Cold-responsive element gene transcriptions: Difference between revisions

Revision as of 06:43, 1 February 2022

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

A "putative cold-responsive element (CRE) [...] is specified by a conserved 5-bp core sequence (CCGAC) typical for C-repeat (CRT)/dehydration-responsive elements (DRE) that are recognized by cold-specific transcription factors (TFs) [16]."^[1]

Consensus sequences

A "conserved 5-bp core sequence (CCGAC) [is] typical for C-repeat (CRT)/dehydration-responsive elements (DRE)".^[1]

Cold-responsive element samplings

Copying a responsive elements consensus sequence CCGAC 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 CCGAC (starting with SuccessablesCold.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: 21, CCGAC at 4275, CCGAC at 4144, CCGAC at 3993, CCGAC at 3718, CCGAC at 3223, CCGAC at 3084, CCGAC at 3040, CCGAC at 2695, CCGAC at 2561, CCGAC at 2360, CCGAC at 2225, CCGAC at 2108, CCGAC at 2068, CCGAC at 1799, CCGAC at 1755, CCGAC at 1745, CCGAC at 1463, CCGAC at 1281, CCGAC at 1110, CCGAC at 990, CCGAC at 824.
Positive strand, negative direction: 0.
Negative strand, positive direction: 5, CCGAC at 3800, CCGAC at 1963, CCGAC at 997, CCGAC at 897, CCGAC at 791.
Positive strand, positive direction: 15, CCGAC at 3639, CCGAC at 3587, CCGAC at 3525, CCGAC at 3348, CCGAC at 2914, CCGAC at 2886, CCGAC at 2809, CCGAC at 2769, CCGAC at 2319, CCGAC at 1818, CCGAC at 1030, CCGAC at 480, CCGAC at 416, CCGAC at 276, CCGAC at 263.
inverse complement, negative strand, negative direction: 20, GTCGG at 4490, GTCGG at 4481, GTCGG at 4346, GTCGG at 4034, GTCGG at 3727, GTCGG at 3683, GTCGG at 3295, GTCGG at 3205, GTCGG at 3125, GTCGG at 2767, GTCGG at 2651, GTCGG at 2432, GTCGG at 2265, GTCGG at 2006, GTCGG at 1195, GTCGG at 1062, GTCGG at 896, GTCGG at 729, GTCGG at 505, GTCGG at 36.
inverse complement, negative strand, positive direction: 1, GTCGG at 1529.
inverse complement, positive strand, negative direction: 0.
inverse complement, positive strand, positive direction: 15, GTCGG at 3998, GTCGG at 3896, GTCGG at 3101, GTCGG at 2897, GTCGG at 2527, GTCGG at 2391, GTCGG at 2353, GTCGG at 2009, GTCGG at 1604, GTCGG at 1268, GTCGG at 932, GTCGG at 832, GTCGG at 614, GTCGG at 512, GTCGG at 65.

UTR promoters

Negative strand, negative direction: GTCGG at 4490, GTCGG at 4481, GTCGG at 4346, CCGAC at 4275, CCGAC at 4144, GTCGG at 4034, CCGAC at 3993, GTCGG at 3727, CCGAC at 3718, GTCGG at 3683, GTCGG at 3295, CCGAC at 3223, GTCGG at 3205, GTCGG at 3125, CCGAC at 3084, CCGAC at 3040.
inverse complement, negative strand, negative direction: 20, GTCGG at 2767, GTCGG at 2651, GTCGG at 2432, GTCGG at 2265, GTCGG at 2006, GTCGG at 1195, GTCGG at 1062, GTCGG at 896, GTCGG at 729, GTCGG at 505, GTCGG at 36.

Cold-responsive element proximal promoters

Negative strand, negative direction: GTCGG at 2767, CCGAC at 2695, GTCGG at 2651.

