Endoplasmic reticulum stress response element gene transcriptions: Difference between revisions

Revision as of 07:28, 5 April 2022

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.

ERSE random dataset samplings

ERSEr0: 7, CCAAT at 4457, CCAAT at 3878, CCAAT at 3351, CCAAT at 2733, CCAAT at 2614, CCAAT at 2492, CCAAT at 2231.
RDr1: 0.
RDr2: 0.
RDr3: 0.
RDr4: 0.
RDr5: 0.
RDr6: 0.
RDr7: 0.
RDr8: 0.
RDr9: 0.
RDr0ci: 0.
RDr1ci: 0.
RDr2ci: 0.
RDr3ci: 0.
RDr4ci: 0.
RDr5ci: 0.
RDr6ci: 0.
RDr7ci: 0.
RDr8ci: 0.
RDr9ci: 0.

ERSEr UTRs

ERSEr0: CCAAT at 4457, CCAAT at 3878, CCAAT at 3351.

RDr core promoters

ERSEr proximal promoters

ERSEr0: CCAAT at 2733, CCAAT at 2614.

ERSEr distal promoters

ERSEr0: CCAAT at 2492, CCAAT at 2231.

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.

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.

Random dataset samplings

RDr0: 0.
RDr1: 0.
RDr2: 0.
RDr3: 0.
RDr4: 0.
RDr5: 0.
RDr6: 0.
RDr7: 0.
RDr8: 0.
RDr9: 0.
RDr0ci: 0.
RDr1ci: 0.
RDr2ci: 0.
RDr3ci: 0.
RDr4ci: 0.
RDr5ci: 0.
RDr6ci: 0.
RDr7ci: 0.
RDr8ci: 0.
RDr9ci: 0.

RDr UTRs

RDr core promoters

RDr proximal promoters

RDr distal promoters

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.

[1]

@@ Line 45: / Line 45: @@
 # Positive strand, positive direction: CCAAT at 3024.
-==Random dataset samplings==
+==ERSE random dataset samplings==
-# RDr0: 0.
+# ERSEr0: 7, CCAAT at 4457, CCAAT at 3878, CCAAT at 3351, CCAAT at 2733, CCAAT at 2614, CCAAT at 2492, CCAAT at 2231.
 # RDr1: 0.
 # RDr2: 0.
@@ Line 68: / Line 68: @@
 # RDr9ci: 0.
-===RDr UTRs===
+===ERSEr UTRs===
 {{main|UTR promoter gene transcriptions}}
+# ERSEr0: CCAAT at 4457, CCAAT at 3878, CCAAT at 3351.
 ===RDr core promoters===
 {{main|Core promoter gene transcriptions}}
-===RDr proximal promoters===
+===ERSEr proximal promoters===
 {{main|Proximal promoter gene transcriptions}}
+# ERSEr0: CCAAT at 2733, CCAAT at 2614.
-===RDr distal promoters===
+===ERSEr distal promoters===
 {{main|Distal promoter gene transcriptions}}
+# ERSEr0: CCAAT at 2492, CCAAT at 2231.
 ==CCACG samplings==

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gene transcriptions EIN3 binding site gene transcriptions Enhancer activity copy gene transcriptions E box gene transcriptions Element gene transcriptions Endoplasmic reticulum stress response element gene transcriptions Endosperm expression gene transcriptions Enhancer box gene transcriptions Estrogen response element gene transcriptions Ethylene responsive element gene transcriptions Factor II B recognition element gene transcriptions F box gene transcriptions Focused promoter gene transcriptions Forkhead box gene transcriptions Fur box gene transcriptions GAAC element gene transcriptions Gal4p gene transcriptions Γ-interferon activated sequence gene transcriptions GARE gene transcriptions GA responsive complex gene transcriptions GATA gene transcriptions G box gene transcriptions GC box gene transcriptions GCC box gene transcriptions Gcn4p gene transcriptions Gcr1p gene transcriptions Gene expressions General factor II D gene transcriptions General regulatory factors General transcription factor II A gene transcriptions General transcription factor II B gene transcriptions General transcription factor II D gene transcriptions General transcription factor II F gene transcriptions General transcription factor II H gene transcriptions General transcription factor gene transcriptions Gene transcriptions GGC triplet gene transcriptions Gibberellin responsive element gene transcriptions GLM box gene transcriptions Glucocorticoid response element gene transcriptions Grainy head gene transcriptions Grainy head transcription factor gene transcriptions Growth hormone response element gene transcriptions GT boxes Hac1p gene transcriptions Hair color gene expressions H and ACA box gene transcriptions H box gene transcriptions Heat-responsive element gene transcriptions Hex sequence gene transcriptions HMG box gene transcriptions HNF gene transcriptions Homeobox gene transcriptions Hsf1p gene transcriptions HY box gene transcriptions Hybrid C, A boxes Hybrid C, G boxes Hybrid C, T boxes Hypoxia-inducible factor gene transcriptions Hypoxia response elements I box gene transcriptions Initiator element gene transcriptions Initiator-like element gene transcriptions Inositol/choline-responsive elements Interaction gene transcriptions Interferon regulatory factors Inverse copy gene transcriptions Jasmonic acid-responsive element gene transcriptions K-boxes Kozak sequence gene transcriptions Kruppel-associated box gene transcriptions Krüppel-like factor gene transcriptions L box gene transcriptions Leu3 gene transcriptions M35 box gene transcriptions MADS box gene transcriptions Maf recognition element gene transcriptions M box gene transcriptions Mcm1 regulatory factor gene transcriptions Met31p box gene transcriptions Metal responsive element gene transcriptions Middle sporulation element gene transcriptions Mig1p gene transcriptions Model samplings Motif ten element gene transcriptions Msn2,4p gene transcriptions Musashi binding element gene 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

Endoplasmic reticulum stress response element gene transcriptions: Difference between revisions

Revision as of 07:28, 5 April 2022

Contents

Human genes

Consensus sequences

CCAAT samplings

ERSE UTR

ERSE distal promoters

ERSE random dataset samplings

ERSEr UTRs

RDr core promoters

ERSEr proximal promoters

ERSEr distal promoters

CCACG samplings

ERSE2 UTRs

ERSE2 core promoters

ERSE2 proximal promoters

ERSE2 distal promoters

Random dataset samplings

RDr UTRs

RDr core promoters

RDr proximal promoters

RDr distal promoters

See also

References

External links

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