Circadian control element gene transcriptions: Difference between revisions

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==CCE analysis and results==
==CCE analysis and results==
{{main|Complex locus A1BG and ZNF497#CCEs}}
{{main|Complex locus A1BG and ZNF497#Circadian control elements}}
Circadian control elements (CAANNNNATC).<ref name=Sharma/>
Circadian control elements (CAANNNNATC).<ref name=Sharma/>


Revision as of 00:33, 12 December 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

Circadian control elements (CAANNNNATC).[2]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 1 2 0.5 0.5
Randoms UTR arbitrary negative 2 10 0.2 0.35 ± 0.15
Randoms UTR alternate negative 5 10 0.5 0.35 ± 0.15
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 1 10 0.1 0.05
Randoms Core alternate positive 0 10 0 0.05
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 5 10 0.5 0
Randoms Distal alternate negative 5 10 0.5 0
Reals Distal positive 0 2 0 0
Randoms Distal arbitrary positive 9 10 0.9 0.8
Randoms Distal alternate positive 7 10 0.7 0.8

Comparison:

The occurrences of real CCEs overlaps the high randoms. This suggests that the real CCEs are may be random.

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. ↑ 2.0 2.1 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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