Circadian control element gene transcriptions: Difference between revisions

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Revision as of 23:44, 24 January 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

Circadian control elements (CAANNNNATC).^[2]

Hypotheses

A1BG has no CCEs in either promoter.
A1BG is not transcribed by a CCE.
CCE does not participate in the transcription of A1BG.

CCE 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:

negative strand, negative direction, looking for 5'-CAANNNNATC-3', 0.
negative strand, positive direction, looking for 5'-CAANNNNATC-3', 0.
positive strand, negative direction, looking for 5'-CAANNNNATC-3', 0.
positive strand, positive direction, looking for 5'-CAANNNNATC-3', 0.
complement, negative strand, negative direction, looking for 5'-GTTNNNNTAG-3', 0.
complement, negative strand, positive direction, looking for 5'-GTTNNNNTAG-3', 0.
complement, positive strand, negative direction, looking for 5'-GTTNNNNTAG-3', 0.
complement, positive strand, positive direction, looking for 5'-GTTNNNNTAG-3', 0.
inverse complement, negative strand, negative direction, looking for 5'-GATNNNNTTG-3', 0.
inverse complement, negative strand, positive direction, looking for 5'-GATNNNNTTG-3', 0.
inverse complement, positive strand, negative direction, looking for 5'-GATNNNNTTG-3', 1, 5'-GATGGGGTTG-3' at 3804.
inverse complement, positive strand, positive direction, looking for 5'-GATNNNNTTG-3', 0.
inverse negative strand, negative direction, looking for 5'-CTANNNNAAC-3', 1, 5'-CTACCCCAAC-3' at 3804.
inverse negative strand, positive direction, looking for 5'-CTANNNNAAC-3', 0.
inverse positive strand, negative direction, looking for 5'-CTANNNNAAC-3', 0.
inverse positive strand, positive direction, looking for 5'-CTANNNNAAC-3', 0.

CCE UTR promoters

Positive strand, negative direction: GATGGGGTTG at 3804.

CCE random dataset samplings

CCEr0: 1, CAAGGGTATC at 334.
CCEr1: 0.
CCEr2: 2, CAACCGAATC at 2991, CAAACCGATC at 1749.
CCEr3: 2, CAATCGCATC at 1734, CAAATGCATC at 162.
CCEr4: 1, CAACGTCATC at 3915.
CCEr5: 1, CAATGACATC at 2923.
CCEr6: 2, CAACAATATC at 2053, CAAGGACATC at 793.
CCEr7: 0.
CCEr8: 1, CAACTCTATC at 1916.
CCEr9: 0.
CCEr0ci: 0.
CCEr1ci: 4, GATACAGTTG at 3388, GATGACTTTG at 1638, GATTCCTTTG at 712, GATGTGCTTG at 351.
CCEr2ci: 0.
CCEr3ci: 2, GATTTCCTTG at 4300, GATGGATTTG at 3780.
CCEr4ci: 0.
CCEr5ci: 1, GATTGCCTTG at 3319.
CCEr6ci: 0.
CCEr7ci: 0.
CCEr8ci: 0.
CCEr9ci: 0.

CCEr UTRs

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

CCEr core promoters

CCEr3ci: GATTTCCTTG at 4300.

CCEr distal promoters

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

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

CCE analysis and results

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.

References

↑ 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.
↑ 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

[Wei-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.

[Sharma-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.

[1]

[2]

@@ Line 39: / Line 39: @@
 # CCE does not participate in the transcription of A1BG.
-==Samplings==
+==CCE samplings==
 {{main|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.
@@ Line 63: / Line 63: @@
 ===CCE UTR promoters===
 {{main|UTR promoter gene transcriptions}}
-Negative strand, negative direction: CTACCCCAAC at 3804.
+Positive strand, negative direction: GATGGGGTTG at 3804.
 ==CCE random dataset samplings==
@@ Line 111: / Line 111: @@
 # CCEr5ci: GATTGCCTTG at 3319.
-==Response element analysis and results==
+==CCE analysis and results==
-{{main|Complex locus A1BG and ZNF497#Name of elements}}
+{{main|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==
@@ Line 140: / Line 144: @@
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-[[Category:Resources last modified in November 2020]]

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transcriptions MYB recognition element gene transcriptions Myelocytomatosis transcription factor gene transcriptions Myocyte enhancer factor gene transcriptions N-boxes Ndt80p gene transcriptions Nuclear factor 1 Nuclear factor 𝜿B Nuclear factor gene transcriptions Nuclear factor of activated T cell gene transcriptions (NFAT) Nuclear factor Y gene transcriptions Nutrient-sensing response element gene transcriptions Oaf1p gene transcriptions ORE1 binding site gene transcriptions p53 response element gene transcriptions P63 DNA-binding site gene transcriptions P box gene transcriptions Pdr1,3p gene transcriptions Peroxisome proliferator hormone response element gene transcriptions Phosphate starvation-response transcription factor gene transcriptions Pollen1 element gene transcriptions Polycomb response element gene transcriptions Preinitiation complex Preinitiation complex gene transcriptions Pribnow box gene transcriptions Prolamin box gene transcriptions Promoter gene transcriptions 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