Cat8p gene transcriptions

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

A1BG has no Cat8ps in either promoter.
A1BG is not transcribed by a Cat8p.
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:

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 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 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 CGG(A/C/G/T)(C/G/T)(A/C/G/T)(A/C/G)(A/C)(A/C/T)GGA: 0.
inverse complement, negative strand, negative direction: 2, TCCGTGCCACCG at 2528, TCCGTGCCACCG at 657.
inverse complement, negative strand, positive direction: 0.
inverse complement, positive strand, negative direction: 0.
inverse complement, positive strand, positive direction: 0.

Cat8 negative direction (2596-1) distal promoters

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

Cat8 random dataset samplings

Cat8r0: 0.
Cat8r1: 1, CGGGTTGATGGA at 1079.
Cat8r2: 0.
Cat8r3: 0.
Cat8r4: 0.
Cat8r5: 1, CGGCTCAACGGA at 575.
Cat8r6: 1, CGGGCCAATGGA at 743.
Cat8r7: 0.
Cat8r8: 0.
Cat8r9: 0.
Cat8r0ci: 0.
Cat8r1ci: 0.
Cat8r2ci: 1, TCCTGTACACCG at 1210.
Cat8r3ci: 0.
Cat8r4ci: 1, TCCTGGGCGCCG at 2629.
Cat8r5ci: 0.
Cat8r6ci: 1, TCCAGTTGTCCG at 2642.
Cat8r7ci: 1, TCCATCCGGCCG at 1909.
Cat8r8ci: 1, TCCTGTTGCCCG at 3455.
Cat8r9ci: 0.

Cat8r arbitrary (evens) (4560-2846) UTRs

Cat8r8ci: TCCTGTTGCCCG at 3455.

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

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

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

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

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

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

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.

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.

External links

[Tang-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.

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