Q element gene transcriptions: Difference between revisions

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The consensus sequence for a Q element is 3'-AGGTCA-5'.<ref name=Ye/>
The consensus sequence for a Q element is 3'-AGGTCA-5'.<ref name=Ye/>


==Samplings==
==QE samplings==
{{main|Model samplings}}
Copying the apparent consensus sequence for the QE (AGGTCA) and putting it in "⌘F" finds two located between ZSCAN22 or three between ZNF497 and A1BG as can be found by the computer programs.
 
For the Basic programs testing consensus sequence AGGTCA (starting with SuccessablesQE.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 AGGTCA, 2, AGGTCA at 1532, AGGTCA at 1352.
# positive strand, negative direction, looking for AGGTCA, 7, AGGTCA at 4307, AGGTCA at 2585, AGGTCA at 2248, AGGTCA at 712, AGGTCA at 576, AGGTCA at 568, AGGTCA at 439.
# positive strand, positive direction, looking for AGGTCA, 0.
# negative strand, positive direction, looking for AGGTCA, 3, AGGTCA at 4269, AGGTCA at 2220, AGGTCA at 153.
# complement, negative strand, negative direction, looking for TCCAGT, 7, TCCAGT at 4307, TCCAGT at 2585, TCCAGT at 2248, TCCAGT at 712, TCCAGT at 576, TCCAGT at 568, TCCAGT at 439.
# complement, positive strand, negative direction, looking for TCCAGT, 2, TCCAGT at 1532, TCCAGT at 1352.
# complement, positive strand, positive direction, looking for TCCAGT, 3, TCCAGT at 4269, TCCAGT at 2220, TCCAGT at 153.
# complement, negative strand, positive direction, looking for TCCAGT, 0.
# inverse complement, negative strand, negative direction, looking for TGACCT, 0.
# inverse complement, positive strand, negative direction, looking for TGACCT, 0.
# inverse complement, positive strand, positive direction, looking for TGACCT, 0.
# inverse complement, negative strand, positive direction, looking for TGACCT, 2, TGACCT at 4019, TGACCT at 3785.
# inverse negative strand, negative direction, looking for ACTGGA, 0.
# inverse positive strand, negative direction, looking for ACTGGA, 0.
# inverse positive strand, positive direction, looking for ACTGGA, 2, ACTGGA at 4019, ACTGGA at 3785.
# inverse negative strand, positive direction, looking for ACTGGA, 0.
 
===QE (4560-2846) UTRs===
 
# Positive strand, negative direction: AGGTCA at 4307.
 
===QE positive direction (4445-4265) core promoters===
 
# Negative strand, positive direction: AGGTCA at 4269.
 
===QE negative direction (2596-1) distal promoters===
 
# Negative strand, negative direction: AGGTCA at 1532, AGGTCA at 1352.
# Positive strand, negative direction: AGGTCA at 2585, AGGTCA at 2248, AGGTCA at 712, AGGTCA at 576, AGGTCA at 568, AGGTCA at 439.
 
===QE positive direction (4050-1) distal promoters===
 
# Negative strand, positive direction: AGGTCA at 2220, AGGTCA at 153.
# Negative strand, positive direction: TGACCT at 4019, TGACCT at 3785.
 
==QE random dataset samplings==
# QEr0: 1, AGGTCA at 699.
# QEr1: 1, AGGTCA at 1750.
# QEr2: 2, AGGTCA at 4381, AGGTCA at 3163.
# QEr3: 1, AGGTCA at 2303.
# QEr4: 0.
# QEr5: 1, AGGTCA at 4296.
# QEr6: 0.
# QEr7: 0.
# QEr8: 0.
# QEr9: 0.
# QEr0ci: 0.
# QEr1ci: 0.
# QEr2ci: 0.
# QEr3ci: 2, TGACCT at 4439, TGACCT at 2443.
# QEr4ci: 0.
# QEr5ci: 1, TGACCT at 2538.
# QEr6ci: 0.
# QEr7ci: 1, TGACCT at 3801.
# QEr8ci: 1, TGACCT at 540.
# QEr9ci: 0.
 
===QEr arbitrary (evens) (4560-2846) UTRs===
 
# QEr2: AGGTCA at 4381, AGGTCA at 3163.
 
===QEr alternate (odds) (4560-2846) UTRs===
 
# QEr5: AGGTCA at 4296.
# QEr3ci: TGACCT at 4439.
# QEr7ci: TGACCT at 3801.


Copying the apparent consensus sequence for the QE (AGGTCA) and putting it in "⌘F" finds two located between ZSCAN22 or three between ZNF497 and A1BG as can be found by the computer programs.
===QEr arbitrary positive direction (odds) (4445-4265) core promoters===
 
# QEr5: AGGTCA at 4296.
# QEr3ci: TGACCT at 4439.
 
===QEr alternate positive direction (evens) (4445-4265) core promoters===
 
# QEr2: AGGTCA at 4381.
 
===QEr arbitrary negative direction (evens) (2596-1) distal promoters===
 
# QEr0: AGGTCA at 699.
# QEr8ci: TGACCT at 540.
 
===QEr alternate negative direction (odds) (2596-1) distal promoters===
 
# QEr1: AGGTCA at 1750.
# QEr3: AGGTCA at 2303.
# QEr3ci: TGACCT at 2443.
# QEr5ci: TGACCT at 2538.
 
===QEr arbitrary positive direction (odds) (4050-1) distal promoters===
 
# QEr1: AGGTCA at 1750.
# QEr3: AGGTCA at 2303.
# QEr3ci: TGACCT at 2443.
# QEr5ci: TGACCT at 2538.
# QEr7ci: TGACCT at 3801.
 
