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Name: | glmY |
Gene(s): | glmY Genome Browser M3D Gene expression COLOMBOS |
Note(s): | The glmY gene is transcribed from two overlapping promoters: one of them is σ70 (glmYp2) and the other is σ54 dependent (glmYp1) Reichenbach B,2009 Both promoters start transcription at the same nucleotide; however, they are active during different growth phases, as glmYp1 is mainly active during the transition to stationary phase and glmYp2 is active during exponential phase Reichenbach B,2009 The overlapping of promoters upstream of glmY is a conserved feature in other enterobacterial species Reichenbach B,2009 The glmY gene is located upstream of the gene cluster glrK-yfhG-glrR in the genome of all species of the Enterobacteriaceae family Gopel Y,2011 |
Evidence: | [ICWHO] Inferred computationally without human oversight [LTED] Length of transcript experimentally determined |
Reference(s): | [1] Vogel J., et al., 2003 |
Promoter | |
Name: | glmYp2 |
+1: | 2691340 |
Sigma Factor: | Sigma70 Sigmulon |
Distance from start of the gene: | 0 |
Sequence: |
ataatcagtacgttaccaaactattttctttattggcacagttactgcataatagtaaccAgtggctcattcaccgactta -35 -10 +1 |
Evidence: |
[HIPP] [ICWHO] [IDA] [IHBCE] [RS-EPT-CBR] [TIM] |
Reference(s): |
[2] Huerta AM., et al., 2003 [3] Reichenbach B., et al., 2009 [4] Salgado H, et al., 2012 |
Terminator(s) | |
Type: | rho-independent |
Sequence: | gttcagatacAACAAAGCCGGGAATTACCCGGCTTTGTTatggaataag |
Reference(s): | [5] Urban JH., et al., 2007 |
Name: | glmY | |||||||||
Synonym(s): | sroF | |||||||||
Gene(s): | glmY Genome Browser M3D Gene expression COLOMBOS | |||||||||
Note(s): | The glmY gene is transcribed from two overlapping promoters: one of them is σ70 (glmYp2) and the other is σ54 dependent (glmYp1) Reichenbach B,2009 Both promoters start transcription at the same nucleotide; however, they are active during different growth phases, as glmYp1 is mainly active during the transition to stationary phase and glmYp2 is active during exponential phase Reichenbach B,2009 The overlapping of promoters upstream of glmY is a conserved feature in other enterobacterial species Reichenbach B,2009 The activity of the glmYp1 promoter is dependent on the presence of the transcription factors GlrR and IHF. GlrR binds to three sites, designated ABS1, ABS2, and ABS3Reichenbach B,2009.They are located at -221.5, -188.5, and -125.5 upstream of the transcription start site, respectively Reichenbach B,2009|. While ABS2 and ABS3 are essential for the activity of glmYp1, ABS1 only contributes slightly in the transcription of glmY Reichenbach B,2009. IHF binds to two sites, located at -169 and -52 upstream of the transcription start site Gopel Y,2011 The glmY gene is located upstream of the gene cluster glrK-yfhG-glrR in the genome of all species of the Enterobacteriaceae family Gopel Y,2011 |
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Evidence: | [ICWHO] Inferred computationally without human oversight [LTED] Length of transcript experimentally determined |
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Reference(s): | [1] Vogel J., et al., 2003 | |||||||||
Promoter | ||||||||||
Name: | glmYp1 | |||||||||
+1: | 2691340 | |||||||||
Sigma Factor: | Sigma54 Sigmulon | |||||||||
Distance from start of the gene: | 0 | |||||||||
Sequence: |
ataatcagtacgttaccaaactattttctttattggcacagttactgcataatagtaaccAgtggctcattcaccgactta -24 -12 +1 |
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Evidence: |
[HIPP] [ICWHO] [IDA] [IHBCE] [IMP] [RS-EPT-CBR] [TIM] |
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Reference(s): |
[2] Huerta AM., et al., 2003 [3] Reichenbach B., et al., 2009 [4] Salgado H, et al., 2012 [5] Urban JH., et al., 2007 [1] Vogel J., et al., 2003 |
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Terminator(s) | ||||||||||
Type: | rho-independent | |||||||||
Sequence: | gttcagatacAACAAAGCCGGGAATTACCCGGCTTTGTTatggaataag | |||||||||
Reference(s): | [5] Urban JH., et al., 2007 |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
remote | GlrR-phosphorylated | activator | glmYp1 | 2691457 | 2691474 | -125.5 | tatcttaagtTGTCTCTTTTTAGCGACAcagtggctga | nd | [GEA], [APIORCISFBSCS], [BPP], [SM] | [3] |
remote | GlrR-phosphorylated | activator | glmYp1 | 2691520 | 2691537 | -188.5 | tggtttgccgTGTCGCTTTCTGGCGACActtaactcat | nd | [GEA], [APIORCISFBSCS], [BPP], [SM] | [3] |
remote | GlrR-phosphorylated | activator | glmYp1 | 2691553 | 2691570 | -221.5 | agcttttttgTGTCTGTAAATCACGACAatgggtggtt | nd | [GEA], [APIORCISFBSCS], [BPP], [SM] | [3] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
proximal | IHF | activator | glmYp1 | 2691386 | 2691398 | -52.0 | agcaacgtatAATCAGTACGTTAccaaactatt | nd | [GEA], [APIORCISFBSCS], [BPP] | [6] |
remote | IHF | activator | glmYp1 | 2691503 | 2691515 | -169.0 | gcgacacttaACTCATTGATTTTaatattatct | nd | [GEA], [APIORCISFBSCS], [BPP], [SM] | [3], [6] |
Reference(s) |
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