Endosperm expression gene transcriptions: Difference between revisions

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Revision as of 20:46, 11 December 2022

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 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.

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
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

[Sharma-1] 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.

[1]

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 # Endosperm expression does not participate in the transcription of A1BG.
-==Samplings==
+==Endosperm expression samplings==
-{{main|Model 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.
@@ Line 94: / Line 94: @@
 # EEr5: TGTGTCA at 2839.
-==Response element analysis and results==
+==Endosperm expression analysis and results==
 {{main|Complex locus A1BG and ZNF497#Endosperm expressions}}
 Endosperm expression (TGTGTCA).<ref name=Sharma/>
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-[[Category:Resources last modified in December 2020]]

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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 M-CAT boxes Mcm1 regulatory factor gene transcriptions Met3 gene transcriptions 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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 repressor site 1 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

Endosperm expression gene transcriptions: Difference between revisions

Revision as of 20:46, 11 December 2022

Contents

Human genes

Gene expressions

Consensus sequences

Hypotheses

Endosperm expression samplings

EE UTR

EE distal promoters

Endosperm expression random dataset samplings

EEr UTRs

EEr distal promoters

Endosperm expression analysis and results

Acknowledgements

See also

References

External links

Navigation menu

Endosperm expression gene transcriptions: Difference between revisions

Revision as of 20:46, 11 December 2022

Human genes

Gene expressions

Consensus sequences

Hypotheses

Endosperm expression samplings

EE UTR

EE distal promoters

Endosperm expression random dataset samplings

EEr UTRs

EEr distal promoters

Endosperm expression analysis and results

Acknowledgements

See also

References

External links

Navigation menu

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