Endosperm expression gene transcriptions

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.

Endosperm expression 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 TGTGTCA (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 TGTGTCA, 1, TGTGTCA at 4198.
positive strand, negative direction, looking for TGTGTCA, 0.
negative strand, positive direction, looking for TGTGTCA, 0.
positive strand, positive direction, looking for TGTGTCA, 1, TGTGTCA at 3413.
inverse complement, negative strand, negative direction, looking for TGACACA, 0.
inverse complement, positive strand, negative direction, looking for TGACACA, 0.
inverse complement, negative strand, positive direction, looking for TGACACA, 0.
inverse complement, positive strand, positive direction, looking for TGACACA, 1, TGACACA at 2076.

EE (4560-2846) UTRs

Negative strand, negative direction: TGTGTCA at 4198.

EE positive direction (4050-1) distal promoters

Positive strand, positive direction: TGTGTCA at 3413.
Positive strand, positive direction: TGACACA at 2076.

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 arbitrary (evens) (4560-2846) UTRs

EEr0: TGTGTCA at 3959.

EEr arbitrary negative direction (evens) (2846-2811) core promoters

EEr5: TGTGTCA at 2839.

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

EEr5: TGTGTCA at 2839.

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

EEr0: TGTGTCA at 3959.

Endosperm expression 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 ± 0.5 (--1,+-0)
Randoms	UTR	arbitrary negative	1	10	0.1	0.05 ± 0.05
Randoms	UTR	alternate negative	0	10	0	0.05 ± 0.05
Reals	Core	negative	0	2	0	0
Randoms	Core	arbitrary negative	1	10	0.1	0.05 ± 0.05
Randoms	Core	alternate negative	0	10	0	0.05 ± 0.05
Reals	Core	positive	0	2	0	0
Randoms	Core	arbitrary positive	0	10	0	0
Randoms	Core	alternate positive	0	10	0	0
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	0	10	0	0
Randoms	Distal	alternate negative	0	10	0	0
Reals	Distal	positive	2	2	1	1 ± 1 (-+0,++2)
Randoms	Distal	arbitrary positive	1	10	0.1	0.1 ± 0
Randoms	Distal	alternate positive	1	10	0.1	0.1 ± 0

Comparison:

The occurrences of real EEs are greater than the randoms. This suggests that the real EEs 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.

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