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Name: | gapA |
Gene(s): | gapA Genome Browser M3D Gene expression COLOMBOS |
Evidence: | [BTEI] Boundaries of transcription experimentally identified |
Reference(s): | [1] Shimada T., et al., 2005 |
Promoter | |
Name: | gapAp7 |
+1: | 1862240 |
Distance from start of the gene: | 531 |
Sequence: |
agtctttgatataacgaatggattcttcacttaccggttcgtagaaactgggccagccacAgccggaatcatacttggttt |
Evidence: | [TIM] |
Reference(s): | [1] Shimada T., et al., 2005 |
Name: | gapA |
Gene(s): | gapA Genome Browser M3D Gene expression COLOMBOS |
Evidence: | [BTEI] Boundaries of transcription experimentally identified |
Reference(s): | [1] Shimada T., et al., 2005 |
Promoter | |
Name: | gapAp6 |
+1: | 1862247 |
Distance from start of the gene: | 524 |
Sequence: |
gatataacgaatggattcttcacttaccggttcgtagaaactgggccagccacagccggaAtcatacttggtttgggaatg |
Evidence: | [TIM] |
Reference(s): | [1] Shimada T., et al., 2005 |
Name: | gapA |
Gene(s): | gapA Genome Browser M3D Gene expression COLOMBOS |
Evidence: | [ICWHO] Inferred computationally without human oversight |
Promoter | |
Name: | gapAp4 |
+1: | 1862526 |
Sigma Factor: | Sigma70 Sigmulon |
Distance from start of the gene: | 245 |
Sequence: |
tgactgattctaacaaaacattaacaccaactggcaaaattttgtcctaaacttgatctcGacgaaatggctgcacctaaa -35 -10 +1 |
Note(s): | The gapAp4 promoter does not have a -35 promoter sequence, and it has been suggested that it either requires a transcriptional activator or it represents a secondary RNA polymerase-binding site. |
Evidence: |
[HIPP] [TIM] |
Reference(s): | [2] Charpentier B., et al., 1994 |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
remote | Cra | repressor | gapAp4 | 1862001 | 1862018 | -516.5 | tggaataagtTGCTGAATCGTTTTTTCAaccgttgatt | nd | [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] | [1] |
remote | Cra | repressor | gapAp4 | 1862683 | 1862700 | 166.5 | ttgtcgcaatGATTGACACGATTCCGCTtgacgctgcg | nd | [AIBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] | [1] |
Name: | gapA |
Gene(s): | gapA Genome Browser M3D Gene expression COLOMBOS |
Evidence: | [ICWHO] Inferred computationally without human oversight |
Promoter | |
Name: | gapAp3 |
+1: | 1862597 |
Sigma Factor: | Sigma70 Sigmulon |
Distance from start of the gene: | 174 |
Sequence: |
tgcacctaaatcgtgatgaaaatcacatttttatcgtaattgccctttaaaattcggggcGccgaccccatgtggtctcaa -35 -10 +1 |
Note(s): | Utilization of the gapAp3 promoter is subject to catabolic repression. A potential -10 promoter sequence of the RNA polymerase σ70 is found, and instead of a -35 sequence there is evidence of a potential cAMP-CRP-binding site. |
Evidence: |
[HIPP] [TIM] |
Reference(s): | [2] Charpentier B., et al., 1994 |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
proximal | CRP-cAMP | activator | gapAp3 | 1862545 | 1862566 | -41.5 | gctgcacctaAATCGTGATGAAAATCACATTTttatcgtaat | nd | [APIORCISFBSCS], [CV(GEA)], [GEA] | [2] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
remote | Cra | repressor | gapAp3 | 1862001 | 1862018 | -587.5 | tggaataagtTGCTGAATCGTTTTTTCAaccgttgatt | nd | [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] | [1] |
remote | Cra | repressor | gapAp3 | 1862683 | 1862700 | 95.5 | ttgtcgcaatGATTGACACGATTCCGCTtgacgctgcg | nd | [AIBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] | [1] |
Name: | gapA-yeaD |
