MtbRegList
Internal user
Search
Navigate
Help
Genome
Annotated motifs
Genome
Help
Exporting data
About
Credits
Quickfind:
Annotated Motif Search Type
Root Pattern (Consensus)
DNA Motif (Instance)
Root Patterns Search Parameters
(Example 1)
(Example 2)
Sequence
Contains
Exact Match
Begins with
Ends with
Limit search to a specific pattern box
Limit to
first
second
third
pattern box
Spacing
Minimum:
Equals
<=
>=
Maximum:
Equals
<=
>=
Limit search to a specific spacing
Between
first and second
second and third
pattern boxes
Recognized by
--Any--
None
Rv3744
Rv1909c (FurA)
Rv1033c (TrcR)
Rv0491 (RegX3)
Rv3855 (EthR, Aka, EtaR)
Rv2374c (HrcA)
Rv1994c
Rv3676
Rv2720 (LexA)
Rv0981 (MprA)
Rv1395
Rv2841c (NusA)
Rv2711 (IdeR, DtxR)
Rv0353 (HspR)
Rv3133c (DevR, DosR)
Rv1221 (SigE)
Rv3286c (SigF)
Rv3414c (SigD)
Unknown
Rv3223c (SigH, RpoE)
Rv2069 (SigC)
Rv0735 (SigL)
None
Multiple selection is allowed (use ctrl key)
Category
--Any--
TSS
Regulator
Promoter
Terminator
Multiple selection is allowed (use ctrl key)
Reference
contains
does not contain
Note
contains
does not contain
Check box to display results from that field
DNA Pattern Instances Search Parameters
(Example)
Sequence
Contains
Exact Match
Begins with
Ends with
Limit search to a specific pattern box
Limit to
first
second
third
pattern box
Spacing between boxes
Minimum:
Equals
<=
>=
Maximum:
Equals
<=
>=
Limit search to a specific spacing
Between
first and second
second and third
pattern boxes
Associated Root
--Any--
None => TSS
Rv3744 => AATATATGATCATATGTTCATTTATT
Rv1909c (FurA) => AGTCTTGACTGATTCCAGAAAAG
Rv1033c (TrcR) => ATAAGCGACATTTGAAAAATTTATGAAT
Rv0491 (RegX3) => ATGTGAACGGTAACCGAACAGCTGTGGCGTAGTGTGTGACTT
Rv3855 (EthR, Aka, EtaR) => CCACGCTATCAACGTAATGTCGAGGCCGTCAACGAGATGTCGACACTATCGACAC
Rv2374c (HrcA) => GCACTCT/8-8/GAGTGCTA
Rv1994c => GCTGTTATACCAGTATATGGTGTACTATTTGATCT
Rv3676 => NGTGNNANNNNNCACA
Rv2720 (LexA) => TCGAACNNNNGTTCGA
Rv0981 (MprA) => TCTCNGNN/3-3/TCTCNGNN
Rv1395 => TGAG/4-6/GGACA
Rv2841c (NusA) => TGTTGTTTGAGAA/6-6/AGTGTGTTT
Rv2711 (IdeR, DtxR) => TTAGGNWAGSCTWVCCTAA
Rv0353 (HspR) => TTGAGCG/5-5/GACTCA
Rv3133c (DevR, DosR) => TTSGGGACTWWAGTCCCSAA
Rv1221 (SigE) => GGRMCS/15-19/SGTTG
Rv3286c (SigF) => GGTTTC/16-20/GGGTAT
Rv3414c (SigD) => GTAACGCT/16-16/WNATGT
Unknown => NNNNNN/0-25/NNNNNN
Rv3223c (SigH, RpoE) => SGGAAC/17-22/SGTTS
Rv2069 (SigC) => SSSAAT/16-20/CGTSSS
Rv0735 (SigL) => TGAACC/16-16/CGTGTC
None => TERM
Multiple selection is allowed (use ctrl key)
Number of mismatch
Equals
<=
>=
Search a specific pattern box
Specify a specific pattern box:
Genomic region
Both
Intergenic region
Gene
Strand
Both
positive
negative
Distance
5':
Equals
<=
>=
3':
Equals
<=
>=
Distance is calculated between flanking gene and proximal pattern side on positive strand
Experimental evidence
--Any--
Primer extension analysis
S1 nuclease transcript mapping
Run-off transcription
Electrophoretic mobility shift assay
Footprinting assay (DNase I, DMS, etc.)
Site-directed mutagenesis
DNA microarray and macroarray
Disruption of transcription factor gene
Rapid amplification of cDNA ends
Run-off transcription followed by macroarray
Fusion with a reporter gene
Homology search by authors
Primer extension analysis on RNA from M. Bovis BCG
S1 nuclease transcript mapping on RNA from M. Bovis BCG
Run-off transcription with a M. smegmatis purified polymerase
In vivo M. smegmatis transcription with a reporter fusion gene
Deduced by homology search from an experimentally derived consensus
Predicted in silico by GeSTer algorithm
No Data
Multiple selection is allowed (use ctrl key)
Transcriptional impact
--Any--
Positive
Negative
Positive and negative
Undefined
Multiple selection is allowed (use ctrl key)
Reference
contains
does not contain
Note
contains
does not contain
Check box to display results from that field