Alpha-amylase conserved element gene transcriptions
"A few genes were also noticed with the shoot (GATAatGATG) and root (TGACGTCA) specific elements, cell cycle regulation (CCCAACGGT), seed-specific element (CATGCATG) and alpha-amylase conserved elements (TATCCATCCATCC). The presence of a significant number of the regulatory elements suggests strong participation of the U-box E3 gene family in plant development and responses under abiotic and biotic stress conditions. The data also supports the active involvement of the U-box E3 gene family in hormonal regulatory pathways."

# Consensus sequences
TATCCATCCATCC

# Hypotheses
- A1BG has no A boxes in either promoter.
- A1BG is not transcribed by an ATA box.
- AGCE1 does not participate in the transcription of A1BG.

# Alpha-amylase conserved element samplings
Copying a responsive elements consensus sequence TATCCA 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 TATCCATCCATCC (starting with SuccessablesAAC.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'-TATCCATCCATCC-3', 0.
- negative strand, positive direction, looking for 5'-TATCCATCCATCC-3', 0.
- positive strand, negative direction, looking for 5'-TATCCATCCATCC-3', 0.
- positive strand, positive direction, looking for 5'-TATCCATCCATCC-3', 0.
- complement, negative strand, negative direction, looking for 5'-ATAGGTAGGTAGG-3', 0.
- complement, negative strand, positive direction, looking for 5'-ATAGGTAGGTAGG-3', 0.
- complement, positive strand, negative direction, looking for 5'-ATAGGTAGGTAGG-3', 0.
- complement, positive strand, positive direction, looking for 5'-ATAGGTAGGTAGG-3', 0.
- inverse complement, negative strand, negative direction, looking for 5'-GGATGGATGGATA-3', 0.
- inverse complement, negative strand, positive direction, looking for 5'-GGATGGATGGATA-3', 0.
- inverse complement, positive strand, negative direction, looking for 5'-GGATGGATGGATA-3', 0.
- inverse complement, positive strand, positive direction, looking for 5'-GGATGGATGGATA-3', 0.
- inverse negative strand, negative direction, looking for 5'-CCTACCTACCTAT-3', 0.
- inverse negative strand, positive direction, looking for 5'-CCTACCTACCTAT-3', 0.
- inverse positive strand, negative direction, looking for 5'-CCTACCTACCTAT-3', 0.
- inverse positive strand, positive direction, looking for 5'-CCTACCTACCTAT-3', 0.

# Alpha-amylase conserved element portion samplings
Copying a responsive elements consensus sequence TATCCA 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 TATCCA (starting with SuccessablesAACp.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: 1, TATCCA at 1530.
- Negative strand, positive direction: 0.
- Positive strand, positive direction: 0.
- inverse complement, negative strand, negative direction: 1, TGGATA at 2996.
- inverse complement, positive strand, negative direction: 0.
- inverse complement, negative strand, positive direction: 1, TGGATA at 2737.
- inverse complement, positive strand, positive direction: 0.

## AACp (4560-2846) UTRs
- Negative strand, negative direction: TGGATA at 2996.

## AACp negative direction (2596-1) distal promoters
- Positive strand, negative direction: TATCCA at 1530.

## AACp positive direction (4050-1) distal promoters
- Negative strand, positive direction: TGGATA at 2737.

# Alpha-amylase conserved element portion random dataset samplings
- ACCpr0: 1, TATCCA at 279.
- ACCpr1: 0.
- ACCpr2: 0.
- ACCpr3: 1, TATCCA at 1875.
- ACCpr4: 1, TATCCA at 2560.
- ACCpr5: 1, TATCCA at 651.
- ACCpr6: 4, TATCCA at 2353, TATCCA at 1930, TATCCA at 1762, TATCCA at 1752.
- ACCpr7: 1, TATCCA at 2349.
- ACCpr8: 1, TATCCA at 2418.
- ACCpr9: 0.
- ACCpr0ci: 2, TGGATA at 3537, TGGATA at 2990.
- ACCpr1ci: 1, TGGATA at 2154.
- ACCpr2ci: 0.
- ACCpr3ci: 0.
- ACCpr4ci: 1, TGGATA at 4275.
- ACCpr5ci: 0.
- ACCpr6ci: 0.
- ACCpr7ci: 1, TGGATA at 2719.
- ACCpr8ci: 0.
- ACCpr9ci: 0.

## ACCpr arbitrary (evens) (4560-2846) UTRs
- ACCpr0ci: TGGATA at 3537, TGGATA at 2990.
- ACCpr4ci: TGGATA at 4275.

## ACCpr alternate positive direction (evens) (4445-4265) core promoters
- ACCpr4ci: TGGATA at 4275.

## ACCpr alternate negative direction (odds) (2811-2596) proximal promoters
- ACCpr7ci: TGGATA at 2719.

## ACCpr arbitrary negative direction (evens) (2596-1) distal promoters
- ACCpr0: TATCCA at 279.
- ACCpr4: TATCCA at 2560.
- ACCpr6: TATCCA at 2353, TATCCA at 1930, TATCCA at 1762, TATCCA at 1752.
- ACCpr8: TATCCA at 2418.

## ACCpr alternate negative direction (odds) (2596-1) distal promoters
- ACCpr3: TATCCA at 1875.
- ACCpr7: TATCCA at 2349.

## ACCpr arbitrary positive direction (odds) (4050-1) distal promoters
- ACCpr3: TATCCA at 1875.
- ACCpr7: TATCCA at 2349.
- ACCpr7ci: TGGATA at 2719.

## ACCpr alternate positive direction (evens) (4050-1) distal promoters
- ACCpr0: TATCCA at 279.
- ACCpr4: TATCCA at 2560.
- ACCpr6: TATCCA at 2353, TATCCA at 1930, TATCCA at 1762, TATCCA at 1752.
- ACCpr8: TATCCA at 2418.
- ACCpr0ci: TGGATA at 3537, TGGATA at 2990.

# Alpha-amylase conserved element portion analysis and results
TATCCATCCATCC portion TATCCA.
Comparison:
The occurrences of real AACp UTRs and distals are greater than the randoms. This suggests that the real AACps are likely active or activable.

# Acknowledgements
The content on this page was first contributed by: Henry A. Hoff.