Cat8p gene transcriptions: Difference between revisions

Revision as of 18:37, 11 January 2022

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

Human genes

Interactions

Consensus sequences

The upstream activating sequence (UAS) for Cat8p is 5'-CGGNBNVMHGGA-3', where N = A, C, G, T, B = C, G, T, V = A, C, G, M = A, C, and H = A, C, T; i.e. 5'-CGG(A/C/G/T)(C/G/T)(A/C/G/T)(A/C/G)(A/C)(A/C/T)GGA-3'.^[1]

Hypotheses

A1BG has no Cat8ps in either promoter.
A1BG is not transcribed by a Cat8p.
Cat8p does not participate in the transcription of A1BG.

Samplings

Copying 5'-CGGTCCGC-3' 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 5'-CGG(A/C/G/T)(C/G/T)(A/C/G/T)(A/C/G)(A/C)(A/C/T)GGA-3' (starting with SuccessablesCat8p.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'-CGG(A/C/G/T)(C/G/T)(A/C/G/T)(A/C/G)(A/C)(A/C/T)GGA-3', 0.
negative strand, positive direction, looking for 5'-CGG(A/C/G/T)(C/G/T)(A/C/G/T)(A/C/G)(A/C)(A/C/T)GGA-3', 0.
positive strand, negative direction, looking for 5'-CGG(A/C/G/T)(C/G/T)(A/C/G/T)(A/C/G)(A/C)(A/C/T)GGA-3', 0.
positive strand, positive direction, looking for 5'-CGG(A/C/G/T)(C/G/T)(A/C/G/T)(A/C/G)(A/C)(A/C/T)GGA-3', 0.
complement, negative strand, negative direction, looking for 5'-GCC(A/C/G/T)(A/C/G)(A/C/G/T)(C/G/T)(G/T)(A/G/T)CCT-3', 0.
complement, negative strand, positive direction, looking for 5'-GCC(A/C/G/T)(A/C/G)(A/C/G/T)(C/G/T)(G/T)(A/G/T)CCT-3', 0.
complement, positive strand, negative direction, looking for 5'-GCC(A/C/G/T)(A/C/G)(A/C/G/T)(C/G/T)(G/T)(A/G/T)CCT-3', 0.
complement, positive strand, positive direction, looking for 5'-GCC(A/C/G/T)(A/C/G)(A/C/G/T)(C/G/T)(G/T)(A/G/T)CCT-3', 0.
inverse complement, negative strand, negative direction, looking for 5'-TCC(A/G/T)(G/T)(C/G/T)(A/C/G/T)(A/C/G)(A/C/G/T)CCG-3', 2, 5'-TCCGTGCCACCG-3' at 2528, 5'-TCCGTGCCACCG-3' at 657, and complements.
inverse complement, negative strand, positive direction, looking for 5'-TCC(A/G/T)(G/T)(C/G/T)(A/C/G/T)(A/C/G)(A/C/G/T)CCG-3', 0.
inverse complement, positive strand, negative direction, looking for 5'-TCC(A/G/T)(G/T)(C/G/T)(A/C/G/T)(A/C/G)(A/C/G/T)CCG-3', 0.
inverse complement, positive strand, positive direction, looking for 5'-TCC(A/G/T)(G/T)(C/G/T)(A/C/G/T)(A/C/G)(A/C/G/T)CCG-3', 0.
inverse negative strand, negative direction, looking for 5'-AGG(A/C/T)(A/C)(A/C/G)(A/C/G/T)(C/G/T)(A/C/G/T)GGC-3', 0.
inverse negative strand, positive direction, looking for 5'-AGG(A/C/T)(A/C)(A/C/G)(A/C/G/T)(C/G/T)(A/C/G/T)GGC-3', 0.
inverse positive strand, negative direction, looking for 5'-AGG(A/C/T)(A/C)(A/C/G)(A/C/G/T)(C/G/T)(A/C/G/T)GGC-3', 2, 5'-AGGCACGGTGGC-3' at 2528, 5'-AGGCACGGTGGC-3' at 657.
inverse positive strand, positive direction, looking for 5'-AGG(A/C/T)(A/C)(A/C/G)(A/C/G/T)(C/G/T)(A/C/G/T)GGC-3', 0.

Cat8p distal promoters

Negative strand, negative direction: TCCGTGCCACCG at 2528, TCCGTGCCACCG at 657.

Cat8 random dataset samplings

Cat8r0: 0.
Cat8r1: 1, CGGGTTGATGGA at 1079.
Cat8r2: 0.
Cat8r3: 0.
Cat8r4: 0.
Cat8r5: 1, CGGCTCAACGGA at 575.
Cat8r6: 1, CGGGCCAATGGA at 743.
Cat8r7: 0.
Cat8r8: 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

Cat8 analysis and results

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.

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.

[1]

@@ Line 64: / Line 64: @@
 # Cat8r6: 1, CGGGCCAATGGA at 743.
 # Cat8r7: 0.
-# RDr8: 0.
+# Cat8r8: 0.
 # RDr9: 0.
 # RDr0ci: 0.

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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 Heat shock elements 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 Immunoglobulin like domain containing family 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 Met3 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 Nanos/Pumilio response element 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 actin/cytoskeleton/contractile family TATA box albumin family TATA box aldolase family TATA box alkaline phosphatase family TATA box annexin family TATA box cytochrome superfamily TATA box gene transcriptions TATA box heat shock family TATA box histone family TATA box human genes TATA box keratin family TATA box lipase family TATA box peptidase family TATA box platelet-derived growth factor family TATA box selenium-binding family TATA box serine protease family TATA box serpin superfamily TATA box transforming growth factor superfamily TATA box trefoil family TATA box tumor necrosis factor superfamily TATA box zinc metalloenzyme family 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 Tryptophan residue 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