Estrogen response element gene transcriptions

# Human genes

# Consensus sequences
"The  estrogen response element (ERE)  located on  94 to 80 "AGGTTATTGCCTCCT" on the transcript, respectively."
Note: GGTTA is the complement of CCAAT. AGGTTATTGCCTCCT is the complement of TCCAATAACGGAGGA.
"Our in silico analysis revealed a putative ERE sequence (GGTCAggaTGACA; wherein the non-consensus nucleotide A is underlined) starting at position 242 from the translation initiation codon (ATG, A being +1; )."
"The estrogen receptor (ER)1 is a transcription factor that regulates the expression of estrogen-responsive genes by binding to a specific DNA sequence found in their regulatory regions. This sequence is called the estrogen response element (ERE).  The essential ERE was determined to have the consensus sequence 5-GGTCAnnnTGACC-3 (4, 7)."
The "sequence requirements for a minimal consensus ERE  for ER binding encompasses a wide variety of possible combinations, which display stable ER binding. The optimal binding sequence is 5-C(A/G)GGTCAnnnTGACC(T/C)G-3. Any change from this optimal consensus diminishes ER-ERE affinity. The underlined core consensus sequence represents the minimum length for binding activity."

# ERE (Matsumoto) samplings
Copying an abridged consensus sequence for the estrogen response element of AGGTTA (ci=TAACCT) and putting it in "F" finds none located between ZSCAN22 and A1BG and none between ZNF497 and A1BG as can be found by the computer programs.
For the Basic programs testing consensus sequence AGGTTA (starting with SuccessablesEREM.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:
- negative strand, negative direction: 0.
- positive strand, negative direction: 0.
- negative strand, positive direction: 0.
- positive strand, positive direction: 0.
- inverse complement, negative strand, negative direction: 0.
- inverse complement, positive strand, negative direction: 0.
- inverse complement, negative strand, positive direction: 0.
- inverse complement, positive strand, positive direction: 0.
For the Basic programs testing consensus sequence 5'-AGGTTATTGCCTCCT-3' (starting with SuccessablesERE.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:
- negative strand, negative direction, looking for 5'-AGGTTATTGCCTCCT-3', 0.
- negative strand, positive direction, looking for 5'-AGGTTATTGCCTCCT-3', 0.
- positive strand, negative direction, looking for 5'-AGGTTATTGCCTCCT-3', 0.
- positive strand, positive direction, looking for 5'-AGGTTATTGCCTCCT-3', 0.
- complement, negative strand, negative direction, looking for 5'-TCCAATAACGGAGGA-3', 0.
- complement, negative strand, positive direction, looking for 5'-TCCAATAACGGAGGA-3', 0.
- complement, positive strand, negative direction, looking for 5'-TCCAATAACGGAGGA-3', 0.
- complement, positive strand, positive direction, looking for 5'-TCCAATAACGGAGGA-3', 0.
- inverse complement, negative strand, negative direction, looking for 5'-AGGAGGCAATAACCT-3', 0.
- inverse complement, negative strand, positive direction, looking for 5'-AGGAGGCAATAACCT-3', 0.
- inverse complement, positive strand, negative direction, looking for 5'-AGGAGGCAATAACCT-3', 0.
- inverse complement, positive strand, positive direction, looking for 5'-AGGAGGCAATAACCT-3', 0.
- inverse negative strand, negative direction, looking for 5'-TCCTCCGTTATTGGA-3', 0.
- inverse negative strand, positive direction, looking for 5'-TCCTCCGTTATTGGA-3', 0.
- inverse positive strand, negative direction, looking for 5'-TCCTCCGTTATTGGA-3', 0.
- inverse positive strand, positive direction, looking for 5'-TCCTCCGTTATTGGA-3', 0.

