Cat8p gene transcriptions: Difference between revisions

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# Cat8p does not participate in the transcription of A1BG.
# Cat8p does not participate in the transcription of A1BG.


==Samplings==
==Cat8p samplings==


Copying 5'-CGGTCCGC-3' in "⌘F" yields none between ZSCAN22 and A1BG and none between ZNF497 and A1BG as can be found by the computer programs.
Copying CGGTCCGC in "⌘F" yields none between ZSCAN22 and A1BG and none between ZNF497 and A1BG as can be found by the computer programs.


For the Basic programs testing consensus sequence 5'-CGG(A/C/G/T)(C/G/T)(A/C/G/T)(A/C/G)(A/C)(A/C/T)GGA-3' (starting with SuccessablesCat8p.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:
For the Basic programs testing consensus sequence CGG(A/C/G/T)(C/G/T)(A/C/G/T)(A/C/G)(A/C)(A/C/T)GGA (starting with SuccessablesCat8p.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 5'-CGG(A/C/G/T)(C/G/T)(A/C/G/T)(A/C/G)(A/C)(A/C/T)GGA-3', 0.
# negative strand, negative direction, looking for CGG(A/C/G/T)(C/G/T)(A/C/G/T)(A/C/G)(A/C)(A/C/T)GGA: 0.
# negative strand, positive direction, looking for 5'-CGG(A/C/G/T)(C/G/T)(A/C/G/T)(A/C/G)(A/C)(A/C/T)GGA-3', 0.
# negative strand, positive direction, looking for CGG(A/C/G/T)(C/G/T)(A/C/G/T)(A/C/G)(A/C)(A/C/T)GGA: 0.
# positive strand, negative direction, looking for 5'-CGG(A/C/G/T)(C/G/T)(A/C/G/T)(A/C/G)(A/C)(A/C/T)GGA-3', 0.
# positive strand, negative direction, looking for CGG(A/C/G/T)(C/G/T)(A/C/G/T)(A/C/G)(A/C)(A/C/T)GGA: 0.
# positive strand, positive direction, looking for 5'-CGG(A/C/G/T)(C/G/T)(A/C/G/T)(A/C/G)(A/C)(A/C/T)GGA-3', 0.
# positive strand, positive direction, looking for CGG(A/C/G/T)(C/G/T)(A/C/G/T)(A/C/G)(A/C)(A/C/T)GGA: 0.
# complement, negative strand, negative direction, looking for 5'-GCC(A/C/G/T)(A/C/G)(A/C/G/T)(C/G/T)(G/T)(A/G/T)CCT-3', 0.
# inverse complement, negative strand, negative direction: 2, TCCGTGCCACCG at 2528, TCCGTGCCACCG at 657.
# complement, negative strand, positive direction, looking for 5'-GCC(A/C/G/T)(A/C/G)(A/C/G/T)(C/G/T)(G/T)(A/G/T)CCT-3', 0.
# inverse complement, negative strand, positive direction: 0.
# complement, positive strand, negative direction, looking for 5'-GCC(A/C/G/T)(A/C/G)(A/C/G/T)(C/G/T)(G/T)(A/G/T)CCT-3', 0.
# inverse complement, positive strand, negative direction: 0.
# complement, positive strand, positive direction, looking for 5'-GCC(A/C/G/T)(A/C/G)(A/C/G/T)(C/G/T)(G/T)(A/G/T)CCT-3', 0.
# inverse complement, positive strand, positive direction: 0.
# inverse complement, negative strand, negative direction, looking for 5'-TCC(A/G/T)(G/T)(C/G/T)(A/C/G/T)(A/C/G)(A/C/G/T)CCG-3', 2, 5'-TCCGTGCCACCG-3' at 2528, 5'-TCCGTGCCACCG-3' at 657, and complements.
# inverse complement, negative strand, positive direction, looking for 5'-TCC(A/G/T)(G/T)(C/G/T)(A/C/G/T)(A/C/G)(A/C/G/T)CCG-3', 0.
# inverse complement, positive strand, negative direction, looking for 5'-TCC(A/G/T)(G/T)(C/G/T)(A/C/G/T)(A/C/G)(A/C/G/T)CCG-3', 0.
# inverse complement, positive strand, positive direction, looking for 5'-TCC(A/G/T)(G/T)(C/G/T)(A/C/G/T)(A/C/G)(A/C/G/T)CCG-3', 0.
# inverse negative strand, negative direction, looking for 5'-AGG(A/C/T)(A/C)(A/C/G)(A/C/G/T)(C/G/T)(A/C/G/T)GGC-3', 0.
# inverse negative strand, positive direction, looking for 5'-AGG(A/C/T)(A/C)(A/C/G)(A/C/G/T)(C/G/T)(A/C/G/T)GGC-3', 0.
# inverse positive strand, negative direction, looking for 5'-AGG(A/C/T)(A/C)(A/C/G)(A/C/G/T)(C/G/T)(A/C/G/T)GGC-3', 2, 5'-AGGCACGGTGGC-3' at 2528, 5'-AGGCACGGTGGC-3' at 657.
# inverse positive strand, positive direction, looking for 5'-AGG(A/C/T)(A/C)(A/C/G)(A/C/G/T)(C/G/T)(A/C/G/T)GGC-3', 0.


