Amino acid response element gene transcriptions

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

"Many amino acid transporters contain an amino acid response element (AARE) in their promoters (27). [...] Inspection of the regulatory elements of ASCT1 showed a consensus AARE upstream of the transcriptional start site [...]."[1]

Human genes

Gene ID: 6509 is SLC1A4 solute carrier family 1 member 4 aka ASCT1 on 2p14: "The protein encoded by this gene is a sodium-dependent neutral amino acid transporter for alanine, serine, cysteine, and threonine. Defects in this gene have been associated with developmental delay, microcephaly, and intellectual disability."[2]

Gene expressions

Gene ID: 6509 has broad "expression in brain (RPKM 33.8), adrenal (RPKM 12.8) and 23 other tissues".[2]

Interactions

Gene ID: 6509 interacts with Gene ID: 27161 AGO2 argonaute RISC catalytic component 2.[2]

Consensus sequences

AARE1 (5'-ATTGCATCA-3')[3]

5'-TTTGCATCA-3'.[1][4]

Promoter occurrences

"Inspection of the regulatory elements of ASCT1 showed a consensus AARE upstream of the transcriptional start site [...]."[1]

Hypotheses

  1. A1BG has no Amino acid response elements in either promoter.
  2. A1BG is not transcribed by an Amino acid response element.
  3. Amino acid response element does not participate in the transcription of A1BG.

AARE (Maruyama) samplings

Copying a responsive elements consensus sequence 5'-ATTGCATCA-3' 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 5'-ATTGCATCA-3' (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:

  1. negative strand, negative direction, looking for 5'-ATTGCATCA-3', 0.
  2. negative strand, positive direction, looking for 5'-ATTGCATCA-3', 0.
  3. positive strand, negative direction, looking for 5'-ATTGCATCA-3', 0.
  4. positive strand, positive direction, looking for 5'-ATTGCATCA-3', 0.
  5. complement, negative strand, negative direction, looking for 5'-TAACGTAGT-3', 0.
  6. complement, negative strand, positive direction, looking for 5'-TAACGTAGT-3', 0.
  7. complement, positive strand, negative direction, looking for 5'-TAACGTAGT-3', 0.
  8. complement, positive strand, positive direction, looking for 5'-TAACGTAGT-3', 0.
  9. inverse complement, negative strand, negative direction, looking for 5'-TGATGCAAT-3', 0.
  10. inverse complement, negative strand, positive direction, looking for 5'-TGATGCAAT-3', 0.
  11. inverse complement, positive strand, negative direction, looking for 5'-TGATGCAAT-3', 0.
  12. inverse complement, positive strand, positive direction, looking for 5'-TGATGCAAT-3', 0.
  13. inverse negative strand, negative direction, looking for 5'-ACTACGTTA-3', 0.
  14. inverse negative strand, positive direction, looking for 5'-ACTACGTTA-3', 0.
  15. inverse positive strand, negative direction, looking for 5'-ACTACGTTA-3', 0.
  16. inverse positive strand, positive direction, looking for 5'-ACTACGTTA-3', 0.

AARE-like samplings

Copying a responsive elements consensus sequence 5'-TGGTGAAAG-3' 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.

AARE-like sequence (5′-TGGTGAAAG-3′, named AARE3)[3]

For the Basic programs testing consensus sequence 5'-TGGTGAAAG-3' (starting with SuccessablesAREL.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'-TGGTGAAAG-3', 0.
  2. negative strand, positive direction, looking for 5'-TGGTGAAAG-3', 0.
  3. positive strand, negative direction, looking for 5'-TGGTGAAAG-3', 0.
  4. positive strand, positive direction, looking for 5'-TGGTGAAAG-3', 0.
  5. complement, negative strand, negative direction, looking for 5'-ACCACTTTC-3', 0.
  6. complement, negative strand, positive direction, looking for 5'-ACCACTTTC-3', 0.
  7. complement, positive strand, negative direction, looking for 5'-ACCACTTTC-3', 0.
  8. complement, positive strand, positive direction, looking for 5'-ACCACTTTC-3', 0.
  9. inverse complement, negative strand, negative direction, looking for 5'-CTTTCACCA-3', 0.
  10. inverse complement, negative strand, positive direction, looking for 5'-CTTTCACCA-3', 0.
  11. inverse complement, positive strand, negative direction, looking for 5'-CTTTCACCA-3', 0.
  12. inverse complement, positive strand, positive direction, looking for 5'-CTTTCACCA-3', 0.
  13. inverse negative strand, negative direction, looking for 5'-GAAAGTGGT-3', 0.
  14. inverse negative strand, positive direction, looking for 5'-GAAAGTGGT-3', 0.
  15. inverse positive strand, negative direction, looking for 5'-GAAAGTGGT-3', 0.
  16. inverse positive strand, positive direction, looking for 5'-GAAAGTGGT-3', 0.