# ERE (Yasar) samplings
Copying an abridged consensus sequence for the estrogen response element of GGTCAGGAT and putting it in "F" finds none located between ZSCAN22 and A1BG and none between ZNF497 and A1BG as can be found by the computer programs.
For the Basic programs testing consensus sequence 5'-GGTCAGGATGAC-3' (starting with SuccessablesERE2.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:
- negative strand, negative direction, looking for 5'-GGTCAGGATGAC-3', 0.
- negative strand, positive direction, looking for 5'-GGTCAGGATGAC-3', 0.
- positive strand, negative direction, looking for 5'-GGTCAGGATGAC-3', 0.
- positive strand, positive direction, looking for 5'-GGTCAGGATGAC-3', 0.
- complement, negative strand, negative direction, looking for 5'-CCAGTCCTACTG-3', 0.
- complement, negative strand, positive direction, looking for 5'-CCAGTCCTACTG-3', 0.
- complement, positive strand, negative direction, looking for 5'-CCAGTCCTACTG-3', 0.
- complement, positive strand, positive direction, looking for 5'-CCAGTCCTACTG-3', 0.
- inverse complement, negative strand, negative direction, looking for 5'-GTCATCCTGACC-3', 0.
- inverse complement, negative strand, positive direction, looking for 5'-GTCATCCTGACC-3', 0.
- inverse complement, positive strand, negative direction, looking for 5'-GTCATCCTGACC-3', 0.
- inverse complement, positive strand, positive direction, looking for 5'-GTCATCCTGACC-3', 0.
- inverse negative strand, negative direction, looking for 5'-CAGTAGGACTGG-3', 0.
- inverse negative strand, positive direction, looking for 5'-CAGTAGGACTGG-3', 0.
- inverse positive strand, negative direction, looking for 5'-CAGTAGGACTGG-3', 0.
- inverse positive strand, positive direction, looking for 5'-CAGTAGGACTGG-3', 0.

# ERE1 (Driscoll) samplings
Copying a responsive elements consensus sequence GGTCA and putting the sequence in "F" finds five between ZNF497 and A1BG or six between ZSCAN22 and A1BG as can be found by the computer programs.
For the Basic programs testing consensus sequence GGTCA (starting with SuccessablesERE1.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:
- negative strand, negative direction: 6, GGTCA at 4415, GGTCA at 2654, GGTCA at 2601, GGTCA at 2211, GGTCA at 1532, GGTCA at 1352.
- positive strand, negative direction: 8, GGTCA at 4307, GGTCA at 2585, GGTCA at 2248, GGTCA at 712, GGTCA at 576, GGTCA at 568, GGTCA at 439, GGTCA at 206.
- negative strand, positive direction: 5, GGTCA at 4269, GGTCA at 3820, GGTCA at 2220, GGTCA at 2035, GGTCA at 153.
- positive strand, positive direction: 7, GGTCA at 3841, GGTCA at 3379, GGTCA at 3082, GGTCA at 2996, GGTCA at 2605, GGTCA at 2024, GGTCA at 1250.

## ERE1 (4560-2846) UTRs
- Negative strand, negative direction: GGTCA at 4415.
- Positive strand, negative direction: GGTCA at 4307.

## ERE1 positive direction (4445-4265) core promoters
- Negative strand, positive direction: GGTCA at 4269.

## ERE1 negative direction (2811-2596) proximal promoters
- Negative strand, negative direction: GGTCA at 2654, GGTCA at 2601.

## ERE1 negative direction (2596-1) distal promoters
- Negative strand, negative direction: GGTCA at 2211, GGTCA at 1532, GGTCA at 1352.
- Positive strand, negative direction: GGTCA at 2585, GGTCA at 2248, GGTCA at 712, GGTCA at 576, GGTCA at 568, GGTCA at 439, GGTCA at 206.

## ERE1 positive direction (4050-1) distal promoters
- Negative strand, positive direction: GGTCA at 3820, GGTCA at 2220, GGTCA at 2035, GGTCA at 153.
- Positive strand, positive direction: GGTCA at 3841, GGTCA at 3379, GGTCA at 3082, GGTCA at 2996, GGTCA at 2605, GGTCA at 2024, GGTCA at 1250.

