P63 DNA-binding site gene transcriptions: Difference between revisions

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

"p63 bound preferentially to DNA fragments conforming to the 20 bp sequence 5'-RRRC(A/G)(A/T)GYYYRRRC(A/T)(C/T)GYYY-3'."^[1]

Human genes

Consensus sequences

The apparent consensus sequence is (A/G)(A/G)(A/G)C(A/G)(A/T)G(C/T)(C/T)(C/T).

p63 samplings

Copying an apparent consensus sequence for the p63 (GAGCGAGCCT) and putting it in "⌘F" finds none located between ZSCAN22 and one between ZNF497 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence (A/G)(A/G)(A/G)C(A/G)(A/T)G(C/T)(C/T)(C/T)(A/G)(A/G)(A/G)C(A/T)(C/T)G(C/T)(C/T)(C/T) (starting with SuccessablesP63.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 (A/G)(A/G)(A/G)C(A/G)(A/T)G(C/T)(C/T)(C/T)(A/G)(A/G)(A/G)C(A/T)(C/T)G(C/T)(C/T)(C/T), 0.
positive strand, negative direction, looking for (A/G)(A/G)(A/G)C(A/G)(A/T)G(C/T)(C/T)(C/T)(A/G)(A/G)(A/G)C(A/T)(C/T)G(C/T)(C/T)(C/T), 0.
positive strand, positive direction, looking for (A/G)(A/G)(A/G)C(A/G)(A/T)G(C/T)(C/T)(C/T)(A/G)(A/G)(A/G)C(A/T)(C/T)G(C/T)(C/T)(C/T), 0.
negative strand, positive direction, looking for (A/G)(A/G)(A/G)C(A/G)(A/T)G(C/T)(C/T)(C/T)(A/G)(A/G)(A/G)C(A/T)(C/T)G(C/T)(C/T)(C/T), 0.
complement, negative strand, negative direction, looking for (C/T)(C/T)(C/T)G(C/T)(A/T)C(A/G)(A/G)(A/G)(C/T)(C/T)(C/T)G(A/T)(A/G)C(A/G)(A/G)(A/G), 0.
complement, positive strand, negative direction, looking for (C/T)(C/T)(C/T)G(C/T)(A/T)C(A/G)(A/G)(A/G)(C/T)(C/T)(C/T)G(A/T)(A/G)C(A/G)(A/G)(A/G), 0.
complement, positive strand, positive direction, looking for (C/T)(C/T)(C/T)G(C/T)(A/T)C(A/G)(A/G)(A/G)(C/T)(C/T)(C/T)G(A/T)(A/G)C(A/G)(A/G)(A/G), 0.
complement, negative strand, positive direction, looking for (C/T)(C/T)(C/T)G(C/T)(A/T)C(A/G)(A/G)(A/G)(C/T)(C/T)(C/T)G(A/T)(A/G)C(A/G)(A/G)(A/G), 0.
inverse complement, negative strand, negative direction, looking for (A/G)(A/G)(A/G)C(A/G)(A/T)G(C/T)(C/T)(C/T)(A/G)(A/G)(A/G)C(A/T)(C/T)G(C/T)(C/T)(C/T), 0.
inverse complement, positive strand, negative direction, looking for (A/G)(A/G)(A/G)C(A/G)(A/T)G(C/T)(C/T)(C/T)(A/G)(A/G)(A/G)C(A/T)(C/T)G(C/T)(C/T)(C/T), 0.
inverse complement, positive strand, positive direction, looking for (A/G)(A/G)(A/G)C(A/G)(A/T)G(C/T)(C/T)(C/T)(A/G)(A/G)(A/G)C(A/T)(C/T)G(C/T)(C/T)(C/T), 0.
inverse complement, negative strand, positive direction, looking for (A/G)(A/G)(A/G)C(A/G)(A/T)G(C/T)(C/T)(C/T)(A/G)(A/G)(A/G)C(A/T)(C/T)G(C/T)(C/T)(C/T), 0.
inverse negative strand, negative direction, looking for (C/T)(C/T)(C/T)G(C/T)(A/T)C(A/G)(A/G)(A/G)(C/T)(C/T)(C/T)G(A/T)(A/G)C(A/G)(A/G)(A/G), 0.
inverse positive strand, negative direction, looking for (C/T)(C/T)(C/T)G(C/T)(A/T)C(A/G)(A/G)(A/G)(C/T)(C/T)(C/T)G(A/T)(A/G)C(A/G)(A/G)(A/G), 0.
inverse positive strand, positive direction, looking for (C/T)(C/T)(C/T)G(C/T)(A/T)C(A/G)(A/G)(A/G)(C/T)(C/T)(C/T)G(A/T)(A/G)C(A/G)(A/G)(A/G), 0.
inverse negative strand, positive direction, looking for (C/T)(C/T)(C/T)G(C/T)(A/T)C(A/G)(A/G)(A/G)(C/T)(C/T)(C/T)G(A/T)(A/G)C(A/G)(A/G)(A/G), 0.

