Cell-cycle box gene transcriptions: Difference between revisions
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For the Basic programs testing consensus sequence CACGAAAA (starting with SuccessablesCCB.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: | For the Basic programs testing consensus sequence CACGAAAA (starting with SuccessablesCCB.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 CACGAAAA, 0. | # negative strand, negative direction, looking for CACGAAAA, 0. | ||
# positive strand, negative direction, looking for CACGAAAA, 0. | |||
# positive strand, positive direction, looking for CACGAAAA, 0. | |||
# negative strand, positive direction, looking for CACGAAAA, 0. | |||
# complement, negative strand, negative direction, looking for GTGCTTTT, 0. | |||
# complement, positive strand, negative direction, looking for GTGCTTTT, 0. | |||
# complement, positive strand, positive direction, looking for GTGCTTTT, 0. | |||
# complement, negative strand, positive direction, looking for GTGCTTTT, 0. | |||
# inverse complement, negative strand, negative direction, looking for TTTTCGTG, 0. | |||
# inverse complement, positive strand, negative direction, looking for TTTTCGTG, 0. | |||
# inverse complement, positive strand, positive direction, looking for TTTTCGTG, 0. | |||
# inverse complement, negative strand, positive direction, looking for TTTTCGTG, 0. | |||
# inverse negative strand, negative direction, looking for AAAAGCAC, 0. | |||
# inverse positive strand, negative direction, looking for AAAAGCAC, 0. | |||
# inverse positive strand, positive direction, looking for AAAAGCAC, 0. | |||
# inverse negative strand, positive direction, looking for AAAAGCAC, 0. | |||
==CCB variant 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 AAAAAAAA (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: | |||
# negative strand, negative direction, looking for AAAAAAAA, 0. | |||
# positive strand, negative direction, looking for AAAAAAAA, 0. | # positive strand, negative direction, looking for AAAAAAAA, 0. | ||
# positive strand, positive direction, looking for AAAAAAAA, 0. | # positive strand, positive direction, looking for AAAAAAAA, 0. | ||
# negative strand, positive direction, looking for AAAAAAAA, 0. | # negative strand, positive direction, looking for AAAAAAAA, 0. | ||
# complement, negative strand, negative direction, looking for | # complement, negative strand, negative direction, looking for TTTTTTTT, 0. | ||
# complement, positive 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, positive strand, positive direction, looking for TTTTTTTT, 0. | ||
# complement, negative strand, positive direction, looking for TTTTTTTT, 0. | # complement, negative strand, positive direction, looking for TTTTTTTT, 0. | ||
# inverse complement, negative strand, negative direction, looking for | # inverse complement, negative strand, negative direction, looking for TTTTTTTT, 0. | ||
# inverse complement, positive 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, positive strand, positive direction, looking for TTTTTTTT, 0. | ||
# inverse complement, negative strand, positive direction, looking for TTTTTTTT, 0. | # inverse complement, negative strand, positive direction, looking for TTTTTTTT, 0. | ||
# inverse negative strand, negative direction, looking for | # inverse negative strand, negative direction, looking for AAAAAAAA, 0. | ||
# inverse positive 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 positive strand, positive direction, looking for AAAAAAAA, 0. |
Revision as of 22:13, 19 April 2021
Associate Editor(s)-in-Chief: Henry A. Hoff
"The 5' non-coding part contains the sequence elements characteristic for eukaryotic promoters such as TATA and CAAT boxes as well as an inverted motif typical for cell-cycle regulated genes named "cell-cycle box" (CCB). The consensus sequence of CCB is CACGAAAA (Nasmyth, 1985), however, more relaxed variants such as CACGAAA, ACGAAA and C-CGAAA were described in budding yeast CLN1 and CLN2 (Ogas et al, 1991)."[1]
Human genes
Gene expressions
Interactions
Consensus sequences
Binding site for
Inverse copies
"In our soybean genomic clone CCB is represented as an inverted motif TTTTGGTG at the -66 position. (Breeden and Nasmyth (1987) suggested that the "cell cycle box" is functional in either orientation, acting as an enhancer."[1]
Enhancer activity
Promoter occurrences
Hypotheses
- A1BG has no regulatory elements in either promoter.
- A1BG is not transcribed by a regulatory element.
- No regulatory element participates in the transcription of A1BG.
CCB Samplings
Copying a responsive elements consensus sequence CACGAAAA 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 CACGAAAA (starting with SuccessablesCCB.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 CACGAAAA, 0.
- positive strand, negative direction, looking for CACGAAAA, 0.
- positive strand, positive direction, looking for CACGAAAA, 0.
- negative strand, positive direction, looking for CACGAAAA, 0.
- complement, negative strand, negative direction, looking for GTGCTTTT, 0.
- complement, positive strand, negative direction, looking for GTGCTTTT, 0.
- complement, positive strand, positive direction, looking for GTGCTTTT, 0.
- complement, negative strand, positive direction, looking for GTGCTTTT, 0.
- inverse complement, negative strand, negative direction, looking for TTTTCGTG, 0.
- inverse complement, positive strand, negative direction, looking for TTTTCGTG, 0.
- inverse complement, positive strand, positive direction, looking for TTTTCGTG, 0.
- inverse complement, negative strand, positive direction, looking for TTTTCGTG, 0.
- inverse negative strand, negative direction, looking for AAAAGCAC, 0.
- inverse positive strand, negative direction, looking for AAAAGCAC, 0.
- inverse positive strand, positive direction, looking for AAAAGCAC, 0.
- inverse negative strand, positive direction, looking for AAAAGCAC, 0.
CCB variant 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 AAAAAAAA (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:
- 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.
CCB UTRs
CCB core promoters
CCB proximal promoters
CCB distal promoters
Acknowledgements
The content on this page was first contributed by: Henry A. Hoff.
See also
References
- ↑ 1.0 1.1 Joanna Deckert, Natasha Taranenko, and Peter M. Gresshoff (1994). Peter M. Gresshoff, ed. Cell Cycle Genes and Their Plant Homologues, In: Plant Genome Analysis: Current Topics in Plant Molecular Biology. 2000 Corporate Blvd., N.W., Boca Raton, Florida 33431: CRC Press, Inc. pp. 169–194. ISBN 0-8493-8264-5. Retrieved 19 April 2021.