# ERE1 (Driscoll) random dataset samplings
- ERE1r0: 4, GGTCA at 3832, GGTCA at 1984, GGTCA at 845, GGTCA at 699.
- ERE1r1: 6, GGTCA at 4483, GGTCA at 3425, GGTCA at 2777, GGTCA at 2237, GGTCA at 1750, GGTCA at 1572.
- ERE1r2: 7, GGTCA at 4381, GGTCA at 3905, GGTCA at 3163, GGTCA at 2185, GGTCA at 467, GGTCA at 141, GGTCA at 23.
- ERE1r3: 9, GGTCA at 3843, GGTCA at 3505, GGTCA at 2854, GGTCA at 2303, GGTCA at 2238, GGTCA at 1631, GGTCA at 1051, GGTCA at 747, GGTCA at 600.
- ERE1r4: 1, GGTCA at 3806.
- ERE1r5: 3, GGTCA at 4296, GGTCA at 4051, GGTCA at 2696.
- ERE1r6: 3, GGTCA at 2736, GGTCA at 1832, GGTCA at 60.
- ERE1r7: 4, GGTCA at 4457, GGTCA at 3894, GGTCA at 972, GGTCA at 634.
- ERE1r8: 3, GGTCA at 3493, GGTCA at 3433, GGTCA at 2694.
- ERE1r9: 3, GGTCA at 4379, GGTCA at 3055, GGTCA at 2056.

## ERE1r arbitrary (evens) (4560-2846) UTRs
- ERE1r0: GGTCA at 3832.
- ERE1r2: GGTCA at 4381, GGTCA at 3905, GGTCA at 3163.
- ERE1r4: GGTCA at 3806.
- ERE1r8: GGTCA at 3493, GGTCA at 3433.

## ERE1r alternate (odds) (4560-2846) UTRs
- ERE1r1: GGTCA at 4483, GGTCA at 3425.
- ERE1r3: GGTCA at 3843, GGTCA at 3505, GGTCA at 2854.
- ERE1r5: GGTCA at 4296, GGTCA at 4051.
- ERE1r7: GGTCA at 4457, GGTCA at 3894.
- ERE1r9: GGTCA at 4379, GGTCA at 3055.

## ERE1r arbitrary positive direction (odds) (4445-4265) core promoters
- ERE1r5: GGTCA at 4296.
- ERE1r9: GGTCA at 4379.

## ERE1r alternate positive direction (evens) (4445-4265) core promoters
- ERE1r2: GGTCA at 4381.

## ERR1r arbitrary negative direction (evens) (2811-2596) proximal promoters
- ERE1r6: GGTCA at 2736.
- ERE1r8: GGTCA at 2694.

## ERE1r alternate negative direction (odds) (2811-2596) proximal promoters
- ERE1r1: GGTCA at 2777.
- ERE1r5: GGTCA at 2696.

## ERE1r arbitrary positive direction (odds) (4265-4050) proximal promoters
- ERE1r5: GGTCA at 4051.

## ERE1r arbitrary negative direction (evens) (2596-1) distal promoters
- ERE1r0: GGTCA at 1984, GGTCA at 845, GGTCA at 699.
- ERE1r2: GGTCA at 2185, GGTCA at 467, GGTCA at 141, GGTCA at 23.
- ERE1r6: GGTCA at 1832, GGTCA at 60.

## ERE1r alternate negative direction (odds) (2596-1) distal promoters
- ERE1r1: GGTCA at 2237, GGTCA at 1750, GGTCA at 1572.
- ERE1r3: GGTCA at 2303, GGTCA at 2238, GGTCA at 1631, GGTCA at 1051, GGTCA at 747, GGTCA at 600.
- ERE1r7: GGTCA at 972, GGTCA at 634.
- ERE1r9: GGTCA at 2056.

