Tec1p gene transcriptions: Difference between revisions

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# TECr8: 1, GAATGT at 1428.
# TECr8: 1, GAATGT at 1428.
# TECr9: 1, GAATGT at 4244.
# TECr9: 1, GAATGT at 4244.
# RDr0ci: 0.
# TECr0ci: 2, ACATTC at 2089, ACATTC at 890.
# RDr1ci: 0.
# TECr1ci: 1, ACATTC at 4243.
# RDr2ci: 0.
# TECr2ci: 4, ACATTC at 4047, ACATTC at 3990, ACATTC at 1722, ACATTC at 1637.
# RDr3ci: 0.
# TECr3ci: 0.
# RDr4ci: 0.
# TECr4ci: 1, ACATTC at 3699.
# RDr5ci: 0.
# TECr5ci: 1, ACATTC at 3822.
# RDr6ci: 0.
# TECr6ci: 0.
# RDr7ci: 0.
# TECr7ci: 1, ACATTC at 1945.
# RDr8ci: 0.
# TECr8ci: 0.
# RDr9ci: 0.
# TECr9ci: 1, ACATTC at 3641.


===TECr arbitrary (evens) (4560-2846) UTRs===
===TECr arbitrary (evens) (4560-2846) UTRs===


# TECr2: GAATGT at 4493.
# TECr2: GAATGT at 4493.
# TECr2ci: ACATTC at 4047, ACATTC at 3990.
# TECr4ci: ACATTC at 3699.


===TECr alternate (odds) (4560-2846) UTRs===
===TECr alternate (odds) (4560-2846) UTRs===
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# TECr5: GAATGT at 3386.
# TECr5: GAATGT at 3386.
# TECr9: GAATGT at 4244.
# TECr9: GAATGT at 4244.
 
# TECr1ci: ACATTC at 4243.
===RDr arbitrary negative direction (evens) (2846-2811) core promoters===
# TECr5ci: ACATTC at 3822.
 
# TECr9ci: ACATTC at 3641.
===RDr alternate negative direction (odds) (2846-2811) core promoters===


===TECr arbitrary positive direction (odds) (4445-4265) core promoters===
===TECr arbitrary positive direction (odds) (4445-4265) core promoters===


# TECr3: GAATGT at 4317.
# TECr3: GAATGT at 4317.
===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===


===TECr arbitrary positive direction (odds) (4265-4050) proximal promoters===
===TECr arbitrary positive direction (odds) (4265-4050) proximal promoters===


# TECr9: GAATGT at 4244.
# TECr9: GAATGT at 4244.
 
# TECr1ci: ACATTC at 4243.
===RDr alternate positive direction (evens) (4265-4050) proximal promoters===


===TECr arbitrary negative direction (evens) (2596-1) distal promoters===
===TECr arbitrary negative direction (evens) (2596-1) distal promoters===
Line 106: Line 100:
# TECr4: GAATGT at 1101.
# TECr4: GAATGT at 1101.
# TECr8: GAATGT at 1428.
# TECr8: GAATGT at 1428.
# TECr0ci: ACATTC at 2089, ACATTC at 890.
# TECr2ci: ACATTC at 1722, ACATTC at 1637.


===TECr alternate negative direction (odds) (2596-1) distal promoters===
===TECr alternate negative direction (odds) (2596-1) distal promoters===
Line 111: Line 107:
# TECr5: GAATGT at 2128, GAATGT at 1128.
# TECr5: GAATGT at 2128, GAATGT at 1128.
# TECr7: GAATGT at 104.
# TECr7: GAATGT at 104.
# TECr7ci: ACATTC at 1945.


===TECr arbitrary positive direction (odds) (4050-1) distal promoters===
===TECr arbitrary positive direction (odds) (4050-1) distal promoters===
Line 116: Line 113:
# TECr5: GAATGT at 3386, GAATGT at 2128, GAATGT at 1128.
# TECr5: GAATGT at 3386, GAATGT at 2128, GAATGT at 1128.
# TECr7: GAATGT at 104.
# TECr7: GAATGT at 104.
# TECr5ci: ACATTC at 3822.
# TECr7ci: ACATTC at 1945.
# TECr9ci: ACATTC at 3641.


===TECr alternate positive direction (evens) (4050-1) distal promoters===
===TECr alternate positive direction (evens) (4050-1) distal promoters===
Line 122: Line 122:
# TECr4: GAATGT at 1101.
# TECr4: GAATGT at 1101.
# TECr8: GAATGT at 1428.
# TECr8: GAATGT at 1428.
# TECr0ci: ACATTC at 2089, ACATTC at 890.
# TECr2ci: ACATTC at 4047, ACATTC at 3990, ACATTC at 1722, ACATTC at 1637.
# TECr4ci: ACATTC at 3699.