Acknowledgements

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

References

↑ C A Perez, J Ott, D J Mays & J A Pietenpol (15 November 2007). "p63 consensus DNA-binding site: identification, analysis and application into a p63MH algorithm". Oncogene. 26 (52): 7363–70. doi:10.1038/sj.onc.1210561. PMID 17563751. Retrieved 28 August 2020.

External links

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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 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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

@@ Line 17: / Line 17: @@
 ==Human genes==
+{{main|Human genes}}
 ==Consensus sequences==
+{{main|Consensus sequence gene transcriptions}}
 The apparent consensus sequence is (A/G)(A/G)(A/G)C(A/G)(A/T)G(C/T)(C/T)(C/T).
-==Samplings==
+==p63 samplings==
 {{main|Model samplings}}
-Copying an apparent consensus sequence for the P63 (GAGCGAGCCT) and putting it in "⌘F" finds none located between ZSCAN22 and one between ZNF497 and A1BG as can be found by the computer programs.
+Copying an apparent consensus sequence for the p63 (GAGCGAGCCT) and putting it in "⌘F" finds none located between ZSCAN22 and one between ZNF497 and A1BG as can be found by the computer programs.
 For the Basic programs testing consensus sequence (A/G)(A/G)(A/G)C(A/G)(A/T)G(C/T)(C/T)(C/T)(A/G)(A/G)(A/G)C(A/T)(C/T)G(C/T)(C/T)(C/T) (starting with SuccessablesP63.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 (A/G)(A/G)(A/G)C(A/G)(A/T)G(C/T)(C/T)(C/T)(A/G)(A/G)(A/G)C(A/T)(C/T)G(C/T)(C/T)(C/T), 0.
-# positive strand, negative direction, looking for AAAAAAAA, 0.
+# positive strand, negative direction, looking for (A/G)(A/G)(A/G)C(A/G)(A/T)G(C/T)(C/T)(C/T)(A/G)(A/G)(A/G)C(A/T)(C/T)G(C/T)(C/T)(C/T), 0.
-# positive strand, positive direction, looking for AAAAAAAA, 0.
+# positive strand, positive direction, looking for (A/G)(A/G)(A/G)C(A/G)(A/T)G(C/T)(C/T)(C/T)(A/G)(A/G)(A/G)C(A/T)(C/T)G(C/T)(C/T)(C/T), 0.
-# negative strand, positive direction, looking for AAAAAAAA, 0.
+# negative strand, positive direction, looking for (A/G)(A/G)(A/G)C(A/G)(A/T)G(C/T)(C/T)(C/T)(A/G)(A/G)(A/G)C(A/T)(C/T)G(C/T)(C/T)(C/T), 0.
-# complement, negative strand, negative direction, looking for TTTTTTTT, 0.
+# complement, negative strand, negative direction, looking for (C/T)(C/T)(C/T)G(C/T)(A/T)C(A/G)(A/G)(A/G)(C/T)(C/T)(C/T)G(A/T)(A/G)C(A/G)(A/G)(A/G), 0.
-# complement, positive strand, negative direction, looking for TTTTTTTT, 0.
+# complement, positive strand, negative direction, looking for (C/T)(C/T)(C/T)G(C/T)(A/T)C(A/G)(A/G)(A/G)(C/T)(C/T)(C/T)G(A/T)(A/G)C(A/G)(A/G)(A/G), 0.
-# complement, positive strand, positive direction, looking for TTTTTTTT, 0.
+# complement, positive strand, positive direction, looking for (C/T)(C/T)(C/T)G(C/T)(A/T)C(A/G)(A/G)(A/G)(C/T)(C/T)(C/T)G(A/T)(A/G)C(A/G)(A/G)(A/G), 0.
-# complement, negative strand, positive direction, looking for TTTTTTTT, 0.
+# complement, negative strand, positive direction, looking for (C/T)(C/T)(C/T)G(C/T)(A/T)C(A/G)(A/G)(A/G)(C/T)(C/T)(C/T)G(A/T)(A/G)C(A/G)(A/G)(A/G), 0.
-# inverse complement, negative strand, negative direction, looking for TTTTTTTT, 0.