## ERE1r arbitrary positive direction (odds) (4050-1) distal promoters
- ERE1r1: GGTCA at 3425, GGTCA at 2777, GGTCA at 2237, GGTCA at 1750, GGTCA at 1572.
- ERE1r3: GGTCA at 3843, GGTCA at 3505, GGTCA at 2854, GGTCA at 2303, GGTCA at 2238, GGTCA at 1631, GGTCA at 1051, GGTCA at 747, GGTCA at 600.
- ERE1r5: GGTCA at 2696.
- ERE1r7: GGTCA at 3894, GGTCA at 972, GGTCA at 634.
- ERE1r9: GGTCA at 3055, GGTCA at 2056.

## ERE1r alternate positive direction (evens) (4050-1) distal promoters
- ERE1r0: GGTCA at 3832, GGTCA at 1984, GGTCA at 845, GGTCA at 699.
- ERE1r2: GGTCA at 3905, GGTCA at 3163, GGTCA at 2185, GGTCA at 467, GGTCA at 141, GGTCA at 23.
- ERE1r4: GGTCA at 3806.
- ERE1r6: GGTCA at 2736, GGTCA at 1832, GGTCA at 60.
- ERE1r8: GGTCA at 3493, GGTCA at 3433, GGTCA at 2694.

# ERE1 (Driscoll) analysis and results
"The underlined core consensus sequence  represents the minimum length for binding activity."
Comparison:
The occurrences of real ERE1 UTRs overlap at the high end, cores, proximals and distals are greater than the randoms. This suggests that the real ERE1s are likely active or activable.

# ERE2 (Driscoll) samplings
Copying a responsive elements consensus sequence TGACC and putting the sequence in "F" finds none between ZNF497 and A1BG or none between ZSCAN22 and A1BG as can be found by the computer programs.
For the Basic programs testing consensus sequence TGACC (starting with SuccessablesERE2.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:
- inverse complement, negative strand, negative direction: 1, TGACC at 3749.
- inverse complement, positive strand, negative direction: 2, TGACC at 2189, TGACC at 734.
- inverse complement, negative strand, positive direction: 7, TGACC at 4216, TGACC at 4018, TGACC at 3784, TGACC at 3714, TGACC at 2873, TGACC at 2213, TGACC at 1662.
- inverse complement, positive strand, positive direction: 5, TGACC at 3345, TGACC at 3117, TGACC at 1953, TGACC at 1140, TGACC at 347.

## ERE2 (4560-2846) UTRs
- Negative strand, negative direction: TGACC at 3749.

## ERE2 positive direction (4445-4265) core promoters
- Positive strand, positive direction: TGACC at 3345, TGACC at 3117.

## ERE2 positive direction (4265-4050) proximal promoters
- Negative strand, positive direction: TGACC at 4216.

## ERE2 negative direction (2596-1) distal promoters
- Positive strand, negative direction: TGACC at 2189, TGACC at 734.

## ERE2 positive direction (4050-1) distal promoters
- Negative strand, positive direction: TGACC at 4018, TGACC at 3784, TGACC at 3714, TGACC at 2873, TGACC at 2213, TGACC at 1662.
- Positive strand, positive direction: TGACC at 3345, TGACC at 3117, TGACC at 1953, TGACC at 1140, TGACC at 347.

# ERE2 (Driscoll) random dataset samplings
- ERE2r0ci: 5, TGACC at 4380, TGACC at 2730, TGACC at 1834, TGACC at 1659, TGACC at 727.
- ERE2r1ci: 6, TGACC at 3635, TGACC at 3358, TGACC at 3323, TGACC at 3051, TGACC at 1160, TGACC at 154.
- ERE2r2ci: 4, TGACC at 3755, TGACC at 3580, TGACC at 3542, TGACC at 853.
- ERE2r3ci: 3, TGACC at 4438, TGACC at 3102, TGACC at 2442.
- ERE2r4ci: 3, TGACC at 2892, TGACC at 2131, TGACC at 344.
- ERE2r5ci: 2, TGACC at 2537, TGACC at 505.
- ERE2r6ci: 5, TGACC at 3520, TGACC at 3192, TGACC at 2398, TGACC at 1623, TGACC at 1345.
- ERE2r7ci: 3, TGACC at 3800, TGACC at 3140, TGACC at 898.
- ERE2r8ci: 4, TGACC at 1241, TGACC at 776, TGACC at 539, TGACC at 509.
- ERE2r9ci: 2, TGACC at 4209, TGACC at 3680.