===QEr alternate positive direction (evens) (4050-1) distal promoters===
 
# QEr0: AGGTCA at 699.
# QEr2: AGGTCA at 3163.
# QEr8ci: TGACCT at 540.
 
==QE analysis and results==
{{main|Complex locus A1BG and ZNF497#QEs}}
 
The consensus sequence for a Q element is AGGTCA.<ref name=Ye/>
 
{|class="wikitable"
|-
! Reals or randoms !! Promoters !! direction !! Numbers !! Strands !! Occurrences !! Averages (± 0.1)
|-
| Reals || UTR || negative || 1 || 2 || 0.5 || 0.5 ± 0.5 (--0,+-1)
|-
| Randoms || UTR || arbitrary negative || 2 || 10 || 0.2 || 0.25
|-
| Randoms || UTR || alternate negative || 3 || 10 || 0.3 || 0.25
|-
| 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 || 1 || 2 || 0.5 || 0.5 ± 0.5 (-+1,++0)
|-
| Randoms || Core || arbitrary positive || 2 || 10 || 0.2 || 0.15
|-
| Randoms || Core || alternate positive || 1 || 10 || 0.1 || 0.15
|-
| 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 || 8 || 2 || 4 || 4 ± 2 (—2,+-6)
|-
| Randoms || Distal || arbitrary negative || 2 || 10 || 0.2 || 0.3
|-
| Randoms || Distal || alternate negative || 4 || 10 || 0.4 || 0.3
|-
| Reals || Distal || positive || 4 || 2 || 2 || 2 ± 2 (-+4,++0)
|-
| Randoms || Distal || arbitrary positive || 5 || 10 || 0.5 || 0.4
|-
| Randoms || Distal || alternate positive || 3 || 10 || 0.3 || 0.4
|}
 
Comparison:
The occurrences of real QE UTRs, cores and distals are greater than the randoms. This suggests that the real QEs are likely active or activable.


==See also==
==See also==
{{div col|colwidth=20em}}
{{div col|colwidth=20em}}
* [[Complex locus A1BG and ZNF497]]
* [[Complex locus A1BG and ZNF497]]
* [[Peroxisome proliferator hormone response element gene transcriptions]]
* [[Transcription factor]]
* [[Transcription factor]]
{{Div col end}}
{{Div col end}}

Latest revision as of 04:44, 7 September 2023

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

"The basal regulatory elements identified include a putative TATA-box (−30/−24) for RNA polymerase binding and a CAAT box (−64/−61; [...]). Several putative floral expression-related cis-elements identified included a putative 6-nucleotide Q element (−770/−665), three GTGA boxes (−372/−369, −209/−206 and −164/−161) and four putative highly-conserved POLLEN1 boxes (−737/−733, −711/−707, −150/−146 and −36/−32; [...])."[1]

Human genes

Consensus sequences

The consensus sequence for a Q element is 3'-AGGTCA-5'.[1]

QE samplings

Main article: Model samplings

Copying the apparent consensus sequence for the QE (AGGTCA) and putting it in "⌘F" finds two located between ZSCAN22 or three between ZNF497 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence AGGTCA (starting with SuccessablesQE.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 AGGTCA, 2, AGGTCA at 1532, AGGTCA at 1352.
  2. positive strand, negative direction, looking for AGGTCA, 7, AGGTCA at 4307, AGGTCA at 2585, AGGTCA at 2248, AGGTCA at 712, AGGTCA at 576, AGGTCA at 568, AGGTCA at 439.
  3. positive strand, positive direction, looking for AGGTCA, 0.
  4. negative strand, positive direction, looking for AGGTCA, 3, AGGTCA at 4269, AGGTCA at 2220, AGGTCA at 153.
  5. complement, negative strand, negative direction, looking for TCCAGT, 7, TCCAGT at 4307, TCCAGT at 2585, TCCAGT at 2248, TCCAGT at 712, TCCAGT at 576, TCCAGT at 568, TCCAGT at 439.
  6. complement, positive strand, negative direction, looking for TCCAGT, 2, TCCAGT at 1532, TCCAGT at 1352.
  7. complement, positive strand, positive direction, looking for TCCAGT, 3, TCCAGT at 4269, TCCAGT at 2220, TCCAGT at 153.
  8. complement, negative strand, positive direction, looking for TCCAGT, 0.
  9. inverse complement, negative strand, negative direction, looking for TGACCT, 0.
  10. inverse complement, positive strand, negative direction, looking for TGACCT, 0.
  11. inverse complement, positive strand, positive direction, looking for TGACCT, 0.
  12. inverse complement, negative strand, positive direction, looking for TGACCT, 2, TGACCT at 4019, TGACCT at 3785.
  13. inverse negative strand, negative direction, looking for ACTGGA, 0.
  14. inverse positive strand, negative direction, looking for ACTGGA, 0.
  15. inverse positive strand, positive direction, looking for ACTGGA, 2, ACTGGA at 4019, ACTGGA at 3785.
  16. inverse negative strand, positive direction, looking for ACTGGA, 0.

