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.
complement, negative strand, negative direction, looking for 5'-GGTGC-3', 0.
complement, negative strand, positive direction, looking for 5'-GGTGC-3', 8, 5'-GGTGC-3' at 487, 5'-GGTGC-3' at 782, 5'-GGTGC-3' at 1762, 5'-GGTGC-3' at 2088, 5'-GGTGC-3' at 2333, 5'-GGTGC-3' at 2799, 5'-GGTGC-3' at 3150, 5'-GGTGC-3' at 3882.
complement, positive strand, negative direction, looking for 5'-GGTGC-3', 8, 5'-GGTGC-3' at 378, 5'-GGTGC-3' at 1254, 5'-GGTGC-3' at 2080, 5'-GGTGC-3' at 2195, 5'-GGTGC-3' at 2333, 5'-GGTGC-3' at 3196, 5'-GGTGC-3' at 3880, 5'-GGTGC-3' at 3954, and complements.
complement, positive strand, positive direction, looking for 5'-GGTGC-3', 6, 5'-GGTGC-3' at 241, 5'-GGTGC-3' at 298, 5'-GGTGC-3' at 775, 5'-GGTGC-3' at 868, 5'-GGTGC-3' at 968, 5'-GGTGC-3' at 3604, 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 core promoters

Negative strand, positive direction: 5'-CGTGG-3' at 4377, and complement.

Positive strand, positive direction: 5'-CGTGG-3' at 4343, and complement.

ERSE2 proximal promoters

Positive strand, negative direction: 5'-CGTGG-3' at 4238, and complement.

ERSE2 distal promoters

Negative strand, negative direction: 5'-CCACG-3' at 3954, 5'-CCACG-3' at 3880, 5'-CCACG-3' at 3196, 5'-CGTGG-3' at 2761, 5'-CCACG-3' at 2333, 5'-CCACG-3' at 2195, 5'-CCACG-3' at 2080, 5'-CGTGG-3' at 1339, 5'-CCACG-3' at 1254, 5'-CCACG-3' at 378, and complements.

Positive strand, negative direction: 5'-CGTGG-3' at 3047, 5'-CGTGG-3' at 1897, 5'-CGTGG-3' at 1244, 5'-CGTGG-3' at 741, and complements.

Negative strand, positive direction: 5'-CGTGG-3' at 3813, 5'-CCACG-3' at 3604, 5'-CCACG-3' at 968, 5'-CCACG-3' at 868, 5'-CCACG-3' at 775, 5'-CCACG-3' at 298, 5'-CCACG-3' at 241, and complements.

Positive strand, positive direction: 5'-CGTGG-3' at 3885, 5'-CCACG-3' at 3882, 5'-CGTGG-3' at 3601, 5'-CGTGG-3' at 3322, 5'-CCACG-3' at 3150, 5'-CGTGG-3' at 3044, 5'-CCACG-3' at 2799, 5'-CGTGG-3' at 2566, 5'-CCACG-3' at 2333, 5'-CCACG-3' at 2088, 5'-CCACG-3' at 1762, 5'-CGTGG-3' at 1628, 5'-CGTGG-3' at 1460, 5'-CGTGG-3' at 1360, 5'-CGTGG-3' at 1208, 5'-CGTGG-3' at 1124, 5'-CGTGG-3' at 1040, 5'-CGTGG-3' at 956, 5'-CGTGG-3' at 856, 5'-CGTGG-3' at 788, 5'-CCACG-3' at 782, 5'-CGTGG-3' at 772, 5'-CGTGG-3' at 620, 5'-CCACG-3' at 487, and complements.

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 MYB recognition element gene transcriptions Myelocytomatosis transcription factor gene transcriptions Myocyte enhancer factor gene transcriptions N-boxes Ndt80p gene transcriptions Nuclear factor 1 Nuclear factor 𝜿B Nuclear factor gene transcriptions Nuclear factor of activated T cell gene transcriptions (NFAT) Nuclear factor Y gene transcriptions Nutrient-sensing response element gene transcriptions Oaf1p gene transcriptions ORE1 binding site gene transcriptions p53 response element gene transcriptions P63 DNA-binding site gene transcriptions P box gene transcriptions Pdr1,3p gene transcriptions Peroxisome proliferator hormone response element gene transcriptions Phosphate starvation-response transcription factor gene transcriptions Pollen1 element gene transcriptions Polycomb response element gene transcriptions Preinitiation complex Preinitiation complex gene transcriptions Pribnow box gene transcriptions Prolamin box gene transcriptions Promoter gene transcriptions Proximal promoter gene transcriptions Promoter occurrence gene transcriptions Pyrimidine box gene transcriptions Q element gene transcriptions Rap1 regulatory factor gene transcriptions Reb1 general regulatory factor gene transcriptions Retinoblastoma control element gene transcriptions Retinoic acid response element gene transcriptions Rgt1p gene transcriptions Rlm1p gene transcriptions RNA polymerase II gene transcriptions RNA polymerase II holoenzyme complex Root specific element gene transcriptions ROR-response element gene transcriptions Rox1p gene transcriptions Rpn4p gene transcriptions R response element gene transcriptions SARE gene transcriptions Seed-specific element gene transcriptions Serum response element gene transcriptions Servenius sequence gene transcriptions Shoot specific element gene transcriptions Sip4p gene transcriptions Smp1p gene transcriptions Sp1 gene transcriptions Spaceflight gene expressions Specificity protein gene transcriptions STAT gene transcriptions Ste12p gene transcriptions Sterol response element gene transcriptions Sucrose box gene transcriptions Synaptic Activity-Responsive Elements TACTAAC box gene transcriptions TAGteam gene transcriptions Tapetum box gene transcriptions TATA binding protein associated factor gene transcriptions TATA binding protein gene transcriptions TATA box gene transcriptions TAT box gene transcriptions TATC box gene transcriptions Tbf1 regulatory factor gene transcriptions T box gene transcriptions TCCACCATA element gene transcriptions TC element gene transcriptions TCT gene transcriptions TEA consensus sequence gene transcriptions Tec1p gene transcriptions Telomeric repeat DNA-binding factor gene transcriptions Tetradecanoylphorbol-13-acetate response element gene transcriptions TGF-β control elements (TCEs) TGF-β inhibitory elements (TIEs) Thyroid hormone response element gene transcriptions Transcriptional regulation Transcription bubble gene transcriptions Transcription factor gene 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