Regulated Operon: infC-rpmI-rplT-ysdA

Genes
Genes Synonyms Direction Genome position Function COG ID Genus clusters
infC
- 2951902..2952423 initiation factor IF-3 COG0290 infC-BAC infC-STA infC-STR  
rpmI
- 2951689..2951889 ribosomal protein L35 COG0291 rpmI-BAC rpmI-STA rpmI-STR  
rplT
- 2951298..2951657 ribosomal protein L20 COG0292 rplT-BAC rplT-LAB rplT-MYC rplT-STA rplT-STR  
ysdA
- 2950972..2951241
COG3326  

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 2952552..2952606 AAGCAGAAGCACCCGCTTCTCACCTGATTGACACATGCATGTAGTTGGCAGGTTG Choonee N, et al. (2007): NB RG SDM, in-vitro assay, OV FT, toeprint
SigA Promoter -38:+2 2952623..2952661 CTTGACTAAAGATCCGGTATTGTGTAGAATAGTTATTGA Choonee N, et al. (2007): PE

Terminator

Terminator sequence Absolute position Position from stop codon Free energy
[kcal/mol]
Downstream of
ATGTTCGTAGTGTGGGTGTTTTATAATGCCCACACTTTTTGTTTGCCTGC
         >>>>>>>>>>>    <<<<<<<<<<<
2952494..2952519
-617..-592
-16.7
infC
AAAAAGCAGAAAAGCGTTTAACGCTCTTCTGCTTTTTTTGCGAGTTT
     >>>>>>>>>>>>   <<<<<<<<<<<<
2950942..2950968
4..30
-17.7
ysdA
ATAGAGCCGCTCTCCAGCAGAGCGGCTTTTTCTATATAAAG
     >>>>>>>>     <<<<<<<<
2951268..2951288
10..30
-16.5
rplT

Overview



Upper Region






Copyright: Human Genome Center, Inst. Med. Sci., Univ. Tokyo; 1999-2006
Contact: Kenta Nakai