Curation Information

Publication
Characterization of the SOS regulon of Caulobacter crescentus.;da Rocha RP, Paquola AC, Marques Mdo V, Menck CF, Galhardo RS;Journal of bacteriology 2008 Feb; 190(4):1209-18 [18083815]
TF
LexA [Q9A724, view regulon]
Reported TF sp.
Caulobacter crescentus CB15
Reported site sp.
Caulobacter crescentus CB15
Created by
Erill Lab
Curation notes
-

Experimental Process

Iterative refinement of motif. Starts with known LexA genes, builds motif with Gibbs sampling discovery, searches genome. For high scoring sites analyzes expression with RT-PCR. Strongly induced are used in next round of motif discovery.

Transcription Factor Binding Sites


AATGTTCTCCTGGTGTTCC
AAAGTTCGCGTTATGTTCT
CATGTTCCAGCTTTGTTCG
GATGTTCATGTATTGTTCT
ATCGTTCTTGATTTGTTCT
CATATTCCGGTTTTGTTCT
AGATTTCTTGTTTTGTTCC
TCTGTTCACAAGATGTTCC
CATGTTCCACTTTTGTTCT
AATGTTCTTGTTATGTTCT
AATGTTCCTGAATTGTTCT
TATGTTCTTGTTATGTTCG
TTTGTTCTCGGCTTGTTCT
CATGTTCCCTTTCTGTTTC
CATGTTCGCAAGATGTTCC
CATGTTCTGACTATGTTCC
AATGTTCCTATAATGTTCT
AATGTTCCTATAATGTTCT
CATGTTCTCGTATTGTTCG
ATTGTTCTTGATATGTTCC
TATGTTCCAACTTCGTTTG
GATGATCCCGTTTCGTTCC
AACGTTCGTTTTTCGTTCT
TATGTTCCTGAAAAGTTCT
CGCGTTCATCATGTGTTCT
TTTGTTCGCCAGATTTTTT
TATGTTCCTGAAAAGTTCT
TTTGTTCGCATCTTGTTCT
CTTGTTCTCGCGACGTTCG
ATTGTTCTTGATATGTTCC
TATGTTCCAACTTCGTTTG
AGAGTTCGCATTATGTTCT
TTTGTTCTCATAACGTTCT
TTTGTTCTCGAAAGGTTTC
GTTTTTCCGGATTTGTTCT
CATGTTCTGACTATGTTCC
TTTGTTCGCATCTTGTTCT
CTTGTTCTCGCGACGTTCG
CATATTCCGGTTTTGTTCT
AGATTTCTTGTTTTGTTCC
TCTGTTCACAAGATGTTCC
CATGTTCGCAAGATGTTCC
CATGTTCCACTTTTGTTCT
AATGTTCTCCTGGTGTTCC
AAAGTTCGCGTTATGTTCT
CATGTTCCAGCTTTGTTCG
GATGTTCATGTATTGTTCT
ATCGTTCTTGATTTGTTCT
CATATTCCGGTTTTGTTCT
AGATTTCTTGTTTTGTTCC
TCTGTTCACAAGATGTTCC
CATGTTCCACTTTTGTTCT
AATGTTCTTGTTATGTTCT
AATGTTCCTGAATTGTTCT
TATGTTCTTGTTATGTTCG
TTTGTTCTCGGCTTGTTCT
CATGTTCCCTTTCTGTTTC
CATGTTCGCAAGATGTTCC
CATGTTCTGACTATGTTCC
AATGTTCCTATAATGTTCT
AATGTTCCTATAATGTTCT
CATGTTCTCGTATTGTTCG
ATTGTTCTTGATATGTTCC
TATGTTCCAACTTCGTTTG
GATGATCCCGTTTCGTTCC
AACGTTCGTTTTTCGTTCT
TATGTTCCTGAAAAGTTCT
CGCGTTCATCATGTGTTCT
TTTGTTCGCCAGATTTTTT
TATGTTCCTGAAAAGTTCT
TTTGTTCGCATCTTGTTCT
CTTGTTCTCGCGACGTTCG
ATTGTTCTTGATATGTTCC
TATGTTCCAACTTCGTTTG
AGAGTTCGCATTATGTTCT
TTTGTTCTCATAACGTTCT
TTTGTTCTCGAAAGGTTTC
GTTTTTCCGGATTTGTTCT
CATGTTCTGACTATGTTCC
TTTGTTCGCATCTTGTTCT
CTTGTTCTCGCGACGTTCG
CATATTCCGGTTTTGTTCT
AGATTTCTTGTTTTGTTCC
TCTGTTCACAAGATGTTCC
CATGTTCGCAAGATGTTCC
CATGTTCCACTTTTGTTCT

Gene Regulation

Regulated genes for each binding site are displayed below. Gene regulation diagrams show binding sites, positively-regulated genes, negatively-regulated genes, both positively and negatively regulated genes, genes with unspecified type of regulation. For each indvidual site, experimental techniques used to determine the site are also given.

