Aft1p gene transcriptions
Aft1 is Affinity Capture-Western; Two-hybrid.

# Consensus sequences
The upstream activating sequence (UAS) for Aft1p is PyPuCACCCPu or (C/T)(A/G)CACCC(A/G).

# Hypotheses
- A1BG has no Aft1p in either promoter.
- A1BG is not transcribed by an Aft1p.
- Aft1p does not participate in the transcription of A1BG.

# AFT1 samplings
Copying TGCACCC in "F" yields none between ZSCAN22 and A1BG and one TGCACCCG between ZNF497 and A1BG as can be found by the computer programs.
For the Basic programs testing consensus sequence (C/T)(A/G)CACCC(A/G) (starting with SuccessablesAFT.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 (C/T)(A/G)CACCC(A/G), 0.
- negative strand, positive direction, looking for (C/T)(A/G)CACCC(A/G), 1, TGCACCCG at 3324.
- positive strand, negative direction, looking for (C/T)(A/G)CACCC(A/G), 0.
- positive strand, positive direction, looking for (C/T)(A/G)CACCC(A/G), 0.
- inverse complement, negative strand, negative direction, looking for (C/T)GGGTG(C/T)(A/G), 1, TGGGTGTG at 1804.
- inverse complement, negative strand, positive direction, looking for (C/T)GGGTG(C/T)(A/G), 0.
- inverse complement, positive strand, negative direction, looking for (C/T)GGGTG(C/T)(A/G), 3, TGGGTGTG at 3185, CGGGTGCG at 2196, CGGGTGCG at 379.
- inverse complement, positive strand, positive direction, looking for (C/T)GGGTG(C/T)(A/G), 0.

## AFT (4560-2846) UTRs
- Positive strand, negative direction: TGGGTGTG at 3185.

## AFT negative direction (2596-1) distal promoters
- Negative strand, negative direction: TGGGTGTG at 1804.
- Positive strand, negative direction: CGGGTGCG at 2196, CGGGTGCG at 379.

## AFT positive direction (4050-1) distal promoters
- Negative strand, positive direction: TGCACCCG at 3324.

# AFT random dataset samplings
- AFTr0: 0.
- AFTr1: 1, CGCACCCA at 237.
- AFTr2: 0.
- AFTr3: 0.
- AFTr4: 0.
- AFTr5: 0.
- AFTr6: 0.
- AFTr7: 0.
- AFTr8: 1, CACACCCG at 1053.
- AFTr9: 0.
- AFTr0ci: 1, TGGGTGCG at 643.
- AFTr1ci: 2, TGGGTGTA at 4170, TGGGTGTA at 2489.
- AFTr2ci: 1, TGGGTGCA at 2005.
- AFTr3ci: 0.
- AFTr4ci: 0.
- AFTr5ci: 1, TGGGTGTA at 2219.
- AFTr6ci: 0.
- AFTr7ci: 0.
- AFTr8ci: 0.
- AFTr9ci: 1, TGGGTGCG at 3727.

## AFTr alternate (odds) (4560-2846) UTRs
- AFTr1ci: TGGGTGTA at 4170.
- AFTr9ci: TGGGTGCG at 3727.

## AFTr arbitrary positive direction (odds) (4265-4050) proximal promoters
- AFTr1ci: TGGGTGTA at 4170.

## AFTr arbitrary negative direction (evens) (2596-1) distal promoters
- AFTr8: CACACCCG at 1053.
- AFTr0ci: TGGGTGCG at 643.
- AFTr2ci: TGGGTGCA at 2005.

## AFTr alternate negative direction (odds) (2596-1) distal promoters
- AFTr1: CGCACCCA at 237.
- AFTr1ci: TGGGTGTA at 2489.
- AFTr5ci: TGGGTGTA at 2219.

## AFTr arbitrary positive direction (odds) (4050-1) distal promoters
- AFTr1: CGCACCCA at 237.
- AFTr1ci: TGGGTGTA at 2489.
- AFTr5ci: TGGGTGTA at 2219.
- AFTr9ci: TGGGTGCG at 3727.

## AFTr alternate positive direction (evens) (4050-1) distal promoters
- AFTr8: CACACCCG at 1053.
- AFTr0ci: TGGGTGCG at 643.
- AFTr2ci: TGGGTGCA at 2005.

# AFT analysis and results
The upstream activating sequence (UAS) for Aft1p is PyPuCACCCPu or (C/T)(A/G)CACCC(A/G).
Comparison:
The occurrences of real AFTs are greater than the randoms. This suggests that the real AFTs are likely active or activable.

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