Tec1p gene transcriptions: Difference between revisions

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|pmid=32781665
|pmid=32781665
|accessdate=18 September 2020 }}</ref>
|accessdate=18 September 2020 }}</ref>
"These genes include those that affect mating (MAT locus, a number of STE genes, and the TYE genes) and another gene without known cellular function, the TEC1 gene (previously named ROC1 [19]; since the name ROC1 has been previously attributed to another gene, we have renamed this locus TEC1, for transposon enhancement control)."<ref name=Laloux>{{ cite journal
|author=Isabelle Laloux, Evelyne Dubois, Marianne Dewerchin, and Eric Jacobs
|title=''TEC1'', a Gene Involved in the Activation of Ty1 and Ty1-Mediated Gene Expression in ''Saccharomyces cerevisiae'': Cloning and Molecular Analysis
|journal=Molecular and Cellular Biology
|date=July 1990
|volume=10
|issue=7
|pages=3541-3550
|url=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC360789/pdf/molcellb00043-0265.pdf
|arxiv=
|bibcode=
|doi=
|pmid= }}</ref>


==Tec1 samplings==
==Tec1 samplings==
Line 50: Line 64:
==TEC random dataset samplings==
==TEC random dataset samplings==


# RDr0: 0.
# TECr0: 0.
# RDr1: 0.
# TECr1: 0.
# RDr2: 0.
# TECr2: 3, GAATGT at 4493, GAATGT at 1294, GAATGT at 918.
# RDr3: 0.
# TECr3: 1, GAATGT at 4317.
# RDr4: 0.
# TECr4: 1, GAATGT at 1101.
# RDr5: 0.
# TECr5: 3, GAATGT at 3386, GAATGT at 2128, GAATGT at 1128.
# RDr6: 0.
# TECr6: 0.
# RDr7: 0.
# TECr7: 1, GAATGT at 104.
# RDr8: 0.
# TECr8: 1, GAATGT at 1428.
# RDr9: 0.
# TECr9: 1, GAATGT at 4244.
# RDr0ci: 0.
# TECr0ci: 2, ACATTC at 2089, ACATTC at 890.
# RDr1ci: 0.
# TECr1ci: 1, ACATTC at 4243.
# RDr2ci: 0.
# TECr2ci: 4, ACATTC at 4047, ACATTC at 3990, ACATTC at 1722, ACATTC at 1637.
# RDr3ci: 0.
# TECr3ci: 0.
# RDr4ci: 0.
# TECr4ci: 1, ACATTC at 3699.
# RDr5ci: 0.
# TECr5ci: 1, ACATTC at 3822.
# RDr6ci: 0.
# TECr6ci: 0.
# RDr7ci: 0.
# TECr7ci: 1, ACATTC at 1945.
# RDr8ci: 0.
# TECr8ci: 0.
# RDr9ci: 0.
# TECr9ci: 1, ACATTC at 3641.
 
===TECr arbitrary (evens) (4560-2846) UTRs===
 
# TECr2: GAATGT at 4493.
# TECr2ci: ACATTC at 4047, ACATTC at 3990.
# TECr4ci: ACATTC at 3699.


===RDr arbitrary (evens) (4560-2846) UTRs===
===TECr alternate (odds) (4560-2846) UTRs===


===RDr alternate (odds) (4560-2846) UTRs===
# TECr3: GAATGT at 4317.
# TECr5: GAATGT at 3386.
# TECr9: GAATGT at 4244.
# TECr1ci: ACATTC at 4243.
# TECr5ci: ACATTC at 3822.
# TECr9ci: ACATTC at 3641.


===RDr arbitrary negative direction (evens) (2846-2811) core promoters===
===TECr arbitrary positive direction (odds) (4445-4265) core promoters===


===RDr alternate negative direction (odds) (2846-2811) core promoters===
# TECr3: GAATGT at 4317.


===RDr arbitrary positive direction (odds) (4445-4265) core promoters===
===TECr arbitrary positive direction (odds) (4265-4050) proximal promoters===


===RDr alternate positive direction (evens) (4445-4265) core promoters===
# TECr9: GAATGT at 4244.
# TECr1ci: ACATTC at 4243.


