M35 box gene transcriptions: Difference between revisions

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# M35r1ci: 1, TGTCAA at 3514.
# M35r1ci: 1, TGTCAA at 3514.
# M35r2ci: 1, TGTCAA at 2691.
# M35r2ci: 1, TGTCAA at 2691.
# RDr3ci: 0.
# M35r3ci: 2, TGTCAA at 3612, TGTCAA at 102.
# RDr4ci: 0.
# M35r4ci: 0.
# RDr5ci: 0.
# M35r5ci: 0.
# RDr6ci: 0.
# M35r6ci: 0.
# RDr7ci: 0.
# M35r7ci: 1, TGTCAA at 1534.
# RDr8ci: 0.
# M35r8ci: 1, TGTCAA at 591.
# RDr9ci: 0.
# M35r9ci: 2, TGTCAA at 3574, TGTCAA at 1821.


===M35r arbitrary (evens) (4560-2846) UTRs===
===M35r arbitrary (evens) (4560-2846) UTRs===
Line 98: Line 98:
# M35r7: TTGACA at 3816.
# M35r7: TTGACA at 3816.
# M35r1ci: TGTCAA at 3514.
# M35r1ci: TGTCAA at 3514.
 
# M35r3ci: TGTCAA at 3612.
===RDr arbitrary negative direction (evens) (2846-2811) core promoters===
# M35r9ci: TGTCAA at 3574.
 
===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===


===M35r arbitrary negative direction (evens) (2811-2596) proximal promoters===
===M35r arbitrary negative direction (evens) (2811-2596) proximal promoters===


# M35r2ci: TGTCAA at 2691.
# M35r2ci: TGTCAA at 2691.
===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===


===M35r arbitrary negative direction (evens) (2596-1) distal promoters===
===M35r arbitrary negative direction (evens) (2596-1) distal promoters===
Line 121: Line 109:
# M35r4: TTGACA at 1412.
# M35r4: TTGACA at 1412.
# M35r0ci: TGTCAA at 1157.
# M35r0ci: TGTCAA at 1157.
# M35r8ci: TGTCAA at 591.


===M35r alternate negative direction (odds) (2596-1) distal promoters===
===M35r alternate negative direction (odds) (2596-1) distal promoters===


# M35r8: TTGACA at 1179.
# M35r8: TTGACA at 1179.
# M35r3ci: TGTCAA at 102.
# M35r7ci: TGTCAA at 1534.
# M35r9ci: TGTCAA at 1821.


===M35r arbitrary positive direction (odds) (4050-1) distal promoters===
===M35r arbitrary positive direction (odds) (4050-1) distal promoters===
Line 131: Line 123:
# M35r7: TTGACA at 3816.
# M35r7: TTGACA at 3816.
# M35r1ci: TGTCAA at 3514.
# M35r1ci: TGTCAA at 3514.
# M35r3ci: TGTCAA at 102.
# M35r7ci: TGTCAA at 1534.
# M35r9ci: TGTCAA at 3574, TGTCAA at 1821.


===M35r alternate positive direction (evens) (4050-1) distal promoters===
===M35r alternate positive direction (evens) (4050-1) distal promoters===
Line 139: Line 134:
# M35r0ci: TGTCAA at 3593, TGTCAA at 1157.
# M35r0ci: TGTCAA at 3593, TGTCAA at 1157.
# M35r2ci: TGTCAA at 2691.
# M35r2ci: TGTCAA at 2691.
# M35r8ci: TGTCAA at 591.


==M35 analysis and results==
==M35 analysis and results==

Revision as of 19:58, 24 June 2022

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

File:Escherichia coli - MUSE.jpg
Escherichia coli - Sculpture is in vitro. Credit: Luke Jerram.{{free media}}

"The trp promoter does not have a consensus Pribnow box sequence (T-T-A-A-C-T) but it does have a consensus -35 sequence (T-T-G-A-C-A)."[1]

The "degenerate -35 sequence, and the location of the Fis binding site, which forces a suboptimal 16 bp spacing between the -35 and -10 elements, allow only σs but not σ70 to function at proP (P2).[2]

Consensus sequences

"Two domains upstream of the start site of transcription have been identified for which a consensus sequence has been formulated (1-5). [One of these domains is] the -35 sequence (5'-T-T-G-A-C-A-3')".[1]

A1BG sampling

For the Basic programs (starting with SuccessablesM35.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 SuccessablesM35--.bas, looking for 3'-TTGACA-5', 2, 2, TTGACA at 4399, TTGACA at 477.
  2. negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesM35-+.bas, looking for 3'-TTGACA-5', 0,
  3. positive strand in the negative direction is SuccessablesM35+-.bas, looking for 3'-TTGACA-5', 0,
  4. positive strand in the positive direction is SuccessablesM35++.bas, looking for 3'-TTGACA-5', 0,
  5. complement, negative strand, negative direction is SuccessablesM35c--.bas, looking for 3'-AACTGT-5', 0,
  6. complement, negative strand, positive direction is SuccessablesM35c-+.bas, looking for 3'-AACTGT-5', 0,
  7. complement, positive strand, negative direction is SuccessablesM35c+-.bas, looking for 3'-AACTGT-5', 2, 3'-AACTGT-5', 477, 3'-AACTGT-5', 4399,
  8. complement, positive strand, positive direction is SuccessablesM35c++.bas, looking for 3'-AACTGT-5', 0,
  9. inverse complement, negative strand, negative direction is SuccessablesM35ci--.bas, looking for 3'-TGTCAA-5', 0,
  10. inverse complement, negative strand, positive direction is SuccessablesM35ci-+.bas, looking for 3'-TGTCAA-5', 0,
  11. inverse complement, positive strand, negative direction is SuccessablesM35ci+-.bas, looking for 3'-TGTCAA-5', 0,
  12. inverse complement, positive strand, positive direction is SuccessablesM35ci++.bas, looking for 3'-TGTCAA-5', 0,
  13. inverse, negative strand, negative direction, is SuccessablesM35i--.bas, looking for 3'-ACAGTT-5', 0,
  14. inverse, negative strand, positive direction, is SuccessablesM35i-+.bas, looking for 3'-ACAGTT-5', 0,
  15. inverse, positive strand, negative direction, is SuccessablesM35i+-.bas, looking for 3'-ACAGTT-5', 0,
  16. inverse, positive strand, positive direction, is SuccessablesM35i++.bas, looking for 3'-ACAGTT-5', 0.

