D box gene transcriptions

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

File:RF00071.jpg
This example of a C/D box is a small nucleolar RNA 73 (snoRNA U73). Credit: Rfam database (RF00071).{{free media}}

For "box C/D snoRNAs, boxes C and D and an adjoining stem form a vital structure, known as the box C/D motif."[1]

In snoRNA U73 on the right, from the right side, the D box is AGUCY. In 5' to 3' direction, the D box is YCUGA.

Degenerate nucleotides

Main articles: Degenerate nucleotide gene transcriptions and Degenerate nucleotides

For transcription, U (in RNA) is T, Y=(C or T) and R=(A or G).

Consensus sequences

Main articles: Consensus sequence gene transcriptions and Consensus sequences
File:U14 snoRNA.png
This U14 snoRNA from Saccharomyces cerevisiae shows structure and genomic organization. Credit: Dmitry A.Samarsky, Maurille J.Fournier, Robert H.Singer and Edouard Bertrand.{{fairuse}}

Shown in the image on the right is the D box (3'-AGUCUG-5'). Substituting T for U yields D box = 3'-AGTCTG-5' in the transcription direction on the template strand.

"Members of the box C/D snoRNA family, which are the subject of the present report, possess characteristic sequence elements known as box C (UGAUGA) and box D (GUCUGA)."[1]

D-box (TGAGTGG).[2]

Hypotheses

  1. The D boxes are not involved in the transcription of A1BG.
  2. The promoters of A1BG do not contain a Samarsky D box.

(Samarsky) samplings

Main article: Sampling models

For the Basic programs (starting with SuccessablesDbox.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 SuccessablesDbox--.bas, looking for 3'-AGTCTG-5', 1, 3'-AGTCTG-5', 2947,
  2. negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesDbox-+.bas, looking for 3'-AGTCTG-5', 1, 3'-AGTCTG-5', 3923,
  3. positive strand in the negative direction is SuccessablesDbox+-.bas, looking for 3'-AGTCTG-5', 1, 3'-AGTCTG-5', 1355,
  4. positive strand in the positive direction is SuccessablesDbox++.bas, looking for 3'-AGTCTG-5', 0,
  5. complement, negative strand, negative direction is SuccessablesDboxc--.bas, looking for 3'-TCAGAC-5', 1, 3'-TCAGAC-5', 1355,
  6. complement, negative strand, positive direction is SuccessablesDboxc-+.bas, looking for 3'-TCAGAC-5', 0,
  7. complement, positive strand, negative direction is SuccessablesDboxc+-.bas, looking for 3'-TCAGAC-5', 1, 3'-TCAGAC-5', 2947,
  8. complement, positive strand, positive direction is SuccessablesDboxc++.bas, looking for 3'-TCAGAC-5', 1, 3'-TCAGAC-5', 3923,
  9. inverse complement, negative strand, negative direction is SuccessablesDboxci--.bas, looking for 3'-CAGACT-5', 0,
  10. inverse complement, negative strand, positive direction is SuccessablesDboxci-+.bas, looking for 3'-CAGACT-5', 2, 3'-CAGACT-5', 1744, 3'-CAGACT-5', 2416,
  11. inverse complement, positive strand, negative direction is SuccessablesDboxci+-.bas, looking for 3'-CAGACT-5', 2, 3'-CAGACT-5', 15, 3'-CAGACT-5', 1616,
  12. inverse complement, positive strand, positive direction is SuccessablesDboxci++.bas, looking for 3'-CAGACT-5', 3, 3'-CAGACT-5', 2943, 3'-CAGACT-5', 3006, 3'-CAGACT-5', 3924,
  13. inverse, negative strand, negative direction, is SuccessablesDboxi--.bas, looking for 3'-GTCTGA-5', 2, 3'-GTCTGA-5', 15, 3'-GTCTGA-5', 1616,
  14. inverse, negative strand, positive direction, is SuccessablesDboxi-+.bas, looking for 3'-GTCTGA-5', 3, 3'-GTCTGA-5', 2943, 3'-GTCTGA-5', 3006, 3'-GTCTGA-5', 3924,
  15. inverse, positive strand, negative direction, is SuccessablesDboxi+-.bas, looking for 3'-GTCTGA-5', 0,
  16. inverse, positive strand, positive direction, is SuccessablesDboxi++.bas, looking for 3'-GTCTGA-5', 2, 3'-GTCTGA-5', 1744, 3'-GTCTGA-5', 2416.

