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==Binding site for==
==Binding site for==
==Complement copies==
{{main|Complement copy gene transcriptions}}


==Inverse copies==
==Inverse copies==
{{main|Inverse copy gene transcriptions}}
==Complement-inverse copies==
{{main|Complement-inverse copy gene transcriptions}}


==Enhancer activity==
==Enhancer activity==
{{main|Enhancer activity copy gene transcriptions}}


==Promoter occurrences==
==Promoter occurrences==
{{main|Promoter occurrence gene transcriptions}}


==Hypotheses==
==Hypotheses==
{{main|Hypotheses}}
# A1BG has no regulatory elements in either promoter.
# A1BG is not transcribed by a regulatory element.
# No regulatory element participates in the transcription of A1BG.
==Response element samplings==
Copying a responsive elements consensus sequence AAAAAAAA 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 AAAAAAAA (starting with SuccessablesAAA.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===
==Response element 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===


# A1BG has no A boxes in either promoter.
===RDr alternate negative direction (odds) (2596-1) distal promoters===
# A1BG is not transcribed by an ATA box.
# AGCE1 does not participate in the transcription of A1BG.


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


Copying a responsive elements consensus sequence 5'-AAAAAAAA-3' 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.
===RDr alternate positive direction (evens) (4050-1) distal promoters===


For the Basic programs testing consensus sequence 5'-AAAAAAAA-3' (starting with SuccessablesAAA.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:
==Response element analysis and results==
# negative strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesAAA--.bas, looking for 5'-AAAAAAAA-3', 0.
{{main|Complex locus A1BG and ZNF497#Name of response elements}}
# negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesAAA-+.bas, looking for 5'-AAAAAAAA-3', 0.
The Pax-4 homeodomain [HD] was shown to preferentially dimerize on DNA sequences consisting of an inverted TAAT motif, separated by 4-nucleotide spacing."<ref name=Kalousova/>
# positive strand, negative direction is SuccessablesAAA+-.bas, looking for 5'-AAAAAAAA-3', 0.
# positive strand, positive direction is SuccessablesAAA++.bas, looking for 5'-AAAAAAAA-3', 0.
# complement, negative strand, negative direction is SuccessablesAAAc--.bas, looking for 5'-TTTTTTTT-3', 0.
# complement, negative strand, positive direction is SuccessablesAAAc-+.bas, looking for 5'-TTTTTTTT-3', 0.
# complement, positive strand, negative direction is SuccessablesAAAc+-.bas, looking for 5'-TTTTTTTT-3', 0.
# complement, positive strand, positive direction is SuccessablesAAAc++.bas, looking for 5'-TTTTTTTT-3', 0.
# inverse complement, negative strand, negative direction is SuccessablesAAAci--.bas, looking for 5'-TTTTTTTT-3', 0.
# inverse complement, negative strand, positive direction is SuccessablesAAAci-+.bas, looking for 5'-TTTTTTTT-3', 0.
# inverse complement, positive strand, negative direction is SuccessablesAAAci+-.bas, looking for 5'-TTTTTTTT-3', 0.
# inverse complement, positive strand, positive direction is SuccessablesAAAci++.bas, looking for 5'-TTTTTTTT-3', 0.
# inverse negative strand, negative direction is SuccessablesAAAi--.bas, looking for 5'-AAAAAAAA-3', 0.
# inverse negative strand, positive direction is SuccessablesAAAi-+.bas, looking for 5'-AAAAAAAA-3', 0.
# inverse positive strand, negative direction is SuccessablesAAAi+-.bas, looking for 5'-AAAAAAAA-3', 0.
# inverse positive strand, positive direction is SuccessablesAAAi++.bas, looking for 5'-AAAAAAAA-3', 0.


===AAA core promoters===
{|class="wikitable"
{{main|Core promoter gene transcriptions}}
|-
! 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
|}


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


==AAA distal promoters===
The occurrences of real responsive element consensus sequences are greater than the randoms. This suggests that the real responsive element consensus sequences are likely active or activable.
{{main|Distal promoter gene transcriptions}}


==Acknowledgements==
==Acknowledgements==
Line 73: Line 185:
==See also==
==See also==
{{div col|colwidth=20em}}
{{div col|colwidth=20em}}
* [[A1BG gene transcription core promoters]]
* [[A1BG gene transcriptions]]
* [[A1BG gene transcriptions]]
* [[A1BG regulatory elements and regions]]
* [[A1BG response element gene transcriptions]]
* [[A1BG response element negative results]]
* [[A1BG response element positive results]]
* [[Complex locus A1BG and ZNF497]]
* [[Complex locus A1BG and ZNF497]]
{{Div col end}}
{{Div col end}}
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<!-- footer categories -->
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[[Category:Resources last modified in October 2020]]


This user is also an author, contributor, and editor at
This user is also an author, contributor, and editor at

Revision as of 18:46, 27 June 2022

Editor-In-Chief: Henry A. Hoff

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

Human genes

Main article: Human genes

Gene expressions

Main article: Gene expressions

Interactions

Main article: Interaction gene transcriptions

Consensus sequences

Main article: Consensus sequence gene transcriptions

Binding site for

Complement copies

Main article: Complement copy gene transcriptions

Inverse copies

Main article: Inverse copy gene transcriptions

Complement-inverse copies

Main article: Complement-inverse copy gene transcriptions

Enhancer activity

Main article: Enhancer activity copy gene transcriptions

Promoter occurrences

Main article: Promoter occurrence gene transcriptions

Hypotheses

Main article: Hypotheses
  1. A1BG has no regulatory elements in either promoter.
  2. A1BG is not transcribed by a regulatory element.
  3. No regulatory element participates in the transcription of A1BG.

Response element samplings

Copying a responsive elements consensus sequence AAAAAAAA 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 AAAAAAAA (starting with SuccessablesAAA.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

Response element 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

Response element analysis and results

Main article: Complex locus A1BG and ZNF497 § Name of response elements

The Pax-4 homeodomain [HD] was shown to preferentially dimerize on DNA sequences consisting of an inverted TAAT motif, separated by 4-nucleotide spacing."[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 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 responsive element consensus sequences are greater 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.

Initial content for this page in some instances came from Wikiversity.

Initial content for this page in some instances came from Wikipedia.

Initial content for this page in some instances incorporates text from the United States National Library of Medicine.

See also

References

  1. ↑

External links


This user is also an author, contributor, and editor at

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