicate16:DH5alpha_replicate2
7:DH5alphaF_replicate18:DH5alphaF_replicate2
IG_929_1489875_1490493_fwd_st
more

External Database Connections

ECK120002663
EB4289
2847728
ABE-0047249
JWR0235
EG31127
G0-9611
b4429


Department of Biological Science and Technology,

Institute of Bioinformatics National Chiao Tung University, Hsinchu, Taiwan

Contact with: bryan@mail.NCTU.edu.tw