ROR-response element gene transcriptions: Difference between revisions

Revision as of 02:09, 22 February 2021

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

RAR-related orphan receptor "ROR-γ binds DNA with specific sequence motifs AA/TNTAGGTCA (the classic RORE motif) or CT/AG/AGGNCA (the variant RORE motif)^{13, 31}."^[1]

Human genes

Consensus sequences

The consensus sequences for the ROR-response elements are 5'-A(A/T)NTAGGTCA-3' (classic RORE motif) and 5'-C(T/A)(G/A)GGNCA-3' (variant RORE).^[1]

RORE samplings

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

Copying the apparent consensus sequence for the variant RORE (CTGGGACA) and putting it in "⌘F" finds two located between ZSCAN22 and A1BG and one between ZNF497 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence A(A/T)NTAGGTCA (starting with SuccessablesRORE.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(A/T)NTAGGTCA, 1, ATATAGGTCA at 1532.
positive strand, negative direction, looking for A(A/T)NTAGGTCA, 0.
positive strand, positive direction, looking for A(A/T)NTAGGTCA, 0.
negative strand, positive direction, looking for A(A/T)NTAGGTCA, 0.
complement, negative strand, negative direction, looking for T(A/T)NATCCAGT, 0.
complement, positive strand, negative direction, looking for T(A/T)NATCCAGT, 1, ATATAGGTCA at 1532.
complement, positive strand, positive direction, looking for T(A/T)NATCCAGT, 0.
complement, negative strand, positive direction, looking for T(A/T)NATCCAGT, 0.
inverse complement, negative strand, negative direction, looking for TGACCTAN(A/T)T, 0.
inverse complement, positive strand, negative direction, looking for TGACCTAN(A/T)T, 0.
inverse complement, positive strand, positive direction, looking for TGACCTAN(A/T)T, 0.
inverse complement, negative strand, positive direction, looking for TGACCTAN(A/T)T, 0.
inverse negative strand, negative direction, looking for ACTGGATN(A/T)A, 0.
inverse positive strand, negative direction, looking for ACTGGATN(A/T)A, 0.
inverse positive strand, positive direction, looking for ACTGGATN(A/T)A, 0.
inverse negative strand, positive direction, looking for ACTGGATN(A/T)A, 0.

RORE distal promoters

Negative strand: ATATAGGTCA at 1532.

RORE variant samplings

Copying a responsive elements consensus sequence C(T/A)(G/A)GGNCA 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 C(T/A)(G/A)GGNCA (starting with SuccessablesVRORE.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 C(T/A)(G/A)GGNCA, 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 G(T/A)(C/T)CCNGT, 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 TGNCC(C/T)(A/T)G, 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 ACNGG(A/G)(A/T)C, 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.

VRORE UTRs

VRORE core promoters

VRORE proximal promoters

VRORE distal promoters

Acknowledgements

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

References

↑ ^1.0 ^1.1 Junjian Wang, June X. Zou, Xiaoqian Xue, Demin Cai, Yan Zhang, Zhijian Duan, Qiuping Xiang, Joy C. Yang, Maggie C. Louie, Alexander D. Borowsky, Allen C. Gao, Christopher P. Evans, Kit S. Lam, Jianzhen Xu, Hsing-Jien Kung, Ronald M. Evans, Yong Xu, and Hong-Wu Chen (May 2016). "ROR-γ drives androgen receptor expression and represents a therapeutic target in castration-resistant prostate cancer". Nature Medicine. 22 (5): 488–496. doi:10.1038/nm.4070. PMID 27019329. Retrieved 6 September 2020.

External links

[Wang-1] 1.0 ^1.1 Junjian Wang, June X. Zou, Xiaoqian Xue, Demin Cai, Yan Zhang, Zhijian Duan, Qiuping Xiang, Joy C. Yang, Maggie C. Louie, Alexander D. Borowsky, Allen C. Gao, Christopher P. Evans, Kit S. Lam, Jianzhen Xu, Hsing-Jien Kung, Ronald M. Evans, Yong Xu, and Hong-Wu Chen (May 2016). "ROR-γ drives androgen receptor expression and represents a therapeutic target in castration-resistant prostate cancer". Nature Medicine. 22 (5): 488–496. doi:10.1038/nm.4070. PMID 27019329. Retrieved 6 September 2020.

[1]

@@ Line 50: / Line 50: @@
 Negative strand: ATATAGGTCA at 1532.
-==Samplings==
+==RORE variant 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 C(T/A)(G/A)GGNCA 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 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 C(T/A)(G/A)GGNCA (starting with SuccessablesVRORE.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 C(T/A)(G/A)GGNCA, 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, negative strand, negative direction, looking for G(T/A)(C/T)CCNGT, 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, negative strand, negative direction, looking for TGNCC(C/T)(A/T)G, 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 negative strand, negative direction, looking for ACNGG(A/G)(A/T)C, 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 UTRs===
+===VRORE UTRs===
 {{main|UTR promoter gene transcriptions}}
-===AAA core promoters===
+===VRORE core promoters===
 {{main|Core promoter gene transcriptions}}
-===AAA proximal promoters===
+===VRORE proximal promoters===
 {{main|Proximal promoter gene transcriptions}}
-===AAA distal promoters===
+===VRORE distal promoters===
 {{main|Distal promoter gene transcriptions}}

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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 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