Circadian control element gene transcriptions: Difference between revisions

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# CCEr9ci: 0.
# CCEr9ci: 0.


===CCEr UTRs===
===CCEr arbitrary (evens) (4560-2846) UTRs===
{{main|UTR promoter gene transcriptions}}
 
# CCEr2: CAACCGAATC at 2991.
# CCEr2: CAACCGAATC at 2991.
# CCEr4: CAACGTCATC at 3915.
# CCEr4: CAACGTCATC at 3915.


===CCEr core promoters===
===CCEr alternate (odds) (4560-2846) UTRs===
{{main|Core promoter gene transcriptions}}
 
# CCEr5: CAATGACATC at 2923.
# CCEr1ci: GATACAGTTG at 3388.
# CCEr3ci: GATTTCCTTG at 4300, GATGGATTTG at 3780.
# CCEr5ci: GATTGCCTTG at 3319.
 
===CCEr arbitrary positive direction (odds) (4445-4265) core promoters===
 
# CCEr3ci: GATTTCCTTG at 4300.
# CCEr3ci: GATTTCCTTG at 4300.


===CCEr distal promoters===
===CCEr arbitrary negative direction (evens) (2596-1) distal promoters===
{{main|Distal promoter gene transcriptions}}
 
# CCEr0: CAAGGGTATC at 334.
# CCEr0: CAAGGGTATC at 334.
# CCEr2: CAAACCGATC at 1749.
# CCEr2: CAAACCGATC at 1749.
Line 104: Line 111:
# CCEr8: CAACTCTATC at 1916.
# CCEr8: CAACTCTATC at 1916.


===CCEr alternate negative direction (odds) (2596-1) distal promoters===
# CCEr3: CAATCGCATC at 1734, CAAATGCATC at 162.
# CCEr1ci: GATGACTTTG at 1638, GATTCCTTTG at 712, GATGTGCTTG at 351.
===CCEr arbitrary positive direction (odds) (4050-1) distal promoters===


# CCEr3: CAATCGCATC at 1734, CAAATGCATC at 162.
# CCEr3: CAATCGCATC at 1734, CAAATGCATC at 162.
Line 110: Line 123:
# CCEr3ci: GATGGATTTG at 3780.
# CCEr3ci: GATGGATTTG at 3780.
# CCEr5ci: GATTGCCTTG at 3319.
# CCEr5ci: GATTGCCTTG at 3319.
===CCEr alternate positive direction (evens) (4050-1) distal promoters===
# CCEr0: CAAGGGTATC at 334.
# CCEr2: CAACCGAATC at 2991, CAAACCGATC at 1749.
# CCEr4: CAACGTCATC at 3915.
# CCEr6: CAACAATATC at 2053, CAAGGACATC at 793.
# CCEr8: CAACTCTATC at 1916.


==CCE analysis and results==
==CCE analysis and results==

Revision as of 19:29, 23 October 2022

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

"The circadian control element (circadian; Anderson et al., 1994) was found in 10 FvTCP genes."[1]

Consensus sequences

Main article: Consensus sequence gene transcriptions

Circadian control elements (CAANNNNATC).[2]

Hypotheses

Main article: Hypotheses
  1. A1BG has no CCEs in either promoter.
  2. A1BG is not transcribed by a CCE.
  3. CCE does not participate in the transcription of A1BG.

CCE samplings

Main article: Model samplings

Copying the consensus of the CCE: 5'-CAACTTTA-3' and putting the sequence in "⌘F" finds no locations between ZSCAN22 and A1BG and no locations between ZNF497 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence 5'-CAANNNNATC-3' (starting with SuccessablesCCE.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 5'-CAANNNNATC-3', 0.
  2. negative strand, positive direction, looking for 5'-CAANNNNATC-3', 0.
  3. positive strand, negative direction, looking for 5'-CAANNNNATC-3', 0.
  4. positive strand, positive direction, looking for 5'-CAANNNNATC-3', 0.
  5. complement, negative strand, negative direction, looking for 5'-GTTNNNNTAG-3', 0.
  6. complement, negative strand, positive direction, looking for 5'-GTTNNNNTAG-3', 0.
  7. complement, positive strand, negative direction, looking for 5'-GTTNNNNTAG-3', 0.
  8. complement, positive strand, positive direction, looking for 5'-GTTNNNNTAG-3', 0.
  9. inverse complement, negative strand, negative direction, looking for 5'-GATNNNNTTG-3', 0.
  10. inverse complement, negative strand, positive direction, looking for 5'-GATNNNNTTG-3', 0.
  11. inverse complement, positive strand, negative direction, looking for 5'-GATNNNNTTG-3', 1, 5'-GATGGGGTTG-3' at 3804.
  12. inverse complement, positive strand, positive direction, looking for 5'-GATNNNNTTG-3', 0.
  13. inverse negative strand, negative direction, looking for 5'-CTANNNNAAC-3', 1, 5'-CTACCCCAAC-3' at 3804.
  14. inverse negative strand, positive direction, looking for 5'-CTANNNNAAC-3', 0.
  15. inverse positive strand, negative direction, looking for 5'-CTANNNNAAC-3', 0.
  16. inverse positive strand, positive direction, looking for 5'-CTANNNNAAC-3', 0.

