Ste12p gene transcriptions: Difference between revisions

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# positive strand, positive direction, looking for TGAAAC, 0.
# positive strand, positive direction, looking for TGAAAC, 0.
# negative strand, positive direction, looking for TGAAAC, 1, TGAAAC at 2147.
# negative strand, positive direction, looking for TGAAAC, 1, TGAAAC at 2147.
# complement, negative strand, negative direction, looking for ACTTTG, 8, ACTTTG at 3147, ACTTTG at 2620, ACTTTG at 2283, ACTTTG at 1856, ACTTTG at 1583, ACTTTG at 1213, ACTTTG at 474, ACTTTG at 127.
# complement, positive strand, negative direction, looking for ACTTTG, 12, ACTTTG at 4462, ACTTTG at 3985, ACTTTG at 3076, ACTTTG at 2553, ACTTTG at 2217, ACTTTG at 2100, ACTTTG at 1791, ACTTTG at 1688, ACTTTG at 1146, ACTTTG at 682, ACTTTG at 546, ACTTTG at 409.
# complement, positive strand, positive direction, looking for ACTTTG, 1, ACTTTG at 2147.
# complement, negative strand, positive direction, looking for ACTTTG, 0.
# inverse complement, negative strand, negative direction, looking for GTTTCA, 0.
# inverse complement, negative strand, negative direction, looking for GTTTCA, 0.
# inverse complement, positive strand, negative direction, looking for GTTTCA, 0.
# inverse complement, positive strand, negative direction, looking for GTTTCA, 0.
# inverse complement, positive strand, positive direction, looking for GTTTCA, 0.
# inverse complement, positive strand, positive direction, looking for GTTTCA, 0.
# inverse complement, negative strand, positive direction, looking for GTTTCA, 2, GTTTCA at 2302, GTTTCA at 2264.
# inverse complement, negative strand, positive direction, looking for GTTTCA, 2, GTTTCA at 2302, GTTTCA at 2264.
# inverse negative strand, negative direction, looking for CAAAGT, 0.
# inverse positive strand, negative direction, looking for CAAAGT, 0.
# inverse positive strand, positive direction, looking for CAAAGT, 2, CAAAGT at 2302, CAAAGT at 2264.
# inverse negative strand, positive direction, looking for CAAAGT, 0.


===STE UTRs===
===STE (4560-2846) UTRs===
{{main|UTR promoter gene transcriptions}}
Negative strand, negative direction: TGAAAC at 4462, TGAAAC at 3985, TGAAAC at 3076.


Positive strand, negative direction: TGAAAC at 3147.
# Negative strand, negative direction: TGAAAC at 4462, TGAAAC at 3985, TGAAAC at 3076.
# Positive strand, negative direction: TGAAAC at 3147.


===STE proximal promoters===
===STE negative direction (2811-2596) proximal promoters===
{{main|Proximal promoter gene transcriptions}}
Positive strand, negative direction: TGAAAC at 2620.


===STE distal promoters===
# Positive strand, negative direction: TGAAAC at 2620.
{{main|Distal promoter gene transcriptions}}
Negative strand, negative direction: TGAAAC at 2553, TGAAAC at 2217, TGAAAC at 2100, TGAAAC at 1791, TGAAAC at 1688, TGAAAC at 1146, TGAAAC at 682, TGAAAC at 546, TGAAAC at 409.


Positive strand, negative direction: TGAAAC at 2283, TGAAAC at 1856, TGAAAC at 1583, TGAAAC at 1213, TGAAAC at 474, TGAAAC at 127.
===STE negative direction (2596-1) distal promoters===


Negative strand, positive direction: GTTTCA at 2302, GTTTCA at 2264, TGAAAC at 2147.
# Negative strand, negative direction: TGAAAC at 2553, TGAAAC at 2217, TGAAAC at 2100, TGAAAC at 1791, TGAAAC at 1688, TGAAAC at 1146, TGAAAC at 682, TGAAAC at 546, TGAAAC at 409.
# Positive strand, negative direction: TGAAAC at 2283, TGAAAC at 1856, TGAAAC at 1583, TGAAAC at 1213, TGAAAC at 474, TGAAAC at 127.
 
