Adenylate–uridylate rich element gene transcriptions: Difference between revisions
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Copying a responsive elements consensus sequence (A/T)(A/T)(A/T)TATTTAT(A/T)(A/T) 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. | Copying a responsive elements consensus sequence (A/T)(A/T)(A/T)TATTTAT(A/T)(A/T) 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 (A/T)(A/T)(A/T)TATTTAT(A/T)(A/T) (starting with | For the Basic programs testing consensus sequence (A/T)(A/T)(A/T)TATTTAT(A/T)(A/T) (starting with SuccessablesARE.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/T)(A/T)(A/T)TATTTAT(A/T)(A/T), | # negative strand, negative direction, looking for (A/T)(A/T)(A/T)TATTTAT(A/T)(A/T), 1, TTTTATTTATTA at 4076. | ||
# positive strand, negative direction, looking for | # positive strand, negative direction, looking for (A/T)(A/T)(A/T)TATTTAT(A/T)(A/T), 0. | ||
# positive strand, positive direction, looking for | # positive strand, positive direction, looking for (A/T)(A/T)(A/T)TATTTAT(A/T)(A/T), 0. | ||
# negative strand, positive direction, looking for | # negative strand, positive direction, looking for (A/T)(A/T)(A/T)TATTTAT(A/T)(A/T), 0. | ||
# complement, negative strand, negative direction, looking for | # complement, negative strand, negative direction, looking for (A/T)(A/T)(A/T)ATAAATA(A/T)(A/T), 0. | ||
# complement, positive strand, negative direction, looking for (A/T)(A/T)(A/T)ATAAATA(A/T)(A/T), | # complement, positive strand, negative direction, looking for (A/T)(A/T)(A/T)ATAAATA(A/T)(A/T), 1, AAAATAAATAAT at 4076. | ||
# complement, positive strand, positive direction, looking for | # complement, positive strand, positive direction, looking for (A/T)(A/T)(A/T)ATAAATA(A/T)(A/T), 0. | ||
# complement, negative strand, positive direction, looking for | # complement, negative strand, positive direction, looking for (A/T)(A/T)(A/T)ATAAATA(A/T)(A/T), 0. | ||
# inverse complement, negative strand, negative direction, looking for (A/T)(A/T)ATAAATA(A/T)(A/T)(A/T), 0. | # inverse complement, negative strand, negative direction, looking for (A/T)(A/T)ATAAATA(A/T)(A/T)(A/T), 0. | ||
# inverse complement, positive strand, negative direction, looking for (A/T)(A/T)ATAAATA(A/T)(A/T)(A/T), | # inverse complement, positive strand, negative direction, looking for (A/T)(A/T)ATAAATA(A/T)(A/T)(A/T), 1, AAATAAATAATA at 4077. | ||
# inverse complement, positive strand, positive direction, looking for | # inverse complement, positive strand, positive direction, looking for (A/T)(A/T)ATAAATA(A/T)(A/T)(A/T), 0. | ||
# inverse complement, negative strand, positive direction, looking for | # inverse complement, negative strand, positive direction, looking for (A/T)(A/T)ATAAATA(A/T)(A/T)(A/T), 0. | ||
# inverse negative strand, negative direction, looking for (A/T)(A/T)TATTTAT(A/T)(A/T)(A/T), | # inverse negative strand, negative direction, looking for (A/T)(A/T)TATTTAT(A/T)(A/T)(A/T), 1, TTTATTTATTAT at 4077. | ||
# inverse positive strand, negative direction, looking for | # inverse positive strand, negative direction, looking for (A/T)(A/T)TATTTAT(A/T)(A/T)(A/T), 0. | ||
# inverse positive strand, positive direction, looking for | # inverse positive strand, positive direction, looking for (A/T)(A/T)TATTTAT(A/T)(A/T)(A/T), 0. | ||
# inverse negative strand, positive direction, looking for | # inverse negative strand, positive direction, looking for (A/T)(A/T)TATTTAT(A/T)(A/T)(A/T), 0. | ||
===Adenylate–uridylate rich element (Bakheet) UTRs=== | ===Adenylate–uridylate rich element (Bakheet) UTRs=== | ||
{{main|UTR promoter gene transcriptions}} | {{main|UTR promoter gene transcriptions}} | ||
Negative strand, negative direction: TTTTATTTATTA at 4076. | |||
Positive strand, negative direction: AAATAAATAATA at 4077. | |||
==Acknowledgements== | ==Acknowledgements== | ||
Revision as of 17:30, 24 March 2021
Associate Editor(s)-in-Chief: Henry A. Hoff
"Functionally defined and derived adenylate–uridylate rich element (ARE) consensus sequences have been shown to exist in the 3′UTR of selected mRNAs belonging to interferons, cytokines and proto-oncogenes ( 1 ). A 13-bp ARE motif was computationally derived from a list of functionally labile ARE-mRNAs and was the basis of the ARE-mRNA database (ARED) which contains GenBank entries where the 3′UTR matches the motif ( 2 )."[1]
