Pribnow box gene transcriptions: Difference between revisions

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|accessdate=2017-02-19 }}</ref>
|accessdate=2017-02-19 }}</ref>


==Samplings==
==Pribnow box samplings==


For the Basic programs (starting with SuccessablesPrib.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:
For the Basic programs (starting with SuccessablesPrib.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:
Line 52: Line 52:
# inverse, positive strand, negative direction, is SuccessablesPribi+-.bas, looking for 3'-TAATAT-5', 2, 3'-TAATAT-5', 272, 3'-TAATAT-5', 603,
# inverse, positive strand, negative direction, is SuccessablesPribi+-.bas, looking for 3'-TAATAT-5', 2, 3'-TAATAT-5', 272, 3'-TAATAT-5', 603,
# inverse, positive strand, positive direction, is SuccessablesPribi++.bas, looking for 3'-TAATAT-5', 1, 3'-TAATAT-5', 727.
# inverse, positive strand, positive direction, is SuccessablesPribi++.bas, looking for 3'-TAATAT-5', 1, 3'-TAATAT-5', 727.
===Prib (4560-2846) UTRs===
# Negative strand, negative direction: TATAAT at 3468, TATAAT at 3454.
===Prib negative direction (2596-1) distal promoters===
# Negative strand, negative direction: ATTATA at 603, ATTATA at 272.
===Prib positive direction (4050-1) distal promoters===
# Negative strand, positive direction: TATAAT at 729.
# Negative strand, positive direction: ATTATA at 727.
==Pribnow box random dataset samplings==
# RDr0: 0.
# RDr1: 0.
# RDr2: 0.
# RDr3: 0.
# RDr4: 0.
# RDr5: 0.
# RDr6: 0.
# RDr7: 0.
# RDr8: 0.
# RDr9: 0.
# RDr0ci: 0.
# RDr1ci: 0.
# RDr2ci: 0.
# RDr3ci: 0.
# RDr4ci: 0.
# RDr5ci: 0.
# RDr6ci: 0.
# RDr7ci: 0.
# RDr8ci: 0.
# RDr9ci: 0.
===RDr arbitrary (evens) (4560-2846) UTRs===
===RDr alternate (odds) (4560-2846) UTRs===
===RDr arbitrary negative direction (evens) (2846-2811) core promoters===
===RDr alternate negative direction (odds) (2846-2811) core promoters===
===RDr arbitrary positive direction (odds) (4445-4265) core promoters===
===RDr alternate positive direction (evens) (4445-4265) core promoters===
===RDr arbitrary negative direction (evens) (2811-2596) proximal promoters===
===RDr alternate negative direction (odds) (2811-2596) proximal promoters===
===RDr arbitrary positive direction (odds) (4265-4050) proximal promoters===
===RDr alternate positive direction (evens) (4265-4050) proximal promoters===
===RDr arbitrary negative direction (evens) (2596-1) distal promoters===
===RDr alternate negative direction (odds) (2596-1) distal promoters===
===RDr arbitrary positive direction (odds) (4050-1) distal promoters===
===RDr alternate positive direction (evens) (4050-1) distal promoters===
==Pribnow box analysis and results==
{{main|Complex locus A1BG and ZNF497#Pribs}}
The Pribnow box (5'-T-A-T-A-A-T) is in the -10 region.<ref name=Boer/>
{|class="wikitable"
|-
! 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 responsive element consensus sequences are greater than the randoms. This suggests that the real responsive element consensus sequences are likely active or activable.


==Acknowledgements==
==Acknowledgements==

Revision as of 01:45, 14 January 2023

Editor-In-Chief: Henry A. Hoff

"Although the first five bases of the conserved sequence are identical to the first five bases of the Pribnow box (TATAA), the sixth base of the Pribnow box is a 100 per cent conserved T (refs 15-17) while the 100 per cent conserved A found here is actually more similar to eukaryotic promoter sequences20."[1]

"Two domains upstream of the start site of transcription have been identified for which a consensus sequence has been formulated(1-5). These domains are the -35 sequence (5'-T-T-G-A-C-A) and the Pribnow box (5'-T-A-T-A-A-T) in the -10 region. Both domains are in close contact with the RNA polymerase during initiation of RNAsynthesis (2,6)."[2]

