CadC binding domain gene transcriptions: Difference between revisions

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Created page with "{{AE}} Henry A. Hoff "Dimerization of [cadaverine C-terminal] CadC enables the binding of two DBDs to the two Cad1 consensus target sites."<ref name=Schlundt/> ==Consensus s..."
 
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# positive strand, negative direction, looking for 5'-TTANNNNT-3', 6, 5'-TTATTAAT-3' at 4540, 5'-TTAAAAAT-3' at 3355, 5'-TTAGATAT-3' at 2982, 5'-TTATCTTT-3' at 1733, 5'-TTAAGTGT-3' at 322, 5'-TTAAGAAT-3' at 196.
# positive strand, negative direction, looking for 5'-TTANNNNT-3', 6, 5'-TTATTAAT-3' at 4540, 5'-TTAAAAAT-3' at 3355, 5'-TTAGATAT-3' at 2982, 5'-TTATCTTT-3' at 1733, 5'-TTAAGTGT-3' at 322, 5'-TTAAGAAT-3' at 196.
# positive strand, positive direction, looking for 5'-TTANNNNT-3', 5, 5'-TTACTCCT-3' at 4097, 5'-TTATACCT-3' at 3163, 5'-TTATCTTT-3' at 2629, 5'-TTAAAATT-3' at 2443, 5'-TTACACTT-3' at 231.
# positive strand, positive direction, looking for 5'-TTANNNNT-3', 5, 5'-TTACTCCT-3' at 4097, 5'-TTATACCT-3' at 3163, 5'-TTATCTTT-3' at 2629, 5'-TTAAAATT-3' at 2443, 5'-TTACACTT-3' at 231.
# complement, negative strand, negative direction, looking for 5'-TTTTTTTT-3', 0.
# complement, negative strand, negative direction, looking for 5'-AATNNNNA-3', 6, 5'-AATAATTA-3' at 4540, 5'-AATTTTTA-3' at 3355, 5'-AATCTATA-3' at 2982, 5'-AATAGAAA-3' at 1733, 5'-AATTCACA-3' at 322, 5'-AATTCTTA-3' at 196.
# complement, negative strand, positive direction, looking for 5'-TTTTTTTT-3', 0.
# complement, negative strand, positive direction, looking for 5'-AATNNNNA-3', 5, 5'-AATGAGGA-3' at 4097, 5'-AATATGGA-3' at 3163, 5'-AATAGAAA-3' at 2629, 5'-AATTTTAA-3' at 2443, 5'-AATGTGAA-3' at 231.
# complement, positive strand, negative direction, looking for 5'-TTTTTTTT-3', 0.
# complement, positive strand, negative direction, looking for 5'-AATNNNNA-3', 24, 5'-AATAATTA-3' at 4227, 5'-AATAATAA-3' at 4224, 5'-AATAGAAA-3' at 4081, 5'-AATAAATA-3' at 4074, 5'-AATCCCAA-3' at 3978, 5'-AATGGGAA-3' at 3662, 5'-AATACTGA-3' at 3542, 5'-AATTGATA-3' at 3360, 5'-AATAAACA-3' at 3337, 5'-AATGGCTA-3' at 3007, 5'-AATGCTTA-3' at 2935, 5'-AATATATA-3' at 2872, 5'-AATATACA-3' at 2641, 5'-AATAGTAA-3' at 2501, 5'-AATACAAA-3' at 2306, 5'-AATACAAA-3' at 1879, 5'-AATAGAGA-3' at 1712, 5'-AATGCCAA-3' at 1636, 5'-AATACAGA-3' at 1567, 5'-AATCAGGA-3' at 985, 5'-AATACAAA-3' at 770, 5'-AATACAAA-3' at 636, 5'-AATACGAA-3' at 493, 5'-AATTCTAA-3' at 9.
# complement, positive strand, positive direction, looking for 5'-TTTTTTTT-3', 0.