Site sequence Regulated genes Gene diagram Experimental techniques TF function TF type
AATGTTCTCCTGGTGTTCC CC_1902,
... ... CC_1902 CC_1901
Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - Experimental technique details Visual sequence inspection (nan) - repressor dimer
AAAGTTCGCGTTATGTTCT CC_0627,
... ... CC_0627 CC_0626 CC_0625 CC_0624 CC_0623 CC_0622 CC_0621 CC_0620 CC_t05
Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - Experimental technique details Visual sequence inspection (nan) - repressor dimer
CATGTTCCAGCTTTGTTCG CC_3467,
... ... CC_3467 CC_3468 CC_3469
Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - Experimental technique details Visual sequence inspection (nan) - repressor dimer
GATGTTCATGTATTGTTCT CC_3518,
... ... CC_3518 CC_3517 CC_3519
Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - Experimental technique details Visual sequence inspection (nan) - repressor dimer
ATCGTTCTTGATTTGTTCT CC_2332,
... ... CC_2332 CC_2331 CC_2333
Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - Experimental technique details Visual sequence inspection (nan) - repressor dimer
CATATTCCGGTTTTGTTCT CC_1927, dnaE,
... ... CC_1927 dnaE CC_1928 CC_1929 CC_1930 CC_1931
Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - Experimental technique details Visual sequence inspection (nan) - repressor dimer
AGATTTCTTGTTTTGTTCC CC_1927, dnaE,
... ... CC_1927 dnaE CC_1928 CC_1929 CC_1930 CC_1931
Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - Experimental technique details Visual sequence inspection (nan) - repressor dimer
TCTGTTCACAAGATGTTCC CC_1927, dnaE,
... ... CC_1927 dnaE CC_1928 CC_1929 CC_1930 CC_1931
Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - Experimental technique details Visual sequence inspection (nan) - repressor dimer
CATGTTCCACTTTTGTTCT CC_3213,
... ... CC_3213 CC_3214
Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - Experimental technique details Visual sequence inspection (nan) - repressor dimer
AATGTTCTTGTTATGTTCT CC_2272,
... ... CC_2272 CC_2271
Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - Experimental technique details Visual sequence inspection (nan) - repressor dimer
AATGTTCCTGAATTGTTCT CC_3424,
... ... CC_3424 CC_3423 CC_3422 CC_3425 CC_3426 CC_3427 CC_3428
Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - Experimental technique details Visual sequence inspection (nan) - repressor dimer
TATGTTCTTGTTATGTTCG CC_1330,
... ... CC_1330 CC_1329
Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - Experimental technique details Visual sequence inspection (nan) - repressor dimer
TTTGTTCTCGGCTTGTTCT CC_1054,
... ... CC_1054 CC_1053 CC_1055
Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - Experimental technique details Visual sequence inspection (nan) - repressor dimer
CATGTTCCCTTTCTGTTTC CC_2040,
... ... CC_2040 CC_2039 CC_2041
Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - Experimental technique details Visual sequence inspection (nan) - repressor dimer
CATGTTCGCAAGATGTTCC recA,
... ... recA CC_1086
Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - Experimental technique details Visual sequence inspection (nan) - repressor dimer
CATGTTCTGACTATGTTCC CC_2879, CC_2880, uvrC,
... ... CC_2879 CC_2880 uvrC CC_2878 CC_2877
Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - Experimental technique details Visual sequence inspection (nan) - repressor dimer
AATGTTCCTATAATGTTCT CC_3038, CC_3037, CC_3036, CC_3039
... ... CC_3038 CC_3037 CC_3036 CC_3039
Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - Experimental technique details Visual sequence inspection (nan) - repressor dimer
AATGTTCCTATAATGTTCT CC_3037, CC_3036, CC_3039,
... ... CC_3037 CC_3036 CC_3039 CC_3038
Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - Experimental technique details Visual sequence inspection (nan) - repressor dimer
CATGTTCTCGTATTGTTCG CC_3356,
... ... CC_3356 CC_3355 CC_3354 CC_3357
Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - Experimental technique details Visual sequence inspection (nan) - repressor dimer
ATTGTTCTTGATATGTTCC CC_1531,
... ... CC_1531 CC_1532 CC_1530 CC_1533
Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - Experimental technique details Visual sequence inspection (nan) - repressor dimer
TATGTTCCAACTTCGTTTG CC_1531,
... ... CC_1531 CC_1532 CC_1530 CC_1533
Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - Experimental technique details Visual sequence inspection (nan) - repressor dimer
