Pollen1 element gene transcriptions: Difference between revisions

Revision as of 15:05, 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 a responsive elements consensus sequence AAAAAAAA and putting the sequence in "⌘F" finds none between ZNF497 and A1BG or none between ZSCAN22 and A1BG 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 AAAAAAAA, 0.
positive strand, negative direction, looking for AAAAAAAA, 0.
positive strand, positive direction, looking for AAAAAAAA, 0.
negative strand, positive direction, looking for AAAAAAAA, 0.
complement, negative strand, negative direction, looking for TTTTTTTT, 0.
complement, positive strand, negative direction, looking for TTTTTTTT, 0.
complement, positive strand, positive direction, looking for TTTTTTTT, 0.
complement, negative strand, positive direction, looking for TTTTTTTT, 0.
inverse complement, negative strand, negative direction, looking for TTTTTTTT, 0.
inverse complement, positive strand, negative direction, looking for TTTTTTTT, 0.
inverse complement, positive strand, positive direction, looking for TTTTTTTT, 0.
inverse complement, negative strand, positive direction, looking for TTTTTTTT, 0.
inverse negative strand, negative direction, looking for AAAAAAAA, 0.
inverse positive strand, negative direction, looking for AAAAAAAA, 0.
inverse positive strand, positive direction, looking for AAAAAAAA, 0.
inverse negative strand, positive direction, looking for AAAAAAAA, 0.

POL UTR gene transcriptions

POL core promoters

POL proximal promoters

POL distal promoters

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 23: / Line 23: @@
 "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)."<ref name=Ye/>
+==Pollen1 samplings==
+{{main|Model samplings}}
+Copying a responsive elements consensus sequence AAAAAAAA and putting the sequence in "⌘F" finds none between ZNF497 and A1BG or none between ZSCAN22 and A1BG 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 AAAAAAAA, 0.
+# positive strand, negative direction, looking for AAAAAAAA, 0.
+# positive strand, positive direction, looking for AAAAAAAA, 0.
+# negative strand, positive direction, looking for AAAAAAAA, 0.
+# complement, negative strand, negative direction, looking for TTTTTTTT, 0.
+# complement, positive strand, negative direction, looking for TTTTTTTT, 0.
+# complement, positive strand, positive direction, looking for TTTTTTTT, 0.
+# complement, negative strand, positive direction, looking for TTTTTTTT, 0.
+# inverse complement, negative strand, negative direction, looking for TTTTTTTT, 0.
+# inverse complement, positive strand, negative direction, looking for TTTTTTTT, 0.
+# inverse complement, positive strand, positive direction, looking for TTTTTTTT, 0.
+# inverse complement, negative strand, positive direction, looking for TTTTTTTT, 0.
+# inverse negative strand, negative direction, looking for AAAAAAAA, 0.
+# inverse positive strand, negative direction, looking for AAAAAAAA, 0.
+# inverse positive strand, positive direction, looking for AAAAAAAA, 0.
+# inverse negative strand, positive direction, looking for AAAAAAAA, 0.
+===POL UTR gene transcriptions===
+{{main|UTR promoter gene transcriptions}}
+===POL core promoters===
+{{main|Core promoter gene transcriptions}}
+===POL proximal promoters===
+{{main|Proximal promoter gene transcriptions}}
+===POL distal promoters===
+{{main|Distal promoter gene transcriptions}}
 ==Pollen and TCC regulatory element samplings==

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