Tapetum box gene transcriptions: Difference between revisions

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Line 131: Line 131:
! Reals or randoms !! Promoters !! direction !! Numbers !! Strands !! Occurrences !! Averages (± 0.1)  
! Reals or randoms !! Promoters !! direction !! Numbers !! Strands !! Occurrences !! Averages (± 0.1)  
|-
|-
| Reals || UTR || negative || 0 || 2 || 0 || 0  
| Reals || UTR || negative || 3 || 2 || 1.5 || 1.5 ± 0.5 (--2,+-1)
|-
|-
| Randoms || UTR || arbitrary negative || 0 || 10 || 0 || 0  
| Randoms || UTR || arbitrary negative || 1 || 10 || 0.1 || 0.15
|-
|-
| Randoms || UTR || alternate negative || 0 || 10 || 0 || 0  
| Randoms || UTR || alternate negative || 2 || 10 || 0.2 || 0.15
|-
|-
| Reals || Core || negative || 0 || 2 || 0 || 0  
| Reals || Core || negative || 0 || 2 || 0 || 0  
Line 145: Line 145:
| Reals || Core || positive || 0 || 2 || 0 || 0  
| Reals || Core || positive || 0 || 2 || 0 || 0  
|-
|-
| Randoms || Core || arbitrary positive || 0 || 10 || 0 || 0
| Randoms || Core || arbitrary positive || 1 || 10 || 0.1 || 0.05
|-
|-
| Randoms || Core || alternate positive || 0 || 10 || 0 || 0  
| Randoms || Core || alternate positive || 0 || 10 || 0 || 0.05
|-
|-
| Reals || Proximal || negative || 0 || 2 || 0 || 0  
| Reals || Proximal || negative || 0 || 2 || 0 || 0  
|-
|-
| Randoms || Proximal || arbitrary negative || 0 || 10 || 0 || 0  
| Randoms || Proximal || arbitrary negative || 0 || 10 || 0 || 0.05
|-
|-
| Randoms || Proximal || alternate negative || 0 || 10 || 0 || 0  
| Randoms || Proximal || alternate negative || 1 || 10 || 0.1 || 0.05
|-
|-
| Reals || Proximal || positive || 0 || 2 || 0 || 0  
| Reals || Proximal || positive || 0 || 2 || 0 || 0  
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| Reals || Distal || negative || 0 || 2 || 0 || 0  
| Reals || Distal || negative || 0 || 2 || 0 || 0  
|-
|-
| Randoms || Distal || arbitrary negative || 0 || 10 || 0 || 0
| Randoms || Distal || arbitrary negative || 3 || 10 || 0.3 || 0.4
|-
|-
| Randoms || Distal || alternate negative || 0 || 10 || 0 || 0  
| Randoms || Distal || alternate negative || 5 || 10 || 0.5 || 0.4
|-
|-
| Reals || Distal || positive || 0 || 2 || 0 || 0
| Reals || Distal || positive || 2 || 2 || 1 || 1
|-
|-
| Randoms || Distal || arbitrary positive || 0 || 10 || 0 || 0  
| Randoms || Distal || arbitrary positive || 7 || 10 || 0.7 || 0.55
|-
|-
| Randoms || Distal || alternate positive || 0 || 10 || 0 || 0  
| Randoms || Distal || alternate positive || 4 || 10 || 0.4 || 0.55
|}
|}


Comparison:
Comparison:


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


==See also==
==See also==

Revision as of 08:10, 16 February 2023

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

Human genes

Consensus sequences

The consensus sequence for the TAPETUM box is TCGTGT.[1]

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. TAPr3: 2, TCGTGT at 2199.
  5. TAPr4: 0.
  6. TAPr5: 0.
  7. TAPr6: 0.
  8. TAPr7: 2, TCGTGT at 4302, TCGTGT at 1401.
  9. TAPr8: 0.
  10. TAPr9: 0.
  11. TAPr0ci: 1, ACGCGA at 2550.
  12. TAPr1ci: 1, ACGCGA at 1698.
  13. TAPr2ci: 0.
  14. TAPr3ci: 1, ACGCGA at 3964.
  15. TAPr4ci: 0.
  16. TAPr5ci: 2, ACGCGA at 2701, ACGCGA at 2329.
  17. TAPr6ci: 1, ACGCGA at 2872.
  18. TAPr7ci: 0.
  19. TAPr8ci: 1, ACGCGA at 16.
  20. TAPr9ci: 0.

TAPr arbitrary (evens) (4560-2846) UTRs

  1. TAPr6ci: ACGCGA at 2872.

TAPr alternate (odds) (4560-2846) UTRs

  1. TAPr7: TCGTGT at 4302.
  2. TAPr3ci: ACGCGA at 3964.

TAPr arbitrary positive direction (odds) (4445-4265) core promoters

  1. TAPr7: TCGTGT at 4302.

TAPr alternate negative direction (odds) (2811-2596) proximal promoters

  1. TAPr5ci: ACGCGA at 2701.

TAPr arbitrary negative direction (evens) (2596-1) distal promoters

  1. TAPr2: TCGTGT at 1998.
  2. TAPr0ci: ACGCGA at 2550.
  3. TAPr8ci: ACGCGA at 16.

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

  1. TAPr1: TCGTGT at 1378.
  2. TAPr3: TCGTGT at 2199.
  3. TAPr7: TCGTGT at 1401.
  4. TAPr1ci: ACGCGA at 1698.
  5. TAPr5ci: ACGCGA at 2329.

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

  1. TAPr1: TCGTGT at 1378.
  2. TAPr3: TCGTGT at 2199.
  3. TAPr7: TCGTGT at 1401.
  4. TAPr1ci: ACGCGA at 1698.
  5. TAPr3ci: ACGCGA at 3964.
  6. TAPr5ci: ACGCGA at 2701, ACGCGA at 2329.

TAPr alternate positive direction (evens) (4050-1) distal promoters

  1. TAPr2: TCGTGT at 1998.
  2. TAPr0ci: ACGCGA at 2550.
  3. TAPr6ci: ACGCGA at 2872.
  4. TAPr8ci: ACGCGA at 16.

TAP analysis and results

Main article: Complex locus A1BG and ZNF497 § TAPs

The consensus sequence for the TAPETUM box is TCGTGT.[1]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 3 2 1.5 1.5 ± 0.5 (--2,+-1)
Randoms UTR arbitrary negative 1 10 0.1 0.15
Randoms UTR alternate negative 2 10 0.2 0.15
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 1 10 0.1 0.05
Randoms Core alternate positive 0 10 0 0.05
Reals Proximal negative 0 2 0 0
Randoms Proximal arbitrary negative 0 10 0 0.05
Randoms Proximal alternate negative 1 10 0.1 0.05
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 3 10 0.3 0.4
Randoms Distal alternate negative 5 10 0.5 0.4
Reals Distal positive 2 2 1 1
Randoms Distal arbitrary positive 7 10 0.7 0.55
Randoms Distal alternate positive 4 10 0.4 0.55

Comparison:

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

See also

References

  1. ↑ 1.0 1.1 Zi-Wei Ye, Jie Xu, Jianxin Shi, Dabing Zhang and Mee-Len Chye (January 2017). "Kelch-motif containing acyl-CoA binding proteins AtACBP4 and AtACBP5 are differentially expressed and function in floral lipid metabolism" (PDF). Plant Molecular Biology. 93: 209–225. doi:10.1007/s11103-016-0557-5. PMID 27826761. Retrieved 7 May 2020.

External links

Retrieved from "https://www.wikidoc.org/index.php?title=Tapetum_box_gene_transcriptions&oldid=1733137"