Alpha-amylase conserved element gene transcriptions: Difference between revisions

Jump to navigation Jump to search
← Older editNewer edit →
VisualWikitext
Marshallsumter (talk | contribs)
smweditor
13,499 edits
Marshallsumter (talk | contribs)
smweditor
13,499 edits
Line 47: Line 47:
# inverse positive strand, negative direction, looking for 5'-CCTACCTACCTAT-3', 0.
# inverse positive strand, negative direction, looking for 5'-CCTACCTACCTAT-3', 0.
# inverse positive strand, positive direction, looking for 5'-CCTACCTACCTAT-3', 0.
# inverse positive strand, positive direction, looking for 5'-CCTACCTACCTAT-3', 0.
==Alpha-amylase conserved element portion samplings==
Copying a responsive elements consensus sequence TATCCA and putting the sequence in "⌘F" finds none between ZNF497 and A1BG or none between ZSCAN22 and A1BG as can be found by the computer programs.
For the Basic programs testing consensus sequence TATCCA (starting with SuccessablesAACp.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 AAAAAAAA, 0.
# positive strand, negative direction, looking for AAAAAAAA, 0.
# negative strand, positive direction, looking for AAAAAAAA, 0.
# positive strand, positive direction, looking for AAAAAAAA, 0.
# inverse complement, negative strand, negative direction, looking for TTTTTTTT, 0.
# inverse complement, positive strand, negative direction, looking for TTTTTTTT, 0.
# inverse complement, negative strand, positive direction, looking for TTTTTTTT, 0.
# inverse complement, positive strand, positive direction, looking for TTTTTTTT, 0.
===AAA (4560-2846) UTRs===
===AAA negative direction (2846-2811) core promoters===
===AAA positive direction (4445-4265) core promoters===
===AAA negative direction (2811-2596) proximal promoters===
===AAA positive direction (4265-4050) proximal promoters===
===AAA negative direction (2596-1) distal promoters===
===AAA positive direction (4050-1) distal promoters===
==Alpha-amylase conserved element portion random dataset samplings==
# RDr0: 0.
# RDr1: 0.
# RDr2: 0.
# RDr3: 0.
# RDr4: 0.
# RDr5: 0.
# RDr6: 0.
# RDr7: 0.
# RDr8: 0.
# RDr9: 0.
# RDr0ci: 0.
# RDr1ci: 0.
# RDr2ci: 0.
# RDr3ci: 0.
# RDr4ci: 0.
# RDr5ci: 0.
# RDr6ci: 0.
# RDr7ci: 0.
# RDr8ci: 0.
# RDr9ci: 0.
===RDr arbitrary (evens) (4560-2846) UTRs===
===RDr alternate (odds) (4560-2846) UTRs===
===RDr arbitrary negative direction (evens) (2846-2811) core promoters===
===RDr alternate negative direction (odds) (2846-2811) core promoters===
===RDr arbitrary positive direction (odds) (4445-4265) core promoters===
===RDr alternate positive direction (evens) (4445-4265) core promoters===
===RDr arbitrary negative direction (evens) (2811-2596) proximal promoters===
===RDr alternate negative direction (odds) (2811-2596) proximal promoters===
===RDr arbitrary positive direction (odds) (4265-4050) proximal promoters===
===RDr alternate positive direction (evens) (4265-4050) proximal promoters===
===RDr arbitrary negative direction (evens) (2596-1) distal promoters===
===RDr alternate negative direction (odds) (2596-1) distal promoters===
===RDr arbitrary positive direction (odds) (4050-1) distal promoters===
===RDr alternate positive direction (evens) (4050-1) distal promoters===
==Alpha-amylase conserved element portion analysis and results==
{{main|Complex locus A1BG and ZNF497#AACps}}
TATCCATCCATCC<ref name=Sharma/> portion TATCCA.
{|class="wikitable"
|-
! Reals or randoms !! Promoters !! direction !! Numbers !! Strands !! Occurrences !! Averages (± 0.1)
|-
| Reals || UTR || negative || 0 || 2 || 0 || 0
|-
| Randoms || UTR || arbitrary negative || 0 || 10 || 0 || 0
|-
| Randoms || UTR || alternate negative || 0 || 10 || 0 || 0
|-
| 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 || 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 || 0 || 2 || 0 || 0
|-
| Randoms || Distal || arbitrary positive || 0 || 10 || 0 || 0
|-
| Randoms || Distal || alternate positive || 0 || 10 || 0 || 0
|}
Comparison:
The occurrences of real AACps are greater than the randoms. This suggests that the real AACps are likely active or activable.


==Acknowledgements==
==Acknowledgements==

Revision as of 02:51, 11 April 2023

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

"A few genes were also noticed with the shoot (GATAatGATG) and root (TGACGTCA) specific elements, cell cycle regulation (CCCAACGGT), seed-specific element (CATGCATG) and alpha-amylase conserved elements (TATCCATCCATCC). The presence of a significant number of the regulatory elements suggests strong participation of the U-box E3 gene family in plant development and responses under abiotic and biotic stress conditions. The data also supports the active involvement of the U-box E3 gene family in hormonal regulatory pathways."[1]

Consensus sequences

TATCCATCCATCC[1]

Hypotheses

Main article: Hypotheses
  1. A1BG has no A boxes in either promoter.
  2. A1BG is not transcribed by an ATA box.
  3. AGCE1 does not participate in the transcription of A1BG.

