Q element gene transcriptions

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

"The basal regulatory elements identified include a putative TATA-box (−30/−24) for RNA polymerase binding and a CAAT box (−64/−61; [...]). Several putative floral expression-related cis-elements identified included a putative 6-nucleotide Q element (−770/−665), three GTGA boxes (−372/−369, −209/−206 and −164/−161) and four putative highly-conserved POLLEN1 boxes (−737/−733, −711/−707, −150/−146 and −36/−32; [...])."^[1]

Human genes

Consensus sequences

The consensus sequence for a Q element is 3'-AGGTCA-5'.^[1]

QE samplings

Copying the apparent consensus sequence for the QE (AGGTCA) and putting it in "⌘F" finds two located between ZSCAN22 or three between ZNF497 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence AGGTCA (starting with SuccessablesQE.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 AGGTCA, 2, AGGTCA at 1532, AGGTCA at 1352.
positive strand, negative direction, looking for AGGTCA, 7, AGGTCA at 4307, AGGTCA at 2585, AGGTCA at 2248, AGGTCA at 712, AGGTCA at 576, AGGTCA at 568, AGGTCA at 439.
positive strand, positive direction, looking for AGGTCA, 0.
negative strand, positive direction, looking for AGGTCA, 3, AGGTCA at 4269, AGGTCA at 2220, AGGTCA at 153.
complement, negative strand, negative direction, looking for TCCAGT, 7, TCCAGT at 4307, TCCAGT at 2585, TCCAGT at 2248, TCCAGT at 712, TCCAGT at 576, TCCAGT at 568, TCCAGT at 439.
complement, positive strand, negative direction, looking for TCCAGT, 2, TCCAGT at 1532, TCCAGT at 1352.
complement, positive strand, positive direction, looking for TCCAGT, 3, TCCAGT at 4269, TCCAGT at 2220, TCCAGT at 153.
complement, negative strand, positive direction, looking for TCCAGT, 0.
inverse complement, negative strand, negative direction, looking for TGACCT, 0.
inverse complement, positive strand, negative direction, looking for TGACCT, 0.
inverse complement, positive strand, positive direction, looking for TGACCT, 0.
inverse complement, negative strand, positive direction, looking for TGACCT, 2, TGACCT at 4019, TGACCT at 3785.
inverse negative strand, negative direction, looking for ACTGGA, 0.
inverse positive strand, negative direction, looking for ACTGGA, 0.
inverse positive strand, positive direction, looking for ACTGGA, 2, ACTGGA at 4019, ACTGGA at 3785.
inverse negative strand, positive direction, looking for ACTGGA, 0.

QE (4560-2846) UTRs

Positive strand, negative direction: AGGTCA at 4307.

QE positive direction (4445-4265) core promoters

Negative strand, positive direction: AGGTCA at 4269.

QE negative direction (2596-1) distal promoters

Negative strand, negative direction: AGGTCA at 1532, AGGTCA at 1352.
Positive strand, negative direction: AGGTCA at 2585, AGGTCA at 2248, AGGTCA at 712, AGGTCA at 576, AGGTCA at 568, AGGTCA at 439.

QE positive direction (4050-1) distal promoters

Negative strand, positive direction: AGGTCA at 2220, AGGTCA at 153.
Negative strand, positive direction: TGACCT at 4019, TGACCT at 3785.

QE random dataset samplings

QEr0: 1, AGGTCA at 699.
QEr1: 1, AGGTCA at 1750.
QEr2: 2, AGGTCA at 4381, AGGTCA at 3163.
QEr3: 1, AGGTCA at 2303.
QEr4: 0.
QEr5: 1, AGGTCA at 4296.
QEr6: 0.
QEr7: 0.
QEr8: 0.
QEr9: 0.
QEr0ci: 0.
QEr1ci: 0.
QEr2ci: 0.
QEr3ci: 2, TGACCT at 4439, TGACCT at 2443.
QEr4ci: 0.
QEr5ci: 1, TGACCT at 2538.
QEr6ci: 0.
QEr7ci: 1, TGACCT at 3801.
QEr8ci: 1, TGACCT at 540.
QEr9ci: 0.

QEr arbitrary (evens) (4560-2846) UTRs

QEr2: AGGTCA at 4381, AGGTCA at 3163.

QEr alternate (odds) (4560-2846) UTRs

QEr5: AGGTCA at 4296.
QEr3ci: TGACCT at 4439.
QEr7ci: TGACCT at 3801.

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

QEr5: AGGTCA at 4296.
QEr3ci: TGACCT at 4439.

QEr alternate positive direction (evens) (4445-4265) core promoters

QEr2: AGGTCA at 4381.

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

QEr0: AGGTCA at 699.
QEr8ci: TGACCT at 540.

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

QEr1: AGGTCA at 1750.
QEr3: AGGTCA at 2303.
QEr3ci: TGACCT at 2443.
QEr5ci: TGACCT at 2538.

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

QEr1: AGGTCA at 1750.
QEr3: AGGTCA at 2303.
QEr3ci: TGACCT at 2443.
QEr5ci: TGACCT at 2538.
QEr7ci: TGACCT at 3801.

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

QEr0: AGGTCA at 699.
QEr2: AGGTCA at 3163.
QEr8ci: TGACCT at 540.

QE analysis and results

The consensus sequence for a Q element is AGGTCA.^[1]

Reals or randoms	Promoters	direction	Numbers	Strands	Occurrences	Averages (± 0.1)
Reals	UTR	negative	1	2	0.5	0.5 ± 0.5 (--0,+-1)
Randoms	UTR	arbitrary negative	2	10	0.2	0.25
Randoms	UTR	alternate negative	3	10	0.3	0.25
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	1	2	0.5	0.5 ± 0.5 (-+1,++0)
Randoms	Core	arbitrary positive	2	10	0.2	0.15
Randoms	Core	alternate positive	1	10	0.1	0.15
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	8	2	4	4 ± 2 (—2,+-6)
Randoms	Distal	arbitrary negative	2	10	0.2	0.3
Randoms	Distal	alternate negative	4	10	0.4	0.3
Reals	Distal	positive	4	2	2	2 ± 2 (-+4,++0)
Randoms	Distal	arbitrary positive	5	10	0.5	0.4
Randoms	Distal	alternate positive	3	10	0.3	0.4

Comparison: The occurrences of real QE UTRs, cores and distals are greater than the randoms. This suggests that the real QEs are likely active or activable.

References

↑ ^1.0 ^1.1 ^1.2 Zi-Wei Ye, Jie Xu, Jianxin Shi, Dabing Zhang and Mee-Len Chye (January 2017). "Kelch-motif containing acyl-CoA binding proteins AtACBP4 and AtACBP5 are differentially expressed and function in floral lipid metabolism" (PDF). Plant Molecular Biology. 93: 209–225. doi:10.1007/s11103-016-0557-5. PMID 27826761. Retrieved 7 May 2020.

External links

[Ye-1] 1.0 ^1.1 ^1.2 Zi-Wei Ye, Jie Xu, Jianxin Shi, Dabing Zhang and Mee-Len Chye (January 2017). "Kelch-motif containing acyl-CoA binding proteins AtACBP4 and AtACBP5 are differentially expressed and function in floral lipid metabolism" (PDF). Plant Molecular Biology. 93: 209–225. doi:10.1007/s11103-016-0557-5. PMID 27826761. Retrieved 7 May 2020.

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