M35 box gene transcriptions: Difference between revisions

Revision as of 07:57, 24 June 2022

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

Escherichia coli - Sculpture is in vitro. Credit: Luke Jerram.{{free media}}

"The trp promoter does not have a consensus Pribnow box sequence (T-T-A-A-C-T) but it does have a consensus -35 sequence (T-T-G-A-C-A)."^[1]

The "degenerate -35 sequence, and the location of the Fis binding site, which forces a suboptimal 16 bp spacing between the -35 and -10 elements, allow only σ^s but not σ⁷⁰ to function at proP (P2).^[2]

Consensus sequences

"Two domains upstream of the start site of transcription have been identified for which a consensus sequence has been formulated (1-5). [One of these domains is] the -35 sequence (5'-T-T-G-A-C-A-3')".^[1]

A1BG sampling

For the Basic programs (starting with SuccessablesM35.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 in the negative direction (from ZSCAN22 to A1BG) is SuccessablesM35--.bas, looking for 3'-TTGACA-5', 2, 2, TTGACA at 4399, TTGACA at 477.
negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesM35-+.bas, looking for 3'-TTGACA-5', 0,
positive strand in the negative direction is SuccessablesM35+-.bas, looking for 3'-TTGACA-5', 0,
positive strand in the positive direction is SuccessablesM35++.bas, looking for 3'-TTGACA-5', 0,
complement, negative strand, negative direction is SuccessablesM35c--.bas, looking for 3'-AACTGT-5', 0,
complement, negative strand, positive direction is SuccessablesM35c-+.bas, looking for 3'-AACTGT-5', 0,
complement, positive strand, negative direction is SuccessablesM35c+-.bas, looking for 3'-AACTGT-5', 2, 3'-AACTGT-5', 477, 3'-AACTGT-5', 4399,
complement, positive strand, positive direction is SuccessablesM35c++.bas, looking for 3'-AACTGT-5', 0,
inverse complement, negative strand, negative direction is SuccessablesM35ci--.bas, looking for 3'-TGTCAA-5', 0,
inverse complement, negative strand, positive direction is SuccessablesM35ci-+.bas, looking for 3'-TGTCAA-5', 0,
inverse complement, positive strand, negative direction is SuccessablesM35ci+-.bas, looking for 3'-TGTCAA-5', 0,
inverse complement, positive strand, positive direction is SuccessablesM35ci++.bas, looking for 3'-TGTCAA-5', 0,
inverse, negative strand, negative direction, is SuccessablesM35i--.bas, looking for 3'-ACAGTT-5', 0,
inverse, negative strand, positive direction, is SuccessablesM35i-+.bas, looking for 3'-ACAGTT-5', 0,
inverse, positive strand, negative direction, is SuccessablesM35i+-.bas, looking for 3'-ACAGTT-5', 0,
inverse, positive strand, positive direction, is SuccessablesM35i++.bas, looking for 3'-ACAGTT-5', 0.

M35 UTRs

Negative, negative: TTGACA at 4399.

M35 negative direction distal promoters

Negative, negative: TTGACA at 477.

M35 random dataset samplings

M35r0: 2, TTGACA at 3699, TTGACA at 3168.
M35r1: 1, TTGACA at 3785.
M35r2: 0.
M35r3: 0.
M35r4: 1, TTGACA at 1412.
M35r5: 0.
M35r6: 1, TTGACA at 3332.
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.

M35r arbitrary (evens) (4560-2846) UTRs

M35r0: 2, TTGACA at 3699, TTGACA at 3168.
M35r6: TTGACA at 3332.

M35r alternate (odds) (4560-2846) UTRs

M35r1: TTGACA at 3785.

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

M35r arbitrary negative direction (evens) (2596-1) distal promoters

M35r4: TTGACA at 1412.

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

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

M35r1: TTGACA at 3785.

M35r alternate positive direction (evens) (4050-1) distal promoters

M35r0: TTGACA at 3699, TTGACA at 3168.
M35r4: TTGACA at 1412.
M35r6: TTGACA at 3332.

