ORE1 binding site gene transcriptions: Difference between revisions

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

"Nitrogen deficiency (−N) in plants triggers leaf senescence which is regulated by the transcription factor ORE1."^[1]

"As a transcription factor, ORE1 was reported to bind to consensus DNA sequences of [ACG][CA]GT[AG]N{5,6}[CT]AC[AG] [29] or T[TAG][GA]CGT[GA][TCA][TAG] [37]."^[2]

Human genes

Consensus sequences

Consensus sequences are 5'-(A/C/G)(A/C)GT(A/G)N_5,6(C/T)AC(A/G)-3' or 5'-T(A/G/T)(A/G)CGT(A/G)(A/C/T)(A/G/T)-3'.^[2]

Samplings

Copying 5'-TTACGTG-3' in "⌘F" yields none between ZSCAN22 and A1BG and none between ZNF497 and A1BG as can be found by the computer programs.

Copying 5'-TGACGTGAG-3' in "⌘F" yields three between ZSCAN22 and A1BG and none between ZNF497 and A1BG as can be found by the computer programs.

Copying 5'-TAGCGT-3' in "⌘F" yields none between ZSCAN22 and A1BG and none between ZNF497 and A1BG as can be found by the computer programs.

Copying 5'-TAACGTGAG-3' in "⌘F" yields two between ZSCAN22 and A1BG and none between ZNF497 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence AAAAAAAA (starting with SuccessablesAAA.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 AAAAAAAA, 0.
positive strand, negative direction, looking for AAAAAAAA, 0.
positive strand, positive direction, looking for AAAAAAAA, 0.
negative strand, positive direction, looking for AAAAAAAA, 0.
complement, negative strand, negative direction, looking for TTTTTTTT, 0.
complement, positive strand, negative direction, looking for TTTTTTTT, 0.
complement, positive strand, positive direction, looking for TTTTTTTT, 0.
complement, negative strand, positive direction, looking for TTTTTTTT, 0.
inverse complement, negative strand, negative direction, looking for TTTTTTTT, 0.
inverse complement, positive strand, negative direction, looking for TTTTTTTT, 0.
inverse complement, positive strand, positive direction, looking for TTTTTTTT, 0.
inverse complement, negative strand, positive direction, looking for TTTTTTTT, 0.
inverse negative strand, negative direction, looking for AAAAAAAA, 0.
inverse positive strand, negative direction, looking for AAAAAAAA, 0.
inverse positive strand, positive direction, looking for AAAAAAAA, 0.
inverse negative strand, positive direction, looking for AAAAAAAA, 0.

AAA UTR gene transcriptions

AAA core promoters

AAA proximal promoters

AAA distal promoters

Acknowledgements

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

References

↑ Su‐Hyun Park, Jin Seo Jeong, Jun Sung Seo, Bong Soo Park, Nam‐Hai Chua (3 May 2019). "Arabidopsis ubiquitin‐specific proteases UBP12 and UBP13 shape ORE1 levels during leaf senescence induced by nitrogen deficiency". New Phytologist. 223 (3): 1447–1460. doi:10.1111/nph.15879. Retrieved 10 February 2021.
↑ ^2.0 ^2.1 Kai Qiu, Zhongpeng Li, Zhen Yang, Junyi Chen, Shouxin Wu, Xiaoyu Zhu, Shan Gao, Jiong Gao, Guodong Ren, Benke Kuai, and Xin Zhou (July 2015). "EIN3 and ORE1 Accelerate Degreening during Ethylene-Mediated Leaf Senescence by Directly Activating Chlorophyll Catabolic Genes in Arabidopsis". PLoS Genetics. 11 (7): e1005399. doi:10.1371/journal.pgen.1005399. PMID 26218222. Retrieved 4 October 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 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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

@@ Line 1: / Line 1: @@
 {{AE}} Henry A. Hoff
+"Nitrogen deficiency (−N) in plants triggers leaf senescence which is regulated by the transcription factor ORE1."<ref name=Park>{{ cite journal
+|author=Su‐Hyun Park, Jin Seo Jeong, Jun Sung Seo, Bong Soo Park, Nam‐Hai Chua
+|title=Arabidopsis ubiquitin‐specific proteases UBP12 and UBP13 shape ORE1 levels during leaf senescence induced by nitrogen deficiency
+|journal=New Phytologist
+|date=3 May 2019
+|volume=223
+|issue=3
+|pages=1447-1460
+|url=https://nph.onlinelibrary.wiley.com/doi/full/10.1111/nph.15879
+|arxiv=
+|bibcode=
+|doi=10.1111/nph.15879
+|pmid=
+|accessdate=10 February 2021 }}</ref>
 "As a transcription factor, ORE1 was reported to bind to consensus DNA sequences of [ACG][CA]GT[AG]N{5,6}[CT]AC[AG] [29] or T[TAG][GA]CGT[GA][TCA][TAG] [37]."<ref name=Qiu/>