CCE (4560-2846) UTRs

  1. Positive strand, negative direction: GATGGGGTTG at 3804.

CCE random dataset samplings

  1. CCEr0: 1, CAAGGGTATC at 334.
  2. CCEr1: 0.
  3. CCEr2: 2, CAACCGAATC at 2991, CAAACCGATC at 1749.
  4. CCEr3: 2, CAATCGCATC at 1734, CAAATGCATC at 162.
  5. CCEr4: 1, CAACGTCATC at 3915.
  6. CCEr5: 1, CAATGACATC at 2923.
  7. CCEr6: 2, CAACAATATC at 2053, CAAGGACATC at 793.
  8. CCEr7: 0.
  9. CCEr8: 1, CAACTCTATC at 1916.
  10. CCEr9: 0.
  11. CCEr0ci: 0.
  12. CCEr1ci: 4, GATACAGTTG at 3388, GATGACTTTG at 1638, GATTCCTTTG at 712, GATGTGCTTG at 351.
  13. CCEr2ci: 0.
  14. CCEr3ci: 2, GATTTCCTTG at 4300, GATGGATTTG at 3780.
  15. CCEr4ci: 0.
  16. CCEr5ci: 1, GATTGCCTTG at 3319.
  17. CCEr6ci: 0.
  18. CCEr7ci: 0.
  19. CCEr8ci: 0.
  20. CCEr9ci: 0.

CCEr arbitrary (evens) (4560-2846) UTRs

  1. CCEr2: CAACCGAATC at 2991.
  2. CCEr4: CAACGTCATC at 3915.

CCEr alternate (odds) (4560-2846) UTRs

  1. CCEr5: CAATGACATC at 2923.
  2. CCEr1ci: GATACAGTTG at 3388.
  3. CCEr3ci: GATTTCCTTG at 4300, GATGGATTTG at 3780.
  4. CCEr5ci: GATTGCCTTG at 3319.

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

  1. CCEr3ci: GATTTCCTTG at 4300.

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

  1. CCEr0: CAAGGGTATC at 334.
  2. CCEr2: CAAACCGATC at 1749.
  3. CCEr6: CAACAATATC at 2053, CAAGGACATC at 793.
  4. CCEr8: CAACTCTATC at 1916.

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

  1. CCEr3: CAATCGCATC at 1734, CAAATGCATC at 162.
  2. CCEr1ci: GATGACTTTG at 1638, GATTCCTTTG at 712, GATGTGCTTG at 351.

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

  1. CCEr3: CAATCGCATC at 1734, CAAATGCATC at 162.
  2. CCEr5: CAATGACATC at 2923.
  3. CCEr1ci: GATACAGTTG at 3388, GATGACTTTG at 1638, GATTCCTTTG at 712, GATGTGCTTG at 351.
  4. CCEr3ci: GATGGATTTG at 3780.
  5. CCEr5ci: GATTGCCTTG at 3319.

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

  1. CCEr0: CAAGGGTATC at 334.
  2. CCEr2: CAACCGAATC at 2991, CAAACCGATC at 1749.
  3. CCEr4: CAACGTCATC at 3915.
  4. CCEr6: CAACAATATC at 2053, CAAGGACATC at 793.
  5. CCEr8: CAACTCTATC at 1916.

CCE analysis and results

Main article: Complex locus A1BG and ZNF497 § Circadian control elements

In the real promoters there is only one CCE, an inverse complement: GATGGGGTTG at 3804 in the ZSCAN22 - A1BG UTR for an occurrence of 0.5 (its complement CTACCCCAAC is on the negative strand in the negative direction).

The random datasets had two CCEs in the UTR out of ten strands for 0.2. There are also one core promoter for an occurrence of 0.1, no proximal promoter, and five (arbitrary negative direction) and nine (positive direction) distal promoters for 0.5 and 0.9 occurrences, respectively.

Comparing the real and random results, the one CCE in the real promoters is likely active or activable.

Acknowledgements

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

See also

References

  1. ↑ Wei Wei, Yang Hu, Meng-Yuan Cui, Yong-Tao Han, Kuan Gao, and Jia-Yue Feng (22 December 2016). "Identification and Transcript Analysis of the TCP Transcription Factors in the Diploid Woodland Strawberry Fragaria vesca". Frontiers in Plant Science. 7: 1937. doi:10.3389/fpls.2016.01937. PMID 28066489. Retrieved 29 November 2020.
  2. ↑ Bhaskar Sharma & Joemar Taganna (12 June 2020). "Genome-wide analysis of the U-box E3 ubiquitin ligase enzyme gene family in tomato". Scientific Reports. 10 (9581). doi:10.1038/s41598-020-66553-1. PMID 32533036 Check |pmid= value (help). Retrieved 27 August 2020.

External links


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