Pdr1,3p gene transcriptions: Difference between revisions

Revision as of 19:42, 28 April 2023

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

Human genes

Interactions

Consensus sequences

The upstream activating sequence (UAS) for the Pdr1p/Pdr3p is 5'-TCCGCGGA-3'.^[1]

Pdr1p binds to sequence TCCGYGGR (TCCG(C/T)GG(A/G)) of PDRE, which is located within the promoter sequences of its target genes.^[2]^[3]

Pdr samplings

Copying TCCGCGGA in "⌘F" yields none 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 TCCGCGGA (starting with SuccessablesPdr.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 TCCGCGGA, 0.
positive strand, negative direction, looking for TCCGCGGA, 0.
positive strand, positive direction, looking for TCCGCGGA, 0.
negative strand, positive direction, looking for TCCGCGGA, 0.
complement, negative strand, negative direction, looking for AGGCGCCT, 0.
complement, positive strand, negative direction, looking for AGGCGCCT, 0.
complement, positive strand, positive direction, looking for AGGCGCCT, 0.
complement, negative strand, positive direction, looking for AGGCGCCT, 0.
inverse complement, negative strand, negative direction, looking for TCCGCGGA, 0.
inverse complement, positive strand, negative direction, looking for TCCGCGGA, 0.
inverse complement, positive strand, positive direction, looking for TCCGCGGA, 0.
inverse complement, negative strand, positive direction, looking for TCCGCGGA, 0.
inverse negative strand, negative direction, looking for AGGCGCCT, 0.
inverse positive strand, negative direction, looking for AGGCGCCT, 0.
inverse positive strand, positive direction, looking for AGGCGCCT, 0.
inverse negative strand, positive direction, looking for AGGCGCCT, 0.

Pdr1 (Salin) samplings

Copying a responsive elements consensus sequence TCCG(C/T)GG(A/G) 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 TCCG(C/T)GG(A/G) (starting with SuccessablesPdrS.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: 0.
Positive strand, negative direction: 0.
Negative strand, positive direction: 0.
Positive strand, positive direction: 0.
inverse complement, negative strand, negative direction: 3, CCCACGGA at 3198, CCCACGGA at 2335, CCCACGGA at 1256.
inverse complement, positive strand, negative direction: 0.
inverse complement, negative strand, positive direction: 1, TCCACGGA at 300.
inverse complement, positive strand, positive direction: 0.

PdrS (4560-2846) UTRs

Negative strand, negative direction: CCCACGGA at 3198.

PdrS negative direction (2596-1) distal promoters

Negative strand, negative direction: CCCACGGA at 2335, CCCACGGA at 1256.

PdrS positive direction (4050-1) distal promoters

Negative strand, positive direction: TCCACGGA at 300.

Pdr (Salin 2008) 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 arbitrary (evens) (4560-2846) UTRs

RDr alternate (odds) (4560-2846) UTRs

RDr arbitrary negative direction (evens) (2846-2811) core promoters

RDr alternate negative direction (odds) (2846-2811) core promoters

RDr arbitrary positive direction (odds) (4445-4265) core promoters

RDr alternate positive direction (evens) (4445-4265) core promoters

RDr arbitrary negative direction (evens) (2811-2596) proximal promoters

RDr alternate negative direction (odds) (2811-2596) proximal promoters

RDr arbitrary positive direction (odds) (4265-4050) proximal promoters

RDr alternate positive direction (evens) (4265-4050) proximal promoters

RDr arbitrary negative direction (evens) (2596-1) distal promoters

RDr alternate negative direction (odds) (2596-1) distal promoters

RDr arbitrary positive direction (odds) (4050-1) distal promoters

RDr alternate positive direction (evens) (4050-1) distal promoters

Acknowledgements

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

References

↑ Hongting Tang, Yanling Wu, Jiliang Deng, Nanzhu Chen, Zhaohui Zheng, Yongjun Wei, Xiaozhou Luo, and Jay D. Keasling (6 August 2020). "Promoter Architecture and Promoter Engineering in Saccharomyces cerevisiae". Metabolites. 10 (8): 320–39. doi:10.3390/metabo10080320. PMID 32781665 Check |pmid= value (help). Retrieved 18 September 2020.
↑ Salin H, Fardeau V, Piccini E, Lelandais G, Tanty V, Lemoine S, Jacq C, Devaux F (July 2008). "Structure and properties of transcriptional networks driving selenite stress response in yeasts". BMC Genomics. 9: 333. doi:10.1186/1471-2164-9-333. PMC 2515152. PMID 18627600.
↑ Katzmann DJ, Burnett PE, Golin J, Mahé Y, Moye-Rowley WS (July 1994). "Transcriptional control of the yeast PDR5 gene by the PDR3 gene product". Molecular and Cellular Biology. 14 (7): 4653–61. doi:10.1128/MCB.14.7.4653. PMC 358838. PMID 8007969.

External links

[Tang-1] Hongting Tang, Yanling Wu, Jiliang Deng, Nanzhu Chen, Zhaohui Zheng, Yongjun Wei, Xiaozhou Luo, and Jay D. Keasling (6 August 2020). "Promoter Architecture and Promoter Engineering in Saccharomyces cerevisiae". Metabolites. 10 (8): 320–39. doi:10.3390/metabo10080320. PMID 32781665 Check |pmid= value (help). Retrieved 18 September 2020.

[Salin-2] Salin H, Fardeau V, Piccini E, Lelandais G, Tanty V, Lemoine S, Jacq C, Devaux F (July 2008). "Structure and properties of transcriptional networks driving selenite stress response in yeasts". BMC Genomics. 9: 333. doi:10.1186/1471-2164-9-333. PMC 2515152. PMID 18627600.

[Katzmann-3] Katzmann DJ, Burnett PE, Golin J, Mahé Y, Moye-Rowley WS (July 1994). "Transcriptional control of the yeast PDR5 gene by the PDR3 gene product". Molecular and Cellular Biology. 14 (7): 4653–61. doi:10.1128/MCB.14.7.4653. PMC 358838. PMID 8007969.

[1]

[2]

[3]

@@ Line 71: / Line 71: @@
 # Negative strand, positive direction: TCCACGGA at 300.
+==Pdr (Salin 2008) 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 arbitrary (evens) (4560-2846) UTRs===
+===RDr alternate (odds) (4560-2846) UTRs===
+===RDr arbitrary negative direction (evens) (2846-2811) core promoters===
+===RDr alternate negative direction (odds) (2846-2811) core promoters===
+===RDr arbitrary positive direction (odds) (4445-4265) core promoters===
+===RDr alternate positive direction (evens) (4445-4265) core promoters===
+===RDr arbitrary negative direction (evens) (2811-2596) proximal promoters===
+===RDr alternate negative direction (odds) (2811-2596) proximal promoters===
+===RDr arbitrary positive direction (odds) (4265-4050) proximal promoters===
+===RDr alternate positive direction (evens) (4265-4050) proximal promoters===
+===RDr arbitrary negative direction (evens) (2596-1) distal promoters===
+===RDr alternate negative direction (odds) (2596-1) distal promoters===
+===RDr arbitrary positive direction (odds) (4050-1) distal promoters===
+===RDr alternate positive direction (evens) (4050-1) distal promoters===
 ==Acknowledgements==

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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