===STE positive direction (4050-1) distal promoters===
 
# Negative strand, positive direction: TGAAAC at 2147.
# Negative strand, positive direction: GTTTCA at 2302, GTTTCA at 2264.
 
==STE random dataset samplings==
 
# STEr0: 3, TGAAAC at 3417, TGAAAC at 1932, TGAAAC at 902.
# STEr1: 2, TGAAAC at 3795, TGAAAC at 2244.
# STEr2: 2, TGAAAC at 1991, TGAAAC at 1629.
# STEr3: 0.
# STEr4: 2, TGAAAC at 3254, TGAAAC at 819.
# STEr5: 0.
# STEr6: 2, TGAAAC at 1714, TGAAAC at 1098.
# STEr7: 3, TGAAAC at 4202, TGAAAC at 3828, TGAAAC at 3531.
# STEr8: 0.
# STEr9: 2, TGAAAC at 3845, TGAAAC at 1746.
# STEr0ci: 0.
# STEr1ci: 1, GTTTCA at 550.
# STEr2ci: 4, GTTTCA at 3273, GTTTCA at 1655, GTTTCA at 1058, GTTTCA at 67.
# STEr3ci: 1, GTTTCA at 2785.
# STEr4ci: 1, GTTTCA at 281.
# STEr5ci: 4, GTTTCA at 4110, GTTTCA at 1882, GTTTCA at 1661, GTTTCA at 934.
# STEr6ci: 0.
# STEr7ci: 2, GTTTCA at 768, GTTTCA at 610.
# STEr8ci: 2, GTTTCA at 1787, GTTTCA at 369.
# STEr9ci: 2, GTTTCA at 3029, GTTTCA at 1239.
 
===STEr arbitrary (evens) (4560-2846) UTRs===
 
# STEr0: TGAAAC at 3417.
# STEr4: TGAAAC at 3254.
# STEr2ci: GTTTCA at 3273.
 
===STEr alternate (odds) (4560-2846) UTRs===
 
# STEr1: TGAAAC at 3795.
# STEr7: TGAAAC at 4202, TGAAAC at 3828, TGAAAC at 3531.
# STEr9: TGAAAC at 3845.
# STEr5ci: GTTTCA at 4110.
# STEr9ci: GTTTCA at 3029, GTTTCA at 1239.
 
===STEr alternate negative direction (odds) (2811-2596) proximal promoters===
 
# STEr3ci: GTTTCA at 2785.
 
===STEr arbitrary positive direction (odds) (4265-4050) proximal promoters===
 
# STEr7: TGAAAC at 4202.
# STEr5ci: GTTTCA at 4110.
 
===STEr arbitrary negative direction (evens) (2596-1) distal promoters===
 
# STEr0: TGAAAC at 1932, TGAAAC at 902.
# STEr2: TGAAAC at 1991, TGAAAC at 1629.
# STEr4: TGAAAC at 819.
# STEr6: TGAAAC at 1714, TGAAAC at 1098.
# STEr2ci: GTTTCA at 1655, GTTTCA at 1058, GTTTCA at 67.
# STEr4ci: GTTTCA at 281.
# STEr8ci: GTTTCA at 1787, GTTTCA at 369.
 
===STEr alternate negative direction (odds) (2596-1) distal promoters===
 
# STEr1: TGAAAC at 2244.
# STEr9: TGAAAC at 1746.
# STEr1ci: GTTTCA at 550.
# STEr5ci: GTTTCA at 1882, GTTTCA at 1661, GTTTCA at 934.
# STEr7ci: GTTTCA at 768, GTTTCA at 610.
# STEr9ci: GTTTCA at 1239.
 
===STEr arbitrary positive direction (odds) (4050-1) distal promoters===
 
# STEr1: TGAAAC at 3795, TGAAAC at 2244.
# STEr7: TGAAAC at 3828, TGAAAC at 3531.
# STEr9: TGAAAC at 3845, TGAAAC at 1746.
# STEr1ci: GTTTCA at 550.
# STEr3ci: GTTTCA at 2785.
# STEr5ci: GTTTCA at 1882, GTTTCA at 1661, GTTTCA at 934.
# STEr7ci: GTTTCA at 768, GTTTCA at 610.
# STEr9ci: GTTTCA at 3029, GTTTCA at 1239.
 
