Musashi binding element gene transcriptions: Difference between revisions

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For the Basic programs testing consensus sequence (A/G)TTAGT (starting with SuccessablesMBE2.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 (A/G)TTAGT (starting with SuccessablesMBE2.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 (A/G)TTAGT, 0.
# negative strand, negative direction, looking for (A/G)TTAGT, 1, ATTAGT at 982.
# positive strand, negative direction, looking for AAAAAAAA, 0.
# positive strand, negative direction, looking for (A/G)TTAGT, 1, ATTAGT at 155.
# positive strand, positive direction, looking for AAAAAAAA, 0.
# positive strand, positive direction, looking for (A/G)TTAGT, 2, ATTAGT at 4147, GTTAGT at 2338.
# negative strand, positive direction, looking for AAAAAAAA, 0.
# negative strand, positive direction, looking for (A/G)TTAGT, 0.
# inverse complement, negative strand, negative direction, looking for ACTAA(C/T), 0.
# inverse complement, negative strand, negative direction, looking for ACTAA(C/T), 0.
# inverse complement, positive strand, negative direction, looking for TTTTTTTT, 0.
# inverse complement, positive strand, negative direction, looking for ACTAA(C/T), 0.
# inverse complement, positive strand, positive direction, looking for TTTTTTTT, 0.
# inverse complement, positive strand, positive direction, looking for ACTAA(C/T), 3, ACTAAT at 4164, ACTAAT at 4157, ACTAAC at 2677.
# inverse complement, negative strand, positive direction, looking for TTTTTTTT, 0.
# inverse complement, negative strand, positive direction, looking for ACTAA(C/T), 0.


For the Basic programs testing consensus sequence (A/G)TTTAGT (starting with SuccessablesMBE3.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 (A/G)TTTAGT (starting with SuccessablesMBE3.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:
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===MBE proximal promoters===
===MBE proximal promoters===
{{main|Proximal promoter gene transcriptions}}
{{main|Proximal promoter gene transcriptions}}
Positive strand, positive direction: ATAGT at 4124, GTAGT at 4116, GTAGT at 4085.
Positive strand, positive direction: ACTAAT at 4164, ACTAAT at 4157, ATTAGT at 4147, ATAGT at 4124, GTAGT at 4116, GTAGT at 4085.


===MBE distal promoters===
===MBE distal promoters===
{{main|Distal promoter gene transcriptions}}
{{main|Distal promoter gene transcriptions}}
Negative strand, negative direction: ACTAT at 1702, ACTAT at 1665, ACTAT at 353, ACTAC at 142.
Negative strand, negative direction: ACTAT at 1702, ACTAT at 1665, ATTAGT at 982, ACTAT at 353, ACTAC at 142.


Positive strand, negative direction: GTAGT at 2541, ATAGT at 2499, GTAGT at 2340, ATAGT at 1704, ATAGT at 469, ATAGT at 251, ACTAT at 210.
Positive strand, negative direction: GTAGT at 2541, ATAGT at 2499, GTAGT at 2340, ATAGT at 1704, ATAGT at 469, ATAGT at 251, ACTAT at 210, ATTAGT at 155.


Negative strand, positive direction: ACTAC at 2427, ATAGT at 1839.
Negative strand, positive direction: ACTAC at 2427, ATAGT at 1839.


Positive strand, positive direction: ACTAC at 3845, GTAGT at 3251, ACTAC at 2143.
Positive strand, positive direction: ACTAC at 3845, GTAGT at 3251, ACTAAC at 2677, GTTAGT at 2338, ACTAC at 2143.


