Circadian control element gene transcriptions
"The circadian control element (circadian; Anderson et al., 1994) was found in 10 FvTCP genes."

# Consensus sequences
Circadian control elements (CAANNNNATC).

# Hypotheses
- A1BG has no CCEs in either promoter.
- A1BG is not transcribed by a CCE.
- CCE does not participate in the transcription of A1BG.

# CCE samplings
Copying the consensus of the CCE: 5'-CAACTTTA-3' and putting the sequence in "F" finds no locations between ZSCAN22 and A1BG and no locations between ZNF497 and A1BG as can be found by the computer programs.
For the Basic programs testing consensus sequence 5'-CAANNNNATC-3' (starting with SuccessablesCCE.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'-CAANNNNATC-3', 0.
- negative strand, positive direction, looking for 5'-CAANNNNATC-3', 0.
- positive strand, negative direction, looking for 5'-CAANNNNATC-3', 0.
- positive strand, positive direction, looking for 5'-CAANNNNATC-3', 0.
- complement, negative strand, negative direction, looking for 5'-GTTNNNNTAG-3', 0.
- complement, negative strand, positive direction, looking for 5'-GTTNNNNTAG-3', 0.
- complement, positive strand, negative direction, looking for 5'-GTTNNNNTAG-3', 0.
- complement, positive strand, positive direction, looking for 5'-GTTNNNNTAG-3', 0.
- inverse complement, negative strand, negative direction, looking for 5'-GATNNNNTTG-3', 0.
- inverse complement, negative strand, positive direction, looking for 5'-GATNNNNTTG-3', 0.
- inverse complement, positive strand, negative direction, looking for 5'-GATNNNNTTG-3', 1, 5'-GATGGGGTTG-3' at 3804.
- inverse complement, positive strand, positive direction, looking for 5'-GATNNNNTTG-3', 0.
- inverse negative strand, negative direction, looking for 5'-CTANNNNAAC-3', 1, 5'-CTACCCCAAC-3' at 3804.
- inverse negative strand, positive direction, looking for 5'-CTANNNNAAC-3', 0.
- inverse positive strand, negative direction, looking for 5'-CTANNNNAAC-3', 0.
- inverse positive strand, positive direction, looking for 5'-CTANNNNAAC-3', 0.

## CCE (4560-2846) UTRs
- Positive strand, negative direction: GATGGGGTTG at 3804.

# CCE random dataset samplings
- CCEr0: 1, CAAGGGTATC at 334.
- CCEr1: 0.
- CCEr2: 2, CAACCGAATC at 2991, CAAACCGATC at 1749.
- CCEr3: 2, CAATCGCATC at 1734, CAAATGCATC at 162.
- CCEr4: 1, CAACGTCATC at 3915.
- CCEr5: 1, CAATGACATC at 2923.
- CCEr6: 2, CAACAATATC at 2053, CAAGGACATC at 793.
- CCEr7: 0.
- CCEr8: 1, CAACTCTATC at 1916.
- CCEr9: 0.
- CCEr0ci: 0.
- CCEr1ci: 4, GATACAGTTG at 3388, GATGACTTTG at 1638, GATTCCTTTG at 712, GATGTGCTTG at 351.
- CCEr2ci: 0.
- CCEr3ci: 2, GATTTCCTTG at 4300, GATGGATTTG at 3780.
- CCEr4ci: 0.
- CCEr5ci: 1, GATTGCCTTG at 3319.
- CCEr6ci: 0.
- CCEr7ci: 0.
- CCEr8ci: 0.
- CCEr9ci: 0.

## CCEr arbitrary (evens) (4560-2846) UTRs
- CCEr2: CAACCGAATC at 2991.
- CCEr4: CAACGTCATC at 3915.

## CCEr alternate (odds) (4560-2846) UTRs
- CCEr5: CAATGACATC at 2923.
- CCEr1ci: GATACAGTTG at 3388.
- CCEr3ci: GATTTCCTTG at 4300, GATGGATTTG at 3780.
- CCEr5ci: GATTGCCTTG at 3319.

## CCEr arbitrary positive direction (odds) (4445-4265) core promoters
- CCEr3ci: GATTTCCTTG at 4300.

## CCEr arbitrary negative direction (evens) (2596-1) distal promoters
- CCEr0: CAAGGGTATC at 334.
- CCEr2: CAAACCGATC at 1749.
- CCEr6: CAACAATATC at 2053, CAAGGACATC at 793.
- CCEr8: CAACTCTATC at 1916.

## CCEr alternate negative direction (odds) (2596-1) distal promoters
- CCEr3: CAATCGCATC at 1734, CAAATGCATC at 162.
- CCEr1ci: GATGACTTTG at 1638, GATTCCTTTG at 712, GATGTGCTTG at 351.

## CCEr arbitrary positive direction (odds) (4050-1) distal promoters
- CCEr3: CAATCGCATC at 1734, CAAATGCATC at 162.
- CCEr5: CAATGACATC at 2923.
- CCEr1ci: GATACAGTTG at 3388, GATGACTTTG at 1638, GATTCCTTTG at 712, GATGTGCTTG at 351.
- CCEr3ci: GATGGATTTG at 3780.
- CCEr5ci: GATTGCCTTG at 3319.

## CCEr alternate positive direction (evens) (4050-1) distal promoters
- CCEr0: CAAGGGTATC at 334.
- CCEr2: CAACCGAATC at 2991, CAAACCGATC at 1749.
- CCEr4: CAACGTCATC at 3915.
- CCEr6: CAACAATATC at 2053, CAAGGACATC at 793.
- CCEr8: CAACTCTATC at 1916.

# CCE analysis and results
Circadian control elements (CAANNNNATC).
Comparison:
The occurrences of real CCEs overlaps the high randoms. This suggests that the real CCEs are may be random.

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