M35 UTRs

  1. Negative, negative: TTGACA at 4399.

M35 negative direction distal promoters

  1. Negative, negative: TTGACA at 477.

M35 random dataset samplings

  1. M35r0: 2, TTGACA at 3699, TTGACA at 3168.
  2. M35r1: 1, TTGACA at 3785.
  3. M35r2: 0.
  4. M35r3: 0.
  5. M35r4: 1, TTGACA at 1412.
  6. M35r5: 0.
  7. M35r6: 1, TTGACA at 3332.
  8. M35r7: 1, TTGACA at 3816.
  9. M35r8: 1, TTGACA at 1179.
  10. M35r9: 0.
  11. M35r0ci: 2, TGTCAA at 3593, TGTCAA at 1157.
  12. M35r1ci: 1, TGTCAA at 3514.
  13. M35r2ci: 1, TGTCAA at 2691.
  14. M35r3ci: 2, TGTCAA at 3612, TGTCAA at 102.
  15. M35r4ci: 0.
  16. M35r5ci: 0.
  17. M35r6ci: 0.
  18. M35r7ci: 1, TGTCAA at 1534.
  19. M35r8ci: 1, TGTCAA at 591.
  20. M35r9ci: 2, TGTCAA at 3574, TGTCAA at 1821.

M35r arbitrary (evens) (4560-2846) UTRs

  1. M35r0: TTGACA at 3699, TTGACA at 3168.
  2. M35r6: TTGACA at 3332.
  3. M35r0ci: TGTCAA at 3593.

M35r alternate (odds) (4560-2846) UTRs

  1. M35r1: TTGACA at 3785.
  2. M35r7: TTGACA at 3816.
  3. M35r1ci: TGTCAA at 3514.
  4. M35r3ci: TGTCAA at 3612.
  5. M35r9ci: TGTCAA at 3574.

M35r arbitrary negative direction (evens) (2811-2596) proximal promoters

  1. M35r2ci: TGTCAA at 2691.

M35r arbitrary negative direction (evens) (2596-1) distal promoters

  1. M35r4: TTGACA at 1412.
  2. M35r0ci: TGTCAA at 1157.
  3. M35r8ci: TGTCAA at 591.

M35r alternate negative direction (odds) (2596-1) distal promoters

  1. M35r8: TTGACA at 1179.
  2. M35r3ci: TGTCAA at 102.
  3. M35r7ci: TGTCAA at 1534.
  4. M35r9ci: TGTCAA at 1821.

M35r arbitrary positive direction (odds) (4050-1) distal promoters

  1. M35r1: TTGACA at 3785.
  2. M35r7: TTGACA at 3816.
  3. M35r1ci: TGTCAA at 3514.
  4. M35r3ci: TGTCAA at 102.
  5. M35r7ci: TGTCAA at 1534.
  6. M35r9ci: TGTCAA at 3574, TGTCAA at 1821.

M35r alternate positive direction (evens) (4050-1) distal promoters

  1. M35r0: TTGACA at 3699, TTGACA at 3168.
  2. M35r4: TTGACA at 1412.
  3. M35r6: TTGACA at 3332.
  4. M35r0ci: TGTCAA at 3593, TGTCAA at 1157.
  5. M35r2ci: TGTCAA at 2691.
  6. M35r8ci: TGTCAA at 591.

M35 analysis and results

Main article: Complex locus A1BG and ZNF497 § Name of response elements

"Two domains upstream of the start site of transcription have been identified for which a consensus sequence has been formulated (1-5). [One of these domains is] the -35 sequence (5'-T-T-G-A-C-A-3')".[1]

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.

Initial content for this page in some instances incorporates text from the United States National Library of Medicine.

See also

References

  1. ↑ 1.0 1.1 1.2 Herman A. de Boer, Lisa J. Comstock, and Mark Vasser (January 1983). "The tac promoter: A functional hybrid derived from the trp and lac promoters" (PDF). Proceedings of the National Academy of Sciences USA. 80 (1): 21–5. Retrieved 2017-02-19.
  2. ↑ Athanasios Typas, Stefano Stella, Reid C. Johnson and Regine Hengge (9 January 2007). "The -35 sequence location and the Fis–sigma factor interface determine σs selectivity of the proP (P2) promoter in Escherichia coli". Molecular Microbiology. 63 (3): 780–796. doi:10.1111/j.1365-2958.2006.05560.x. Retrieved 10 November 2018.

External links

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