D box gene transcriptions: Difference between revisions
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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. | 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), [...].<ref name=Voronina>{{ cite journal | |||
|author=E. N. Voronina, T. D. Kolokol’tsova, E. A. Nechaeva, and M. L. Filipenko | |||
|title=Structural–Functional Analysis of the Human Gene for Ribosomal Protein L11 | |||
|journal=Molecular Biology | |||
|date=2003 | |||
|volume=37 | |||
|issue=3 | |||
|pages=362–371 | |||
|url=https://www.researchgate.net/profile/Elena_Voronina3/publication/263607045_Structural-Functional_Analysis_of_the_Human_Gene_for_Ribosomal_Protein_L11/links/5523af480cf27b5dc3795afa.pdf | |||
|arxiv= | |||
|bibcode= | |||
|doi= | |||
|pmid= | |||
|accessdate=11 April 2019 }}</ref> | |||
TCTCACATT(A/C)AATAAGTCA is a D-box.<ref name=Johnson>{{ cite journal | |||
|author=PA Johnson, D Bunick, NB Hecht | |||
|title=Protein Binding Regions in the Mouse and Rat Protamine-2 Genes | |||
|journal=Biology of Reproduction | |||
|date=1991 | |||
|volume=44 | |||
|issue=1 | |||
|pages=127-134 | |||
|url=https://academic.oup.com/biolreprod/article-pdf/44/1/127/10536199/biolreprod0127.pdf | |||
|arxiv= | |||
|bibcode= | |||
|doi= | |||
|pmid= | |||
|accessdate=6 April 2019 }}</ref> | |||
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]."<ref name=Mracek>{{ cite journal | |||
|author=Philipp Mracek, Cristina Santoriello, M. Laura Idda, Cristina Pagano, Zohar Ben-Moshe, Yoav Gothilf, Daniela Vallone, Nicholas S. Foulkes | |||
|title=Regulation of ''per'' and ''cry'' Genes Reveals a Central Role for the D-Box Enhancer in Light-Dependent Gene Expression | |||
|journal=PLoS ONE | |||
|date=December 6, 2012 | |||
|volume=7 | |||
|issue=12 | |||
|pages=e51278 | |||
|url=https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0051278 | |||
|arxiv= | |||
|bibcode= | |||
|doi=10.1371/journal.pone.0051278 | |||
|pmid= | |||
|accessdate=10 February 2019 }}</ref> | |||
==See also== | ==See also== | ||
Revision as of 07:57, 25 December 2019
Associate Editor(s)-in-Chief: Henry A. Hoff
{{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
For transcription, U (in RNA) is T, Y=(C or T) and R=(A or G).
Consensus sequences
{{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]
Samplings
Regarding hypothesis 1
The D boxes are not involved in the transcription of A1BG.
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:
- negative strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesDbox--.bas, looking for 3'-AGTCTG-5', 1, 3'-AGTCTG-5', 2947,
- negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesDbox-+.bas, looking for 3'-AGTCTG-5', 1, 3'-AGTCTG-5', 3923,
- positive strand in the negative direction is SuccessablesDbox+-.bas, looking for 3'-AGTCTG-5', 1, 3'-AGTCTG-5', 1355,
- positive strand in the positive direction is SuccessablesDbox++.bas, looking for 3'-AGTCTG-5', 0,
- complement, negative strand, negative direction is SuccessablesDboxc--.bas, looking for 3'-TCAGAC-5', 1, 3'-TCAGAC-5', 1355,
- complement, negative strand, positive direction is SuccessablesDboxc-+.bas, looking for 3'-TCAGAC-5', 0,
- complement, positive strand, negative direction is SuccessablesDboxc+-.bas, looking for 3'-TCAGAC-5', 1, 3'-TCAGAC-5', 2947,
- complement, positive strand, positive direction is SuccessablesDboxc++.bas, looking for 3'-TCAGAC-5', 1, 3'-TCAGAC-5', 3923,
- inverse complement, negative strand, negative direction is SuccessablesDboxci--.bas, looking for 3'-CAGACT-5', 0,
- inverse complement, negative strand, positive direction is SuccessablesDboxci-+.bas, looking for 3'-CAGACT-5', 2, 3'-CAGACT-5', 1744, 3'-CAGACT-5', 2416,
- inverse complement, positive strand, negative direction is SuccessablesDboxci+-.bas, looking for 3'-CAGACT-5', 2, 3'-CAGACT-5', 15, 3'-CAGACT-5', 1616,
- 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,
- inverse, negative strand, negative direction, is SuccessablesDboxi--.bas, looking for 3'-GTCTGA-5', 2, 3'-GTCTGA-5', 15, 3'-GTCTGA-5', 1616,
- 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,
- inverse, positive strand, negative direction, is SuccessablesDboxi+-.bas, looking for 3'-GTCTGA-5', 0,
- 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
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), [...].[2]
TCTCACATT(A/C)AATAAGTCA is a D-box.[3]
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]."[4]
See also
References
- ↑ 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.
- ↑ 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.
- ↑ 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.
- ↑ 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.