Hex sequence gene transcriptions: Difference between revisions

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==Response element analysis and results==
==Response element analysis and results==
{{main|Complex locus A1BG and ZNF497#Name of response elements}}
{{main|Complex locus A1BG and ZNF497#Hex sequences}}
Response element (AAAAAA).<Author reference>
The Hex sequence has the consensus (TGACGTGGC).<ref name=Song/>


{|class="wikitable"
{|class="wikitable"
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| Randoms || Core || alternate negative || 0 || 10 || 0 || 0  
| Randoms || Core || alternate negative || 0 || 10 || 0 || 0  
|-
|-
| Reals || Core || positive || 0 || 2 || 0 || 0  
| Reals || Core || positive || 1 || 2 || 0.5 || 0.5
|-
|-
| Randoms || Core || arbitrary positive || 0 || 10 || 0 || 0
| Randoms || Core || arbitrary positive || 0 || 10 || 0 || 0

Revision as of 06:47, 17 May 2022

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

Human genes

Consensus sequences

The Hex sequence has the consensus (TGACGTGGC)[1]

Hypotheses

  1. A1BG has no Hex sequences in either promoter.
  2. A1BG is not transcribed by a Hex sequence.
  3. No Hex sequence participates in the transcription of A1BG.

Hex core samplings

Copying a responsive elements consensus sequence TGACGTGGC 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 TGACGTGGC (starting with SuccessablesHex.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 TGACGTGGC, 0.
  2. negative strand, positive direction, looking for TGACGTGGC, 0.
  3. positive strand, negative direction, looking for TGACGTGGC, 0.
  4. positive strand, positive direction, looking for TGACGTGGC, 1, TGACGTGGC at 4344.
  5. complement, negative strand, negative direction, looking for ACTGCACCG, 0.
  6. complement, negative strand, positive direction, looking for ACTGCACCG, 1, ACTGCACCG at 4344.
  7. complement, positive strand, negative direction, looking for ACTGCACCG, 0.
  8. complement, positive strand, positive direction, looking for ACTGCACCG, 0.
  9. inverse complement, negative strand, negative direction, looking for GCCACGTCA, 0.
  10. inverse complement, negative strand, positive direction, looking for GCCACGTCA, 0.
  11. inverse complement, positive strand, negative direction, looking for GCCACGTCA, 0.
  12. inverse complement, positive strand, positive direction, looking for GCCACGTCA, 0.
  13. inverse negative strand, negative direction, looking for CGGTGCAGT, 0.
  14. inverse negative strand, positive direction, looking for CGGTGCAGT, 0.
  15. inverse positive strand, negative direction, looking for CGGTGCAGT, 0.
  16. inverse positive strand, positive direction, looking for CGGTGCAGT, 0.

Hex core promoters

  1. Positive strand, positive direction: TGACGTGGC at 4344.

Hex sequence 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 UTRs

RDr alternate UTRs

RDr arbitrary negative direction core promoters

RDr alternate negative direction core promoters

RDr arbitrary positive direction core promoters

RDr alternate positive direction core promoters

RDr arbitrary negative direction proximal promoters

RDr alternate negative direction proximal promoters

RDr arbitrary positive direction proximal promoters

RDr alternate positive direction proximal promoters

RDr arbitrary negative direction distal promoters

RDr alternate negative direction distal promoters

RDr arbitrary positive direction distal promoters

RDr alternate positive direction distal promoters

Response element analysis and results

The Hex sequence has the consensus (TGACGTGGC).[1]

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 1 2 0.5 0.5
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 responsive element consensus sequences are larger than the randoms. This suggests that the real responsive element consensus sequences 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 Young Hun Song; Cheol Min Yoo; An Pio Hong; Seong Hee Kim; Hee Jeong Jeong; Su Young Shin; Hye Jin Kim; Dae-Jin Yun; Chae Oh Lim; Jeong Dong Bahk; Sang Yeol Lee; Ron T. Nagao; Joe L. Key; Jong Chan Hong (April 2008). "DNA-Binding Study Identifies C-Box and Hybrid C/G-Box or C/A-Box Motifs as High-Affinity Binding Sites for STF1 and LONG HYPOCOTYL5 Proteins" (PDF). Plant Physiology. 146 (4): 1862–1877. doi:10.1104/pp.107.113217. PMID 18287490. Retrieved 26 March 2019.

External links