M35 analysis and results

"Two domains upstream of the start site of transcription have been identified for which a consensus sequence has been formulated (1-5). [One of these domains is] the -35 sequence (5'-T-T-G-A-C-A-3')".^[1]

Reals or randoms	Promoters	direction	Strands
Reals	UTR	negative	2
Randoms	UTR	arbitrary negative	10
Randoms	UTR	alternate negative	10
Reals	Core	negative	2
Randoms	Core	arbitrary negative	10
Randoms	Core	alternate negative	10
Reals	Core	positive	2
Randoms	Core	arbitrary positive	10
Randoms	Core	alternate positive	10
Reals	Proximal	negative	2
Randoms	Proximal	arbitrary negative	10
Randoms	Proximal	alternate negative	10
Reals	Proximal	positive	2
Randoms	Proximal	arbitrary positive	10
Randoms	Proximal	alternate positive	10
Reals	Distal	negative	2
Randoms	Distal	arbitrary negative	10
Randoms	Distal	alternate negative	10
Reals	Distal	positive	2
Randoms	Distal	arbitrary positive	10
Randoms	Distal	alternate positive	10

Comparison:

The occurrences of real responsive element consensus sequences are greater than the randoms. This suggests that the real responsive element consensus sequences are likely active or activable.

Acknowledgements

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

Initial content for this page in some instances came from Wikiversity.

Initial content for this page in some instances incorporates text from the United States National Library of Medicine.

References

↑ ^1.0 ^1.1 ^1.2 Herman A. de Boer, Lisa J. Comstock, and Mark Vasser (January 1983). "The tac promoter: A functional hybrid derived from the trp and lac promoters" (PDF). Proceedings of the National Academy of Sciences USA. 80 (1): 21–5. Retrieved 2017-02-19.
↑ Athanasios Typas, Stefano Stella, Reid C. Johnson and Regine Hengge (9 January 2007). "The -35 sequence location and the Fis–sigma factor interface determine σ^s selectivity of the proP (P2) promoter in Escherichia coli". Molecular Microbiology. 63 (3): 780–796. doi:10.1111/j.1365-2958.2006.05560.x. Retrieved 10 November 2018.

External links

Template:Sisterlinks

[Boer-1] 1.0 ^1.1 ^1.2 Herman A. de Boer, Lisa J. Comstock, and Mark Vasser (January 1983). "The tac promoter: A functional hybrid derived from the trp and lac promoters" (PDF). Proceedings of the National Academy of Sciences USA. 80 (1): 21–5. Retrieved 2017-02-19.

[Typas-2] Athanasios Typas, Stefano Stella, Reid C. Johnson and Regine Hengge (9 January 2007). "The -35 sequence location and the Fis–sigma factor interface determine σ^s selectivity of the proP (P2) promoter in Escherichia coli". Molecular Microbiology. 63 (3): 780–796. doi:10.1111/j.1365-2958.2006.05560.x. Retrieved 10 November 2018.

[1]

[2]

@@ Line 68: / Line 68: @@
 # M35r0: 2, TTGACA at 3699, TTGACA at 3168.
 # M35r1: 1, TTGACA at 3785.
-# RDr2: 0.
+# M35r2: 0.
-# RDr3: 0.
+# M35r3: 0.
-# RDr4: 0.
+# M35r4: 1, TTGACA at 1412.
-# RDr5: 0.
+# M35r5: 0.
-# RDr6: 0.
+# M35r6: 1, TTGACA at 3332.
 # RDr7: 0.
 # RDr8: 0.
@@ Line 90: / Line 90: @@
 # M35r0: 2, TTGACA at 3699, TTGACA at 3168.
+# M35r6: TTGACA at 3332.
-===RDr alternate (odds) (4560-2846) UTRs===
+===M35r alternate (odds) (4560-2846) UTRs===
 # M35r1: TTGACA at 3785.
@@ Line 111: / Line 112: @@
 ===RDr alternate positive direction (evens) (4265-4050) proximal promoters===
-===RDr arbitrary negative direction (evens) (2596-1) distal promoters===
+===M35r arbitrary negative direction (evens) (2596-1) distal promoters===
+# M35r4: TTGACA at 1412.
 ===RDr alternate negative direction (odds) (2596-1) distal promoters===
@@ Line 122: / Line 125: @@
 # M35r0: TTGACA at 3699, TTGACA at 3168.
+# M35r4: TTGACA at 1412.
+# M35r6: TTGACA at 3332.
 ==M35 analysis and results==

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box gene transcriptions EIF4E basal element 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 Families of TATA box genes 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 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 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 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 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 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