Cytoplasmic polyadenylation element gene transcriptions: Difference between revisions

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

"The most well-understood mechanism for controlling cytoplasmic polyadenylation is regulation of mRNAs containing the cytoplasmic polyadenylation element (CPE; consensus UUUUUAU) by CPE-binding protein (CPEB)1."^[1]

Human genes

CPEB1

Gene expressions

Interactions

Consensus sequences

"Cytoplasmic polyadenylation is determined by the cytoplasmic polyadenylation element (CPE; consensus sequence UUUUUAU) that resides in mRNA 3′ untranslated regions (UTRs)."^[2]

"CPE: cytoplasmic polyadenylation element [consensus (U)4–5(A)1-2U]".^[1]

Binding site for

Hypotheses

A1BG has no regulatory elements in either promoter.
A1BG is not transcribed by a regulatory element.
No regulatory element participates in the transcription of A1BG.

CPE samplings

Copying a responsive elements consensus sequence TTTTTAT and putting the sequence in "⌘F" finds none between ZNF497 and A1BG or seven between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence TTTTTAT (starting with SuccessablesCPE.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 TTTTTAT, 7, TTTTTAT at 4220, TTTTTAT at 4070, TTTTTAT at 2302, TTTTTAT at 1875, TTTTTAT at 766, TTTTTAT at 632, TTTTTAT at 489.
positive strand, negative direction, looking for TTTTTAT, 1, TTTTTAT at 218.
positive strand, positive direction, looking for TTTTTAT, 0.
negative strand, positive direction, looking for TTTTTAT, 0.
complement, negative strand, negative direction, looking for AAAAATA, 1, AAAAATA at 218.
complement, positive strand, negative direction, looking for AAAAATA, 7, AAAAATA at 4220, AAAAATA at 4070, AAAAATA at 2302, AAAAATA at 1875, AAAAATA at 766, AAAAATA at 632, AAAAATA at 489.
complement, positive strand, positive direction, looking for AAAAATA, 0.
complement, negative strand, positive direction, looking for AAAAATA, 0.
inverse complement, negative strand, negative direction, looking for ATAAAAA, 0.
inverse complement, positive strand, negative direction, looking for ATAAAAA, 1, ATAAAAA at 3172.
inverse complement, positive strand, positive direction, looking for ATAAAAA, 0.
inverse complement, negative strand, positive direction, looking for ATAAAAA, 0.
inverse negative strand, negative direction, looking for TATTTTT, 1, TATTTTT at 3172.
inverse positive strand, negative direction, looking for TATTTTT, 0.
inverse positive strand, positive direction, looking for TATTTTT, 0.
inverse negative strand, positive direction, looking for TATTTTT, 0.

CPE UTRs

Negative strand, negative direction: TTTTTAT at 4220, TTTTTAT at 4070.

Positive strand, negative direction: ATAAAAA at 3172.

CPE distal promoters

Negative strand, negative direction: TTTTTAT at 2302, TTTTTAT at 1875, TTTTTAT at 766, TTTTTAT at 632, TTTTTAT at 489.

Positive strand, negative direction: TTTTTAT at 218.

Acknowledgements

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

References

↑ ^1.0 ^1.1 Andrew C Lin, Chin Lik Tan, Chien-Ling Lin, Laure Strochlic, Yi-Shuian Huang, Joel D Richter & Christine E Holt (2 March 2009). "Cytoplasmic polyadenylation and cytoplasmic polyadenylation element-dependent mRNA regulation are involved in Xenopus retinal axon development". Neural Development. 4: 8. doi:10.1186/1749-8104-4-8. |access-date= requires |url= (help)
↑ Maria Ivshina, Paul Lasko, and Joel D. Richter (October 2014). "Cytoplasmic polyadenylation element binding proteins in development, health, and disease". Annual Review of Cell and Developmental Biology. 30: 393–415. doi:10.1146/annurev-cellbio-101011-155831. Retrieved 17 April 2021.