==Acknowledgements==
==Acknowledgements==

Revision as of 05:53, 18 April 2021

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

"The 24-nt Xenopus Mos [polyadenylation response element] PRE (Charlesworth et al, 2002) contained a match to the SELEX-derived murine Musashi RNA binding consensus sequence (G/AU1−3AGU) (Imai et al, 2001), and included a 3′ U residue essential for PRE function (Charlesworth et al, 2002) [...]."[1]

"Regarding the 3′ UTR cis-regulatory sequences such as AREs (PAS) [110], BRD-Box [111] and MBE [112] mediates negative post-transcriptional regulation by affecting mRNA transcript stability and translational efficiency [110], [140]. In our case, the 3′ cis-regulatory signals, BRD-Box and MBE, located upstream and downstream PAS [...] may regulate tissue-specific alternative polyadenylation which has been detected in approximately 54% of human genes [142]."[2]

Human genes

Main article: Human genes

Gene expressions

Main article: Gene expressions

Interactions

Main article: Interaction gene transcriptions

Consensus sequences

Main article: Consensus sequence gene transcriptions

"The [Musashi-binding element] MBE consensus sequence is (G/A)U1–3AGU."[3]

"Musashi did not form a complex with the Mos UTR when the Musashi binding site was disrupted (AUAGU to AUccU [...])."[1]

Binding site for

Enhancer activity

Main article: Enhancer activity copy gene transcriptions

Promoter occurrences

Main article: Promoter occurrence gene transcriptions

Hypotheses

Main article: Hypotheses
  1. A1BG has no regulatory elements in either promoter.
  2. A1BG is not transcribed by a regulatory element.
  3. No regulatory element participates in the transcription of A1BG.

MBE samplings

Main article: Model samplings

Copying a responsive elements consensus sequence (A/G)T1–3AGT and putting the sequenceS in "⌘F" GTAGT, GTTAGT, GTTTAGT finds none or three, or ATTTAGT finds one to three between ZNF497 and A1BG or GTAGT three to six, GTTAGT, GTTTAGT or none between ZSCAN22 and A1BG, or ATAGT none, ATTAGT one, ATTTAGT none as can be found by the computer programs.

For the Basic programs testing consensus sequence (A/G)TAGT (starting with SuccessablesMBE1.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 (A/G)TAGT, 8, GTAGT at 3616, GTAGT at 3521, GTAGT at 3418, GTAGT at 3415, GTAGT at 3394, GTAGT at 2944, GTAGT at 2941, GTAGT at 2888.
  2. positive strand, negative direction, looking for (A/G)TAGT, 8, GTAGT at 4124, ATAGT at 4047, GTAGT at 2541, ATAGT at 2499, GTAGT at 2340, ATAGT at 1704, ATAGT at 469, ATAGT at 251.
  3. positive strand, positive direction, looking for (A/G)TAGT, 5, GTAGT at 4362, ATAGT at 4124, GTAGT at 4116, GTAGT at 4085, GTAGT at 3251.
  4. negative strand, positive direction, looking for (A/G)TAGT, 1, ATAGT at 1839.
  5. inverse complement, negative strand, negative direction, looking for ACTA(C/T), 9, ACTAC at 3807, ACTAC at 3798, ACTAT at 3544, ACTAT at 3535, ACTAT at 3360, ACTAT at 1702, ACTAT at 1665, ACTAT at 353, ACTAC at 142.
  6. inverse complement, positive strand, negative direction, looking for ACTA(C/T), 4, ACTAC at 3736, ACTAT at 3526, ACTAT at 2975, ACTAT at 210.
  7. inverse complement, positive strand, positive direction, looking for ACTA(C/T), 2, ACTAC at 3845, ACTAC at 2143.
  8. inverse complement, negative strand, positive direction, looking for ACTA(C/T), 1, ACTAC at 2427.

For the Basic programs testing consensus sequence (A/G)TTAGT (starting with SuccessablesMBE2.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 (A/G)TTAGT, 1, ATTAGT at 982.
  2. positive strand, negative direction, looking for (A/G)TTAGT, 1, ATTAGT at 155.
  3. positive strand, positive direction, looking for (A/G)TTAGT, 2, ATTAGT at 4147, GTTAGT at 2338.
  4. negative strand, positive direction, looking for (A/G)TTAGT, 0.
  5. inverse complement, negative strand, negative direction, looking for ACTAA(C/T), 0.
  6. inverse complement, positive strand, negative direction, looking for ACTAA(C/T), 0.
  7. inverse complement, positive strand, positive direction, looking for ACTAA(C/T), 3, ACTAAT at 4164, ACTAAT at 4157, ACTAAC at 2677.
  8. inverse complement, negative strand, positive direction, looking for ACTAA(C/T), 0.