Cold-responsive element distal promoters

Negative strand, negative direction: CCGAC at 2561, GTCGG at 2432, CCGAC at 2360, GTCGG at 2265, CCGAC at 2225, CCGAC at 2108, CCGAC at 2068, GTCGG at 2006, CCGAC at 1799, CCGAC at 1755, CCGAC at 1745, CCGAC at 1463, CCGAC at 1281, GTCGG at 1195, CCGAC at 1110, GTCGG at 1062, CCGAC at 990, GTCGG at 896, CCGAC at 824, GTCGG at 729, GTCGG at 505, GTCGG at 36.

Negative strand, positive direction: CCGAC at 3800, CCGAC at 1963, GTCGG at 1529, CCGAC at 997, CCGAC at 897, CCGAC at 791.
Positive strand, positive direction: 15, GTCGG at 3998, GTCGG at 3896, CCGAC at 3639, CCGAC at 3587, CCGAC at 3525, CCGAC at 3348, GTCGG at 3101, CCGAC at 2914, GTCGG at 2897, CCGAC at 2886, CCGAC at 2809, CCGAC at 2769, GTCGG at 2527, GTCGG at 2391, GTCGG at 2353, CCGAC at 2319, GTCGG at 2009, CCGAC at 1818, GTCGG at 1604, GTCGG at 1268, CCGAC at 1030, GTCGG at 932, GTCGG at 832, GTCGG at 614, GTCGG at 512, CCGAC at 480, CCGAC at 416, CCGAC at 276, CCGAC at 263, GTCGG at 65.

Cold-responsive element random dataset samplings

Coldr0: 6, CCGAC at 3063, CCGAC at 2510, CCGAC at 1598, CCGAC at 1318, CCGAC at 878, CCGAC at 48.
Coldr1: 7, CCGAC at 3037, CCGAC at 2353, CCGAC at 2132, CCGAC at 1838, CCGAC at 1765, CCGAC at 1729, CCGAC at 958.
Coldr2: 3, CCGAC at 3706, CCGAC at 1868, CCGAC at 1718.
Coldr3: 3, CCGAC at 4506, CCGAC at 2428, CCGAC at 2363.
Coldr4: 4, CCGAC at 4356, CCGAC at 3678, CCGAC at 398, CCGAC at 383.
Coldr5: 2, CCGAC at 1543, CCGAC at 96.
Coldr6: 4, CCGAC at 4297, CCGAC at 3539, CCGAC at 3407, CCGAC at 2843.
Coldr7: 3, CCGAC at 3556, CCGAC at 2419, CCGAC at 2412.
Coldr8: 5, CCGAC at 2906, CCGAC at 1992, CCGAC at 1942, CCGAC at 1105, CCGAC at 430.
Coldr9: 9, CCGAC at 4192, CCGAC at 4078, CCGAC at 2767, CCGAC at 2520, CCGAC at 1568, CCGAC at 976, CCGAC at 511, CCGAC at 391, CCGAC at 50.
Coldr0ci: 4, GTCGG at 4188, GTCGG at 4121, GTCGG at 1418, GTCGG at 867.
Coldr1ci: 7, GTCGG at 4548, GTCGG at 3559, GTCGG at 3004, GTCGG at 1165, GTCGG at 1070, GTCGG at 592, GTCGG at 511.
Coldr2ci: 4, GTCGG at 3197, GTCGG at 1606, GTCGG at 90, GTCGG at 11.
Coldr3ci: 3, GTCGG at 1888, GTCGG at 1485, GTCGG at 645.
Coldr4ci: 4, GTCGG at 4242, GTCGG at 2663, GTCGG at 2470, GTCGG at 2028.
Coldr5ci: 6, GTCGG at 3539, GTCGG at 3177, GTCGG at 2902, GTCGG at 2880, GTCGG at 1053, GTCGG at 463.
Coldr6ci: 4, GTCGG at 2689, GTCGG at 1230, GTCGG at 515, GTCGG at 475.
RDr7ci: 3, GTCGG at 3352, GTCGG at 2048, GTCGG at 1473.
RDr8ci: 0.
RDr9ci: 0.

