Regulated Operon: rrnD

Genes
Genes Synonyms Direction Genome position Function COG ID Genus clusters
rrnD-16S
+ 946030..947583 ribosomal RNA-16S
 
rrnD-23S
+ 947751..950679 ribosomal RNA-23S
 
rrnD-5S
+ 950791..950906 ribosomal RNA-5S
 
trnD-Asn trnR + 950916..950990 transfer RNA-Asn
 
trnD-Ser trnR + 950996..951087 transfer RNA-Ser
 
trnD-Glu trnR + 951122..951196 transfer RNA-Glu
 
trnD-Val trnR + 951203..951278 transfer RNA-Val
 
trnD-Met trnR + 951288..951364 transfer RNA-Met
 
trnD-Asp trnR + 951376..951452 transfer RNA-Asp
 
trnD-Phe trnR + 951465..951540 transfer RNA-Phe
 
trnD-Thr trnR + 951546..951621 transfer RNA-Thr
 
trnD-Tyr trnR + 951641..951725 transfer RNA-Tyr
 
trnD-Trp trnR + 951731..951804 transfer RNA-Trp
 
trnD-His trnR + 951829..951904 transfer RNA-His
 
trnD-Gln trnR + 951914..951988 transfer RNA-Gln
 
trnD-Gly trnR + 952035..952109 transfer RNA-Gly
 
trnD-Cys trnR + 952115..952188 transfer RNA-Cys
 
trnD-Leu1 trnR + 952193..952281 transfer RNA-Leu
 
trnD-Leu2 trnR + 952547..952631 transfer RNA-Leu
 

Operon evidence: Northern blotting; S1 nuclease mapping
Reference: Wawrousek EF, et al. (1984), Vold BS, et al. (1988)
Comments: The Northern blotting experiments showed the position of the terminators, but did not determine if all genes belong to the same operon. The readthrough terminator downstream of trnD-Leu1 prevents most transcripts to continue into trnD-Leu2, which is therefore mainly transcribed from its own promoter.

Promoters

Binding
factor		 Regulation Location Absolute position Binding seq.(cis-element) Experimental evidence
SigA Promoter ND 945714..945776 AAAAAGGTGTTGACTCTGATTCTTGACCGTGTTATATTATTAAACGTCGCTGATGCGCTTCTG Jarvis ED, et al. (1990): HM
SigA Promoter ND 945811..945873 AAAAAAACATTTGACAAAAGAAAGTCAAAATGTTATATTAATAAAGTCGCTTCAACAAGAAGT Jarvis ED, et al. (1990): HM
SigA Promoter -39:+12 950737..950787 AACACTTGATTTTCTCAAGAATACATAGTATAATGTTAAATGTCACTGAAA Vold BS, et al. (1988): S1
SigA Promoter -47:+13 952472..952531 TTTTTTGAAATACGTTGACACTTTATGAGATCCATGATATATTTATATTCGTCGGTTAGA Vold BS, et al. (1988): S1

Terminator

Terminator sequence Absolute position Position from stop codon Free energy
[kcal/mol]		 Downstream of
GAAAACCCGTTTCTTAACAGAAACGGGTTTTTATTTTTTATT
     >>>>>>>>>    <<<<<<<<<
952639..952660
8..29
-14.6
 trnD-Leu2
GAAAAGGAGCCTCGGCTCCTTTTTATACTTACTC
     >>>>>    <<<<<
952684..952697
53..66
-8.4
 trnD-Leu2
ATTAATGATCTACATAAGTAGATCATTTTTTTAATGCTTT
     >>>>>>>>    <<<<<<<<
952345..952364
64..83
-11.7
 trnD-Leu1

Overview



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