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sRNA Annotations

2nd structure
(RNAfold)
sRNAG0059Get Sequence
Gene Name spf
Synonyms ECK3856;b3864;
Position 4047922.....4048030
Length 109 bp
Strand forward
Gene Class Spf RNA
Species Escherichia coli K12 MG1655
Evidence Inferred from physical interaction;Inferred from mutant phenotype;
Source regulonDB

Genome position Promoter site

Structural RNA alignment
(RNALogo)
Get alignment sequences

Descriptions


    "The spf gene encodes a nontranslated RNA (Rice PW,1987) that is involved in wild-type DNA polymerase I activity (Polayes DA,1988). Spf is responsible for selective inhibition of translation of a particular gene (galK) within the mRNA transcribed from the galactose operon; Spf occludes interaction of the ribosome with the galK Shine-Dalgarno sequence (Moller T,2002). The spf RNA shows some interaction with ribosomes but is not translated (Rice PW,1987). The Hfq protein stimulates pairing of Spf regions with complementary RNA sequences (Moller.....

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References

Møller T, Franch T, Højrup P, Keene DR, Bächinger HP, Brennan RG, and Valentin-Hansen P (2002) "Hfq: a bacterial Sm-like protein that mediates RNA-RNA interaction." Mol Cell 9 (1)  PubMed
Hatfull GF, and Joyce CM (1986) "Deletion of the spf (spot 42 RNA) gene of Escherichia coli." J Bacteriol 166 (3)  PubMed
Rice PW, and Dahlberg JE (1982) "A gene between polA and glnA retards growth of Escherichia coli when present in multiple copies: physiological effects of the gene for spot 42 RNA." J Bacteriol 152 (3)  PubMed
Polayes DA, Rice PW, and Dahlberg JE (1988) "DNA polymerase I activity in Escherichia coli is influenced by spot 42 RNA." J Bacteriol 170 (5)  PubMed
Møller T, Franch T, Udesen C, Gerdes K, and Valentin-Hansen P (2002) "Spot 42 RNA mediates discoordinate expression of the E. coli galactose operon." Genes Dev 16 (13)  PubMed
more..

Computational Records


Gene NameStartEndStrand
IS197 4047475 4047593 forward

score promoter_score=54.221;terminator_score=-20.16
Note GenBank_annotation:spf sRNA gene (Spot42 sRNA)
Methods "profile-based search method(profile search program, pftools2.2) to identify putative promoters in the E. coli genome."
Species Escherichia coli K12 MG1655
Sequence Get Sequence
PMID PubMed

Comparative Genomics by UCSC Genome Browser

Network Visualization

Regulators/sRNAs


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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
spf_b3864_st
more

External Database Connections

ECK120002540
EB4261
948354
ABE-0012621
EG30098
EG30098
b3864
334
RF00021


Department of Biological Science and Technology,

Institute of Bioinformatics National Chiao Tung University, Hsinchu, Taiwan

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