Endosperm expression gene transcriptions: Difference between revisions

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

Human genes

Gene expressions

Consensus sequences

Endosperm expression (TGTGTCA).^[1]

Hypotheses

A1BG has no Endosperm expression in either promoter.
A1BG is not transcribed by Endosperm expression.
Endosperm expression does not participate in the transcription of A1BG.

Samplings

Copying an apparent consensus sequence of TGTGTCA and putting it in "⌘F" finds one located 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 5'-TGTGTCA-3' (starting with SuccessablesEE.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'-TGTGTCA-3', 1, 5'-TGTGTCA-3' at 4198.
negative strand, positive direction, looking for 5'-TGTGTCA-3', 0.
positive strand, negative direction, looking for 5'-TGTGTCA-3', 0.
positive strand, positive direction, looking for 5'-TGTGTCA-3', 1, 5'-TGTGTCA-3' at 3413.
complement, negative strand, negative direction, looking for 5'-ACACAGT-3', 0.
complement, negative strand, positive direction, looking for 5'-ACACAGT-3', 1, 5'-ACACAGT-3' at 3413.
complement, positive strand, negative direction, looking for 5'-ACACAGT-3', 1, 5'-ACACAGT-3' at 4198.
complement, positive strand, positive direction, looking for 5'-ACACAGT-3', 0.
inverse complement, negative strand, negative direction, looking for 5'-TGACACA-3', 0.
inverse complement, negative strand, positive direction, looking for 5'-TGACACA-3', 0.
inverse complement, positive strand, negative direction, looking for 5'-TGACACA-3', 0.
inverse complement, positive strand, positive direction, looking for 5'-TGACACA-3', 1, 5'-TGACACA-3' at 2076.
inverse negative strand, negative direction, looking for 5'-ACTGTGT-3', 0.
inverse negative strand, positive direction, looking for 5'-ACTGTGT-3', 1, 5'-ACTGTGT-3' at 2076.
inverse positive strand, negative direction, looking for 5'-ACTGTGT-3', 0.
inverse positive strand, positive direction, looking for 5'-ACTGTGT-3', 0.

EE UTR

Negative strand, negative direction: TGTGTCA at 4198.

EE distal promoters

Negative strand, positive direction: TGACACA at 2076.

Positive strand, positive direction: TGTGTCA at 3413.

Endosperm expression random dataset samplings

EEr0: 1, TGTGTCA at 3959.
EEr1: 0.
EEr2: 0.
EEr3: 0.
EEr4: 0.
EEr5: 1, TGTGTCA at 2839.
EEr6: 0.
EEr7: 0.
EEr8: 0.
EEr9: 0.
EEr0ci: 0.
EEr1ci: 0.
EEr2ci: 0.
EEr3ci: 0.
EEr4ci: 0.
EEr5ci: 0.
EEr6ci: 0.
EEr7ci: 0.
EEr8ci: 0.
EEr9ci: 0.

EEr UTRs

EEr0: TGTGTCA at 3959.

EEr distal promoters

EEr5: TGTGTCA at 2839.

Response element analysis and results

Endosperm expression (TGTGTCA).^[1]

Reals or randoms	Promoters	direction	Numbers	Strands	Occurrences	Averages (± 0.1)
Reals	UTR	negative	1	2	0.5	0.5
Randoms	UTR	arbitrary negative	1	10	0.1	0.05
Randoms	UTR	alternate negative	0	10	0	0.05
Reals	Core	negative	0	2	0	0
Randoms	Core	negative	0	10	0	0
Reals	Core	positive	0	2	0	0
Randoms	Core	positive	0	10	0	0
Reals	Proximal	negative	0	2	0	0
Randoms	Proximal	negative	0	10	0	0
Reals	Proximal	positive	0	2	0	0
Randoms	Proximal	positive	0	10	0	0
Reals	Distal	negative	0	2	0	0
Randoms	Distal	negative	0	10	0	0.05
Reals	Distal	positive	2	2	1.0	0.5
Randoms	Distal	positive	1	10	0.1	0.05

Comparison:

The occurrences of real endosperm expression consensus sequences are larger than the randoms. This suggests that the endosperm expression consensus sequences are likely active or activable.

Acknowledgements

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

References

↑ ^1.0 ^1.1 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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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 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 gene transcriptions 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 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

@@ Line 96: / Line 96: @@
 ==Response element analysis and results==
 {{main|Complex locus A1BG and ZNF497#Endosperm expressions}}
+Endosperm expression (TGTGTCA).<ref name=Sharma/>
+{|class="wikitable"
+|-
+! Reals or randoms !! Promoters !! direction !! Numbers !! Strands !! Occurrences !! Averages (± 0.1)
+|-
+| Reals || UTR || negative || 1 || 2 || 0.5 || 0.5
+|-
+| Randoms || UTR || arbitrary negative || 1 || 10 || 0.1 || 0.05
+|-
+| Randoms || UTR || alternate negative || 0 || 10 || 0 || 0.05
+|-
+| Reals || Core || negative || 0 || 2 || 0 || 0
+|-
+| Randoms || Core || negative || 0 || 10 || 0 || 0
+|-
+| Reals || Core || positive || 0 || 2 || 0 || 0
+|-
+| Randoms || Core || positive || 0 || 10 || 0 || 0
+|-
+| Reals || Proximal || negative || 0 || 2 || 0 || 0
+|-
+| Randoms || Proximal || negative || 0 || 10 || 0 || 0
+|-
+| Reals || Proximal || positive || 0 || 2 || 0 || 0
+|-
+| Randoms || Proximal || positive || 0 || 10 || 0 || 0
+|-
+| Reals || Distal || negative || 0 || 2 || 0 || 0
+|-
+| Randoms || Distal || negative || 0 || 10 || 0 || 0.05
+|-
+| Reals || Distal || positive || 2 || 2 || 1.0 || 0.5
+|-
+| Randoms || Distal || positive || 1 || 10 || 0.1 || 0.05
+|}
+Comparison:
+The occurrences of real endosperm expression consensus sequences are larger than the randoms. This suggests that the endosperm expression consensus sequences are likely active or activable.
 ==Acknowledgements==