# complement, positive strand, positive direction, looking for 5'-AATNNNNA-3', 9, 5'-AATATTAA-3' at 4169, 5'-AATAACTA-3' at 4162, 5'-AATTAGTA-3' at 4148, 5'-AATAATTA-3' at 4145, 5'-AATAGTGA-3' at 4126, 5'-AATACTGA-3' at 3029, 5'-AATCCCGA-3' at 2768, 5'-AATTTTAA-3' at 2447, 5'-AATTTGTA-3' at 2139.
# inverse complement, negative strand, negative direction, looking for 5'-TTTTTTTT-3', 0.
# inverse complement, negative strand, negative direction, looking for 5'-ANNNNTAA-3', 10, 5'-ATAATTAA-3' at 4541, 5'-AAGTGTAA-3' at 4533, 5'-ATTATTAA-3' at 4226, 5'-ATCTATAA-3' at 3467, 5'-ATTTTTAA-3' at 3356, 5'-ATTTTTAA-3' at 3174, 5'-ATGGATAA-3' at 2997, 5'-ATCTCTAA-3' at 1714, 5'-ACCCTTAA-3' at 1694, 5'-ATATATAA-3' at 1601.
# inverse complement, negative strand, positive direction, looking for 5'-TTTTTTTT-3', 0.
# inverse complement, negative strand, positive direction, looking for 5'-ANNNNTAA-3', 2, 5'-AATTTTAA-3' at 2443, 5'-ACAGTTAA-3' at 2135.
# inverse complement, positive strand, negative direction, looking for 5'-TTTTTTTT-3', 0.
# inverse complement, positive strand, negative direction, looking for 5'-ANNNNTAA-3', 28, 5'-AATAATAA-3' at 4224, 5'-AAAAATAA-3' at 4221, 5'-ATAAATAA-3' at 4075, 5'-AAAAATAA-3' at 4071, 5'-ACCTGTAA-3' at 3972, 5'-AGGGATAA-3' at 3656, 5'-ATTACTAA-3' at 3472, 5'-ATTGATAA-3' at 3361, 5'-ACAAATAA-3' at 3334, 5'-AAACATAA-3' at 3169, 5'-AAAACTAA-3' at 3030, 5'-ATGGCTAA-3' at 3008, 5'-ATGCTTAA-3' at 2936, 5'-ATATATAA-3' at 2873, 5'-AATAGTAA-3' at 2501, 5'-ATCTTTAA-3' at 1735, 5'-AAACCTAA-3' at 1591, 5'-ACACTTAA-3' at 1546, 5'-ACCTGTAA-3' at 1133, 5'-ACCTGTAA-3' at 803, 5'-ACACGTAA-3' at 533, 5'-ACCTGTAA-3' at 396, 5'-AGTGCTAA-3' at 337, 5'-AACCTTAA-3' at 318, 5'-AGATGTAA-3' at 247, 5'-AGGTATAA-3' at 181, 5'-ACACCTAA-3' at 64, 5'-AATTCTAA-3' at 9.
# inverse complement, positive strand, positive direction, looking for 5'-TTTTTTTT-3', 0.
# inverse complement, positive strand, positive direction, looking for 5'-ANNNNTAA-3', 10, 5'-AATATTAA-3' at 4169, 5'-ATAACTAA-3' at 4163, 5'-ACTAATAA-3' at 4159, 5'-AGAACTAA-3' at 4133, 5'-ATCCATAA-3' at 2643, 5'-AACCCTAA-3' at 2545, 5'-AATTTTAA-3' at 2447, 5'-ACAAATAA-3' at 2347, 5'-ACCGATAA-3' at 1976, 5'-AAACATAA-3' at 115.
# inverse negative strand, negative direction, looking for 5'-AAAAAAAA-3', 0.
# inverse negative strand, negative direction, looking for 5'-TNNNNATT-3', 0.
# inverse negative strand, positive direction, looking for 5'-AAAAAAAA-3', 0.
# inverse negative strand, positive direction, looking for 5'-TNNNNATT-3', 0.
# inverse positive strand, negative direction, looking for 5'-AAAAAAAA-3', 0.
# inverse positive strand, negative direction, looking for 5'-TNNNNATT-3', 0.
# inverse positive strand, positive direction, looking for 5'-AAAAAAAA-3', 0.
# inverse positive strand, positive direction, looking for 5'-TNNNNATT-3', 0.