===RDr arbitrary negative direction (evens) (2811-2596) proximal promoters===
===TECr arbitrary negative direction (evens) (2596-1) distal promoters===


===RDr alternate negative direction (odds) (2811-2596) proximal promoters===
# TECr2: GAATGT at 1294, GAATGT at 918.
# TECr4: GAATGT at 1101.
# TECr8: GAATGT at 1428.
# TECr0ci: ACATTC at 2089, ACATTC at 890.
# TECr2ci: ACATTC at 1722, ACATTC at 1637.


===RDr arbitrary positive direction (odds) (4265-4050) proximal promoters===
===TECr alternate negative direction (odds) (2596-1) distal promoters===


===RDr alternate positive direction (evens) (4265-4050) proximal promoters===
# TECr5: GAATGT at 2128, GAATGT at 1128.
# TECr7: GAATGT at 104.
# TECr7ci: ACATTC at 1945.


===RDr arbitrary negative direction (evens) (2596-1) distal promoters===
===TECr arbitrary positive direction (odds) (4050-1) distal promoters===


===RDr alternate negative direction (odds) (2596-1) distal promoters===
# TECr5: GAATGT at 3386, GAATGT at 2128, GAATGT at 1128.
# TECr7: GAATGT at 104.
# TECr5ci: ACATTC at 3822.
# TECr7ci: ACATTC at 1945.
# TECr9ci: ACATTC at 3641.


===RDr arbitrary positive direction (odds) (4050-1) distal promoters===
===TECr alternate positive direction (evens) (4050-1) distal promoters===


===RDr alternate positive direction (evens) (4050-1) distal promoters===
# TECr2: GAATGT at 1294, GAATGT at 918.
# TECr4: GAATGT at 1101.
# TECr8: GAATGT at 1428.
# TECr0ci: ACATTC at 2089, ACATTC at 890.
# TECr2ci: ACATTC at 4047, ACATTC at 3990, ACATTC at 1722, ACATTC at 1637.
# TECr4ci: ACATTC at 3699.


==TEC analysis and results==
==TEC analysis and results==
Line 109: Line 150:
| Reals || UTR || negative || 0 || 2 || 0 || 0  
| Reals || UTR || negative || 0 || 2 || 0 || 0  
|-
|-
| Randoms || UTR || arbitrary negative || 0 || 10 || 0 || 0  
| Randoms || UTR || arbitrary negative || 4 || 10 || 0.4 || 0.5
|-
|-
| Randoms || UTR || alternate negative || 0 || 10 || 0 || 0  
| Randoms || UTR || alternate negative || 6 || 10 || 0.6 || 0.5
|-
|-
| Reals || Core || negative || 0 || 2 || 0 || 0  
| Reals || Core || negative || 0 || 2 || 0 || 0  
Line 121: Line 162:
| Reals || Core || positive || 0 || 2 || 0 || 0  
| Reals || Core || positive || 0 || 2 || 0 || 0  
|-
|-
| Randoms || Core || arbitrary positive || 0 || 10 || 0 || 0
| Randoms || Core || arbitrary positive || 1 || 10 || 0.1 || 0.05
|-
|-
| Randoms || Core || alternate positive || 0 || 10 || 0 || 0  
| Randoms || Core || alternate positive || 0 || 10 || 0 || 0.05
|-
|-
| Reals || Proximal || negative || 0 || 2 || 0 || 0  
| Reals || Proximal || negative || 0 || 2 || 0 || 0  
Line 133: Line 174:
| Reals || Proximal || positive || 0 || 2 || 0 || 0  
| Reals || Proximal || positive || 0 || 2 || 0 || 0  
|-
|-
| Randoms || Proximal || arbitrary positive || 0 || 10 || 0 || 0  
| Randoms || Proximal || arbitrary positive || 2 || 10 || 0.2 || 0.1
|-
|-
| Randoms || Proximal || alternate positive || 0 || 10 || 0 || 0  
| Randoms || Proximal || alternate positive || 0 || 10 || 0 || 0.1
|-
|-
| Reals || Distal || negative || 0 || 2 || 0 || 0  
| Reals || Distal || negative || 0 || 2 || 0 || 0  
|-
|-
| Randoms || Distal || arbitrary negative || 0 || 10 || 0 || 0
| Randoms || Distal || arbitrary negative || 0 || 10 || 0 || 0.2
|-
|-
| Randoms || Distal || alternate negative || 0 || 10 || 0 || 0  
| Randoms || Distal || alternate negative || 4 || 10 || 0.4 || 0.2
|-
|-
| Reals || Distal || positive || 1 || 2 || 0.5 || 0.5 ± 0.5 (-+0,++1)  
| Reals || Distal || positive || 1 || 2 || 0.5 || 0.5 ± 0.5 (-+0,++1)  
|-
|-
| Randoms || Distal || arbitrary positive || 0 || 10 || 0 || 0  
| Randoms || Distal || arbitrary positive || 7 || 10 || 0.7 || 0.9 ± 0.2 (0.7,1.1)
|-
|-
| Randoms || Distal || alternate positive || 0 || 10 || 0 || 0  
| Randoms || Distal || alternate positive || 11 || 10 || 1.1 || 0.9
|}
|}


