A box gene transcriptions

Jump to navigation Jump to search

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

The GC boxes are not apparently associated with the A box, B box, C box, and D box.[1]

"AS/T, serine/threonine-rich subdomain within the A box".[1] "AQ, glutamine-rich subdomain within the A box".[1]

Consensus sequences

Main article: Consensus sequence gene transcriptions

"The human [Transforming growth factor b1] TGFB1 promoter region contains two binding sequences for [Activator protein-1] AP-1, designated AP-1 box A (TGACTCT) and box B (TGTCTCA), which mediate the upregulation of promoter activity via a PKC-dependent pathway after exposure of cells to a high-glucose environment (Refs 37, 38)."[2]

Most bZIP proteins show high binding affinity for the ACGT motifs, which include [...] TACGTA (A box) [...].[3][4][5]

"The human TGF-β1 promoter region contains two binding sequences for AP-1, designated AP-1 box A (TGACTCT) and box B (TGTCTCA), which mediate the up-regulation of promoter activity after [High glucose] HG stimulation."[6]

Hypotheses

  1. A1BG has no A boxes in either promoter.
  2. A1BG is not transcribed by an A box.
  3. An A box does not participate in the transcription of A1BG.

Box A samplings

Box A 3-TGACTCT-5' was not found using "⌘F" to locate any consensus sequences.

Hypothesis 1: A1BG is not transcribed by box A.

For the Basic programs testing consensus sequence 3'-TGACTCT-5' (starting with SuccessablesAbox.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:

  1. negative strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesAbox--.bas, looking for 3'-TGACTCT-5', 0.
  2. negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesAbox-+.bas, looking for 3'-TGACTCT-5', 0.
  3. positive strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesAbox+-.bas, looking for 3'-TGACTCT-5', 1, 3'-TGACTCT-5' at 2788.
  4. positive strand in the positive direction (from ZNF497 to A1BG) is SuccessablesAbox++.bas, looking for 3'-TGACTCT-5', 0.
  5. complement, negative strand, negative direction is SuccessablesAboxc--.bas, looking for 3'-ACTGAGA-5', 1, 3'-ACTGAGA-5' at 2788.
  6. complement, negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesAboxc-+.bas, looking for 3'-ACTGAGA-5', 0.
  7. complement, positive strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesAboxc+-.bas, looking for 3'-ACTGAGA-5', 0.
  8. complement, positive strand in the positive direction (from ZNF497 to A1BG) is SuccessablesAboxc++.bas, looking for 3'-ACTGAGA-5', 0.
  9. inverse complement, negative strand, negative direction is SuccessablesAboxci--.bas, looking for 3'-AGAGTCA-5', 0.
  10. inverse complement, negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesAboxci-+.bas, looking for 3'-AGAGTCA-5', 1, 3'-AGAGTCA-5' at 2613.
  11. inverse complement, positive strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesAboxci+-.bas, looking for 3'-AGAGTCA-5', 0.
  12. inverse complement, positive strand in the positive direction (from ZNF497 to A1BG) is SuccessablesAboxci++.bas, looking for 3'-AGAGTCA-5', 0.
  13. inverse negative strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesAboxi--.bas, looking for 3'-TCTCAGT-5', 0.
  14. inverse negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesAboxi-+.bas, looking for 3'-TCTCAGT-5', 0.
  15. inverse positive strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesAboxi+-.bas, looking for 3'-TCTCAGT-5', 0.
  16. inverse positive strand in the positive direction (from ZNF497 to A1BG) is SuccessablesAboxi++.bas, looking for 3'-TCTCAGT-5', 1, 3'-TCTCAGT-5' at 2613.

Box A distal promoters

Positive strand, negative direction: TGACTCT at 2788.

Positive strand, positive direction: TCTCAGT at 2613.

Box A random dataset samplings

  1. Aboxr0: 0.
  2. Aboxr1: 0.
  3. Aboxr2: 0.
  4. Aboxr3: 2, TGACTCT at 4481, TGACTCT at 2451.
  5. Aboxr4: 0.
  6. Aboxr5: 0.
  7. Aboxr6: 0.
  8. Aboxr7: 0.
  9. Aboxr8: 0.
  10. Aboxr9: 1, TGACTCT at 3523.
  11. Aboxr0ci: 0.
  12. Aboxr1ci: 0.
  13. Aboxr2ci: 0.
  14. Aboxr3ci: 0.
  15. Aboxr4ci: 0.
  16. Aboxr5ci: 0.
  17. Aboxr6ci: 3, AGAGTCA at 4503, AGAGTCA at 4449, AGAGTCA at 1109.
  18. Aboxr7ci: 0.
  19. Aboxr8ci: 0.
  20. Aboxr9ci: 0.

Aboxr UTRs

Main article: UTR promoter gene transcriptions
  1. Aboxr6ci: AGAGTCA at 4503, AGAGTCA at 4449.

Aboxr core promoters

Main article: Core promoter gene transcriptions
  1. Aboxr3: TGACTCT at 4481.

Aboxr distal promoters

Main article: Distal promoter gene transcriptions
  1. Aboxr6ci: AGAGTCA at 1109.