===CadC core promoters===
===CadC core promoters===

Revision as of 08:33, 6 November 2020

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

"Dimerization of [cadaverine C-terminal] CadC enables the binding of two DBDs to the two Cad1 consensus target sites."[1]

Consensus sequences

Main article: Consensus sequence gene transcriptions

"Altogether, the specific contacts observed suggest a consensus binding motif of 5′-T-T-A-x-x-x-x-T-3′."[1]

"The DNA consensus sequence 5′-T-T-A-x-x-x-x-T-3′ is present once in the quasi-palindromic Cad1 17-mer DNA, consistent with the formation of a 1:1 complex. However, a second consensus facilitates the formation of the 2:1 complex of CadC with Cad1 41-mer DNA as evidenced by the CadC model with the minimal Cad1 26-mer DNA that spans the two AT-rich regions, i.e. consensus sites."[1]

Hypotheses

Main article: Hypotheses
  1. A1BG has no CadC binding domain in either promoter.
  2. A1BG is not transcribed by a CadC binding domain.
  3. CadC binding domain does not participate in the transcription of A1BG.

Samplings

Main article: Model samplings

Copying the cadaverine C-terminal binding domain consensus sequence 5'-T-T-A-x-x-x-x-T-3' and putting the sequence in "⌘F" finds one location between ZNF497 and A1BG or four locations between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence 5'-TTANNNNT-3' (starting with SuccessablesCadC.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'-TTANNNNT-3', 24, 5'-TTATTAAT-3' at 4227, 5'-TTATTATT-3' at 4224, '-TTATCTTT-3' at 4081, 5'-TTATTTAT-3' at 4074, 5'-TTAGGGTT-3' at 3978, 5'-TTACCCTT-3' at 3662, 5'-TTATGACT-3' at 3542, 5'-TTAACTAT-3' at 3360, 5'-TTATTTGT-3' at 3337, 5'-TTACCGAT-3' at 3007, 5'-TTACGAAT-3' at 2935, 5'-TTATATAT-3' at 2872, 5'-TTATATGT-3' at 2641, 5'-TTATCATT-3' at 2501, 5'-TTATGTTT-3' at 2306, 5'-TTATGTTT-3' at 1879, 5'-TTATCTCT-3' at 1712, 5'-TTACGGTT-3' at 1636, 5'-TTATGTCT-3' at 1567, 5'-TTAGTCCT-3' at 985, 5'-TTATGTTT-3' at 770, 5'-TTATGTTT-3' at 636, 5'-TTATGCTT-3' at 493, 5'-TTAAGATT-3' at 9, and complements.
  2. negative strand, positive direction, looking for 5'-TTANNNNT-3', 9, 5'-TTATAATT-3' at 4169, 5'-TTATTGAT-3' at 4162, 5'-TTAATCAT-3' at 4148, 5'-TTATTAAT-3' at 4145, 5'-TTATCACT-3' at 4126, 5'-TTATGACT-3' at 3029, 5'-TTAGGGCT-3' at 2768, 5'-TTAAAATT-3' at 2447, 5'-TTAAACAT-3' at 2139.
  3. positive strand, negative direction, looking for 5'-TTANNNNT-3', 6, 5'-TTATTAAT-3' at 4540, 5'-TTAAAAAT-3' at 3355, 5'-TTAGATAT-3' at 2982, 5'-TTATCTTT-3' at 1733, 5'-TTAAGTGT-3' at 322, 5'-TTAAGAAT-3' at 196.
  4. positive strand, positive direction, looking for 5'-TTANNNNT-3', 5, 5'-TTACTCCT-3' at 4097, 5'-TTATACCT-3' at 3163, 5'-TTATCTTT-3' at 2629, 5'-TTAAAATT-3' at 2443, 5'-TTACACTT-3' at 231.
  5. complement, negative strand, negative direction, looking for 5'-AATNNNNA-3', 6, 5'-AATAATTA-3' at 4540, 5'-AATTTTTA-3' at 3355, 5'-AATCTATA-3' at 2982, 5'-AATAGAAA-3' at 1733, 5'-AATTCACA-3' at 322, 5'-AATTCTTA-3' at 196.