==TEC analysis and results==
==TEC analysis and results==

Revision as of 22:48, 26 February 2023

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

Human genes

Interactions

Consensus sequences

The upstream activating sequence (UAS) for Tec1p is 5'-GAATGT-3'.[1]

Tec1 samplings

Copying GAATGT in "⌘F" yields none between ZSCAN22 and A1BG and none between ZNF497 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence GAATGT (starting with SuccessablesTEC.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 GAATGT, 0.
  2. positive strand, negative direction, looking for GAATGT, 0.
  3. positive strand, positive direction, looking for GAATGT, 0.
  4. negative strand, positive direction, looking for GAATGT, 0.
  5. complement, negative strand, negative direction, looking for CTTACA, 0.
  6. complement, positive strand, negative direction, looking for CTTACA, 0.
  7. complement, positive strand, positive direction, looking for CTTACA, 0.
  8. complement, negative strand, positive direction, looking for CTTACA, 0.
  9. inverse complement, negative strand, negative direction, looking for ACATTC, 0.
  10. inverse complement, positive strand, negative direction, looking for ACATTC, 0.
  11. inverse complement, positive strand, positive direction, looking for ACATTC, 1, ACATTC at 2456.
  12. inverse complement, negative strand, positive direction, looking for ACATTC, 0.
  13. inverse negative strand, negative direction, looking for TGTAAG, 0.
  14. inverse positive strand, negative direction, looking for TGTAAG, 0.
  15. inverse positive strand, positive direction, looking for TGTAAG, 0.
  16. inverse negative strand, positive direction, looking for TGTAAG, 1, TGTAAG at 2456.

TEC positive direction (4050-1) distal promoters

  1. Positive strand, positive direction: ACATTC at 2456.

TEC random dataset samplings

  1. TECr0: 0.
  2. TECr1: 0.
  3. TECr2: 3, GAATGT at 4493, GAATGT at 1294, GAATGT at 918.
  4. TECr3: 1, GAATGT at 4317.
  5. TECr4: 1, GAATGT at 1101.
  6. TECr5: 3, GAATGT at 3386, GAATGT at 2128, GAATGT at 1128.
  7. TECr6: 0.
  8. TECr7: 1, GAATGT at 104.
  9. TECr8: 1, GAATGT at 1428.
  10. TECr9: 1, GAATGT at 4244.
  11. TECr0ci: 2, ACATTC at 2089, ACATTC at 890.
  12. TECr1ci: 1, ACATTC at 4243.
  13. TECr2ci: 4, ACATTC at 4047, ACATTC at 3990, ACATTC at 1722, ACATTC at 1637.
  14. TECr3ci: 0.
  15. TECr4ci: 1, ACATTC at 3699.
  16. TECr5ci: 1, ACATTC at 3822.
  17. TECr6ci: 0.
  18. TECr7ci: 1, ACATTC at 1945.
  19. TECr8ci: 0.
  20. TECr9ci: 1, ACATTC at 3641.

TECr arbitrary (evens) (4560-2846) UTRs

  1. TECr2: GAATGT at 4493.
  2. TECr2ci: ACATTC at 4047, ACATTC at 3990.
  3. TECr4ci: ACATTC at 3699.

TECr alternate (odds) (4560-2846) UTRs

  1. TECr3: GAATGT at 4317.
  2. TECr5: GAATGT at 3386.
  3. TECr9: GAATGT at 4244.
  4. TECr1ci: ACATTC at 4243.
  5. TECr5ci: ACATTC at 3822.
  6. TECr9ci: ACATTC at 3641.

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

  1. TECr3: GAATGT at 4317.

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

  1. TECr9: GAATGT at 4244.
  2. TECr1ci: ACATTC at 4243.

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

  1. TECr2: GAATGT at 1294, GAATGT at 918.
  2. TECr4: GAATGT at 1101.
  3. TECr8: GAATGT at 1428.
  4. TECr0ci: ACATTC at 2089, ACATTC at 890.
  5. TECr2ci: ACATTC at 1722, ACATTC at 1637.

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

  1. TECr5: GAATGT at 2128, GAATGT at 1128.
  2. TECr7: GAATGT at 104.
  3. TECr7ci: ACATTC at 1945.

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

  1. TECr5: GAATGT at 3386, GAATGT at 2128, GAATGT at 1128.
  2. TECr7: GAATGT at 104.
  3. TECr5ci: ACATTC at 3822.
  4. TECr7ci: ACATTC at 1945.
  5. TECr9ci: ACATTC at 3641.

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

  1. TECr2: GAATGT at 1294, GAATGT at 918.
  2. TECr4: GAATGT at 1101.
  3. TECr8: GAATGT at 1428.
  4. TECr0ci: ACATTC at 2089, ACATTC at 890.
  5. TECr2ci: ACATTC at 4047, ACATTC at 3990, ACATTC at 1722, ACATTC at 1637.
  6. TECr4ci: ACATTC at 3699.

TEC analysis and results

Main article: Complex locus A1BG and ZNF497 § TECs

The upstream activating sequence (UAS) for Tec1p is GAATGT.[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 1 2 0.5 0.5 ± 0.5 (-+0,++1)
Randoms Distal arbitrary positive 0 10 0 0
Randoms Distal alternate positive 0 10 0 0

Comparison:

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

See also

References

  1. ↑ 1.0 1.1 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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