Endoplasmic reticulum stress response element gene transcriptions

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

Human genes

Consensus sequences

"The released aminoterminal of ATF6 (ATF6-N) then migrates to the nucleus and binds to the ER stress response element (ERSE) containing the consensus sequence CCAAT-N9-CCACG to activate genes encoding ER chaperones, ERAD components, and XBP1 (Chen et al., 2010; Yamamoto et al., 2004; Yoshida et al., 2001)."^[1]

CCAAT samplings

Copying an apparent consensus sequence of CCAAT and putting it in "⌘F" finds none located between ZSCAN22 and A1BG on the negative strand and finds one on the positive strand but CCAAT-1A-2T-3T-4T5T-6A-7A-8A-9GT finds none and CCAAT occurs once between ZNF497 and A1BG but CCAAT-1G-2G-3G-4C-5T-6G-7A-8A-9AC finds none between ZNF497 and A1BG on the negative strand and CCAAT occurs once between ZNF497 and A1BG but CCAAT-1A-2C-3T-4G-5A-6A-7G-8T-9CCG finds none on the positive strand as can be found by the computer programs.

For the Basic programs testing consensus sequence CCAAT (starting with SuccessablesERSE.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 CCAAT, 0.
negative strand, positive direction, looking for CCAAT, 1, CCAAT at 2908.
positive strand, negative direction, looking for CCAAT, 1, CCAAT at 2848.
positive strand, positive direction, looking for CCAAT, 1, CCAAT at 3024.
inverse complement, negative strand, negative direction, looking for ATTGG, 1, ATTGG at 614.
inverse complement, negative strand, positive direction, looking for ATTGG, 1, ATTGG at 24.
inverse complement, positive strand, negative direction, looking for ATTGG, 3, ATTGG at 643, ATTGG at 1045, ATTGG at 3529.
inverse complement, positive strand, positive direction, looking for ATTGG, 0.

ERSE UTR

Positive strand, negative direction: ATTGG at 3529, CCAAT at 2848.

ERSE distal promoters

Negative strand, negative direction: ATTGG at 614.
Positive strand, negative direction: ATTGG at 1045, ATTGG at 643.

Negative strand, positive direction: CCAAT at 2908, ATTG at 24.
Positive strand, positive direction: CCAAT at 3024.

CCACG samplings

Copying an apparent consensus sequence of CCACG and putting it in "⌘F" finds eight located between ZSCAN22 and A1BG on the negative strand and none on the positive strand and six on the negative strand between ZNF497 and eight on the positive strand and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence 5'-CCACG-3' (starting with SuccessablesERSE2.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 5'-CCACG-3', 8, 5'-CCACG-3' at 378, 5'-CCACG-3' at 1254, 5'-CCACG-3' at 2080, 5'-CCACG-3' at 2195, 5'-CCACG-3' at 2333, 5'-CCACG-3' at 3196, 5'-CCACG-3' at 3880, 5'-CCACG-3' at 3954, and complements.
negative strand, positive direction, looking for 5'-CCACG-3', 6, 5'-CCACG-3' at 241, 5'-CCACG-3' at 298, 5'-CCACG-3' at 775, 5'-CCACG-3' at 868, 5'-CCACG-3' at 968, 5'-CCACG-3' at 3604, and complements.
positive strand, negative direction, looking for 5'-CCACG-3', 0.
positive strand, positive direction, looking for 5'-CCACG-3', 8, 5'-CCACG-3' at 487, 5'-CCACG-3' at 782, 5'-CCACG-3' at 1762, 5'-CCACG-3' at 2088, 5'-CCACG-3' at 2333, 5'-CCACG-3' at 2799, 5'-CCACG-3' at 3150, 5'-CCACG-3' at 3882, and complements.
inverse complement, negative strand, negative direction, looking for 5'-CGTGG-3', 2, 5'-CGTGG-3' at 1339, 5'-CGTGG-3' at 2761, and complements.
inverse complement, negative strand, positive direction, looking for 5'-CGTGG-3', 2, 5'-CGTGG-3' at 3813, 5'-CGTGG-3' at 4377, and complements.
inverse complement, positive strand, negative direction, looking for 5'-CGTGG-3', 5, 5'-CGTGG-3' at 741, 5'-CGTGG-3' at 1244, 5'-CGTGG-3' at 1897, 5'-CGTGG-3' at 3047, 5'-CGTGG-3' at 4238, and complements.
inverse complement, positive strand, positive direction, looking for 5'-CGTGG-3', 17, 5'-CGTGG-3' at 620, 5'-CGTGG-3' at 772, 5'-CGTGG-3' at 788, 5'-CGTGG-3' at 856, 5'-CGTGG-3' at 956, 5'-CGTGG-3' at 1040, 5'-CGTGG-3' at 1124, 5'-CGTGG-3' at 1208, 5'-CGTGG-3' at 1360, 5'-CGTGG-3' at 1460, 5'-CGTGG-3' at 1628, 5'-CGTGG-3' at 2566, 5'-CGTGG-3' at 3044, 5'-CGTGG-3' at 3322, 5'-CGTGG-3' at 3601, 5'-CGTGG-3' at 3885, 5'-CGTGG-3' at 4343, and complements.
inverse negative strand, negative direction, looking for 5'-GCACC-3', 5, 5'-GCACC-3' at 741, 5'-GCACC-3' at 1244, 5'-GCACC-3' at 1897, 5'-GCACC-3' at 3047, 5'-GCACC-3' at 4238.
inverse negative strand, positive direction, looking for 5'-GCACC-3', 17, 5'-GCACC-3' at 620, 5'-GCACC-3' at 772, 5'-GCACC-3' at 788, 5'-GCACC-3' at 856, 5'-GCACC-3' at 956, 5'-GCACC-3' at 1040, 5'-GCACC-3' at 1124, 5'-GCACC-3' at 1208, 5'-GCACC-3' at 1360, 5'-GCACC-3' at 1460, 5'-GCACC-3' at 1628, 5'-GCACC-3' at 2566, 5'-GCACC-3' at 3044, 5'-GCACC-3' at 3322, 5'-GCACC-3' at 3601, 5'-GCACC-3' at 3885, 5'-GCACC-3' at 4343.
inverse positive strand, negative direction, looking for 5'-GCACC-3', 2, 5'-GCACC-3' at 1339, 5'-GCACC-3' at 2761.
inverse positive strand, positive direction, looking for 5'-GCACC-3', 2, 5'-GCACC-3' at 3813, 5'-GCACC-3' at 4377.