Distal promoter D boxes

Main articles: Gene transcriptions/Distal promoters and Distal promoters

Using an estimate of 2 knts, a distal promoter to A1BG would be expected after nucleotide number 2460 in the negative direction.

There is one D box in the distal promoter: 3'-AGTCTG-5' at 2947 on the negative strand in the negative direction and its complement on the positive strand.

Using an estimate of 2 knts, a distal promoter to A1BG would be expected after nucleotide number 2300 in the positive direction.

There is one D box in the distal promoter: 3'-AGTCTG-5' at 3923 on the negative strand in the positive direction and its complement on the positive strand.

D boxes

The human ribosomal protein L11 gene (HRPL11) has [...] two potential snRNA-coding sequences in intron 4: [...] a D box beginning at +4237 (TCCTG), [...].[3]

(Voronina) samplings

For the Basic programs testing consensus sequence 5'-TCCTG-3' (starting with SuccessablesAAA.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, negative direction, looking for 5'-TCCTG-3', 4, 5'-TCCTG-3' at 4467, 5'-TCCTG-3' at 3755, 5'-TCCTG-3' at 3639, 5'-TCCTG-3' at 3388, and complements.
  2. negative strand, positive direction, looking for 5'-TCCTG-3', 10, 5'-TCCTG-3' at 4408, 5'-TCCTG-3' at 4185, 5'-TCCTG-3' at 3621, 5'-TCCTG-3' at 3295, 5'-TCCTG-3' at 2519, 5'-TCCTG-3' at 2500, 5'-TCCTG-3' at 2210, 5'-TCCTG-3' at 1775, 5'-TCCTG-3' at 1117, 5'-TCCTG-3' at 143, and complements.
  3. positive strand, negative direction, looking for 5'-TCCTG-3', 5, 5'-TCCTG-3' at 4545, 5'-TCCTG-3' at 3905, 5'-TCCTG-3' at 1910, 5'-TCCTG-3' at 1840, 5'-TCCTG-3' at 595, and complements.
  4. positive strand, positive direction, looking for 5'-TCCTG-3', 4, 5'-TCCTG-3' at 4251, 5'-TCCTG-3' at 3130, 5'-TCCTG-3' at 2459, 5'-TCCTG-3' at 1669, and complements.
  5. complement, negative strand, negative direction, looking for 5'-TTTTTTTT-3', 0.
  6. complement, negative strand, positive direction, looking for 5'-TTTTTTTT-3', 0.
  7. complement, positive strand, negative direction, looking for 5'-TTTTTTTT-3', 0.
  8. complement, positive strand, positive direction, looking for 5'-TTTTTTTT-3', 0.
  9. inverse complement, negative strand, negative direction, looking for 5'-TTTTTTTT-3', 0.
  10. inverse complement, negative strand, positive direction, looking for 5'-TTTTTTTT-3', 0.
  11. inverse complement, positive strand, negative direction, looking for 5'-TTTTTTTT-3', 0.
  12. inverse complement, positive strand, positive direction, looking for 5'-TTTTTTTT-3', 0.
  13. inverse negative strand, negative direction, looking for 5'-AAAAAAAA-3', 0.
  14. inverse negative strand, positive direction, looking for 5'-AAAAAAAA-3', 0.
  15. inverse positive strand, negative direction, looking for 5'-AAAAAAAA-3', 0.
  16. inverse positive strand, positive direction, looking for 5'-AAAAAAAA-3', 0.

DVor core promoters

Main article: Core promoter gene transcriptions

Negative strand, negative direction: 5'-TCCTG-3' at 4467, and complement.

Positive strand, negative direction: 5'-TCCTG-3' at 4545, and complement.

Negative strand, positive direction: 5'-TCCTG-3' at 4408, and complement.

DVor proximal promoters

Main article: Proximal promoter gene transcriptions

Negative strand, positive direction: 5'-TCCTG-3' at 4185, and complement.

Positive strand, positive direction: 5'-TCCTG-3' at 4251, and complement.

DVor distal promoters

Main article: Distal promoter gene transcriptions

Negative strand, negative direction: 5'-TCCTG-3' at 3755, 5'-TCCTG-3' at 3639, 5'-TCCTG-3' at 3388, and complements.

Positive strand, negative direction: 5'-TCCTG-3' at 3905, 5'-TCCTG-3' at 1910, 5'-TCCTG-3' at 1840, 5'-TCCTG-3' at 595, and complements.

