Endosperm expression gene transcriptions: Difference between revisions

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# Endosperm expression does not participate in the transcription of A1BG.
# 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.
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:
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 5'-TGTGTCA-3', 1, 5'-TGTGTCA-3' at 4198.
# negative strand, negative direction, looking for TGTGTCA, 1, TGTGTCA at 4198.
# negative strand, positive direction, looking for 5'-TGTGTCA-3', 0.
# positive strand, negative direction, looking for TGTGTCA, 0.
# positive strand, negative direction, looking for 5'-TGTGTCA-3', 0.
# negative strand, positive direction, looking for TGTGTCA, 0.
# positive strand, positive direction, looking for 5'-TGTGTCA-3', 1, 5'-TGTGTCA-3' at 3413.
# positive strand, positive direction, looking for TGTGTCA, 1, TGTGTCA at 3413.
# complement, negative strand, negative direction, looking for 5'-ACACAGT-3', 0.
# inverse complement, negative strand, negative direction, looking for TGACACA, 0.
# complement, negative strand, positive direction, looking for 5'-ACACAGT-3', 1, 5'-ACACAGT-3' at 3413.
# inverse complement, positive strand, negative direction, looking for TGACACA, 0.
# complement, positive strand, negative direction, looking for 5'-ACACAGT-3', 1, 5'-ACACAGT-3' at 4198.
# inverse complement, negative strand, positive direction, looking for TGACACA, 0.
# complement, positive strand, positive direction, looking for 5'-ACACAGT-3', 0.
# inverse complement, positive strand, positive direction, looking for TGACACA, 1, TGACACA at 2076.
# inverse complement, negative strand, negative direction, looking for 5'-TGACACA-3', 0.
 
# inverse complement, negative strand, positive direction, looking for 5'-TGACACA-3', 0.
===EE (4560-2846) UTRs===
# 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.
# Negative strand, negative direction: TGTGTCA at 4198.
# 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.
===EE positive direction (4050-1) distal promoters===
# inverse positive strand, negative direction, looking for 5'-ACTGTGT-3', 0.
 
# inverse positive strand, positive direction, looking for 5'-ACTGTGT-3', 0.
# 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.


===EE UTR===
==Endosperm expression analysis and results==
{{main|Complex locus A1BG and ZNF497#Endosperm expressions}}
Endosperm expression (TGTGTCA).<ref name=Sharma/>


Negative strand, negative direction: TGTGTCA at 4198.
{|class="wikitable"
|-
! 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
|}


===EE distal promoters===
Comparison:


Positive strand, positive direction: TGTGTCA at 3413, TGACACA at 2076.
The occurrences of real EEs are greater than the randoms. This suggests that the real EEs are likely active or activable.


==Acknowledgements==
==Acknowledgements==
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[[Category:Resources last modified in December 2020]]

Latest revision as of 17:27, 18 September 2023

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

Human genes

Main article: Human genes

Gene expressions

Main article: Gene expressions

Consensus sequences

Main article: Consensus sequence gene transcriptions

Endosperm expression (TGTGTCA).[1]

Hypotheses

Main article: Hypotheses
  1. A1BG has no Endosperm expression in either promoter.
  2. A1BG is not transcribed by Endosperm expression.
  3. 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:

  1. negative strand, negative direction, looking for TGTGTCA, 1, TGTGTCA at 4198.
  2. positive strand, negative direction, looking for TGTGTCA, 0.
  3. negative strand, positive direction, looking for TGTGTCA, 0.
  4. positive strand, positive direction, looking for TGTGTCA, 1, TGTGTCA at 3413.
  5. inverse complement, negative strand, negative direction, looking for TGACACA, 0.
  6. inverse complement, positive strand, negative direction, looking for TGACACA, 0.
  7. inverse complement, negative strand, positive direction, looking for TGACACA, 0.
  8. inverse complement, positive strand, positive direction, looking for TGACACA, 1, TGACACA at 2076.

EE (4560-2846) UTRs

  1. Negative strand, negative direction: TGTGTCA at 4198.

EE positive direction (4050-1) distal promoters

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

Endosperm expression random dataset samplings

  1. EEr0: 1, TGTGTCA at 3959.
  2. EEr1: 0.
  3. EEr2: 0.
  4. EEr3: 0.
  5. EEr4: 0.
  6. EEr5: 1, TGTGTCA at 2839.
  7. EEr6: 0.
  8. EEr7: 0.
  9. EEr8: 0.
  10. EEr9: 0.
  11. EEr0ci: 0.
  12. EEr1ci: 0.
  13. EEr2ci: 0.
  14. EEr3ci: 0.
  15. EEr4ci: 0.
  16. EEr5ci: 0.
  17. EEr6ci: 0.
  18. EEr7ci: 0.
  19. EEr8ci: 0.
  20. EEr9ci: 0.

EEr arbitrary (evens) (4560-2846) UTRs

  1. EEr0: TGTGTCA at 3959.

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

  1. EEr5: TGTGTCA at 2839.

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

  1. EEr5: TGTGTCA at 2839.

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

  1. EEr0: TGTGTCA at 3959.

Endosperm expression analysis and results

Main article: Complex locus A1BG and ZNF497 § Endosperm expressions

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.

See also

References

  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.

External links


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