ERSE2 UTRs

Negative strand, negative direction: CGTGG at 4238, CCACG at 3954, CCACG at 3880, CCACG at 3196, CGTGG at 3047.

ERSE2 core promoters

Negative strand, positive direction: CGTGG at 4377.
Positive strand, positive direction: CGTGG at 4343.

ERSE2 proximal promoters

Negative strand, negative direction: CGTGG at 2761.

@ Positive strand, negative direction: CGTGG at 4238.

ERSE2 distal promoters

Negative strand, negative direction: CCACG at 2333, CCACG at 2195, CCACG at 2080, CGTGG at 1339, CCACG at 1254, CCACG at 378.
Positive strand, negative direction: CGTGG at 1897, CGTGG at 1244, CGTGG at 741.

Negative strand, positive direction: CGTGG at 3813, CCACG at 3604, CCACG at 968, CCACG at 868, CCACG at 775, CCACG at 298, CCACG at 241.
Positive strand, positive direction: CGTGG at 3885, CCACG at 3882, CGTGG at 3601, CGTGG at 3322, CCACG at 3150, CGTGG at 3044, CCACG at 2799, CGTGG at 2566, CCACG at 2333, CCACG at 2088, CCACG at 1762, CGTGG at 1628, CGTGG at 1460, CGTGG at 1360, CGTGG at 1208, CGTGG at 1124, CGTGG at 1040, CGTGG at 956, CGTGG at 856, CGTGG at 788, CCACG at 782, CGTGG at 772, CGTGG at 620, CCACG at 487.

References

↑ Jae-Seon So (31 August 2018). "Roles of Endoplasmic Reticulum Stress in Immune Responses". Molecules and Cells. 41 (8): 705–16. doi:10.14348/molcells.2018.0241. PMID 30078231. Retrieved 5 September 2020.

External links

[So-1] Jae-Seon So (31 August 2018). "Roles of Endoplasmic Reticulum Stress in Immune Responses". Molecules and Cells. 41 (8): 705–16. doi:10.14348/molcells.2018.0241. PMID 30078231. Retrieved 5 September 2020.

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transcriptions Transcription factor 3 gene transcriptions Transcription factory gene transcriptions Transcription start site gene transcriptions Translational control sequence gene transcriptions U box gene transcriptions Unfolded protein response element gene transcriptions Upstream response element gene transcriptions Upstream stimulatory factor gene transcriptions UTR promoter gene transcriptions V and P box gene transcriptions V box gene transcriptions Vhr1p gene transcriptions Vitamin D response element gene transcriptions W box gene transcriptions X box gene transcriptions Xbp1p gene transcriptions X core promoter element gene transcriptions Xenobiotic response element gene transcriptions Xenobiotic responsive element gene transcriptions Yap1p,2p gene transcriptions Y box gene transcriptions YY1 gene transcriptions Zap1p gene transcriptions Z box gene transcriptions Zinc responsive element gene transcriptions