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==Human genes==
==Human genes==
{{main|Human genes}}
 


==Gene expressions==
==Gene expressions==
Line 11: Line 11:


==Interactions==
==Interactions==
{{main|Interaction gene transcriptions}}
 


==Consensus sequences==
==Consensus sequences==
{{main|Consensus sequence gene transcriptions}}
 


==Binding site for==
==Binding site for==
Line 25: Line 25:


==Complement-inverse copies==
==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==
Line 39: Line 39:
# No regulatory element participates in the transcription of A1BG.
# No regulatory element participates in the transcription of A1BG.


==Samplings==
==Response element samplings==
{{main|Model 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.
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.


Line 46: Line 46:
# negative strand, negative direction, looking for AAAAAAAA, 0.
# negative strand, negative direction, looking for AAAAAAAA, 0.
# positive 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.
# positive strand, positive direction, looking for AAAAAAAA, 0.
# negative strand, positive direction, looking for AAAAAAAA, 0.
# complement, negative strand, negative direction, looking for TTTTTTTT, 0.
# complement, positive strand, negative direction, looking for TTTTTTTT, 0.
# complement, positive strand, positive direction, looking for TTTTTTTT, 0.
# complement, negative strand, positive direction, looking for TTTTTTTT, 0.
# inverse complement, negative strand, negative direction, looking for TTTTTTTT, 0.
# inverse complement, negative strand, negative direction, looking for TTTTTTTT, 0.
# inverse complement, positive 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.
# inverse complement, positive strand, positive direction, looking for TTTTTTTT, 0.
# inverse complement, negative strand, positive direction, looking for TTTTTTTT, 0.
# inverse negative strand, negative direction, looking for AAAAAAAA, 0.
# inverse positive strand, negative direction, looking for AAAAAAAA, 0.
# inverse positive strand, positive direction, looking for AAAAAAAA, 0.
# inverse negative strand, positive direction, looking for AAAAAAAA, 0.


===AAA UTRs===
===AAA (4560-2846) UTRs===
{{main|UTR promoter gene transcriptions}}
 
===AAA negative direction (2846-2811) core promoters===
 
===AAA positive direction (4445-4265) core promoters===
 
===AAA negative direction (2811-2596) proximal promoters===


===AAA core promoters===
===AAA positive direction (4265-4050) proximal promoters===
{{main|Core promoter gene transcriptions}}


===AAA proximal promoters===
===AAA negative direction (2596-1) distal promoters===
{{main|Proximal promoter gene transcriptions}}


===AAA distal promoters===
===AAA positive direction (4050-1) distal promoters===
{{main|Distal promoter gene transcriptions}}


==Random dataset samplings==
==Response element random dataset samplings==


# RDr0: 0.
# RDr0: 0.
Line 96: Line 90:
# RDr9ci: 0.
# RDr9ci: 0.


===RDr UTRs===
===RDr arbitrary (evens) (4560-2846) UTRs===


===RDr alternate (odds) (4560-2846) UTRs===


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


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


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


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


===RDr distal 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==
==Response element analysis and results==
{{main|Complex locus A1BG and ZNF497#Name of elements}}
{{main|Complex locus A1BG and ZNF497#Name of response elements}}
Response element (AAAAAA).<Author reference>
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=Zhang>{{ cite journal
|author=Bosen Zhang, Liwei Song, Jiali Cai, Lei Li, Hong Xu, Mengying Li, Jiamin Wang, Minmin Shi, Hao Chen, Hao Jia, and Zhaoyuan Hou
|title=The LIM protein Ajuba/SP1 complex forms a feed forward loop to induce SP1 target genes and promote pancreatic cancer cell proliferation
|journal=Journal of Experimental and Clinical Cancer Research
|date=17 May 2019
|volume=38
|issue=
|pages=205
|url=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6525466/
|arxiv=
|bibcode=
|doi=10.1186/s13046-019-1203-2
|pmid=31101117
|accessdate=27 February 2021 }}</ref>


{|class="wikitable"
{|class="wikitable"
Line 123: Line 147:
| Reals || Core || negative || 0 || 2 || 0 || 0  
| Reals || Core || negative || 0 || 2 || 0 || 0  
|-
|-
| Randoms || Core || negative || 0 || 10 || 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  
| Reals || Core || positive || 0 || 2 || 0 || 0  
|-
|-
| Randoms || Core || positive || 0 || 10 || 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  
| Reals || Proximal || negative || 0 || 2 || 0 || 0  
|-
|-
| Randoms || Proximal || negative || 0 || 10 || 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  
| Reals || Proximal || positive || 0 || 2 || 0 || 0  
|-
|-
| Randoms || Proximal || positive || 0 || 10 || 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
|-
|-
| Reals || Distal || negative || 1 || 2 || 0.5 || 0.5
| Randoms || Distal || alternate negative || 0 || 10 || 0 || 0  
|-
|-
| Randoms || Distal || negative || 1 || 10 || 0.1 || 0.05
| Reals || Distal || positive || 0 || 2 || 0 || 0  
|-
|-
| Reals || Distal || positive || 1 || 2 || 0.5 || 0.5
| Randoms || Distal || arbitrary positive || 0 || 10 || 0 || 0  
|-
|-
| Randoms || Distal || positive || 0 || 10 || 0 || 0.05
| Randoms || Distal || alternate positive || 0 || 10 || 0 || 0  
|}
|}


Comparison:
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.
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==
==Acknowledgements==
Line 182: Line 218:


<!-- footer templates -->
<!-- footer templates -->
{{Gene project}}
{{Gene project}}{{tlx|Phosphate biochemistry}}{{Transcription factors and intracellular receptors}}


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[[Category:Resources last modified in August 2021]]


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

Latest revision as of 05:24, 29 January 2023

Editor-In-Chief: Henry A. Hoff

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

Human genes

Gene expressions

Main article: Gene expressions

Interactions

Consensus sequences

Binding site for

Complement copies

Main article: Complement copy gene transcriptions

Inverse copies

Main article: Inverse copy gene transcriptions

Complement-inverse copies

Enhancer activity

Promoter occurrences

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. ↑ Bosen Zhang, Liwei Song, Jiali Cai, Lei Li, Hong Xu, Mengying Li, Jiamin Wang, Minmin Shi, Hao Chen, Hao Jia, and Zhaoyuan Hou (17 May 2019). "The LIM protein Ajuba/SP1 complex forms a feed forward loop to induce SP1 target genes and promote pancreatic cancer cell proliferation". Journal of Experimental and Clinical Cancer Research. 38: 205. doi:10.1186/s13046-019-1203-2. PMID 31101117. Retrieved 27 February 2021.

External links

{{Phosphate biochemistry}}


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

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