QE (4560-2846) UTRs

  1. Positive strand, negative direction: AGGTCA at 4307.

QE positive direction (4445-4265) core promoters

  1. Negative strand, positive direction: AGGTCA at 4269.

QE negative direction (2596-1) distal promoters

  1. Negative strand, negative direction: AGGTCA at 1532, AGGTCA at 1352.
  2. Positive strand, negative direction: AGGTCA at 2585, AGGTCA at 2248, AGGTCA at 712, AGGTCA at 576, AGGTCA at 568, AGGTCA at 439.

QE positive direction (4050-1) distal promoters

  1. Negative strand, positive direction: AGGTCA at 2220, AGGTCA at 153.
  2. Negative strand, positive direction: TGACCT at 4019, TGACCT at 3785.

QE random dataset samplings

  1. QEr0: 1, AGGTCA at 699.
  2. QEr1: 1, AGGTCA at 1750.
  3. QEr2: 2, AGGTCA at 4381, AGGTCA at 3163.
  4. QEr3: 1, AGGTCA at 2303.
  5. QEr4: 0.
  6. QEr5: 1, AGGTCA at 4296.
  7. QEr6: 0.
  8. QEr7: 0.
  9. QEr8: 0.
  10. QEr9: 0.
  11. QEr0ci: 0.
  12. QEr1ci: 0.
  13. QEr2ci: 0.
  14. QEr3ci: 2, TGACCT at 4439, TGACCT at 2443.
  15. QEr4ci: 0.
  16. QEr5ci: 1, TGACCT at 2538.
  17. QEr6ci: 0.
  18. QEr7ci: 1, TGACCT at 3801.
  19. QEr8ci: 1, TGACCT at 540.
  20. QEr9ci: 0.

QEr arbitrary (evens) (4560-2846) UTRs

  1. QEr2: AGGTCA at 4381, AGGTCA at 3163.

QEr alternate (odds) (4560-2846) UTRs

  1. QEr5: AGGTCA at 4296.
  2. QEr3ci: TGACCT at 4439.
  3. QEr7ci: TGACCT at 3801.

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

  1. QEr5: AGGTCA at 4296.
  2. QEr3ci: TGACCT at 4439.

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

  1. QEr2: AGGTCA at 4381.

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

  1. QEr0: AGGTCA at 699.
  2. QEr8ci: TGACCT at 540.

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

  1. QEr1: AGGTCA at 1750.
  2. QEr3: AGGTCA at 2303.
  3. QEr3ci: TGACCT at 2443.
  4. QEr5ci: TGACCT at 2538.

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

  1. QEr1: AGGTCA at 1750.
  2. QEr3: AGGTCA at 2303.
  3. QEr3ci: TGACCT at 2443.
  4. QEr5ci: TGACCT at 2538.
  5. QEr7ci: TGACCT at 3801.

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

  1. QEr0: AGGTCA at 699.
  2. QEr2: AGGTCA at 3163.
  3. QEr8ci: TGACCT at 540.

QE analysis and results

Main article: Complex locus A1BG and ZNF497 § QEs

The consensus sequence for a Q element is AGGTCA.[1]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 1 2 0.5 0.5 ± 0.5 (--0,+-1)
Randoms UTR arbitrary negative 2 10 0.2 0.25
Randoms UTR alternate negative 3 10 0.3 0.25
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 1 2 0.5 0.5 ± 0.5 (-+1,++0)
Randoms Core arbitrary positive 2 10 0.2 0.15
Randoms Core alternate positive 1 10 0.1 0.15
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 8 2 4 4 ± 2 (—2,+-6)
Randoms Distal arbitrary negative 2 10 0.2 0.3
Randoms Distal alternate negative 4 10 0.4 0.3
Reals Distal positive 4 2 2 2 ± 2 (-+4,++0)
Randoms Distal arbitrary positive 5 10 0.5 0.4
Randoms Distal alternate positive 3 10 0.3 0.4

Comparison: The occurrences of real QE UTRs, cores and distals are greater than the randoms. This suggests that the real QEs are likely active or activable.

See also

References

  1. ↑ 1.0 1.1 1.2 Zi-Wei Ye, Jie Xu, Jianxin Shi, Dabing Zhang and Mee-Len Chye (January 2017). "Kelch-motif containing acyl-CoA binding proteins AtACBP4 and AtACBP5 are differentially expressed and function in floral lipid metabolism" (PDF). Plant Molecular Biology. 93: 209–225. doi:10.1007/s11103-016-0557-5. PMID 27826761. Retrieved 7 May 2020.

External links

Retrieved from "https://www.wikidoc.org/index.php?title=Q_element_gene_transcriptions&oldid=1736012"