Human genes
The ARE-mRNA database (ARED) "demonstrated that ARE-mRNAs represent as much as 5–8% of human genes and encode functionally diverse proteins that are important in many transient biological processes including cell growth and differentiation, signal transduction, transcriptional and translational control, hematopoiesis, apoptosis, nutrient transport, and metabolism ( 2 )."[1]
"The 3′UTRs were searched for the 13-bp pattern WWWUAUUUAUWW with mismatch=−1 which was computationally derived as previously described ( 2 ). The pattern was further statistically validated against larger sets of mRNA data (10 872 mRNA with 3′UTR; GenBank 119) showing occurrence of the motif in 6.8% of human mRNA."[1]
"The ARED website ( http://rc.kfshrc.edu.sa/ared ) offers a query search engine that allows searches for ARE-genes using multiple identifier numbers or descriptions such as UniGene IDs, UniGene definition, RefSeq IDs, accession numbers, alternative names, official Gene symbols and mouse homologs (MGD) ( 10 )."[1]
Gene expressions
"3′ untranslated regions play an important role in regulating mRNA fate by complexing with RNA binding proteins that help control mRNA localization, translation, and stability [1, 2, 3]. Identification of a consensus UUAUUUAU sequence in the 3′ UTRs of human and mouse mRNAs encoding tumor necrosis factor (TNF-α) and a variety of other inflammatory mediators led to the suggestion that these AU-rich elements AREs) could be important for regulating gene expression [4]."[2]
Interactions
Consensus sequences
WWWUAUUUAUWW=(A/T)(A/T)(A/T)TATTTAT(A/T)(A/T).[1]
Binding site for
Adenylate–uridylate rich element (Bakheet) samplings
Copying a responsive elements consensus sequence (A/T)(A/T)(A/T)TATTTAT(A/T)(A/T) 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 (A/T)(A/T)(A/T)TATTTAT(A/T)(A/T) (starting with SuccessablesARE.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/T)(A/T)(A/T)TATTTAT(A/T)(A/T), 1, TTTTATTTATTA at 4076.
- positive strand, negative direction, looking for (A/T)(A/T)(A/T)TATTTAT(A/T)(A/T), 0.
- positive strand, positive direction, looking for (A/T)(A/T)(A/T)TATTTAT(A/T)(A/T), 0.
- negative strand, positive direction, looking for (A/T)(A/T)(A/T)TATTTAT(A/T)(A/T), 0.
- complement, negative strand, negative direction, looking for (A/T)(A/T)(A/T)ATAAATA(A/T)(A/T), 0.
- complement, positive strand, negative direction, looking for (A/T)(A/T)(A/T)ATAAATA(A/T)(A/T), 1, AAAATAAATAAT at 4076.
- complement, positive strand, positive direction, looking for (A/T)(A/T)(A/T)ATAAATA(A/T)(A/T), 0.
- complement, negative strand, positive direction, looking for (A/T)(A/T)(A/T)ATAAATA(A/T)(A/T), 0.
- inverse complement, negative strand, negative direction, looking for (A/T)(A/T)ATAAATA(A/T)(A/T)(A/T), 0.
- inverse complement, positive strand, negative direction, looking for (A/T)(A/T)ATAAATA(A/T)(A/T)(A/T), 1, AAATAAATAATA at 4077.
- inverse complement, positive strand, positive direction, looking for (A/T)(A/T)ATAAATA(A/T)(A/T)(A/T), 0.
- inverse complement, negative strand, positive direction, looking for (A/T)(A/T)ATAAATA(A/T)(A/T)(A/T), 0.
- inverse negative strand, negative direction, looking for (A/T)(A/T)TATTTAT(A/T)(A/T)(A/T), 1, TTTATTTATTAT at 4077.
- inverse positive strand, negative direction, looking for (A/T)(A/T)TATTTAT(A/T)(A/T)(A/T), 0.
- inverse positive strand, positive direction, looking for (A/T)(A/T)TATTTAT(A/T)(A/T)(A/T), 0.
- inverse negative strand, positive direction, looking for (A/T)(A/T)TATTTAT(A/T)(A/T)(A/T), 0.
Adenylate–uridylate rich element (Bakheet) UTRs
Negative strand, negative direction: TTTTATTTATTA at 4076.
Positive strand, negative direction: AAATAAATAATA at 4077.
Acknowledgements
The content on this page was first contributed by: Henry A. Hoff.
See also
References
- ↑ 1.0 1.1 1.2 1.3 1.4 Tala Bakheet, Bryan R. G. Williams, and Khalid S. A. Khabar (1 January 2003). "ARED 2.0: an update of AU-rich element mRNA database". Nucleic Acids Research. 31 (1): 421–423. doi:10.1093/nar/gkg023. Retrieved 23 March 2021.
- ↑ David A. Siegel, Olivier Le Tonqueze, Anne Biton, Noah Zaitlen, and David J. Erle (12 February 2020). "Massively Parallel Analysis of Human 3′ UTRs Reveals that AU-Rich Element Length and Registration Predict mRNA Destabilization" (PDF). bioRxiv. doi:10.1101/2020.02.12.945063. Retrieved 23 March 2021.