Hex sequence gene transcriptions: Difference between revisions

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# No Hex sequence participates in the transcription of A1BG.
# No Hex sequence participates in the transcription of A1BG.


==Samplings==
==Hex core samplings==
{{main|Model 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.
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.


Line 53: Line 53:
# complement, positive strand, negative direction, looking for ACTGCACCG, 0.
# complement, positive strand, negative direction, looking for ACTGCACCG, 0.
# complement, positive strand, positive direction, looking for ACTGCACCG, 0.
# complement, positive strand, positive direction, looking for ACTGCACCG, 0.
# inverse complement, negative strand, negative direction, looking for TTTTTTTT, 0.
# inverse complement, negative strand, negative direction, looking for GCCACGTCA, 0.
# inverse complement, negative strand, positive direction, looking for TTTTTTTT, 0.
# inverse complement, negative strand, positive direction, looking for GCCACGTCA, 0.
# inverse complement, positive strand, negative direction, looking for TTTTTTTT, 0.
# inverse complement, positive strand, negative direction, looking for GCCACGTCA, 0.
# inverse complement, positive strand, positive direction, looking for TTTTTTTT, 0.
# inverse complement, positive strand, positive direction, looking for GCCACGTCA, 0.
# inverse negative strand, negative direction, looking for AAAAAAAA, 0.
# inverse negative strand, negative direction, looking for CGGTGCAGT, 0.
# inverse negative strand, positive direction, looking for AAAAAAAA, 0.
# inverse negative strand, positive direction, looking for CGGTGCAGT, 0.
# inverse positive strand, negative direction, looking for AAAAAAAA, 0.
# inverse positive strand, negative direction, looking for CGGTGCAGT, 0.
# inverse positive strand, positive direction, looking for AAAAAAAA, 0.
# inverse positive strand, positive direction, looking for CGGTGCAGT, 0.


===Hex core promoters===
===Hex core promoters===
{{main|Core promoter gene transcriptions}}
{{main|Core promoter gene transcriptions}}
Positive strand: TGACGTGGC at 4344, and complement.
# Positive strand, positive direction: TGACGTGGC at 4344.
 
==Hex sequence random dataset samplings==
 
# Hexr0: 0.
# Hexr1: 0.
# Hexr2: 0.
# Hexr3: 0.
# Hexr4: 0.
# Hexr5: 0.
# Hexr6: 0.
# Hexr7: 0.
# Hexr8: 0.
# Hexr9: 0.
# Hexr0ci: 0.
# Hexr1ci: 0.
# Hexr2ci: 0.
# Hexr3ci: 0.
# Hexr4ci: 0.
# Hexr5ci: 0.
# Hexr6ci: 0.
# Hexr7ci: 0.
# Hexr8ci: 0.
# Hexr9ci: 0.
 
==Hex sequence analysis and results==
{{main|Complex locus A1BG and ZNF497#Hex sequences}}
The Hex sequence has the consensus (TGACGTGGC).<ref name=Song/>
 
{|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 || 1 || 2 || 0.5 || 0.5 ± 0.5 (-+0,++1)
|-
| 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
|}


===Hex proximal promoters===
Comparison:
{{main|Proximal promoter gene transcriptions}}


===Hex distal promoters===
The occurrence of a real Hex sequence is greater than the randoms. This suggests that the real Hex sequence is likely active or activable.
{{main|Distal promoter gene transcriptions}}


==Acknowledgements==
==Acknowledgements==

Latest revision as of 05:49, 30 August 2023

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

Human genes

Main article: Human genes

Consensus sequences

Main article: Consensus sequence gene transcriptions

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

Hypotheses

Main article: 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

Main article: Core promoter gene transcriptions
  1. Positive strand, positive direction: TGACGTGGC at 4344.

Hex sequence random dataset samplings

  1. Hexr0: 0.
  2. Hexr1: 0.
  3. Hexr2: 0.
  4. Hexr3: 0.
  5. Hexr4: 0.
  6. Hexr5: 0.
  7. Hexr6: 0.
  8. Hexr7: 0.
  9. Hexr8: 0.
  10. Hexr9: 0.
  11. Hexr0ci: 0.
  12. Hexr1ci: 0.
  13. Hexr2ci: 0.
  14. Hexr3ci: 0.
  15. Hexr4ci: 0.
  16. Hexr5ci: 0.
  17. Hexr6ci: 0.
  18. Hexr7ci: 0.
  19. Hexr8ci: 0.
  20. Hexr9ci: 0.

Hex sequence analysis and results

Main article: Complex locus A1BG and ZNF497 § Hex sequences

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 ± 0.5 (-+0,++1)
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 occurrence of a real Hex sequence is greater than the randoms. This suggests that the real Hex sequence is 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

Retrieved from "https://www.wikidoc.org/index.php?title=Hex_sequence_gene_transcriptions&oldid=1735925"