Coldr UTRs

RDr0: CCGAC at 3063.
Coldr2: CCGAC at 3706.
Coldr4: CCGAC at 4356, CCGAC at 3678.
Coldr6: CCGAC at 4297, CCGAC at 3539, CCGAC at 3407.
Coldr8: CCGAC at 2906.
Coldr0ci: GTCGG at 4188, GTCGG at 4121.
Coldr2ci: GTCGG at 3197.
Coldr4ci: GTCGG at 4242.

Coldr core promoters

Coldr6: CCGAC at 2843.

Coldr3: CCGAC at 4506.
Coldr1ci: GTCGG at 4548.

Coldr proximal promoters

Coldr4ci:GTCGG at 2663.

Coldr9: CCGAC at 4192, CCGAC at 4078.

Coldr distal promoters

Coldr0: CCGAC at 2510, CCGAC at 1598, CCGAC at 1318, CCGAC at 878, CCGAC at 48.
Coldr2: CCGAC at 1868, CCGAC at 1718.
Coldr4: CCGAC at 398, CCGAC at 383.
Coldr8: CCGAC at 1992, CCGAC at 1942, CCGAC at 1105, CCGAC at 430.
Coldr0ci: GTCGG at 1418, GTCGG at 867.
Coldr2ci: GTCGG at 1606, GTCGG at 90, GTCGG at 11.
Coldr4ci: GTCGG at 2470, GTCGG at 2028.

Coldr1: CCGAC at 3037, CCGAC at 2353, CCGAC at 2132, CCGAC at 1838, CCGAC at 1765, CCGAC at 1729, CCGAC at 958.
Coldr3: CCGAC at 2428, CCGAC at 2363.
Coldr5: CCGAC at 1543, CCGAC at 96.
Coldr7: CCGAC at 3556, CCGAC at 2419, CCGAC at 2412.
Coldr9: CCGAC at 2767, CCGAC at 2520, CCGAC at 1568, CCGAC at 976, CCGAC at 511, CCGAC at 391, CCGAC at 50.
Coldr1ci: GTCGG at 3559, GTCGG at 3004, GTCGG at 1165, GTCGG at 1070, GTCGG at 592, GTCGG at 511.
Coldr3ci: GTCGG at 1888, GTCGG at 1485, GTCGG at 645.
Coldr5ci: GTCGG at 3539, GTCGG at 3177, GTCGG at 2902, GTCGG at 2880, GTCGG at 1053, GTCGG at 463.

Cold-responsive element analysis and results

Acknowledgements

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

References

↑ ^1.0 ^1.1 Björn Pietzenuk, Catarine Markus, Hervé Gaubert, Navratan Bagwan, Aldo Merotto, Etienne Bucher & Ales Pecinka (11 October 2016). "Recurrent evolution of heat-responsiveness in Brassicaceae COPIA elements". Genome Biology. 17: 209. doi:10.1186/s13059-016-1072-3. Retrieved 14 September 2020.

External links

[Pietzenuk-1] 1.0 ^1.1 Björn Pietzenuk, Catarine Markus, Hervé Gaubert, Navratan Bagwan, Aldo Merotto, Etienne Bucher & Ales Pecinka (11 October 2016). "Recurrent evolution of heat-responsiveness in Brassicaceae COPIA elements". Genome Biology. 17: 209. doi:10.1186/s13059-016-1072-3. Retrieved 14 September 2020.

[1]

@@ Line 69: / Line 69: @@
 # Coldr4ci: 4, GTCGG at 4242, GTCGG at 2663, GTCGG at 2470, GTCGG at 2028.
 # Coldr5ci: 6, GTCGG at 3539, GTCGG at 3177, GTCGG at 2902, GTCGG at 2880, GTCGG at 1053, GTCGG at 463.
-# RDr6ci: 0.
+# Coldr6ci: 4, GTCGG at 2689, GTCGG at 1230, GTCGG at 515, GTCGG at 475.
-# RDr7ci: 0.
+# RDr7ci: 3, GTCGG at 3352, GTCGG at 2048, GTCGG at 1473.
 # RDr8ci: 0.
 # RDr9ci: 0.

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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