Comparison:
Comparison:


The occurrences of real TECs are greater than the randoms. This suggests that the real TECs are likely active or activable.
The occurrences of real TECs are within the range the randoms. This suggests that the real TECs are likely random.


==See also==
==See also==

Latest revision as of 04:20, 24 April 2023

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

Human genes

Interactions

Consensus sequences

The upstream activating sequence (UAS) for Tec1p is 5'-GAATGT-3'.[1]

"These genes include those that affect mating (MAT locus, a number of STE genes, and the TYE genes) and another gene without known cellular function, the TEC1 gene (previously named ROC1 [19]; since the name ROC1 has been previously attributed to another gene, we have renamed this locus TEC1, for transposon enhancement control)."[2]

Tec1 samplings

Copying GAATGT 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 GAATGT (starting with SuccessablesTEC.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 GAATGT, 0.
  2. positive strand, negative direction, looking for GAATGT, 0.
  3. positive strand, positive direction, looking for GAATGT, 0.
  4. negative strand, positive direction, looking for GAATGT, 0.
  5. complement, negative strand, negative direction, looking for CTTACA, 0.
  6. complement, positive strand, negative direction, looking for CTTACA, 0.
  7. complement, positive strand, positive direction, looking for CTTACA, 0.
  8. complement, negative strand, positive direction, looking for CTTACA, 0.
  9. inverse complement, negative strand, negative direction, looking for ACATTC, 0.
  10. inverse complement, positive strand, negative direction, looking for ACATTC, 0.
  11. inverse complement, positive strand, positive direction, looking for ACATTC, 1, ACATTC at 2456.
  12. inverse complement, negative strand, positive direction, looking for ACATTC, 0.
  13. inverse negative strand, negative direction, looking for TGTAAG, 0.
  14. inverse positive strand, negative direction, looking for TGTAAG, 0.
  15. inverse positive strand, positive direction, looking for TGTAAG, 0.
  16. inverse negative strand, positive direction, looking for TGTAAG, 1, TGTAAG at 2456.

TEC positive direction (4050-1) distal promoters

  1. Positive strand, positive direction: ACATTC at 2456.

TEC random dataset samplings

  1. TECr0: 0.
  2. TECr1: 0.
  3. TECr2: 3, GAATGT at 4493, GAATGT at 1294, GAATGT at 918.
  4. TECr3: 1, GAATGT at 4317.
  5. TECr4: 1, GAATGT at 1101.
  6. TECr5: 3, GAATGT at 3386, GAATGT at 2128, GAATGT at 1128.
  7. TECr6: 0.
  8. TECr7: 1, GAATGT at 104.
  9. TECr8: 1, GAATGT at 1428.
  10. TECr9: 1, GAATGT at 4244.
  11. TECr0ci: 2, ACATTC at 2089, ACATTC at 890.
  12. TECr1ci: 1, ACATTC at 4243.
  13. TECr2ci: 4, ACATTC at 4047, ACATTC at 3990, ACATTC at 1722, ACATTC at 1637.
  14. TECr3ci: 0.
  15. TECr4ci: 1, ACATTC at 3699.
  16. TECr5ci: 1, ACATTC at 3822.
  17. TECr6ci: 0.
  18. TECr7ci: 1, ACATTC at 1945.
  19. TECr8ci: 0.
  20. TECr9ci: 1, ACATTC at 3641.

