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sRNA Annotations

2nd structure
(RNAfold)
sRNAG0058Get Sequence
Gene Name sokC
Synonyms ECK0019;sof;b4413;
Position 16952.....17006
Length 55 bp
Strand forward
Gene Class antisense RNA blocking mokC and hokC 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


    "sokC appears to be an antisense RNA that regulates the translation of MokC and HokC. The hokC locus codes for a hok/sok toxin/antitoxin system, but appears to have been inactivated by insertion of an IS186 insertion sequence. This locus is poorly translated (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). HokC is regulated translationally by the antisense RNA sokC (Poulsen LK,1991). Both the hokC and sokC RNAs are processed at thei.....

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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
Poulsen LK, Refn A, Molin S, and Andersson P (1991) "The gef gene from Escherichia coli is regulated at the level of translation." Mol Microbiol 5 (7)  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_16_16558_17488_fwd_f_st
more

External Database Connections

ECK120002653
EB4290
2847745
ABE-0047238
JWR0224
EG31128
G0-9581
b4413


Department of Biological Science and Technology,

Institute of Bioinformatics National Chiao Tung University, Hsinchu, Taiwan

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