AARE (Garaeva) samplings

Copying a responsive elements consensus sequence 5'-TTTGCATCA-3' 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 5'-TTTGCATCA-3' (starting with SuccessablesAREG.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'-TTTGCATCA-3', 0.
  2. negative strand, positive direction, looking for 5'-TTTGCATCA-3', 0.
  3. positive strand, negative direction, looking for 5'-TTTGCATCA-3', 0.
  4. positive strand, positive direction, looking for 5'-TTTGCATCA-3', 0.
  5. complement, negative strand, negative direction, looking for 5'-AAACGTAGT-3', 0.
  6. complement, negative strand, positive direction, looking for 5'-AAACGTAGT-3', 0.
  7. complement, positive strand, negative direction, looking for 5'-AAACGTAGT-3', 0.
  8. complement, positive strand, positive direction, looking for 5'-AAACGTAGT-3', 0.
  9. inverse complement, negative strand, negative direction, looking for 5'-TGATGCAAA-3', 0.
  10. inverse complement, negative strand, positive direction, looking for 5'-TGATGCAAA-3', 0.
  11. inverse complement, positive strand, negative direction, looking for 5'-TGATGCAAA-3', 0.
  12. inverse complement, positive strand, positive direction, looking for 5'-TGATGCAAA-3', 0.
  13. inverse negative strand, negative direction, looking for 5'-ACTACGTTT-3', 0.
  14. inverse negative strand, positive direction, looking for 5'-ACTACGTTT-3', 0.
  15. inverse positive strand, negative direction, looking for 5'-ACTACGTTT-3', 0.
  16. inverse positive strand, positive direction, looking for 5'-ACTACGTTT-3', 0.

Acknowledgements

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

See also

References

  1. 1.0 1.1 1.2 Angelika Bröer, Gregory Gauthier-Coles, Farid Rahimi, Michelle van Geldermalsen, Dieter Dorsch, Ansgar Wegener, Jeff Holst, and Stefan Bröer (March 15, 2019). "Ablation of the ASCT2 (SLC1A5) gene encoding a neutral amino acid transporter reveals transporter plasticity and redundancy in cancer cells" (PDF). Journal of Biological Chemistry. 294 (11): 4012–4026. doi:10.1074/jbc.RA118.006378. Retrieved 4 October 2020.
  2. 2.0 2.1 2.2 RefSeq (January 2017). "SLC1A4 solute carrier family 1 member 4 [ Homo sapiens (human) ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 31 October 2020.
  3. 3.0 3.1 Ryuto Maruyama, Makoto Shimizu, Juan Li, Jun Inoue & Ryuichiro Sato (24 March 2016). "Fibroblast growth factor 21 induction by activating transcription factor 4 is regulated through three amino acid response elements in its promoter region". Bioscience, Biotechnology, and Biochemistry. 80 (5): 929–934. doi:10.1080/09168451.2015.1135045. Retrieved 4 October 2020.
  4. Alisa A. Garaeva, Irina E. Kovaleva, Peter M. Chumakov & Alexandra G. Evstafieva (15 January 2016). "Mitochondrial dysfunction induces SESN2 gene expression through Activating Transcription Factor 4". Cell Cycle. 15 (1): 64–71. doi:10.1080/15384101.2015.1120929. PMID 26771712. Retrieved 5 September 2020.

External links