Circadian control element gene transcriptions

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 (4560-2846) UTRs

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 arbitrary (evens) (4560-2846) UTRs

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

CCEr alternate (odds) (4560-2846) UTRs

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.

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

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

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

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 ± 0.5 (--0,+-1)
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 are greater than the randoms. This suggests that the real CCEs are 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.
↑ ^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

[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] 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.

[1]

[2]

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recognition element gene transcriptions DREB box gene transcriptions E2 box gene transcriptions EIF4E basal element gene transcriptions EIN3 binding site gene transcriptions Enhancer activity copy gene transcriptions E box gene transcriptions Element gene transcriptions Endoplasmic reticulum stress response element gene transcriptions Endosperm expression gene transcriptions Enhancer box gene transcriptions Estrogen response element gene transcriptions Ethylene responsive element gene transcriptions Families of TATA box genes F box gene transcriptions Focused promoter gene transcriptions Forkhead box gene transcriptions Fur box gene transcriptions GAAC element gene transcriptions Gal4p gene transcriptions Γ-interferon activated sequence gene transcriptions GARE gene transcriptions GA responsive complex gene transcriptions GATA gene transcriptions G box gene transcriptions GC box gene transcriptions GCC box gene transcriptions Gcn4p gene transcriptions Gcr1p gene transcriptions Gene expressions General factor II D gene transcriptions General regulatory factors General transcription factor II A gene transcriptions General transcription factor II B gene transcriptions General transcription factor II D gene transcriptions General transcription factor II F gene transcriptions General transcription factor II H gene transcriptions General transcription factor gene transcriptions Gene transcriptions GGC triplet gene transcriptions Gibberellin responsive element gene transcriptions GLM box gene transcriptions Glucocorticoid response element gene transcriptions Grainy head gene transcriptions Grainy head transcription factor gene transcriptions Growth hormone response element gene transcriptions GT boxes Hac1p gene transcriptions Hair color gene expressions H and ACA box gene transcriptions H box gene transcriptions Heat-responsive element gene transcriptions Heat shock elements Hex sequence gene transcriptions HMG box gene transcriptions HNF gene transcriptions Homeobox gene transcriptions Hsf1p gene transcriptions HY box gene transcriptions Hybrid C, A boxes Hybrid C, G boxes Hybrid C, T boxes Hypoxia-inducible factor gene transcriptions Hypoxia response elements I box gene transcriptions Immunoglobulin like domain containing family Initiator element gene transcriptions Initiator-like element gene transcriptions Inositol/choline-responsive elements Interaction gene transcriptions Interferon regulatory factors Inverse copy gene transcriptions Jasmonic acid-responsive element gene transcriptions K-boxes Kozak sequence gene transcriptions Kruppel-associated box gene transcriptions Krüppel-like factor gene transcriptions L box gene transcriptions Leu3 gene transcriptions M35 box gene transcriptions MADS box gene transcriptions Maf recognition element gene transcriptions M box gene transcriptions Mcm1 regulatory factor gene transcriptions Met3 gene transcriptions Met31p box gene transcriptions Metal responsive element gene transcriptions Middle sporulation element gene transcriptions Mig1p gene transcriptions Model samplings Motif ten element gene transcriptions Msn2,4p gene transcriptions Musashi binding element gene transcriptions MYB recognition element gene transcriptions Myelocytomatosis transcription factor gene transcriptions Myocyte enhancer factor gene transcriptions N-boxes Nanos/Pumilio response element 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 Proximal promoter gene transcriptions Promoter occurrence gene transcriptions Pyrimidine box gene transcriptions Q element gene transcriptions Rap1 regulatory factor gene transcriptions Reb1 general regulatory factor gene transcriptions Retinoblastoma control element gene transcriptions Retinoic acid response element gene transcriptions Rgt1p gene transcriptions Rlm1p gene transcriptions RNA polymerase II gene transcriptions RNA polymerase II holoenzyme complex Root specific element gene transcriptions ROR-response element gene transcriptions Rox1p gene transcriptions Rpn4p gene transcriptions R response element gene transcriptions SARE gene transcriptions Seed-specific element gene transcriptions Serum response element gene transcriptions Servenius sequence gene transcriptions Shoot specific element gene transcriptions Sip4p gene transcriptions Smp1p gene transcriptions Sp1 gene transcriptions Spaceflight gene expressions Specificity protein gene transcriptions STAT gene transcriptions Ste12p gene transcriptions Sterol response element gene transcriptions Sucrose box gene transcriptions Synaptic Activity-Responsive Elements TACTAAC box gene transcriptions TAGteam gene transcriptions Tapetum box gene transcriptions TATA binding protein associated factor gene transcriptions TATA binding protein gene transcriptions TATA box actin/cytoskeleton/contractile family TATA box albumin family TATA box aldolase family TATA box alkaline phosphatase family TATA box annexin family TATA box cytochrome superfamily TATA box gene transcriptions TATA box heat shock family TATA box histone family TATA box human genes TATA box keratin family TATA box lipase family TATA box peptidase family TATA box platelet-derived growth factor family TATA box selenium-binding family TATA box serine protease family TATA box serpin superfamily TATA box transforming growth factor superfamily TATA box trefoil family TATA box tumor necrosis factor superfamily TATA box zinc metalloenzyme family TAT box gene transcriptions TATC box gene transcriptions Tbf1 regulatory factor gene transcriptions T box gene transcriptions TCCACCATA element gene transcriptions TC element gene transcriptions TCT gene transcriptions TEA consensus sequence gene transcriptions Tec1p gene transcriptions Telomeric repeat DNA-binding factor gene transcriptions Tetradecanoylphorbol-13-acetate response element gene transcriptions TGF-β control elements (TCEs) TGF-β inhibitory elements (TIEs) Thyroid hormone response element gene transcriptions Transcriptional regulation Transcription bubble gene transcriptions Transcription factor gene transcriptions Transcription factor 3 gene transcriptions Transcription factory gene transcriptions Transcription start site gene transcriptions Translational control sequence gene transcriptions Tryptophan residue U box gene transcriptions Unfolded protein response element gene transcriptions Upstream response element gene transcriptions Upstream stimulatory factor gene transcriptions UTR promoter gene transcriptions V and P box gene transcriptions V box gene transcriptions Vhr1p gene transcriptions Vitamin D response element gene transcriptions W box gene transcriptions X box gene transcriptions Xbp1p gene transcriptions X core promoter element gene transcriptions Xenobiotic response element gene transcriptions Xenobiotic responsive element gene transcriptions Yap1p,2p gene transcriptions Y box gene transcriptions YY1 gene transcriptions Zap1p gene transcriptions Z box gene transcriptions Zinc responsive element gene transcriptions