===Cat8p distal promoters===
===Cat8 negative direction (2596-1) distal promoters===
{{main|Distal promoter gene transcriptions}}
 
Negative strand, negative direction: TCCGTGCCACCG at 2528, TCCGTGCCACCG at 657.
# Negative strand, negative direction: 2, TCCGTGCCACCG at 2528, TCCGTGCCACCG at 657.


==Cat8 random dataset samplings==
==Cat8 random dataset samplings==


# RDr0: 0.
# Cat8r0: 0.
# RDr1: 0.
# Cat8r1: 1, CGGGTTGATGGA at 1079.
# RDr2: 0.
# Cat8r2: 0.
# RDr3: 0.
# Cat8r3: 0.
# RDr4: 0.
# Cat8r4: 0.
# RDr5: 0.
# Cat8r5: 1, CGGCTCAACGGA at 575.
# RDr6: 0.
# Cat8r6: 1, CGGGCCAATGGA at 743.
# RDr7: 0.
# Cat8r7: 0.
# RDr8: 0.
# Cat8r8: 0.
# RDr9: 0.
# Cat8r9: 0.
# RDr0ci: 0.
# Cat8r0ci: 0.
# RDr1ci: 0.
# Cat8r1ci: 0.
# RDr2ci: 0.
# Cat8r2ci: 1, TCCTGTACACCG at 1210.
# RDr3ci: 0.
# Cat8r3ci: 0.
# RDr4ci: 0.
# Cat8r4ci: 1, TCCTGGGCGCCG at 2629.
# RDr5ci: 0.
# Cat8r5ci: 0.
# RDr6ci: 0.
# Cat8r6ci: 1, TCCAGTTGTCCG at 2642.
# RDr7ci: 0.
# Cat8r7ci: 1, TCCATCCGGCCG at 1909.
# RDr8ci: 0.
# Cat8r8ci: 1, TCCTGTTGCCCG at 3455.
# RDr9ci: 0.
# Cat8r9ci: 0.
 
===Cat8r arbitrary (evens) (4560-2846) UTRs===
 
# Cat8r8ci: TCCTGTTGCCCG at 3455.
 
===Cat8r arbitrary negative direction (evens) (2811-2596) proximal promoters===


===RDr UTRs===
# Cat8r4ci: TCCTGGGCGCCG at 2629.
{{main|UTR promoter gene transcriptions}}
# Cat8r6ci: TCCAGTTGTCCG at 2642.


===RDr core promoters===
===Cat8r arbitrary negative direction (evens) (2596-1) distal promoters===
{{main|Core promoter gene transcriptions}}


===RDr proximal promoters===
# Cat8r6: CGGGCCAATGGA at 743.
{{main|Proximal promoter gene transcriptions}}
# Cat8r2ci: TCCTGTACACCG at 1210.


===RDr distal promoters===
===Cat8r alternate negative direction (odds) (2596-1) distal promoters===
{{main|Distal promoter gene transcriptions}}
 
# Cat8r1: CGGGTTGATGGA at 1079.
# Cat8r5: CGGCTCAACGGA at 575.
# Cat8r7ci: TCCATCCGGCCG at 1909.
 
===Cat8r arbitrary positive direction (odds) (4050-1) distal promoters===
 
# Cat8r1: CGGGTTGATGGA at 1079.
# Cat8r5: CGGCTCAACGGA at 575.
# Cat8r7ci: TCCATCCGGCCG at 1909.
 
===Cat8r alternate positive direction (evens) (4050-1) distal promoters===
 
# Cat8r6: CGGGCCAATGGA at 743.
# Cat8r2ci: TCCTGTACACCG at 1210.
# Cat8r4ci: TCCTGGGCGCCG at 2629.
# Cat8r6ci: TCCAGTTGTCCG at 2642.
# Cat8r8ci: TCCTGTTGCCCG at 3455.


