Pollen1 element gene transcriptions: Difference between revisions

Revision as of 17:01, 13 February 2021

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

"Electrophoretic mobility shift assays identified a pollen-specific cis-acting element POLLEN1 (AGAAA) mapped at AtACBP4 (−157/−153) which interacted with nuclear proteins from flower and this was substantiated by DNase I footprinting."^[1]

"POLLEN1 and the TCCACCATA element are co-dependent regulatory elements responsible for pollen-specific activation of tomato LAT52 (Bate and Twell 1998)."^[1]

Human genes

Consensus sequences

"Given that AtACBP4pro::GUS (−156/−67) could drive promoter activity for pollen expression, [electrophoretic mobility shift assays] EMSAs were carried out to investigate the role of the putative POLLEN1 cis-element, AGAAA (−150/−146), and its adjacent co-dependent regulatory element TCCACCATA (–141/–133)."^[1]

Pollen1 samplings

Copying the consensus for POLLEN1: 3'-AGAAA-5' and putting the sequence in "⌘F" finds many locations for this sequence in the A1BG directions as can be found by the computer programs.

For the Basic programs testing consensus sequence AGAAA (starting with SuccessablesPOL.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 AGAAA, 5, AGAAA at 1733, AGAAA at 1418, AGAAA at 347, AGAAA at 47, AGAAA at 25.
positive strand, negative direction, looking for AGAAA, 23, AGAAA at 4394, AGAAA at 4389, AGAAA at 4382, AGAAA at 4085, AGAAA at 4081, AGAAA at 3591, AGAAA at 3376, AGAAA at 3342, AGAAA at 2838, AGAAA at 2831, AGAAA at 2821, AGAAA at 2814, AGAAA at 2804, AGAAA at 2800, AGAAA at 2505, AGAAA at 2055, AGAAA at 1630, AGAAA at 357, AGAAA at 303, AGAAA at 226, AGAAA at 135, AGAAA at 102, AGAAA at 52.
positive strand, positive direction, looking for AGAAA, 6, AGAAA at 4382, AGAAA at 3397, AGAAA at 2585, AGAAA at 2278, AGAAA at 1981, AGAAA at 110.
negative strand, positive direction, looking for AGAAA, 2, AGAAA at 3918, AGAAA at 2629.
complement, negative strand, negative direction, looking for TCTTT, 23, TCTTT at 4394, TCTTT at 4389, TCTTT at 4382, TCTTT at 4085, TCTTT at 4081, TCTTT at 3591, TCTTT at 3376, TCTTT at 3342, TCTTT at 2838, TCTTT at 2831, TCTTT at 2821, TCTTT at 2814, TCTTT at 2804, TCTTT at 2800, TCTTT at 2505, TCTTT at 2055, TCTTT at 1630, TCTTT at 357, TCTTT at 303, TCTTT at 226, TCTTT at 135, TCTTT at 102, TCTTT at 52.
complement, positive strand, negative direction, looking for TCTTT, 5, TCTTT at 1733, TCTTT at 1418, TCTTT at 347, TCTTT at 47, TCTTT at 25.
complement, positive strand, positive direction, looking for TCTTT, 2, TCTTT at 3918, TCTTT at 2629.
complement, negative strand, positive direction, looking for TCTTT, 6, TCTTT at 4382, TCTTT at 3397, TCTTT at 2585, TCTTT at 2278, TCTTT at 1981, TCTTT at 110.
inverse complement, negative strand, negative direction, looking for TTTCT, 22, TTTCT at 4505, TTTCT at 4392, TTTCT at 4387, TTTCT at 4380, TTTCT at 4083, TTTCT at 3924, TTTCT at 3665, TTTCT at 3378, TTTCT at 2892, TTTCT at 2836, TTTCT at 2824, TTTCT at 2819, TTTCT at 2807, TTTCT at 2802, TTTCT at 2798, TTTCT at 2175, TTTCT at 2053, TTTCT at 1628, TTTCT at 1549, TTTCT at 1400, TTTCT at 224, TTTCT at 55.
inverse complement, positive strand, negative direction, looking for TTTCT, 2, TTTCT at 1604, TTTCT at 23.
inverse complement, positive strand, positive direction, looking for TTTCT, 2, TTTCT at 3929, TTTCT at 3065.
inverse complement, negative strand, positive direction, looking for TTTCT, 5, TTTCT at 4384, TTTCT at 2276, TTTCT at 2165, TTTCT at 1979, TTTCT at 137.
inverse negative strand, negative direction, looking for AAAGA, 2, AAAGA at 1604, AAAGA at 23.
inverse positive strand, negative direction, looking for AAAGA, 22, AAAGA at 4505, AAAGA at 4392, AAAGA at 4387, AAAGA at 4380, AAAGA at 4083, AAAGA at 3924, AAAGA at 3665, AAAGA at 3378, AAAGA at 2892, AAAGA at 2836, AAAGA at 2824, AAAGA at 2819, AAAGA at 2807, AAAGA at 2802, AAAGA at 2798, AAAGA at 2175, AAAGA at 2053, AAAGA at 1628, AAAGA at 1549, AAAGA at 1400, AAAGA at 224, AAAGA at 55.
inverse positive strand, positive direction, looking for AAAGA, 5, AAAGA at 4384, AAAGA at 2276, AAAGA at 2165, AAAGA at 1979, AAAGA at 137.
inverse negative strand, positive direction, looking for AAAGA, 2, AAAGA at 3929, AAAGA at 3065.