Gene(s): | gapA, yeaD Genome Browser M3D Gene expression COLOMBOS |
Evidence: | [ITC] Inferred through co-regulation |
Reference(s): | [3] Nonaka G., et al., 2006 |
Promoter | |
Name: | gapAp2 |
+1: | 1862618 |
Sigma Factor: | Sigma32 Sigmulon |
Distance from start of the gene: | 153 |
Sequence: |
atcacatttttatcgtaattgccctttaaaattcggggcgccgaccccatgtggtctcaaGcccaaaggaagagtgaggcg -35 -10 +1 |
Note(s): | The sole effect of transcription of the gapAp2 promoter during heat shock is to maintain the gapA gene transcription level. |
Evidence: |
[AIPP] [CV(TIM)] [HIPP] [IDA] [TIM] |
Reference(s): |
[4] Charpentier B., et al., 1998 [2] Charpentier B., et al., 1994 [3] Nonaka G., et al., 2006 [5] Olvera L., et al., 2009 [6] Wade JT., et al., 2006 |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
remote | Cra | repressor | gapAp2 | 1862001 | 1862018 | -608.5 | tggaataagtTGCTGAATCGTTTTTTCAaccgttgatt | nd | [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] | [1] |
remote | Cra | repressor | gapAp2 | 1862683 | 1862700 | 74.5 | ttgtcgcaatGATTGACACGATTCCGCTtgacgctgcg | nd | [AIBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] | [1] |
Name: | gapA |
Gene(s): | gapA Genome Browser M3D Gene expression COLOMBOS |
Evidence: | [ICWHO] Inferred computationally without human oversight |
Promoter | |
Name: | gapAp1 |
+1: | 1862735 |
Sigma Factor: | Sigma70, Sigma38 |
Distance from start of the gene: | 36 |
Sequence: |
gtcgcaatgattgacacgattccgcttgacgctgcgtaaggtttttgtaattttacaggcAaccttttattcactaacaaa -35 -10 +1 |
Note(s): | gapAp1 utilization is very strong at the beginning of the exponential phase and seems to depend upon growth phase. Glucose stimulates the gapAp1 activity. |
Evidence: |
[CV(RS-EPT-CBR)] [CV(TIM)] [HIPP] [HTIM] [IMP] [RS-EPT-CBR] [TIM] |
Reference(s): |
[4] Charpentier B., et al., 1998 [2] Charpentier B., et al., 1994 [5] Olvera L., et al., 2009 [7] Salgado H, et al., 2012 [8] Thouvenot B., et al., 2004 |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
remote | Cra | repressor | gapAp1 | 1862001 | 1862018 | -725.5 | tggaataagtTGCTGAATCGTTTTTTCAaccgttgatt | nd | [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] | [1] |
proximal | Cra | repressor | gapAp1 | 1862683 | 1862700 | -43.5 | ttgtcgcaatGATTGACACGATTCCGCTtgacgctgcg | nd | [AIBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] | [1] |
Gene(s): | yeaD Genome Browser M3D Gene expression COLOMBOS |
Evidence: | [ICWHO] Inferred computationally without human oversight |
RNA cis-regulatory element | ![]() |
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Regulation, transcriptional elongation | |
Attenuator type: | Transcriptional |
Strand: | forward |
Structure type | Energy | LeftPos | RightPos | Sequence (RNA-strand) | |
---|---|---|---|---|---|
terminator | -17.5 | 1863790 | 1863819 | gtgatctaaaAAGAGCGACTTCGGTCGCTCTTTTTTTTAcctgataaaa | |
anti-terminator | -4.7 | 1863765 | 1863801 | tctccaaataAGTTGAGATGACACTGTGATCTAAAAAGAGCGACTTcggtcgctct | |
anti-anti-terminator | -6.2 | 1863725 | 1863773 | accggttactCCAACAAAGTTCTGGACCTGATCGCTCACATCTCCAAATAAGTTGAGAtgacactgtg |
Notes: "The provided "Sequence" is that of the RNA strand, i.e. U's are shown instead of T's and regulators on the reverse strand will appear as the reverse complement of the sequence delimited by LeftPos-RigtPos" |
Reference(s) |
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