DBSCR - List of revised TLS

   Database of transcriptional regulation in Streptomyces coelicolor and its closest reltives
Home
 Transcription factors
 Regulated genes
 Revised TLS
 Search
 Contacts

List of revised translation start sites (TLSs)

Based on experimentally validated transcription start sites, we listed probable mis-annotations of translation start sites in NCBI file.

S. coelicolor

Genes NCBI file Experimental data
Position Direction Sequence Position Sequence Reference Comment
rpmB2 3791191..3791412 + ATGCTGACCGGGGCCCGGCCCGGCTTCGGC- 3791176 GTGTCCGCCCACTGCATGCTGACCGGGGCC- Owen GA, et al. (2007) (may not be suitable citation..)
ssgB 1650311..1650790 + GTGGCATGTCGATTTCGCCGACGTGCGAAT- 1650377 ATGAACACCACGGTCAGCTGCGAGCTGCAC- Kormanec J, et al. (2002) Translation start site on NCBI file is overlapping with -10 motif.
bldN 3675442..3675975 + ATGGAGCTGGTCGAGCGGGCCCAGGCCGGC- 3675181 GTGTACCCACACGTCGGGGTTGACGCCTCG- Bibb MJ, et al. (2003) Actual translation start site locates 261bp upstream of the position on NCBI file, although this region does not have sequence homology with ECF sigma factors.
crtB 173768..174946 + GTGCGGACAACCGAGAGTGAGAAGGGGCTG- - - Takano H, et al. (2005) The translation start site on NCBI file locates 116bp upstream of the transcription start site.
actI-orf1 5529801..5531204 + GTGCCGCTGGACGCGGCGCCGGTGGATCCG- - - Arias P, et al. (1999) The translation start site on NCBI file locates upstream of the transcription start site.
ramC 7419664..7422456 + GTGACAGCCGCAACTGTCCGAGGCGGTACG- 7419742 GTGAACAAGGGCTACGCCGTGTACTGCGAC- O'Connor TJ, et al. (2005) The translation start site on NCBI file seems to locate upstream of the transcription start site.
ragA 4468763..4469743 - ATGCAAACGAACGAGCACGAACACGTGATT- 4469719 GTGATTGAGGTCACCGACCTTCGGCGTGTG- San Paolo S, et al. (2006) The translation start site on NCBI file seems to locate upstream of the transcription start site.
pqrA 1678678..1679247 - GTGGGTTATTGTTGTCTCATGGCCGTTGAT- 1679229 ATGGCCGTTGATCGTGAACAGGTACTGCGC- Cho YH, et al. (2003) The translation start site on NCBI file locates just after the transcription start site.
redD 6432566-6433618 + ATGACGGGTGGGGGAGTGCTTGCCACGATG- - - Kang JG, et al. (1997) Translation start site on NCBI file is overlapping with -35 motif.
SCE87.13 3463996..3465258 + GTGGCGGTTGCATCCACTGTCACGGGCGAC- - - Paget MS, et al. (2001) The translation start site on NCBI file locates upstream of the transcription start site.

S. griseus

Genes NCBI file Experimental data
Position Direction Sequence Position Sequence Reference Comment
sprD 6762850..6764028 + GTGTGCGTTTCGCGGCGTCGGAATAGTGGG... 6762943 TTGAAGCATCGACGCATATCCAGGAAGCGC... Tomono A, et al. (2005) The translation satrt site on NCBI file locates around -35 motif.
SGR_2391 2819856..2820875 + GTGGAATTCACCATCGGCGGACGGCTGGAAGT... 2820004 ATGTGCTCTCGATCACACGAAAGAGCGGGGAA... Ueda K, et al. (1998) The translation satrt site on NCBI file locates upstream of the transcription start site.

DBSCR:

Copyright: BASE, RIKEN
Contact: Yuko Makita