===STEr alternate positive direction (evens) (4050-1) distal promoters===
 
# STEr0: TGAAAC at 3417, TGAAAC at 1932, TGAAAC at 902.
# STEr2: TGAAAC at 1991, TGAAAC at 1629.
# STEr4: TGAAAC at 3254, TGAAAC at 819.
# STEr6: TGAAAC at 1714, TGAAAC at 1098.
# STEr2ci: GTTTCA at 3273, GTTTCA at 1655, GTTTCA at 1058, GTTTCA at 67.
# STEr4ci: GTTTCA at 281.
# STEr8ci: GTTTCA at 1787, GTTTCA at 369.
 
==STE analysis and results==
{{main|Complex locus A1BG and ZNF497#STEs}}
The upstream activating sequence (UAS) for Ste12p is TGAAAC.<ref name=Tang/>
 
{|class="wikitable"
|-
! Reals or randoms !! Promoters !! direction !! Numbers !! Strands !! Occurrences !! Averages (± 0.1)
|-
| Reals || UTR || negative || 4 || 2 || 2 || 2 ± 1 (--3,+-1)
|-
| Randoms || UTR || arbitrary negative || 3 || 10 || 0.3 || 0
|-
| Randoms || UTR || alternate negative || 8 || 10 || 0.8 || 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 || 1 || 2 || 0.5 || 0.5 ± 0.5 (--0,+-1)
|-
| Randoms || Proximal || arbitrary negative || 0 || 10 || 0 || 0.05 ± 0.05
|-
| Randoms || Proximal || alternate negative || 1 || 10 || 0.1 || 0.05 ± 0.05
|-
| Reals || Proximal || positive || 0 || 2 || 0 || 0
|-
| Randoms || Proximal || arbitrary positive || 2 || 10 || 0.2 || 0.1 ± 0.1
|-
| Randoms || Proximal || alternate positive || 0 || 10 || 0 || 0.1 ± 0.1
|-
| Reals || Distal || negative || 15 || 2 || 7.5 || 7.5 ± 1.5 (--9,+-6)
|-
| Randoms || Distal || arbitrary negative || 13 || 10 || 1.3 || 1.1 ± 0.2
|-
| Randoms || Distal || alternate negative || 9 || 10 || 0.9 || 1.1 ± 0.2
|-
| Reals || Distal || positive || 3 || 2 || 1.5 || 1.5 ± 0.5 (-+3,++0)
|-
| Randoms || Distal || arbitrary positive || 15 || 10 || 1.5 || 1.55 ± 0.05
|-
| Randoms || Distal || alternate positive || 16 || 10 || 1.6 || 1.55 ± 0.05
|}
 
Comparison:
 
The occurrences of real STEs are greater than the randoms. This suggests that the real STEs are likely active or activable.


==Acknowledgements==
==Acknowledgements==
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[[Category:Resources last modified in February 2021]]

Latest revision as of 17:04, 8 September 2023

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

"The [Sterile12] STE12 gene encodes a transcription factor that activates genes involved in yeast mating (thus ste12 mutants are sterile) 4."[1]

Human genes

Main article: Human genes

Interactions

Main article: Interaction gene transcriptions

Consensus sequences

Main article: Consensus sequence gene transcriptions

The upstream activating sequence (UAS) for Ste12p is 5'-TGAAAC-3'.[2]

STE samplings

Main article: Model samplings

Copying TGAAAC in "⌘F" yields eleven between ZSCAN22 and A1BG and one between ZNF497 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence TGAAAC (starting with SuccessablesSTE.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 TGAAAC, 12, TGAAAC at 4462, TGAAAC at 3985, TGAAAC at 3076, TGAAAC at 2553, TGAAAC at 2217, TGAAAC at 2100, TGAAAC at 1791, TGAAAC at 1688, TGAAAC at 1146, TGAAAC at 682, TGAAAC at 546, TGAAAC at 409.
  2. positive strand, negative direction, looking for TGAAAC, 8, TGAAAC at 3147, TGAAAC at 2620, TGAAAC at 2283, TGAAAC at 1856, TGAAAC at 1583, TGAAAC at 1213, TGAAAC at 474, TGAAAC at 127.
  3. positive strand, positive direction, looking for TGAAAC, 0.
  4. negative strand, positive direction, looking for TGAAAC, 1, TGAAAC at 2147.
  5. inverse complement, negative strand, negative direction, looking for GTTTCA, 0.
  6. inverse complement, positive strand, negative direction, looking for GTTTCA, 0.
  7. inverse complement, positive strand, positive direction, looking for GTTTCA, 0.
  8. inverse complement, negative strand, positive direction, looking for GTTTCA, 2, GTTTCA at 2302, GTTTCA at 2264.