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Transcription resources	A1BG gene transcription core promoters A1BG gene transcriptions A1BG regulatory elements and regions A1BG response element gene transcriptions A1BG response element negative results A1BG response element positive results ABA-response element gene transcriptions Abf1 regulatory factor gene transcriptions A box gene transcriptions ACGT-containing element gene transcriptions Activating protein gene transcriptions Activating transcription factor gene transcriptions Adenylate–uridylate rich element gene transcriptions Adr1p gene transcriptions Aft1p gene transcriptions AGC box gene transcriptions AGCE gene transcriptions Alpha-amylase conserved element gene transcriptions Amino acid response element gene transcriptions AARE-like Androgen response element gene transcriptions Angiotensinogen core promoter element gene transcriptions Antioxidant-electrophile responsive element gene transcriptions ATA box gene transcriptions Auxin response factor gene transcriptions B 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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 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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 55: / Line 55: @@
 ==CPE samplings==
 {{main|Model samplings}}
-Copying a responsive elements consensus sequence AAAAAAAA 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.
+Copying a responsive elements consensus sequence TTTTTAT and putting the sequence in "⌘F" finds none between ZNF497 and A1BG or seven between ZSCAN22 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:
+For the Basic programs testing consensus sequence TTTTTAT (starting with SuccessablesCPE.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.
+# negative strand, negative direction, looking for TTTTTAT, 7, TTTTTAT at 4220, TTTTTAT at 4070, TTTTTAT at 2302, TTTTTAT at 1875, TTTTTAT at 766, TTTTTAT at 632, TTTTTAT at 489.
-# positive strand, negative direction, looking for AAAAAAAA, 0.
+# positive strand, negative direction, looking for TTTTTAT, 1, TTTTTAT at 218.
-# positive strand, positive direction, looking for AAAAAAAA, 0.
+# positive strand, positive direction, looking for TTTTTAT, 0.
-# negative strand, positive direction, looking for AAAAAAAA, 0.
+# negative strand, positive direction, looking for TTTTTAT, 0.
-# complement, negative strand, negative direction, looking for TTTTTTTT, 0.
+# complement, negative strand, negative direction, looking for AAAAATA, 1, AAAAATA at 218.
-# complement, positive strand, negative direction, looking for TTTTTTTT, 0.
+# complement, positive strand, negative direction, looking for AAAAATA, 7, AAAAATA at 4220, AAAAATA at 4070, AAAAATA at 2302, AAAAATA at 1875, AAAAATA at 766, AAAAATA at 632, AAAAATA at 489.
-# complement, positive strand, positive direction, looking for TTTTTTTT, 0.
+# complement, positive strand, positive direction, looking for AAAAATA, 0.
-# complement, negative strand, positive direction, looking for TTTTTTTT, 0.
+# complement, negative strand, positive direction, looking for AAAAATA, 0.
-# inverse complement, negative strand, negative direction, looking for TTTTTTTT, 0.
+# inverse complement, negative strand, negative direction, looking for ATAAAAA, 0.
-# inverse complement, positive strand, negative direction, looking for TTTTTTTT, 0.
+# inverse complement, positive strand, negative direction, looking for ATAAAAA, 1, ATAAAAA at 3172.
-# inverse complement, positive strand, positive direction, looking for TTTTTTTT, 0.
+# inverse complement, positive strand, positive direction, looking for ATAAAAA, 0.
-# inverse complement, negative strand, positive direction, looking for TTTTTTTT, 0.
+# inverse complement, negative strand, positive direction, looking for ATAAAAA, 0.
-# inverse negative strand, negative direction, looking for AAAAAAAA, 0.
+# inverse negative strand, negative direction, looking for TATTTTT, 1, TATTTTT at 3172.
-# inverse positive strand, negative direction, looking for AAAAAAAA, 0.
+# inverse positive strand, negative direction, looking for TATTTTT, 0.
-# inverse positive strand, positive direction, looking for AAAAAAAA, 0.
+# inverse positive strand, positive direction, looking for TATTTTT, 0.
-# inverse negative strand, positive direction, looking for AAAAAAAA, 0.
+# inverse negative strand, positive direction, looking for TATTTTT, 0.
 ===CPE UTRs===
 {{main|UTR promoter gene transcriptions}}
+Negative strand, negative direction: TTTTTAT at 4220, TTTTTAT at 4070.
-===CPE core promoters===
+Positive strand, negative direction: ATAAAAA at 3172.
-{{main|Core promoter gene transcriptions}}
-===CPE proximal promoters===
+===CPE distal promoters===
-{{main|Proximal promoter gene transcriptions}}
+{{main|Distal promoter gene transcriptions}}
+Negative strand, negative direction: TTTTTAT at 2302, TTTTTAT at 1875, TTTTTAT at 766, TTTTTAT at 632, TTTTTAT at 489.
-===AAA distal promoters===
+Positive strand, negative direction: TTTTTAT at 218.
-{{main|Distal promoter gene transcriptions}}
 ==Acknowledgements==