Negative strand, positive direction: 5'-TCCTG-3' at 3621, 5'-TCCTG-3' at 3295, 5'-TCCTG-3' at 2519, 5'-TCCTG-3' at 2500, 5'-TCCTG-3' at 2210, 5'-TCCTG-3' at 1775, 5'-TCCTG-3' at 1117, 5'-TCCTG-3' at 143, and complements.

Positive strand, positive direction: 5'-TCCTG-3' at 3130, 5'-TCCTG-3' at 2459, 5'-TCCTG-3' at 1669, and complements.

(Johnson) samplings

TCTCACATT(A/C)AATAAGTCA is a D-box.[4]

For the Basic programs testing consensus sequence 5'-AAAAAAAA-3' (starting with SuccessablesAAA.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, negative direction, looking for 5'-AAAAAAAA-3', 0.
  2. negative strand, positive direction, looking for 5'-AAAAAAAA-3', 0.
  3. positive strand, negative direction, looking for 5'-AAAAAAAA-3', 0.
  4. positive strand, positive direction, looking for 5'-AAAAAAAA-3', 0.
  5. complement, negative strand, negative direction, looking for 5'-TTTTTTTT-3', 0.
  6. complement, negative strand, positive direction, looking for 5'-TTTTTTTT-3', 0.
  7. complement, positive strand, negative direction, looking for 5'-TTTTTTTT-3', 0.
  8. complement, positive strand, positive direction, looking for 5'-TTTTTTTT-3', 0.
  9. inverse complement, negative strand, negative direction, looking for 5'-TTTTTTTT-3', 0.
  10. inverse complement, negative strand, positive direction, looking for 5'-TTTTTTTT-3', 0.
  11. inverse complement, positive strand, negative direction, looking for 5'-TTTTTTTT-3', 0.
  12. inverse complement, positive strand, positive direction, looking for 5'-TTTTTTTT-3', 0.
  13. inverse negative strand, negative direction, looking for 5'-AAAAAAAA-3', 0.
  14. inverse negative strand, positive direction, looking for 5'-AAAAAAAA-3', 0.
  15. inverse positive strand, negative direction, looking for 5'-AAAAAAAA-3', 0.
  16. inverse positive strand, positive direction, looking for 5'-AAAAAAAA-3', 0.

AAA core promoters

Main article: Core promoter gene transcriptions

AAA proximal promoters

Main article: Proximal promoter gene transcriptions

AAA distal promoters

Main article: Distal promoter gene transcriptions

(Mracek) samplings

There is another promoter D box, or D-box: "Located in the region [...] is a single D-box element (5′-GTTGTATAAC-3′) with a distinct sequence from that of the functional D-box identified in the per2 promoter (5′-CTTATGTAAA-3′) [21]."[5]

For the Basic programs testing consensus sequence 5'-AAAAAAAA-3' (starting with SuccessablesAAA.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, negative direction, looking for 5'-AAAAAAAA-3', 0.
  2. negative strand, positive direction, looking for 5'-AAAAAAAA-3', 0.
  3. positive strand, negative direction, looking for 5'-AAAAAAAA-3', 0.
  4. positive strand, positive direction, looking for 5'-AAAAAAAA-3', 0.
  5. complement, negative strand, negative direction, looking for 5'-TTTTTTTT-3', 0.
  6. complement, negative strand, positive direction, looking for 5'-TTTTTTTT-3', 0.
  7. complement, positive strand, negative direction, looking for 5'-TTTTTTTT-3', 0.
  8. complement, positive strand, positive direction, looking for 5'-TTTTTTTT-3', 0.
  9. inverse complement, negative strand, negative direction, looking for 5'-TTTTTTTT-3', 0.
  10. inverse complement, negative strand, positive direction, looking for 5'-TTTTTTTT-3', 0.
  11. inverse complement, positive strand, negative direction, looking for 5'-TTTTTTTT-3', 0.
  12. inverse complement, positive strand, positive direction, looking for 5'-TTTTTTTT-3', 0.
  13. inverse negative strand, negative direction, looking for 5'-AAAAAAAA-3', 0.
  14. inverse negative strand, positive direction, looking for 5'-AAAAAAAA-3', 0.
  15. inverse positive strand, negative direction, looking for 5'-AAAAAAAA-3', 0.
  16. inverse positive strand, positive direction, looking for 5'-AAAAAAAA-3', 0.