TECr arbitrary (evens) (4560-2846) UTRs

  1. TECr2: GAATGT at 4493.
  2. TECr2ci: ACATTC at 4047, ACATTC at 3990.
  3. TECr4ci: ACATTC at 3699.

TECr alternate (odds) (4560-2846) UTRs

  1. TECr3: GAATGT at 4317.
  2. TECr5: GAATGT at 3386.
  3. TECr9: GAATGT at 4244.
  4. TECr1ci: ACATTC at 4243.
  5. TECr5ci: ACATTC at 3822.
  6. TECr9ci: ACATTC at 3641.

TECr arbitrary positive direction (odds) (4445-4265) core promoters

  1. TECr3: GAATGT at 4317.

TECr arbitrary positive direction (odds) (4265-4050) proximal promoters

  1. TECr9: GAATGT at 4244.
  2. TECr1ci: ACATTC at 4243.

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

  1. TECr2: GAATGT at 1294, GAATGT at 918.
  2. TECr4: GAATGT at 1101.
  3. TECr8: GAATGT at 1428.
  4. TECr0ci: ACATTC at 2089, ACATTC at 890.
  5. TECr2ci: ACATTC at 1722, ACATTC at 1637.

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

  1. TECr5: GAATGT at 2128, GAATGT at 1128.
  2. TECr7: GAATGT at 104.
  3. TECr7ci: ACATTC at 1945.

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

  1. TECr5: GAATGT at 3386, GAATGT at 2128, GAATGT at 1128.
  2. TECr7: GAATGT at 104.
  3. TECr5ci: ACATTC at 3822.
  4. TECr7ci: ACATTC at 1945.
  5. TECr9ci: ACATTC at 3641.

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

  1. TECr2: GAATGT at 1294, GAATGT at 918.
  2. TECr4: GAATGT at 1101.
  3. TECr8: GAATGT at 1428.
  4. TECr0ci: ACATTC at 2089, ACATTC at 890.
  5. TECr2ci: ACATTC at 4047, ACATTC at 3990, ACATTC at 1722, ACATTC at 1637.
  6. TECr4ci: ACATTC at 3699.

TEC analysis and results

Main article: Complex locus A1BG and ZNF497 § TECs

The upstream activating sequence (UAS) for Tec1p is GAATGT.[1]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 0 2 0 0
Randoms UTR arbitrary negative 4 10 0.4 0.5
Randoms UTR alternate negative 6 10 0.6 0.5
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 1 10 0.1 0.05
Randoms Core alternate positive 0 10 0 0.05
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 2 10 0.2 0.1
Randoms Proximal alternate positive 0 10 0 0.1
Reals Distal negative 0 2 0 0
Randoms Distal arbitrary negative 0 10 0 0.2
Randoms Distal alternate negative 4 10 0.4 0.2
Reals Distal positive 1 2 0.5 0.5 ± 0.5 (-+0,++1)
Randoms Distal arbitrary positive 7 10 0.7 0.9 ± 0.2 (0.7,1.1)
Randoms Distal alternate positive 11 10 1.1 0.9

Comparison:

The occurrences of real TECs are within the range the randoms. This suggests that the real TECs are likely random.

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.
  2. ↑ Isabelle Laloux, Evelyne Dubois, Marianne Dewerchin, and Eric Jacobs (July 1990). "TEC1, a Gene Involved in the Activation of Ty1 and Ty1-Mediated Gene Expression in Saccharomyces cerevisiae: Cloning and Molecular Analysis" (PDF). Molecular and Cellular Biology. 10 (7): 3541–3550.

External links

Retrieved from "https://www.wikidoc.org/index.php?title=Tec1p_gene_transcriptions&oldid=1733713"