Pribnow box samplings

For the Basic programs (starting with SuccessablesPrib.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 in the negative direction (from ZSCAN22 to A1BG) is SuccessablesPrib--.bas, looking for 3'-TATAAT-5', 2, 3'-TATAAT-5', 3454, 3'-TATAAT-5', 3468,
  2. negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesPrib-+.bas, looking for 3'-TATAAT-5', 1, 3'-TATAAT-5', 729,
  3. positive strand in the negative direction is SuccessablesPrib+-.bas, looking for 3'-TATAAT-5', 0,
  4. positive strand in the positive direction is SuccessablesPrib++.bas, looking for 3'-TATAAT-5', 0,
  5. complement, negative strand, negative direction is SuccessablesPribc--.bas, looking for 3'-ATATTA-5', 0,
  6. complement, negative strand, positive direction is SuccessablesPribc-+.bas, looking for 3'-ATATTA-5', 0,
  7. complement, positive strand, negative direction is SuccessablesPribc+-.bas, looking for 3'-ATATTA-5', 2, 3'-ATATTA-5', 3454, 3'-ATATTA-5', 3468,
  8. complement, positive strand, positive direction is SuccessablesPribc++.bas, looking for 3'-ATATTA-5', 1, 3'-ATATTA-5', 729,
  9. inverse complement, negative strand, negative direction is SuccessablesPribci--.bas, looking for 3'-ATTATA-5', 2, 3'-ATTATA-5', 272, 3'-ATTATA-5', 603,
  10. inverse complement, negative strand, positive direction is SuccessablesPribci-+.bas, looking for 3'-ATTATA-5', 1, 3'-ATTATA-5', 727,
  11. inverse complement, positive strand, negative direction is SuccessablesPribci+-.bas, looking for 3'-ATTATA-5', 0,
  12. inverse complement, positive strand, positive direction is SuccessablesPribci++.bas, looking for 3'-ATTATA-5', 0,
  13. inverse, negative strand, negative direction, is SuccessablesPribi--.bas, looking for 3'-TAATAT-5', 0,
  14. inverse, negative strand, positive direction, is SuccessablesPribi-+.bas, looking for 3'-TAATAT-5', 0,
  15. inverse, positive strand, negative direction, is SuccessablesPribi+-.bas, looking for 3'-TAATAT-5', 2, 3'-TAATAT-5', 272, 3'-TAATAT-5', 603,
  16. inverse, positive strand, positive direction, is SuccessablesPribi++.bas, looking for 3'-TAATAT-5', 1, 3'-TAATAT-5', 727.

Prib (4560-2846) UTRs

  1. Negative strand, negative direction: TATAAT at 3468, TATAAT at 3454.

Prib negative direction (2596-1) distal promoters

  1. Negative strand, negative direction: ATTATA at 603, ATTATA at 272.

Prib positive direction (4050-1) distal promoters

  1. Negative strand, positive direction: TATAAT at 729.
  2. Negative strand, positive direction: ATTATA at 727.

Pribnow box random dataset samplings

  1. RDr0: 0.
  2. RDr1: 0.
  3. RDr2: 0.
  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.

RDr arbitrary (evens) (4560-2846) UTRs

RDr alternate (odds) (4560-2846) UTRs

RDr arbitrary negative direction (evens) (2846-2811) core promoters

RDr alternate negative direction (odds) (2846-2811) core promoters

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

RDr alternate positive direction (evens) (4445-4265) core promoters

RDr arbitrary negative direction (evens) (2811-2596) proximal promoters

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

RDr arbitrary positive direction (odds) (4265-4050) proximal promoters

RDr alternate positive direction (evens) (4265-4050) proximal promoters

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

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

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

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

Pribnow box analysis and results

Main article: Complex locus A1BG and ZNF497 § Pribs

The Pribnow box (5'-T-A-T-A-A-T) is in the -10 region.[2]

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 responsive element consensus sequences are greater than the randoms. This suggests that the real responsive element consensus sequences are likely active or activable.

Acknowledgements

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

Initial content for this page in some instances came from Wikiversity.

See also

References

  1. ↑ Alan C. Christensen & Elton T. Young (1982). "T4 late transcripts are initiated near a conserved DNA sequence". Nature. 299 (5881): 369–71. doi:10.1038/299369a0. Retrieved 2017-02-19. Unknown parameter |month= ignored (help)
  2. ↑ 2.0 2.1 Herman A. de Boer, Lisa J. Comstock, and Mark Vasser (1983). "The tac promoter: A functional hybrid derived from the trpand lac promoters" (PDF). Proceedings of the National Academy of Sciences USA. 80 (1): 21–5. Retrieved 2017-02-19. Unknown parameter |month= ignored (help)

External links

Template:Sisterlinks

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