Tapetum box gene transcriptions

Associate Editor(s)-in-Chief: Henry A. Hoff

Consensus sequences

The consensus sequence for the TAPETUM box is TCGTGT.

Tapetum box samplings

Copying the consensus Tapetum box: TCGTGT and putting the sequence in "⌘F" finds one location between ZNF497 and A1BG and one between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence TCGTGT (starting with SuccessablesTAP.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:

1. negative strand, negative direction, looking for TCGTGT, 1, TCGTGT at 3915.
2. positive strand, negative direction, looking for TCGTGT, 0.
3. positive strand, positive direction, looking for TCGTGT, 1, TCGTGT at 3740.
4. negative strand, positive direction, looking for TCGTGT, 1, TCGTGT at 80.
5. complement, negative strand, negative direction, looking for AGCACA, 0.
6. complement, positive strand, negative direction, looking for AGCACA, 1, AGCACA at 3915.
7. complement, positive strand, positive direction, looking for AGCACA, 1, AGCACA at 80.
8. complement, negative strand, positive direction, looking for AGCACA, 1, AGCACA at 3740.
9. inverse complement, negative strand, negative direction, looking for ACACGA, 1, ACACGA at 4402.
10. inverse complement, positive strand, negative direction, looking for ACACGA, 1, ACACGA at 4471.
11. inverse complement, positive strand, positive direction, looking for ACACGA, 0.
12. inverse complement, negative strand, positive direction, looking for ACACGA, 0.
13. inverse negative strand, negative direction, looking for TGTGCT, 1, TGTGCT at 4471.
14. inverse positive strand, negative direction, looking for TGTGCT, 1, TGTGCT at 4402.
15. inverse positive strand, positive direction, looking for TGTGCT, 0.
16. inverse negative strand, positive direction, looking for TGTGCT, 0.

TAP (4560-2846) UTRs

1. Negative strand, negative direction: TCGTGT at 3915.
2. Negative strand, negative direction: ACACGA at 4402.
3. Positive strand, negative direction: ACACGA at 4471.

TAP positive direction (4050-1) distal promoters

1. Negative strand, positive direction: TCGTGT at 80.
2. Positive strand, positive direction: TCGTGT at 3740.

TAP random dataset samplings

1. TAPr0: 0.
2. TAPr1: 1, TCGTGT at 1378.
3. TAPr2: 1, TCGTGT at 1998.
4. RDr3: 0.
5. RDr4: 0.
6. RDr5: 0.
7. RDr6: 0.
8. RDr7: 0.
9. RDr8: 0.
10. RDr9: 0.
11. RDr0ci: 0.
12. RDr1ci: 0.
13. RDr2ci: 0.
14. RDr3ci: 0.
15. RDr4ci: 0.
16. RDr5ci: 0.
17. RDr6ci: 0.
18. RDr7ci: 0.
19. RDr8ci: 0.
20. RDr9ci: 0.

TAPr alternate negative direction (odds) (2596-1) distal promoters

1. TAPr1: TCGTGT at 1378.

TAPr arbitrary positive direction (odds) (4050-1) distal promoters

1. TAPr1: TCGTGT at 1378.

TAP analysis and results

Main article: Complex locus A1BG and ZNF497 § TAPs

The consensus sequence for the TAPETUM box is TCGTGT.

Reals or randoms	Promoters	direction	Numbers	Strands	Occurrences	Averages (± 0.1)
Reals	UTR	negative	0	2	0	0
Randoms	UTR	arbitrary negative	0	10	0	0
Randoms	UTR	alternate negative	0	10	0	0
Reals	Core	negative	0	2	0	0
Randoms	Core	arbitrary negative	0	10	0	0
Randoms	Core	alternate negative	0	10	0	0
Reals	Core	positive	0	2	0	0
Randoms	Core	arbitrary positive	0	10	0	0
Randoms	Core	alternate positive	0	10	0	0
Reals	Proximal	negative	0	2	0	0
Randoms	Proximal	arbitrary negative	0	10	0	0
Randoms	Proximal	alternate negative	0	10	0	0
Reals	Proximal	positive	0	2	0	0
Randoms	Proximal	arbitrary positive	0	10	0	0
Randoms	Proximal	alternate positive	0	10	0	0
Reals	Distal	negative	0	2	0	0
Randoms	Distal	arbitrary negative	0	10	0	0
Randoms	Distal	alternate negative	0	10	0	0
Reals	Distal	positive	0	2	0	0
Randoms	Distal	arbitrary positive	0	10	0	0
Randoms	Distal	alternate positive	0	10	0	0

Comparison:

The occurrences of real TAPs are greater than the randoms. This suggests that the real TAPs are likely active or activable.

See also

• Complex locus A1BG and ZNF497
• Transcription factor