  1. Aboxr3: TGACTCT at 2451.
  2. Aboxr9: TGACTCT at 3523.

A box samplings

A box 5'-TACGTA-3' using "⌘F" has one location between ZSCAN22 and A1BG and none between ZNF497 and A1BG.

Hypothesis 1: A1BG is not transcribed by an A box.

For the Basic programs testing consensus sequence 3'-TACGTA-5' (starting with SuccessablesAbox1.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:

  1. negative strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesAbox1--.bas, looking for 3'-TACGTA-5', 1, 3'-TACGTA-5' at 4246.
  2. negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesAbox1-+.bas, looking for 3'-TACGTA-5', 0.
  3. positive strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesAbox1+-.bas, looking for 3'-TACGTA-5', 0.
  4. positive strand in the positive direction (from ZNF497 to A1BG) is SuccessablesAbox1++.bas, looking for 3'-TACGTA-5', 1, 3'-TACGTA-5', 3071.
  5. complement, negative strand, negative direction is SuccessablesAbox1c--.bas, looking for 3'-ATGCAT-5', 0.
  6. complement, negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesAbox1c-+.bas, looking for 3'-ATGCAT-5', 1, 3'-ATGCAT-5', 3071.
  7. complement, positive strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesAbox1c+-.bas, looking for 3'-ATGCAT-5', 1, 3'-ATGCAT-5', 4246.
  8. complement, positive strand in the positive direction (from ZNF497 to A1BG) is SuccessablesAbox1c++.bas, looking for 3'-ACTGAGA-5', 0.
  9. complement inverse is TACGTA.

A box proximal promoters

Main article: Proximal promoter gene transcriptions

Negative strand, negative direction: 5'-TACGTA-3' at 4246 and complement.

A box distal promoters

Main article: Distal promoter gene transcriptions

Positive strand, positive direction: 5'-TACGTA-3' at 3071 and complement.

Abox1 random dataset samplings

  1. Abox1r0: 1, TACGTA at 398.
  2. Abox1r1: 0.
  3. Abox1r2: 0.
  4. Abox1r3: 0.
  5. Abox1r4: 0.
  6. Abox1r5: 1, TACGTA at 3126.
  7. Abox1r6: 1, TACGTA at 2107.
  8. Abox1r7: 0.
  9. Abox1r8: 0.
  10. Abox1r9: 1, TACGTA at 3688.

Abox1r UTRs

Main article: UTR promoter gene transcriptions

Abox1r core promoters

Main article: Core promoter gene transcriptions

Abox1r distal promoters

Main article: Distal promoter gene transcriptions

Acknowledgements

The content on this page was first contributed by: Henry A. Hoff.

See also

References

  1. ↑ 1.0 1.1 1.2 Huajun Jin, Arthi Kanthasamy, Dilshan S. Harischandra, Naveen Kondru, Anamitra Ghosh, Nikhil Panicker, Vellareddy Anantharam, Ajay Rana, and Anumantha G. Kanthasamy (December 12, 2014). "Histone Hyperacetylation Up-regulates Protein Kinase C􏰀 in Dopaminergic Neurons to Induce Cell Death RELEVANCE TO EPIGENETIC MECHANISMS OF NEURODEGENERATION IN PARKINSON DISEASE" (PDF). 289 (50): 34743–34767. doi:10.1074/jbc.M114.576702. Retrieved 10 April 2019.
  2. ↑ Amber Paratore Sanchez and Kumar Sharma (July 2009). "Transcription factors in the pathogenesis of diabetic nephropathy". Expert Reviews in Molecular Medicine. 11: e13. doi:10.1017/S1462399409001057. Retrieved 1 October 2018.
  3. ↑ Landschulz WH, Johnson PF, McKnight SL (June 1988). "The leucine zipper: a hypothetical structure common to a new class of DNA binding proteins". Science. 240 (4860): 1759–64. Bibcode:1988Sci...240.1759L. doi:10.1126/science.3289117. PMID 3289117.
  4. ↑ Z G E, Zhang YP, Zhou JH, Wang L (April 2014). "Mini review roles of the bZIP gene family in rice". Genetics and Molecular Research. 13 (2): 3025–36. doi:10.4238/2014.April.16.11. PMID 24782137. Vancouver style error: name (help)
  5. ↑ Nijhawan A, Jain M, Tyagi AK, Khurana JP (February 2008). "Genomic survey and gene expression analysis of the basic leucine zipper transcription factor family in rice". Plant Physiology. 146 (2): 333–50. doi:10.1104/pp.107.112821. PMID 18065552.
  6. ↑ Keiko Kokoroishi, Ayumu Nakashima, Shigehiro Doi, Toshinori Ueno, Toshiki Doi, Yukio Yokoyama, Kiyomasa Honda, Masami Kanawa, Yukio Kato, Nobuoki Kohno & Takao Masaki (28 May 2015). "High glucose promotes TGF-β1 production by inducing FOS expression in human peritoneal mesothelial cells". Clinical and Experimental Nephrology. 20 (1): 30–8. doi:10.1007/s10157-015-1128-9. PMID 26018137. Retrieved 14 August 2020.

External links


Retrieved from "https://www.wikidoc.org/index.php?title=A_box_gene_transcriptions&oldid=1704886"