  6. complement, negative strand, positive direction, looking for 5'-AATNNNNA-3', 5, 5'-AATGAGGA-3' at 4097, 5'-AATATGGA-3' at 3163, 5'-AATAGAAA-3' at 2629, 5'-AATTTTAA-3' at 2443, 5'-AATGTGAA-3' at 231.
  7. complement, positive strand, negative direction, looking for 5'-AATNNNNA-3', 24, 5'-AATAATTA-3' at 4227, 5'-AATAATAA-3' at 4224, 5'-AATAGAAA-3' at 4081, 5'-AATAAATA-3' at 4074, 5'-AATCCCAA-3' at 3978, 5'-AATGGGAA-3' at 3662, 5'-AATACTGA-3' at 3542, 5'-AATTGATA-3' at 3360, 5'-AATAAACA-3' at 3337, 5'-AATGGCTA-3' at 3007, 5'-AATGCTTA-3' at 2935, 5'-AATATATA-3' at 2872, 5'-AATATACA-3' at 2641, 5'-AATAGTAA-3' at 2501, 5'-AATACAAA-3' at 2306, 5'-AATACAAA-3' at 1879, 5'-AATAGAGA-3' at 1712, 5'-AATGCCAA-3' at 1636, 5'-AATACAGA-3' at 1567, 5'-AATCAGGA-3' at 985, 5'-AATACAAA-3' at 770, 5'-AATACAAA-3' at 636, 5'-AATACGAA-3' at 493, 5'-AATTCTAA-3' at 9.
  8. complement, positive strand, positive direction, looking for 5'-AATNNNNA-3', 9, 5'-AATATTAA-3' at 4169, 5'-AATAACTA-3' at 4162, 5'-AATTAGTA-3' at 4148, 5'-AATAATTA-3' at 4145, 5'-AATAGTGA-3' at 4126, 5'-AATACTGA-3' at 3029, 5'-AATCCCGA-3' at 2768, 5'-AATTTTAA-3' at 2447, 5'-AATTTGTA-3' at 2139.
  9. inverse complement, negative strand, negative direction, looking for 5'-ANNNNTAA-3', 10, 5'-ATAATTAA-3' at 4541, 5'-AAGTGTAA-3' at 4533, 5'-ATTATTAA-3' at 4226, 5'-ATCTATAA-3' at 3467, 5'-ATTTTTAA-3' at 3356, 5'-ATTTTTAA-3' at 3174, 5'-ATGGATAA-3' at 2997, 5'-ATCTCTAA-3' at 1714, 5'-ACCCTTAA-3' at 1694, 5'-ATATATAA-3' at 1601.
  10. inverse complement, negative strand, positive direction, looking for 5'-ANNNNTAA-3', 2, 5'-AATTTTAA-3' at 2443, 5'-ACAGTTAA-3' at 2135.
  11. inverse complement, positive strand, negative direction, looking for 5'-ANNNNTAA-3', 28, 5'-AATAATAA-3' at 4224, 5'-AAAAATAA-3' at 4221, 5'-ATAAATAA-3' at 4075, 5'-AAAAATAA-3' at 4071, 5'-ACCTGTAA-3' at 3972, 5'-AGGGATAA-3' at 3656, 5'-ATTACTAA-3' at 3472, 5'-ATTGATAA-3' at 3361, 5'-ACAAATAA-3' at 3334, 5'-AAACATAA-3' at 3169, 5'-AAAACTAA-3' at 3030, 5'-ATGGCTAA-3' at 3008, 5'-ATGCTTAA-3' at 2936, 5'-ATATATAA-3' at 2873, 5'-AATAGTAA-3' at 2501, 5'-ATCTTTAA-3' at 1735, 5'-AAACCTAA-3' at 1591, 5'-ACACTTAA-3' at 1546, 5'-ACCTGTAA-3' at 1133, 5'-ACCTGTAA-3' at 803, 5'-ACACGTAA-3' at 533, 5'-ACCTGTAA-3' at 396, 5'-AGTGCTAA-3' at 337, 5'-AACCTTAA-3' at 318, 5'-AGATGTAA-3' at 247, 5'-AGGTATAA-3' at 181, 5'-ACACCTAA-3' at 64, 5'-AATTCTAA-3' at 9.
  12. inverse complement, positive strand, positive direction, looking for 5'-ANNNNTAA-3', 10, 5'-AATATTAA-3' at 4169, 5'-ATAACTAA-3' at 4163, 5'-ACTAATAA-3' at 4159, 5'-AGAACTAA-3' at 4133, 5'-ATCCATAA-3' at 2643, 5'-AACCCTAA-3' at 2545, 5'-AATTTTAA-3' at 2447, 5'-ACAAATAA-3' at 2347, 5'-ACCGATAA-3' at 1976, 5'-AAACATAA-3' at 115.
  13. inverse negative strand, negative direction, looking for 5'-TNNNNATT-3', 0.
  14. inverse negative strand, positive direction, looking for 5'-TNNNNATT-3', 0.
  15. inverse positive strand, negative direction, looking for 5'-TNNNNATT-3', 0.
  16. inverse positive strand, positive direction, looking for 5'-TNNNNATT-3', 0.