AAA core promoters

Main article: Core promoter gene transcriptions

AAA proximal promoters

Main article: Proximal promoter gene transcriptions

AAA distal promoters

Main article: Distal promoter gene transcriptions

Consensus sequence (Motojima)

D-box (TGAGTGG).[2]

(Motojima) samplings

Copying the consensus of the D-box: 5'-TGAGTGG-3' and putting the sequence in "⌘F" finds no locations between ZSCAN22 and A1BG and one between ZNF497 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence 5'-AAAAAAAA-3' (starting with SuccessablesAAA.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, negative direction, looking for 5'-AAAAAAAA-3', 0.
  2. negative strand, positive direction, looking for 5'-AAAAAAAA-3', 0.
  3. positive strand, negative direction, looking for 5'-AAAAAAAA-3', 0.
  4. positive strand, positive direction, looking for 5'-AAAAAAAA-3', 0.
  5. complement, negative strand, negative direction, looking for 5'-TTTTTTTT-3', 0.
  6. complement, negative strand, positive direction, looking for 5'-TTTTTTTT-3', 0.
  7. complement, positive strand, negative direction, looking for 5'-TTTTTTTT-3', 0.
  8. complement, positive strand, positive direction, looking for 5'-TTTTTTTT-3', 0.
  9. inverse complement, negative strand, negative direction, looking for 5'-TTTTTTTT-3', 0.
  10. inverse complement, negative strand, positive direction, looking for 5'-TTTTTTTT-3', 0.
  11. inverse complement, positive strand, negative direction, looking for 5'-TTTTTTTT-3', 0.
  12. inverse complement, positive strand, positive direction, looking for 5'-TTTTTTTT-3', 0.
  13. inverse negative strand, negative direction, looking for 5'-AAAAAAAA-3', 0.
  14. inverse negative strand, positive direction, looking for 5'-AAAAAAAA-3', 0.
  15. inverse positive strand, negative direction, looking for 5'-AAAAAAAA-3', 0.
  16. inverse positive strand, positive direction, looking for 5'-AAAAAAAA-3', 0.

AAA core promoters

Main article: Core promoter gene transcriptions

AAA proximal promoters

Main article: Proximal promoter gene transcriptions

AAA distal promoters

Main article: Distal promoter gene transcriptions

Acknowledgements

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

Initial content for this page in some instances came from Wikiversity.

See also

References

  1. ↑ 1.0 1.1 Dmitry A.Samarsky, Maurille J.Fournier, Robert H.Singer and Edouard Bertrand (1 July 1998). "The snoRNA box C/D motif directs nucleolar targeting and also couples snoRNA synthesis and localization" (PDF). The European Molecular Biology Organization (EMBO) Journal. 17 (13): 3747–3757. doi:10.1093/emboj/17.13.3747. PMID 9649444. Retrieved 2017-02-04.
  2. ↑ 2.0 2.1 Masaru Motojima, Takao Ando and Toshimasa Yoshioka (10 July 2000). "Sp1-like activity mediates angiotensin-II-induced plasminogen-activator inhibitor type-1 (PAI-1) gene expression in mesangial cells" (PDF). Biomedical Journal. 349 (2): 435–441. doi:10.1042/0264-6021:3490435. PMID 10880342. Retrieved 13 August 2020.
  3. ↑ E. N. Voronina, T. D. Kolokol’tsova, E. A. Nechaeva, and M. L. Filipenko (2003). "Structural–Functional Analysis of the Human Gene for Ribosomal Protein L11" (PDF). Molecular Biology. 37 (3): 362–371. Retrieved 11 April 2019.
  4. ↑ PA Johnson, D Bunick, NB Hecht (1991). "Protein Binding Regions in the Mouse and Rat Protamine-2 Genes" (PDF). Biology of Reproduction. 44 (1): 127–134. Retrieved 6 April 2019.
  5. ↑ Philipp Mracek, Cristina Santoriello, M. Laura Idda, Cristina Pagano, Zohar Ben-Moshe, Yoav Gothilf, Daniela Vallone, Nicholas S. Foulkes (December 6, 2012). "Regulation of per and cry Genes Reveals a Central Role for the D-Box Enhancer in Light-Dependent Gene Expression". PLoS ONE. 7 (12): e51278. doi:10.1371/journal.pone.0051278. Retrieved 10 February 2019.

External links

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