+# inverse complement, negative strand, negative direction, looking for (A/G)(A/G)(A/G)C(A/G)(A/T)G(C/T)(C/T)(C/T)(A/G)(A/G)(A/G)C(A/T)(C/T)G(C/T)(C/T)(C/T), 0.
-# inverse complement, positive strand, negative direction, looking for TTTTTTTT, 0.
+# inverse complement, positive strand, negative direction, looking for (A/G)(A/G)(A/G)C(A/G)(A/T)G(C/T)(C/T)(C/T)(A/G)(A/G)(A/G)C(A/T)(C/T)G(C/T)(C/T)(C/T), 0.
-# inverse complement, positive strand, positive direction, looking for TTTTTTTT, 0.
+# inverse complement, positive strand, positive direction, looking for (A/G)(A/G)(A/G)C(A/G)(A/T)G(C/T)(C/T)(C/T)(A/G)(A/G)(A/G)C(A/T)(C/T)G(C/T)(C/T)(C/T), 0.
-# inverse complement, negative strand, positive direction, looking for TTTTTTTT, 0.
+# inverse complement, negative strand, positive direction, looking for (A/G)(A/G)(A/G)C(A/G)(A/T)G(C/T)(C/T)(C/T)(A/G)(A/G)(A/G)C(A/T)(C/T)G(C/T)(C/T)(C/T), 0.
-# inverse negative strand, negative direction, looking for AAAAAAAA, 0.
+# inverse negative strand, negative direction, looking for (C/T)(C/T)(C/T)G(C/T)(A/T)C(A/G)(A/G)(A/G)(C/T)(C/T)(C/T)G(A/T)(A/G)C(A/G)(A/G)(A/G), 0.
-# inverse positive strand, negative direction, looking for AAAAAAAA, 0.
+# inverse positive strand, negative direction, looking for (C/T)(C/T)(C/T)G(C/T)(A/T)C(A/G)(A/G)(A/G)(C/T)(C/T)(C/T)G(A/T)(A/G)C(A/G)(A/G)(A/G), 0.
-# inverse positive strand, positive direction, looking for AAAAAAAA, 0.
+# inverse positive strand, positive direction, looking for (C/T)(C/T)(C/T)G(C/T)(A/T)C(A/G)(A/G)(A/G)(C/T)(C/T)(C/T)G(A/T)(A/G)C(A/G)(A/G)(A/G), 0.
-# inverse negative strand, positive direction, looking for AAAAAAAA, 0.
+# inverse negative strand, positive direction, looking for (C/T)(C/T)(C/T)G(C/T)(A/T)C(A/G)(A/G)(A/G)(C/T)(C/T)(C/T)G(A/T)(A/G)C(A/G)(A/G)(A/G), 0.
-===AAA UTRs===
+==Acknowledgements==
-{{main|UTR promoter gene transcriptions}}
-===AAA core promoters===
+The content on this page was first contributed by: Henry A. Hoff.
-{{main|Core promoter gene transcriptions}}
-===AAA proximal promoters===
-{{main|Proximal promoter gene transcriptions}}
-===AAA distal promoters===
-{{main|Distal promoter gene transcriptions}}
 ==See also==
 {{div col|colwidth=20em}}
+* [[A1BG gene transcription core promoters]]
+* [[A1BG gene transcriptions]]
+* [[A1BG regulatory elements and regions]]
+* [[A1BG response element negative results]]
+* [[A1BG response element positive results]]
 * [[Complex locus A1BG and ZNF497]]
-* [[Transcription factor]]
 {{Div col end}}
@@ Line 66: / Line 64: @@
 ==External links==
+* [http://www.genome.jp/ GenomeNet KEGG database]
+* [http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene Home - Gene - NCBI]
+* [http://www.ncbi.nlm.nih.gov/sites/gquery NCBI All Databases Search]
+* [http://www.ncbi.nlm.nih.gov/ncbisearch/ NCBI Site Search]
+* [http://www.ncbi.nlm.nih.gov/pccompound PubChem Public Chemical Database]
 <!-- footer templates -->
@@ Line 71: / Line 74: @@
 <!-- footer categories -->
-[[Category:Resources last modified in September 2020]]
+[[Category:Resources last modified in February 2021]]

P63 DNA-binding site gene transcriptions: Difference between revisions

Latest revision as of 04:18, 14 February 2021

Contents