Tec1p gene transcriptions: Difference between revisions
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==Tec1 samplings== | ==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. | Copying GAATGT in "⌘F" yields none between ZSCAN22 and A1BG and none between ZNF497 and A1BG as can be found by the computer programs. | ||
Line 44: | Line 44: | ||
# inverse negative strand, positive direction, looking for TGTAAG, 1, TGTAAG at 2456. | # inverse negative strand, positive direction, looking for TGTAAG, 1, TGTAAG at 2456. | ||
===TEC distal promoters=== | ===TEC positive direction (4050-1) distal promoters=== | ||
{{main| | |||
# Positive strand, positive direction: ACATTC at 2456. | |||
==TEC 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=== | |||
==TEC analysis and results== | |||
{{main|Complex locus A1BG and ZNF497#TECs}} | |||
The upstream activating sequence (UAS) for Tec1p is GAATGT.<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 || 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 || 1 || 2 || 0.5 || 0.5 ± 0.5 (-+0,++1) | |||
|- | |||
| Randoms || Distal || arbitrary positive || 0 || 10 || 0 || 0 | |||
|- | |||
| Randoms || Distal || alternate positive || 0 || 10 || 0 || 0 | |||
|} | |||
Comparison: | |||
The occurrences of real TECs are greater than the randoms. This suggests that the real TECs are likely active or activable. | |||
==See also== | ==See also== |
Revision as of 06:42, 24 February 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]
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:
- negative strand, negative direction, looking for GAATGT, 0.
- positive strand, negative direction, looking for GAATGT, 0.
- positive strand, positive direction, looking for GAATGT, 0.
- negative strand, positive direction, looking for GAATGT, 0.
- complement, negative strand, negative direction, looking for CTTACA, 0.
- complement, positive strand, negative direction, looking for CTTACA, 0.
- complement, positive strand, positive direction, looking for CTTACA, 0.
- complement, negative strand, positive direction, looking for CTTACA, 0.
- inverse complement, negative strand, negative direction, looking for ACATTC, 0.
- inverse complement, positive strand, negative direction, looking for ACATTC, 0.
- inverse complement, positive strand, positive direction, looking for ACATTC, 1, ACATTC at 2456.
- inverse complement, negative strand, positive direction, looking for ACATTC, 0.
- inverse negative strand, negative direction, looking for TGTAAG, 0.
- inverse positive strand, negative direction, looking for TGTAAG, 0.
- inverse positive strand, positive direction, looking for TGTAAG, 0.
- inverse negative strand, positive direction, looking for TGTAAG, 1, TGTAAG at 2456.
TEC positive direction (4050-1) distal promoters
- Positive strand, positive direction: ACATTC at 2456.
TEC 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
TEC analysis and results
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 | 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 | 1 | 2 | 0.5 | 0.5 ± 0.5 (-+0,++1) |
Randoms | Distal | arbitrary positive | 0 | 10 | 0 | 0 |
Randoms | Distal | alternate positive | 0 | 10 | 0 | 0 |
Comparison:
The occurrences of real TECs are greater than the randoms. This suggests that the real TECs are likely active or activable.
See also
References
- ↑ 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.