CadC core promoters

Main article: Core promoter gene transcriptions

Positive strand, negative direction: 5'-TTATTAAT-3' at 4540, and complement.

CadC proximal promoters

Main article: Proximal promoter gene transcriptions

Negative strand, negative direction: 24, 5'-TTATTAAT-3' at 4227, 5'-TTATTATT-3' at 4224, and complements.

Negative strand, positive direction: 5'-TTATAATT-3' at 4169, 5'-TTATTGAT-3' at 4162, 5'-TTAATCAT-3' at 4148, 5'-TTATTAAT-3' at 4145, 5'-TTATCACT-3' at 4126, and complements.

Positive strand, positive direction: 5'-TTACTCCT-3' at 4097, and complement.

CadC distal promoters

Main article: Distal promoter gene transcriptions

Negative strand, negative direction: 5'-TTATCTTT-3' at 4081, 5'-TTATTTAT-3' at 4074, 5'-TTAGGGTT-3' at 3978, 5'-TTACCCTT-3' at 3662, 5'-TTATGACT-3' at 3542, 5'-TTAACTAT-3' at 3360, 5'-TTATTTGT-3' at 3337, 5'-TTACCGAT-3' at 3007, 5'-TTACGAAT-3' at 2935, 5'-TTATATAT-3' at 2872, 5'-TTATATGT-3' at 2641, 5'-TTATCATT-3' at 2501, 5'-TTATGTTT-3' at 2306, 5'-TTATGTTT-3' at 1879, 5'-TTATCTCT-3' at 1712, 5'-TTACGGTT-3' at 1636, 5'-TTATGTCT-3' at 1567, 5'-TTAGTCCT-3' at 985, 5'-TTATGTTT-3' at 770, 5'-TTATGTTT-3' at 636, 5'-TTATGCTT-3' at 493, 5'-TTAAGATT-3' at 9, and complements.

Negative strand, positive direction: 5'-TTATGACT-3' at 3029, 5'-TTAGGGCT-3' at 2768, 5'-TTAAAATT-3' at 2447, 5'-TTAAACAT-3' at 2139, and complements.

Positive strand, negative direction: 5'-TTAAAAAT-3' at 3355, 5'-TTAGATAT-3' at 2982, 5'-TTATCTTT-3' at 1733, 5'-TTAAGTGT-3' at 322, 5'-TTAAGAAT-3' at 196, and complements.

Positive strand, positive direction: 5'-TTATACCT-3' at 3163, 5'-TTATCTTT-3' at 2629, 5'-TTAAAATT-3' at 2443, 5'-TTACACTT-3' at 231, and complements.

Acknowledgements

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

See also

References

  1. ↑ 1.0 1.1 1.2 Andreas Schlundt, Sophie Buchner, Robert Janowski, Thomas Heydenreich, Ralf Heermann, Jürgen Lassak, Arie Geerlof, Ralf Stehle, Dierk Niessing, Kirsten Jung & Michael Sattler (21 April 2017). "Structure-function analysis of the DNA-binding domain of a transmembrane transcriptional activator". Scientific Reports. 7: 1051. doi:10.1038/s41598-017-01031-9. PMID 28432336. Retrieved 28 August 2020.

External links

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