## ERE2r arbitrary (evens) (4560-2846) UTRs
- ERE2r0ci: TGACC at 4380.
- ERE2r2ci: TGACC at 3755, TGACC at 3580, TGACC at 3542.
- ERE2r4ci: TGACC at 2892.
- ERE2r6ci: TGACC at 3520, TGACC at 3192.

## ERE2r alternate (odds) (4560-2846) UTRs
- ERE2r1ci: TGACC at 3635, TGACC at 3358, TGACC at 3323, TGACC at 3051.
- ERE2r3ci: TGACC at 4438, TGACC at 3102.
- ERE2r7ci: TGACC at 3800, TGACC at 3140.
- ERE2r9ci: TGACC at 4209, TGACC at 3680.

## ERE2r arbitrary positive direction (odds) (4445-4265) core promoters
- ERE2r3ci: TGACC at 4438.

## ERE2r alternate positive direction (evens) (4445-4265) core promoters
- ERE2r0ci: TGACC at 4380.

## ERE2r arbitrary negative direction (evens) (2811-2596) proximal promoters
- ERE2r0ci: TGACC at 2730.

## ERE2r arbitrary positive direction (odds) (4265-4050) proximal promoters
- ERE2r9ci: TGACC at 4209.

## ERE2r arbitrary negative direction (evens) (2596-1) distal promoters
- ERE2r0ci: TGACC at 1834, TGACC at 1659, TGACC at 727.
- ERE2r2ci: TGACC at 853.
- ERE2r4ci: TGACC at 2131, TGACC at 344.
- ERE2r6ci: TGACC at 2398, TGACC at 1623, TGACC at 1345.
- ERE2r8ci: TGACC at 1241, TGACC at 776, TGACC at 539, TGACC at 509.

## ERE2r alternate negative direction (odds) (2596-1) distal promoters
- ERE2r1ci: TGACC at 1160, TGACC at 154.
- ERE2r3ci: TGACC at 2442.
- ERE2r5ci: TGACC at 2537, TGACC at 505.
- ERE2r7ci: TGACC at 898.

## ERE2r arbitrary positive direction (odds) (4050-1) distal promoters
- ERE2r1ci: TGACC at 3635, TGACC at 3358, TGACC at 3323, TGACC at 3051, TGACC at 1160, TGACC at 154.
- ERE2r3ci: TGACC at 3102, TGACC at 2442.
- ERE2r5ci: TGACC at 2537, TGACC at 505.
- ERE2r7ci: TGACC at 3800, TGACC at 3140, TGACC at 898.
- ERE2r9ci: TGACC at 3680.

## ERE2r alternate positive direction (evens) (4050-1) distal promoters
- ERE2r0ci: TGACC at 2730, TGACC at 1834, TGACC at 1659, TGACC at 727.
- ERE2r2ci: TGACC at 3755, TGACC at 3580, TGACC at 3542, TGACC at 853.
- ERE2r4ci: TGACC at 2892, TGACC at 2131, TGACC at 344.
- ERE2r6ci: TGACC at 3520, TGACC at 3192, TGACC at 2398, TGACC at 1623, TGACC at 1345.
- ERE2r8ci: TGACC at 1241, TGACC at 776, TGACC at 539, TGACC at 509.

# ERE2 (Driscoll) analysis and results
"The underlined core consensus sequence  represents the minimum length for binding activity."
Comparison:
The occurrences of real ERE2 UTRs are less than the randoms, cores, proximals and distals are greater than the randoms. This suggests that the real ERE2s are likely active or activable.