POL UTR gene transcriptions

Negative strand, negative direction: TTTCT at 4505, TTTCT at 4392, TTTCT at 4387, TTTCT at 4380, TTTCT at 4083, TTTCT at 3924, TTTCT at 3665, TTTCT at 3378, TTTCT at 2892.

Positive strand, negative direction: AGAAA at 4394, AGAAA at 4389, AGAAA at 4382, AGAAA at 4085, AGAAA at 4081, AGAAA at 3591, AGAAA at 3376, AGAAA at 3342.

POL core promoters

Negative strand, negative direction: TTTCT at 2836, TTTCT at 2824, TTTCT at 2819.

Positive strand, negative direction: AGAAA at 2838, AGAAA at 2831, AGAAA at 2821, AGAAA at 2814.

Negative strand, positive direction: TTTCT at 4384.

Positive strand, positive direction: AGAAA at 4382.

POL proximal promoters

Negative strand, negative direction: TTTCT at 2807, TTTCT at 2802, TTTCT at 2798.

Positive strand, negative direction: AGAAA at 2804, AGAAA at 2800.

POL distal promoters

Negative strand, negative direction: TTTCT at 2175, TTTCT at 2053, AGAAA at 1733, TTTCT at 1628, TTTCT at 1549, AGAAA at 1418, TTTCT at 1400, AGAAA at 347, TTTCT at 224, TTTCT at 55, AGAAA at 47, AGAAA at 25.

Positive strand, negative direction: AGAAA at 2505, AGAAA at 2055, AGAAA at 1630, TTTCT at 1604, AGAAA at 357, AGAAA at 303, AGAAA at 226, AGAAA at 135, AGAAA at 102, AGAAA at 52, TTTCT at 23.

Negative strand, positive direction: AGAAA at 3918, AGAAA at 2629, TTTCT at 2276, TTTCT at 2165, TTTCT at 1979, TTTCT at 137.

Positive strand, positive direction: TTTCT at 3929, AGAAA at 3397, TTTCT at 3065, AGAAA at 2585, AGAAA at 2278, AGAAA at 1981, AGAAA at 110.

Pollen and TCC regulatory element samplings

Copying the consensus for POLLEN1: 3'-AGAAA-5' and putting the sequence in "⌘F" finds many locations for this sequence in the A1BG directions as can be found by the computer programs. POLLEN1, AGAAA (−150/−146), has adjacent co-dependent regulatory element TCCACCATA (–141/–133), so that a combined consensus sequence expected would have AGAAANNNNTCCACCATA.

For the Basic programs testing consensus sequence AGAAANNNNTCCACCATA (starting with SuccessablesPol.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 AGAAANNNNTCCACCATA, 0.
positive strand, negative direction, looking for AGAAANNNNTCCACCATA, 0.
positive strand, positive direction, looking for AGAAANNNNTCCACCATA, 0.
negative strand, positive direction, looking for AGAAANNNNTCCACCATA, 0.
complement, negative strand, negative direction, looking for TCTTTNNNNAGGTGGTAT, 0.
complement, positive strand, negative direction, looking for TCTTTNNNNAGGTGGTAT, 0.
complement, positive strand, positive direction, looking for TCTTTNNNNAGGTGGTAT, 0.
complement, negative strand, positive direction, looking for TCTTTNNNNAGGTGGTAT, 0.
inverse complement, negative strand, negative direction, looking for TATGGTGGANNNNTTTCT, 0.
inverse complement, positive strand, negative direction, looking for TATGGTGGANNNNTTTCT, 0.
inverse complement, positive strand, positive direction, looking for TATGGTGGANNNNTTTCT, 0.
inverse complement, negative strand, positive direction, looking for TATGGTGGANNNNTTTCT, 0.
inverse negative strand, negative direction, looking for ATACCACCTNNNNAAAGA, 0.
inverse positive strand, negative direction, looking for ATACCACCTNNNNAAAGA, 0.
inverse positive strand, positive direction, looking for ATACCACCTNNNNAAAGA, 0.
inverse negative strand, positive direction, looking for ATACCACCTNNNNAAAGA, 0.

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.

[1]

@@ Line 102: / Line 102: @@
 ==See also==
 {{div col|colwidth=20em}}
+* [[A1BG gene transcription core promoters]]
+* [[A1BG gene transcriptions]]
+* [[A1BG regulatory elements and regions]]
+* [[A1BG response element negative results]]
+* [[A1BG response element positive results]]
 * [[Complex locus A1BG and ZNF497]]
-* [[Transcription factor]]
+* [[TCCACCATA element gene transcriptions]]
 {{Div col end}}

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