GATGATCCCGTTTCGTTCC CC_1983,
... ... CC_1983 CC_1984
Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - Experimental technique details Visual sequence inspection (nan) - repressor dimer
AACGTTCGTTTTTCGTTCT CC_0140,
... ... CC_0140 CC_0139 CC_0141
Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - Experimental technique details Visual sequence inspection (nan) - repressor dimer
TATGTTCCTGAAAAGTTCT CC_0383,
... ... CC_0383 CC_0382 CC_0381 CC_0380
Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - Experimental technique details Visual sequence inspection (nan) - repressor dimer
CGCGTTCATCATGTGTTCT CC_3238, CC_3237, ruvB,
... ... CC_3238 CC_3237 ruvB CC_3235 CC_3234 CC_3239
Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - Experimental technique details Visual sequence inspection (nan) - repressor dimer
TTTGTTCGCCAGATTTTTT CC_3225,
... ... CC_3225 CC_3224 CC_3226
Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - Experimental technique details Visual sequence inspection (nan) - repressor dimer
TATGTTCCTGAAAAGTTCT CC_0382,
... ... CC_0382 CC_0381 CC_0380 CC_0383
Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - Experimental technique details Visual sequence inspection (nan) - repressor dimer
TTTGTTCGCATCTTGTTCT uvrA,
... ... uvrA CC_2589
Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - Experimental technique details Visual sequence inspection (nan) - repressor dimer
CTTGTTCTCGCGACGTTCG uvrA,
... ... uvrA CC_2589 CC_2588
Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - Experimental technique details Visual sequence inspection (nan) - repressor dimer
ATTGTTCTTGATATGTTCC CC_1532,
... ... CC_1532 CC_1531 CC_1530 CC_1533
Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - Experimental technique details Visual sequence inspection (nan) - repressor dimer
TATGTTCCAACTTCGTTTG CC_1532,
... ... CC_1532 CC_1531 CC_1530 CC_1533
Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - Experimental technique details Visual sequence inspection (nan) - repressor dimer
AGAGTTCGCATTATGTTCT CC_3515,
... ... CC_3515 CC_3514 CC_3516
Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - Experimental technique details Visual sequence inspection (nan) - repressor dimer
TTTGTTCTCATAACGTTCT CC_1468,
... ... CC_1468 CC_1467 CC_1466
Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - Experimental technique details Visual sequence inspection (nan) - repressor dimer
TTTGTTCTCGAAAGGTTTC CC_3130,
... ... CC_3130 CC_3131 CC_3132 CC_3133
Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - Experimental technique details Visual sequence inspection (nan) - repressor dimer
GTTTTTCCGGATTTGTTCT CC_3130,
... ... CC_3130 CC_3131 CC_3132 CC_3133
Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - Experimental technique details Visual sequence inspection (nan) - repressor dimer
CATGTTCTGACTATGTTCC CC_2878,
... ... CC_2878 CC_2879 CC_2877 CC_2880 uvrC
Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - Experimental technique details Visual sequence inspection (nan) - repressor dimer
TTTGTTCGCATCTTGTTCT CC_2589, uvrA
... ... CC_2589 uvrA
Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - Experimental technique details Visual sequence inspection (nan) - repressor dimer
CTTGTTCTCGCGACGTTCG CC_2589, uvrA,
... ... CC_2589 uvrA CC_2588
Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - Experimental technique details Visual sequence inspection (nan) - repressor dimer
CATATTCCGGTTTTGTTCT CC_1928,
... ... CC_1928 CC_1927 dnaE CC_1929 CC_1930 CC_1931
Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - Experimental technique details Visual sequence inspection (nan) - repressor dimer
AGATTTCTTGTTTTGTTCC CC_1928,
... ... CC_1928 CC_1927 dnaE CC_1929 CC_1930 CC_1931
Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - Experimental technique details Visual sequence inspection (nan) - repressor dimer
TCTGTTCACAAGATGTTCC
... ... CC_1927 dnaE CC_1928 CC_1929 CC_1930 CC_1931
Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - Experimental technique details Visual sequence inspection (nan) - repressor dimer
CATGTTCGCAAGATGTTCC CC_1086, recA
... ... CC_1086 recA
Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - Experimental technique details Visual sequence inspection (nan) - repressor dimer
CATGTTCCACTTTTGTTCT CC_3214,
... ... CC_3214 CC_3213
Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - Experimental technique details Visual sequence inspection (nan) - repressor dimer