Alpha-amylase conserved element samplings

Main article: Model samplings

Copying a responsive elements consensus sequence TATCCA and putting the sequence in "⌘F" finds none between ZNF497 and A1BG or none between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence TATCCATCCATCC (starting with SuccessablesAAC.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 5'-TATCCATCCATCC-3', 0.
  2. negative strand, positive direction, looking for 5'-TATCCATCCATCC-3', 0.
  3. positive strand, negative direction, looking for 5'-TATCCATCCATCC-3', 0.
  4. positive strand, positive direction, looking for 5'-TATCCATCCATCC-3', 0.
  5. complement, negative strand, negative direction, looking for 5'-ATAGGTAGGTAGG-3', 0.
  6. complement, negative strand, positive direction, looking for 5'-ATAGGTAGGTAGG-3', 0.
  7. complement, positive strand, negative direction, looking for 5'-ATAGGTAGGTAGG-3', 0.
  8. complement, positive strand, positive direction, looking for 5'-ATAGGTAGGTAGG-3', 0.
  9. inverse complement, negative strand, negative direction, looking for 5'-GGATGGATGGATA-3', 0.
  10. inverse complement, negative strand, positive direction, looking for 5'-GGATGGATGGATA-3', 0.
  11. inverse complement, positive strand, negative direction, looking for 5'-GGATGGATGGATA-3', 0.
  12. inverse complement, positive strand, positive direction, looking for 5'-GGATGGATGGATA-3', 0.
  13. inverse negative strand, negative direction, looking for 5'-CCTACCTACCTAT-3', 0.
  14. inverse negative strand, positive direction, looking for 5'-CCTACCTACCTAT-3', 0.
  15. inverse positive strand, negative direction, looking for 5'-CCTACCTACCTAT-3', 0.
  16. inverse positive strand, positive direction, looking for 5'-CCTACCTACCTAT-3', 0.

Alpha-amylase conserved element portion samplings

Copying a responsive elements consensus sequence TATCCA and putting the sequence in "⌘F" finds none between ZNF497 and A1BG or none between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence TATCCA (starting with SuccessablesAACp.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 AAAAAAAA, 0.
  2. positive strand, negative direction, looking for AAAAAAAA, 0.
  3. negative strand, positive direction, looking for AAAAAAAA, 0.
  4. positive strand, positive direction, looking for AAAAAAAA, 0.
  5. inverse complement, negative strand, negative direction, looking for TTTTTTTT, 0.
  6. inverse complement, positive strand, negative direction, looking for TTTTTTTT, 0.
  7. inverse complement, negative strand, positive direction, looking for TTTTTTTT, 0.
  8. inverse complement, positive strand, positive direction, looking for TTTTTTTT, 0.

AAA (4560-2846) UTRs

AAA negative direction (2846-2811) core promoters

AAA positive direction (4445-4265) core promoters

AAA negative direction (2811-2596) proximal promoters

AAA positive direction (4265-4050) proximal promoters

AAA negative direction (2596-1) distal promoters

AAA positive direction (4050-1) distal promoters

Alpha-amylase conserved element portion random dataset samplings

  1. RDr0: 0.
  2. RDr1: 0.
  3. RDr2: 0.
  4. RDr3: 0.
  5. RDr4: 0.
  6. RDr5: 0.
  7. RDr6: 0.
  8. RDr7: 0.
  9. RDr8: 0.
  10. RDr9: 0.
  11. RDr0ci: 0.
  12. RDr1ci: 0.
  13. RDr2ci: 0.
  14. RDr3ci: 0.
  15. RDr4ci: 0.
  16. RDr5ci: 0.
  17. RDr6ci: 0.
  18. RDr7ci: 0.
  19. RDr8ci: 0.
  20. RDr9ci: 0.

RDr arbitrary (evens) (4560-2846) UTRs

RDr alternate (odds) (4560-2846) UTRs

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

RDr alternate negative direction (odds) (2846-2811) core promoters

RDr arbitrary positive direction (odds) (4445-4265) core promoters

RDr alternate positive direction (evens) (4445-4265) core promoters

RDr arbitrary negative direction (evens) (2811-2596) proximal promoters

RDr alternate negative direction (odds) (2811-2596) proximal promoters

RDr arbitrary positive direction (odds) (4265-4050) proximal promoters

RDr alternate positive direction (evens) (4265-4050) proximal promoters

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

RDr alternate negative direction (odds) (2596-1) distal promoters

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

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

Alpha-amylase conserved element portion analysis and results

Main article: Complex locus A1BG and ZNF497 § AACps

TATCCATCCATCC[1] portion TATCCA.

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 0 2 0 0
Randoms UTR arbitrary negative 0 10 0 0
Randoms UTR alternate negative 0 10 0 0
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 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 0 2 0 0
Randoms Distal arbitrary positive 0 10 0 0
Randoms Distal alternate positive 0 10 0 0

Comparison:

The occurrences of real AACps are greater than the randoms. This suggests that the real AACps 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 1.2 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

Retrieved from "https://www.wikidoc.org/index.php?title=Alpha-amylase_conserved_element_gene_transcriptions&oldid=1733596"