==Cat8 analysis and results==
==Cat8 analysis and results==
{{main|Complex locus A1BG and ZNF497#Cat8s}}
{{main|Complex locus A1BG and ZNF497#Cat8s}}
The upstream activating sequence (UAS) for Cat8p is 5'-CGGNBNVMHGGA-3', where N = A, C, G, T, B = C, G, T, V = A, C, G, M = A, C, and H = A, C, T; i.e. 5'-CGG(A/C/G/T)(C/G/T)(A/C/G/T)(A/C/G)(A/C)(A/C/T)GGA-3'.<ref name=Tang/>
{|class="wikitable"
|-
! Reals or randoms !! Promoters !! direction !! Numbers !! Strands !! Occurrences !! Averages (± 0.1)
|-
| Reals || UTR || negative || 0 || 2 || 0 || 0
|-
| Randoms || UTR || arbitrary negative || 1 || 10 || 0.1 || 0.05
|-
| Randoms || UTR || alternate negative || 0 || 10 || 0 || 0.05
|-
| 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 || 2 || 10 || 0.2 || 0.1
|-
| Randoms || Proximal || alternate negative || 0 || 10 || 0 || 0.1
|-
| 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 || 2 || 2 || 1 || 1
|-
| Randoms || Distal || arbitrary negative || 2 || 10 || 0.2 || 0.25
|-
| Randoms || Distal || alternate negative || 3 || 10 || 0.3 || 0.25
|-
| Reals || Distal || positive || 0 || 2 || 0 || 0
|-
| Randoms || Distal || arbitrary positive || 3 || 10 || 0.3 || 0.4
|-
| Randoms || Distal || alternate positive || 5 || 10 || 0.5 || 0.4
|}
Comparison:
The occurrences of real Cat8s are greater than the randoms. This suggests that the real Cat8s are likely active or activable.


==Acknowledgements==
==Acknowledgements==
Line 100: Line 165:
* [[Carbon source-responsive element gene transcriptions]]
* [[Carbon source-responsive element gene transcriptions]]
* [[Complex locus A1BG and ZNF497]]
* [[Complex locus A1BG and ZNF497]]
* [[Transcription factor]]
* [[Sip4p gene transcriptions]]
{{Div col end}}
{{Div col end}}


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[[Category:Resources last modified in November 2020]]

Latest revision as of 22:22, 18 October 2022

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

Human genes

Interactions

Consensus sequences

The upstream activating sequence (UAS) for Cat8p is 5'-CGGNBNVMHGGA-3', where N = A, C, G, T, B = C, G, T, V = A, C, G, M = A, C, and H = A, C, T; i.e. 5'-CGG(A/C/G/T)(C/G/T)(A/C/G/T)(A/C/G)(A/C)(A/C/T)GGA-3'.[1]

Hypotheses

Main article: Hypotheses
  1. A1BG has no Cat8ps in either promoter.
  2. A1BG is not transcribed by a Cat8p.
  3. Cat8p does not participate in the transcription of A1BG.

Cat8p samplings

Copying CGGTCCGC in "⌘F" yields none between ZSCAN22 and A1BG and none between ZNF497 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence CGG(A/C/G/T)(C/G/T)(A/C/G/T)(A/C/G)(A/C)(A/C/T)GGA (starting with SuccessablesCat8p.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 CGG(A/C/G/T)(C/G/T)(A/C/G/T)(A/C/G)(A/C)(A/C/T)GGA: 0.
  2. negative strand, positive direction, looking for CGG(A/C/G/T)(C/G/T)(A/C/G/T)(A/C/G)(A/C)(A/C/T)GGA: 0.
  3. positive strand, negative direction, looking for CGG(A/C/G/T)(C/G/T)(A/C/G/T)(A/C/G)(A/C)(A/C/T)GGA: 0.
  4. positive strand, positive direction, looking for CGG(A/C/G/T)(C/G/T)(A/C/G/T)(A/C/G)(A/C)(A/C/T)GGA: 0.
  5. inverse complement, negative strand, negative direction: 2, TCCGTGCCACCG at 2528, TCCGTGCCACCG at 657.
  6. inverse complement, negative strand, positive direction: 0.
  7. inverse complement, positive strand, negative direction: 0.
  8. inverse complement, positive strand, positive direction: 0.