For the Basic programs testing consensus sequence (A/G)TTTAGT (starting with SuccessablesMBE3.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 (A/G)TTTAGT, 0.
  2. positive strand, negative direction, looking for AAAAAAAA, 0.
  3. positive strand, positive direction, looking for AAAAAAAA, 0.
  4. negative strand, positive direction, looking for AAAAAAAA, 0.
  5. inverse complement, negative strand, negative direction, looking for ACTAAA(C/T), 0.
  6. inverse complement, positive strand, negative direction, looking for TTTTTTTT, 0.
  7. inverse complement, positive strand, positive direction, looking for TTTTTTTT, 0.
  8. inverse complement, negative strand, positive direction, looking for TTTTTTTT, 0.

MBE UTRs

Main article: UTR promoter gene transcriptions

Negative strand, negative direction: ACTAC at 3807, ACTAC at 3798, GTAGT at 3616, ACTAT at 3544, ACTAT at 3535, GTAGT at 3521, GTAGT at 3418, GTAGT at 3415, GTAGT at 3394, ACTAT at 3360, GTAGT at 2944, GTAGT at 2941, GTAGT at 2888.

Positive strand, negative direction: GTAGT at 4124, ATAGT at 4047, ACTAC at 3736, ACTAT at 3526, ACTAT at 2975.

MBE core promoters

Main article: Core promoter gene transcriptions

Positive strand, positive direction: GTAGT at 4362.

MBE proximal promoters

Main article: Proximal promoter gene transcriptions

Positive strand, positive direction: ACTAAT at 4164, ACTAAT at 4157, ATTAGT at 4147, ATAGT at 4124, GTAGT at 4116, GTAGT at 4085.

MBE distal promoters

Main article: Distal promoter gene transcriptions

Negative strand, negative direction: ACTAT at 1702, ACTAT at 1665, ATTAGT at 982, ACTAT at 353, ACTAC at 142.

Positive strand, negative direction: GTAGT at 2541, ATAGT at 2499, GTAGT at 2340, ATAGT at 1704, ATAGT at 469, ATAGT at 251, ACTAT at 210, ATTAGT at 155.

Negative strand, positive direction: ACTAC at 2427, ATAGT at 1839.

Positive strand, positive direction: ACTAC at 3845, GTAGT at 3251, ACTAAC at 2677, GTTAGT at 2338, ACTAC at 2143.

Acknowledgements

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

See also

References

  1. ↑ 1.0 1.1 Amanda Charlesworth, Anna Wilczynska, Prajitha Thampi, Linda L Cox, and Angus M MacNicol (21 June 2006). "Musashi regulates the temporal order of mRNA translation during Xenopus oocyte maturation". The EMBO Journal. 25 (12): 2792–2801. doi:10.1038/sj.emboj.7601159. PMID 16763568. Retrieved 17 April 2021.
  2. ↑ Siva Arumugam Saravanaperuma, Dario Pediconi, Carlo Renieri, Antonietta La Terza (15 June 2012). "Skipping of Exons by Premature Termination of Transcription and Alternative Splicing within Intron-5 of the Sheep SCF Gene: A Novel Splice Variant". PLOS ONE. 7 (6): e38657. doi:10.1371/journal.pone.0038657. Retrieved 17 April 2021.
  3. ↑ Tomoya Kotani, Kaori Maehata, Natsumi Takei (2017). "Regulation of Translationally Repressed mRNAs in Zebrafish and Mouse Oocytes, In: Oocytes. Results and Problems in Cell Differentiation". 63. Cham: Springer: 297–324. doi:10.1007/978-3-319-60855-6_13. Retrieved 17 April 2021.

External links

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