TAGteam gene transcriptions: Difference between revisions

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# inverse negative strand, positive direction, looking for GATGGAC, 0.
# inverse negative strand, positive direction, looking for GATGGAC, 0.


===TAG distal promoters===
===TAG positive direction (4050-1) distal promoters===
{{main|Distal promoter gene transcriptions}}
 
Negative strand, positive direction: CAGGTAG at 4035, CTACCTG at 1198.
# Negative strand, positive direction: CAGGTAG at 4035.
# Negative strand, positive direction: CTACCTG at 1198.
 
==TAGteam 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===
 
===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===
 
==TAGteam analysis and results==
{{main|Complex locus A1BG and ZNF497#TAGteams}}
The "heptamer consensus sequence [is] CAGGTAG".<ref name=Fonseca/>
 
{|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 || 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==
==Acknowledgements==

Revision as of 06:38, 12 February 2023

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

The "heptamer consensus sequence CAGGTAG (i.e., the TAGteam) is overrepresented in regulatory regions of the earliest expressed zygotic genes [2]."[1]

Human genes

Consensus sequences

The "heptamer consensus sequence [is] CAGGTAG".[1]

TAGteam samplings

Main article: Model samplings

Copying the consensus TAGteam: CAGGTAG and putting the sequence in "⌘F" finds one location between ZNF497 and A1BG or no locations between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence CAGGTAG (starting with SuccessablesTAG.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 CAGGTAG, 0.
  2. positive strand, negative direction, looking for CAGGTAG, 0.
  3. positive strand, positive direction, looking for CAGGTAG, 0.
  4. negative strand, positive direction, looking for CAGGTAG, 1, CAGGTAG at 4035.
  5. complement, negative strand, negative direction, looking for GTCCATC, 0.
  6. complement, positive strand, negative direction, looking for GTCCATC, 0.
  7. complement, positive strand, positive direction, looking for GTCCATC, 1, GTCCATC at 4035.
  8. complement, negative strand, positive direction, looking for GTCCATC, 0.
  9. inverse complement, negative strand, negative direction, looking for CTACCTG, 0.
  10. inverse complement, positive strand, negative direction, looking for CTACCTG, 0.
  11. inverse complement, positive strand, positive direction, looking for CTACCTG, 0.
  12. inverse complement, negative strand, positive direction, looking for CTACCTG, 1, CTACCTG at 1198.
  13. inverse negative strand, negative direction, looking for GATGGAC, 0.
  14. inverse positive strand, negative direction, looking for GATGGAC, 0.
  15. inverse positive strand, positive direction, looking for GATGGAC, 1, GATGGAC at 1198.
  16. inverse negative strand, positive direction, looking for GATGGAC, 0.

TAG positive direction (4050-1) distal promoters

  1. Negative strand, positive direction: CAGGTAG at 4035.
  2. Negative strand, positive direction: CTACCTG at 1198.

TAGteam 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

TAGteam analysis and results

Main article: Complex locus A1BG and ZNF497 § TAGteams

The "heptamer consensus sequence [is] CAGGTAG".[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.

See also

References

  1. ↑ 1.0 1.1 1.2 Rodrigo Nunes da Fonseca and Thiago M. Venancio (1 March 2018). "Maternal or zygotic: Unveiling the secrets of the Pancrustacea transcription factor zelda". Plos Genetics. 14 (3): e1007201. doi:10.1371/journal.pgen.1007201. PMID 29494591. Retrieved 5 September 2020.

External links

Retrieved from "https://www.wikidoc.org/index.php?title=TAGteam_gene_transcriptions&oldid=1733111"