Regulated Operon: infC-rpmI-rplT-ysdA

Genes
Genes Synonyms Direction Genome position Function COG ID Conserved groups
infC
- 2952828..2953349
COG0290J infC-BAC infC-STA infC-STR  
rpmI
- 2952615..2952815
COG0291J rpmI-BAC rpmI-STA rpmI-STR  
rplT
- 2952224..2952583
COG0292J rplT-MYC rplT-BAC rplT-LAB rplT-MYC rplT-STA rplT-STR  
ysdA
- 2951898..2952167
COG3326S  

Operon evidence: Northern blotting (1.7 kb transcript)
Reference: Wipat A, et al. (1996), Choonee N, et al. (2007)
Comments: The full-length infC-rpmI-rplT-ysdA transcript is minor; the major transcript has a length of 1.4 kb and includes infC-rpmI-rplT, terminating at the terminator downstream of rplT. Transcriptional readthrough at this terminator was confirmed by RT-PCR experiments. The stem-loop upstream of infC is part of a terminator/antiterminator structure, as shown by Northern blotting, point mutations, lacZ fusions, and in-vitro transcription assays. Binding of the ribosomal protein L20 (RplT) to the nascent mRNA causes transcriptional termination.

Promoters

Binding
factor		 Regulation Location Absolute position Binding seq.(cis-element) Experimental evidence
RplT Negative +19:+73 2953478..2953532 AAGCAGAAGCACCCGCTTCTCACCTGATTGACACATGCATGTAGTTGGCAGGTTG Choonee N, et al. (2007): NB RG SDM, in-vitro assay, OV FT, toeprint
SigA Promoter -37:+2 2953549..2953587 CTTGACTAAAGATCCGGTATTGTGTAGAATAGTTATTGA Choonee N, et al. (2007): PE

Terminator

Terminator sequence Absolute position Position from stop codon Free energy
[kcal/mol]		 Downstream of
ATGTTCGTAGTGTGGGTGTTTTATAATGCCCACACTTTTTGTTTGCCTGC
         >>>>>>>>>>>    <<<<<<<<<<<
2953420..2953445
-617..-592
-16.7
 infC
AAAAAGCAGAAAAGCGTTTAACGCTCTTCTGCTTTTTTTGCGAGTTT
     >>>>>>>>>>>>   <<<<<<<<<<<<
2951868..2951894
4..30
-17.7
 ysdA
ATAGAGCCGCTCTCCAGCAGAGCGGCTTTTTCTATATAAAG
     >>>>>>>>     <<<<<<<<
2952194..2952214
10..30
-16.5
 rplT

Overview



Upper Region
Copyright: Human Genome Center, Inst. Med. Sci., Univ. Tokyo; 1999-2008
Contact: Kenta Nakai