Cat8 negative direction (2596-1) distal promoters

  1. Negative strand, negative direction: 2, TCCGTGCCACCG at 2528, TCCGTGCCACCG at 657.

Cat8 random dataset samplings

  1. Cat8r0: 0.
  2. Cat8r1: 1, CGGGTTGATGGA at 1079.
  3. Cat8r2: 0.
  4. Cat8r3: 0.
  5. Cat8r4: 0.
  6. Cat8r5: 1, CGGCTCAACGGA at 575.
  7. Cat8r6: 1, CGGGCCAATGGA at 743.
  8. Cat8r7: 0.
  9. Cat8r8: 0.
  10. Cat8r9: 0.
  11. Cat8r0ci: 0.
  12. Cat8r1ci: 0.
  13. Cat8r2ci: 1, TCCTGTACACCG at 1210.
  14. Cat8r3ci: 0.
  15. Cat8r4ci: 1, TCCTGGGCGCCG at 2629.
  16. Cat8r5ci: 0.
  17. Cat8r6ci: 1, TCCAGTTGTCCG at 2642.
  18. Cat8r7ci: 1, TCCATCCGGCCG at 1909.
  19. Cat8r8ci: 1, TCCTGTTGCCCG at 3455.
  20. Cat8r9ci: 0.

Cat8r arbitrary (evens) (4560-2846) UTRs

  1. Cat8r8ci: TCCTGTTGCCCG at 3455.

Cat8r arbitrary negative direction (evens) (2811-2596) proximal promoters

  1. Cat8r4ci: TCCTGGGCGCCG at 2629.
  2. Cat8r6ci: TCCAGTTGTCCG at 2642.

Cat8r arbitrary negative direction (evens) (2596-1) distal promoters

  1. Cat8r6: CGGGCCAATGGA at 743.
  2. Cat8r2ci: TCCTGTACACCG at 1210.

Cat8r alternate negative direction (odds) (2596-1) distal promoters

  1. Cat8r1: CGGGTTGATGGA at 1079.
  2. Cat8r5: CGGCTCAACGGA at 575.
  3. Cat8r7ci: TCCATCCGGCCG at 1909.

Cat8r arbitrary positive direction (odds) (4050-1) distal promoters

  1. Cat8r1: CGGGTTGATGGA at 1079.
  2. Cat8r5: CGGCTCAACGGA at 575.
  3. Cat8r7ci: TCCATCCGGCCG at 1909.

Cat8r alternate positive direction (evens) (4050-1) distal promoters

  1. Cat8r6: CGGGCCAATGGA at 743.
  2. Cat8r2ci: TCCTGTACACCG at 1210.
  3. Cat8r4ci: TCCTGGGCGCCG at 2629.
  4. Cat8r6ci: TCCAGTTGTCCG at 2642.
  5. Cat8r8ci: TCCTGTTGCCCG at 3455.

Cat8 analysis and results

Main article: Complex locus A1BG and ZNF497 § Cat8s

The upstream activating sequence (UAS) for Cat8p is 5'-CGGNBNVMHGGA-3', where N = A, C, G, T, B = C, G, T, V = A, C, G, M = A, C, and H = A, C, T; i.e. 5'-CGG(A/C/G/T)(C/G/T)(A/C/G/T)(A/C/G)(A/C)(A/C/T)GGA-3'.[1]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 0 2 0 0
Randoms UTR arbitrary negative 1 10 0.1 0.05
Randoms UTR alternate negative 0 10 0 0.05
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 2 10 0.2 0.1
Randoms Proximal alternate negative 0 10 0 0.1
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 2 2 1 1
Randoms Distal arbitrary negative 2 10 0.2 0.25
Randoms Distal alternate negative 3 10 0.3 0.25
Reals Distal positive 0 2 0 0
Randoms Distal arbitrary positive 3 10 0.3 0.4
Randoms Distal alternate positive 5 10 0.5 0.4

Comparison:

The occurrences of real Cat8s are greater than the randoms. This suggests that the real Cat8s 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 Hongting Tang, Yanling Wu, Jiliang Deng, Nanzhu Chen, Zhaohui Zheng, Yongjun Wei, Xiaozhou Luo, and Jay D. Keasling (6 August 2020). "Promoter Architecture and Promoter Engineering in Saccharomyces cerevisiae". Metabolites. 10 (8): 320–39. doi:10.3390/metabo10080320. PMID 32781665 Check |pmid= value (help). Retrieved 18 September 2020.

External links


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