Alpha-amylase conserved element gene transcriptions: Difference between revisions

Revision as of 03:30, 11 April 2023

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

"A few genes were also noticed with the shoot (GATAatGATG) and root (TGACGTCA) specific elements, cell cycle regulation (CCCAACGGT), seed-specific element (CATGCATG) and alpha-amylase conserved elements (TATCCATCCATCC). The presence of a significant number of the regulatory elements suggests strong participation of the U-box E3 gene family in plant development and responses under abiotic and biotic stress conditions. The data also supports the active involvement of the U-box E3 gene family in hormonal regulatory pathways."^[1]

Consensus sequences

TATCCATCCATCC^[1]

Hypotheses

A1BG has no A boxes in either promoter.
A1BG is not transcribed by an ATA box.
AGCE1 does not participate in the transcription of A1BG.

Alpha-amylase conserved element samplings

Copying a responsive elements consensus sequence TATCCA 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 TATCCATCCATCC (starting with SuccessablesAAC.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 5'-TATCCATCCATCC-3', 0.
negative strand, positive direction, looking for 5'-TATCCATCCATCC-3', 0.
positive strand, negative direction, looking for 5'-TATCCATCCATCC-3', 0.
positive strand, positive direction, looking for 5'-TATCCATCCATCC-3', 0.
complement, negative strand, negative direction, looking for 5'-ATAGGTAGGTAGG-3', 0.
complement, negative strand, positive direction, looking for 5'-ATAGGTAGGTAGG-3', 0.
complement, positive strand, negative direction, looking for 5'-ATAGGTAGGTAGG-3', 0.
complement, positive strand, positive direction, looking for 5'-ATAGGTAGGTAGG-3', 0.
inverse complement, negative strand, negative direction, looking for 5'-GGATGGATGGATA-3', 0.
inverse complement, negative strand, positive direction, looking for 5'-GGATGGATGGATA-3', 0.
inverse complement, positive strand, negative direction, looking for 5'-GGATGGATGGATA-3', 0.
inverse complement, positive strand, positive direction, looking for 5'-GGATGGATGGATA-3', 0.
inverse negative strand, negative direction, looking for 5'-CCTACCTACCTAT-3', 0.
inverse negative strand, positive direction, looking for 5'-CCTACCTACCTAT-3', 0.
inverse positive strand, negative direction, looking for 5'-CCTACCTACCTAT-3', 0.
inverse positive strand, positive direction, looking for 5'-CCTACCTACCTAT-3', 0.

Alpha-amylase conserved element portion samplings

Copying a responsive elements consensus sequence TATCCA 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 TATCCA (starting with SuccessablesAACp.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: 0.
Positive strand, negative direction: 1, TATCCA at 1530.
Negative strand, positive direction: 0.
Positive strand, positive direction: 0.
inverse complement, negative strand, negative direction: 1, TGGATA at 2996.
inverse complement, positive strand, negative direction: 0.
inverse complement, negative strand, positive direction: 1, TGGATA at 2737.
inverse complement, positive strand, positive direction: 0.

AACp (4560-2846) UTRs

Negative strand, negative direction: TGGATA at 2996.

AACp negative direction (2596-1) distal promoters

Positive strand, negative direction: TATCCA at 1530.

AACp positive direction (4050-1) distal promoters

Negative strand, positive direction: TGGATA at 2737.

Alpha-amylase conserved element portion random dataset samplings

RDr0: 0.
RDr1: 0.
RDr2: 0.
RDr3: 0.
RDr4: 0.
RDr5: 0.
RDr6: 0.
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.

RDr arbitrary (evens) (4560-2846) UTRs

RDr alternate (odds) (4560-2846) UTRs

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

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

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

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

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

Alpha-amylase conserved element portion analysis and results

TATCCATCCATCC^[1] portion TATCCA.

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 AACps are greater than the randoms. This suggests that the real AACps are likely active or activable.

Acknowledgements

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

References

↑ ^1.0 ^1.1 ^1.2 Bhaskar Sharma & Joemar Taganna (12 June 2020). "Genome-wide analysis of the U-box E3 ubiquitin ligase enzyme gene family in tomato". Scientific Reports. 10 (9581). doi:10.1038/s41598-020-66553-1. PMID 32533036 Check |pmid= value (help). Retrieved 27 August 2020.

External links

[Sharma-1] 1.0 ^1.1 ^1.2 Bhaskar Sharma & Joemar Taganna (12 June 2020). "Genome-wide analysis of the U-box E3 ubiquitin ligase enzyme gene family in tomato". Scientific Reports. 10 (9581). doi:10.1038/s41598-020-66553-1. PMID 32533036 Check |pmid= value (help). Retrieved 27 August 2020.

[1]

@@ Line 53: / Line 53: @@
 For the Basic programs testing consensus sequence TATCCA (starting with SuccessablesAACp.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: 0.
-# positive strand, negative direction, looking for AAAAAAAA, 0.
+# Positive strand, negative direction: 1, TATCCA at 1530.
-# negative strand, positive direction, looking for AAAAAAAA, 0.
+# Negative strand, positive direction: 0.
-# positive strand, positive direction, looking for AAAAAAAA, 0.
+# Positive strand, positive direction: 0.
-# inverse complement, negative strand, negative direction, looking for TTTTTTTT, 0.
+# inverse complement, negative strand, negative direction: 1, TGGATA at 2996.
-# inverse complement, positive strand, negative direction, looking for TTTTTTTT, 0.
+# inverse complement, positive strand, negative direction: 0.
-# inverse complement, negative strand, positive direction, looking for TTTTTTTT, 0.
+# inverse complement, negative strand, positive direction: 1, TGGATA at 2737.
-# inverse complement, positive strand, positive direction, looking for TTTTTTTT, 0.
+# inverse complement, positive strand, positive direction: 0.
-===AAA (4560-2846) UTRs===
+===AACp (4560-2846) UTRs===
-===AAA negative direction (2846-2811) core promoters===
+# Negative strand, negative direction: TGGATA at 2996.
-===AAA positive direction (4445-4265) core promoters===
+===AACp negative direction (2596-1) distal promoters===
-===AAA negative direction (2811-2596) proximal promoters===
+# Positive strand, negative direction: TATCCA at 1530.
-===AAA positive direction (4265-4050) proximal promoters===
+===AACp positive direction (4050-1) distal promoters===
-===AAA negative direction (2596-1) distal promoters===
+# Negative strand, positive direction: TGGATA at 2737.
-===AAA positive direction (4050-1) distal promoters===
 ==Alpha-amylase conserved element portion random dataset samplings==

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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 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 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