STE (4560-2846) UTRs

  1. Negative strand, negative direction: TGAAAC at 4462, TGAAAC at 3985, TGAAAC at 3076.
  2. Positive strand, negative direction: TGAAAC at 3147.

STE negative direction (2811-2596) proximal promoters

  1. Positive strand, negative direction: TGAAAC at 2620.

STE negative direction (2596-1) distal promoters

  1. Negative strand, negative direction: TGAAAC at 2553, TGAAAC at 2217, TGAAAC at 2100, TGAAAC at 1791, TGAAAC at 1688, TGAAAC at 1146, TGAAAC at 682, TGAAAC at 546, TGAAAC at 409.
  2. Positive strand, negative direction: TGAAAC at 2283, TGAAAC at 1856, TGAAAC at 1583, TGAAAC at 1213, TGAAAC at 474, TGAAAC at 127.

STE positive direction (4050-1) distal promoters

  1. Negative strand, positive direction: TGAAAC at 2147.
  2. Negative strand, positive direction: GTTTCA at 2302, GTTTCA at 2264.

STE random dataset samplings

  1. STEr0: 3, TGAAAC at 3417, TGAAAC at 1932, TGAAAC at 902.
  2. STEr1: 2, TGAAAC at 3795, TGAAAC at 2244.
  3. STEr2: 2, TGAAAC at 1991, TGAAAC at 1629.
  4. STEr3: 0.
  5. STEr4: 2, TGAAAC at 3254, TGAAAC at 819.
  6. STEr5: 0.
  7. STEr6: 2, TGAAAC at 1714, TGAAAC at 1098.
  8. STEr7: 3, TGAAAC at 4202, TGAAAC at 3828, TGAAAC at 3531.
  9. STEr8: 0.
  10. STEr9: 2, TGAAAC at 3845, TGAAAC at 1746.
  11. STEr0ci: 0.
  12. STEr1ci: 1, GTTTCA at 550.
  13. STEr2ci: 4, GTTTCA at 3273, GTTTCA at 1655, GTTTCA at 1058, GTTTCA at 67.
  14. STEr3ci: 1, GTTTCA at 2785.
  15. STEr4ci: 1, GTTTCA at 281.
  16. STEr5ci: 4, GTTTCA at 4110, GTTTCA at 1882, GTTTCA at 1661, GTTTCA at 934.
  17. STEr6ci: 0.
  18. STEr7ci: 2, GTTTCA at 768, GTTTCA at 610.
  19. STEr8ci: 2, GTTTCA at 1787, GTTTCA at 369.
  20. STEr9ci: 2, GTTTCA at 3029, GTTTCA at 1239.

STEr arbitrary (evens) (4560-2846) UTRs

  1. STEr0: TGAAAC at 3417.
  2. STEr4: TGAAAC at 3254.
  3. STEr2ci: GTTTCA at 3273.

STEr alternate (odds) (4560-2846) UTRs

  1. STEr1: TGAAAC at 3795.
  2. STEr7: TGAAAC at 4202, TGAAAC at 3828, TGAAAC at 3531.
  3. STEr9: TGAAAC at 3845.
  4. STEr5ci: GTTTCA at 4110.
  5. STEr9ci: GTTTCA at 3029, GTTTCA at 1239.

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

  1. STEr3ci: GTTTCA at 2785.

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

  1. STEr7: TGAAAC at 4202.
  2. STEr5ci: GTTTCA at 4110.

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

  1. STEr0: TGAAAC at 1932, TGAAAC at 902.
  2. STEr2: TGAAAC at 1991, TGAAAC at 1629.
  3. STEr4: TGAAAC at 819.
  4. STEr6: TGAAAC at 1714, TGAAAC at 1098.
  5. STEr2ci: GTTTCA at 1655, GTTTCA at 1058, GTTTCA at 67.
  6. STEr4ci: GTTTCA at 281.
  7. STEr8ci: GTTTCA at 1787, GTTTCA at 369.

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

  1. STEr1: TGAAAC at 2244.
  2. STEr9: TGAAAC at 1746.
  3. STEr1ci: GTTTCA at 550.
  4. STEr5ci: GTTTCA at 1882, GTTTCA at 1661, GTTTCA at 934.
  5. STEr7ci: GTTTCA at 768, GTTTCA at 610.
  6. STEr9ci: GTTTCA at 1239.

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

  1. STEr1: TGAAAC at 3795, TGAAAC at 2244.
  2. STEr7: TGAAAC at 3828, TGAAAC at 3531.
  3. STEr9: TGAAAC at 3845, TGAAAC at 1746.
  4. STEr1ci: GTTTCA at 550.
  5. STEr3ci: GTTTCA at 2785.
  6. STEr5ci: GTTTCA at 1882, GTTTCA at 1661, GTTTCA at 934.
  7. STEr7ci: GTTTCA at 768, GTTTCA at 610.
  8. STEr9ci: GTTTCA at 3029, GTTTCA at 1239.

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

  1. STEr0: TGAAAC at 3417, TGAAAC at 1932, TGAAAC at 902.
  2. STEr2: TGAAAC at 1991, TGAAAC at 1629.
  3. STEr4: TGAAAC at 3254, TGAAAC at 819.
  4. STEr6: TGAAAC at 1714, TGAAAC at 1098.
  5. STEr2ci: GTTTCA at 3273, GTTTCA at 1655, GTTTCA at 1058, GTTTCA at 67.
  6. STEr4ci: GTTTCA at 281.
  7. STEr8ci: GTTTCA at 1787, GTTTCA at 369.

STE analysis and results

Main article: Complex locus A1BG and ZNF497 § STEs

The upstream activating sequence (UAS) for Ste12p is TGAAAC.[2]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 4 2 2 2 ± 1 (--3,+-1)
Randoms UTR arbitrary negative 3 10 0.3 0
Randoms UTR alternate negative 8 10 0.8 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 1 2 0.5 0.5 ± 0.5 (--0,+-1)
Randoms Proximal arbitrary negative 0 10 0 0.05 ± 0.05
Randoms Proximal alternate negative 1 10 0.1 0.05 ± 0.05
Reals Proximal positive 0 2 0 0
Randoms Proximal arbitrary positive 2 10 0.2 0.1 ± 0.1
Randoms Proximal alternate positive 0 10 0 0.1 ± 0.1
Reals Distal negative 15 2 7.5 7.5 ± 1.5 (--9,+-6)
Randoms Distal arbitrary negative 13 10 1.3 1.1 ± 0.2
Randoms Distal alternate negative 9 10 0.9 1.1 ± 0.2
Reals Distal positive 3 2 1.5 1.5 ± 0.5 (-+3,++0)
Randoms Distal arbitrary positive 15 10 1.5 1.55 ± 0.05
Randoms Distal alternate positive 16 10 1.6 1.55 ± 0.05

Comparison:

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

Acknowledgements

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

See also

References

  1. ↑ Nitasha Sehgal, M. Eileen Sylves, Ansuman Sahoo, Jacky Chow, Sarah E. Walker, Paul J. Cullen, James O. Berry (November/December 2018). "CRISPR Gene Editing in Yeast: An Experimental Protocol for an Upper‐Division Undergraduate Laboratory Course". Biochemistry and Molecular Biology Education. 46 (6): 592–601. doi:10.1002/bmb.21175. Retrieved 28 February 2021. Check date values in: |date= (help)
  2. ↑ 2.0 2.1 Hongting Tang, Yanling Wu, Jiliang Deng, Nanzhu Chen, Zhaohui Zheng, Yongjun Wei, Xiaozhou Luo, and Jay D. Keasling (6 August 2020). "Promoter Architecture and Promoter Engineering in Saccharomyces cerevisiae". Metabolites. 10 (8): 320–39. doi:10.3390/metabo10080320. PMID 32781665 Check |pmid= value (help). Retrieved 18 September 2020.

External links


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