Q element gene transcriptions: Difference between revisions

Revision as of 08:30, 18 January 2023

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

"The basal regulatory elements identified include a putative TATA-box (−30/−24) for RNA polymerase binding and a CAAT box (−64/−61; [...]). Several putative floral expression-related cis-elements identified included a putative 6-nucleotide Q element (−770/−665), three GTGA boxes (−372/−369, −209/−206 and −164/−161) and four putative highly-conserved POLLEN1 boxes (−737/−733, −711/−707, −150/−146 and −36/−32; [...])."^[1]

Human genes

Consensus sequences

The consensus sequence for a Q element is 3'-AGGTCA-5'.^[1]

QE samplings

Copying the apparent consensus sequence for the QE (AGGTCA) and putting it in "⌘F" finds two located between ZSCAN22 or three between ZNF497 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence AGGTCA (starting with SuccessablesQE.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 AGGTCA, 2, AGGTCA at 1532, AGGTCA at 1352.
positive strand, negative direction, looking for AGGTCA, 7, AGGTCA at 4307, AGGTCA at 2585, AGGTCA at 2248, AGGTCA at 712, AGGTCA at 576, AGGTCA at 568, AGGTCA at 439.
positive strand, positive direction, looking for AGGTCA, 0.
negative strand, positive direction, looking for AGGTCA, 3, AGGTCA at 4269, AGGTCA at 2220, AGGTCA at 153.
complement, negative strand, negative direction, looking for TCCAGT, 7, TCCAGT at 4307, TCCAGT at 2585, TCCAGT at 2248, TCCAGT at 712, TCCAGT at 576, TCCAGT at 568, TCCAGT at 439.
complement, positive strand, negative direction, looking for TCCAGT, 2, TCCAGT at 1532, TCCAGT at 1352.
complement, positive strand, positive direction, looking for TCCAGT, 3, TCCAGT at 4269, TCCAGT at 2220, TCCAGT at 153.
complement, negative strand, positive direction, looking for TCCAGT, 0.
inverse complement, negative strand, negative direction, looking for TGACCT, 0.
inverse complement, positive strand, negative direction, looking for TGACCT, 0.
inverse complement, positive strand, positive direction, looking for TGACCT, 0.
inverse complement, negative strand, positive direction, looking for TGACCT, 2, TGACCT at 4019, TGACCT at 3785.
inverse negative strand, negative direction, looking for ACTGGA, 0.
inverse positive strand, negative direction, looking for ACTGGA, 0.
inverse positive strand, positive direction, looking for ACTGGA, 2, ACTGGA at 4019, ACTGGA at 3785.
inverse negative strand, positive direction, looking for ACTGGA, 0.

QE (4560-2846) UTRs

Positive strand, negative direction: AGGTCA at 4307.

QE positive direction (4445-4265) core promoters

Negative strand, positive direction: AGGTCA at 4269.

QE negative direction (2596-1) distal promoters

Negative strand, negative direction: AGGTCA at 1532, AGGTCA at 1352.
Positive strand, negative direction: AGGTCA at 2585, AGGTCA at 2248, AGGTCA at 712, AGGTCA at 576, AGGTCA at 568, AGGTCA at 439.

QE positive direction (4050-1) distal promoters

Negative strand, positive direction: AGGTCA at 2220, AGGTCA at 153.
Negative strand, positive direction: TGACCT at 4019, TGACCT at 3785.

QE random dataset samplings

QEr0: 1, AGGTCA at 699.
QEr1: 1, AGGTCA at 1750.
QEr2: 2, AGGTCA at 4381, AGGTCA at 3163.
QEr3: 1, AGGTCA at 2303.
QEr4: 0.
QEr5: 1, AGGTCA at 4296.
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.

QEr arbitrary (evens) (4560-2846) UTRs

QEr2: AGGTCA at 4381, AGGTCA at 3163.

QEr alternate (odds) (4560-2846) UTRs

QEr5: AGGTCA at 4296.

RDr arbitrary negative direction (evens) (2846-2811) core promoters

QEr alternate negative direction (odds) (2846-2811) core promoters

QEr arbitrary positive direction (odds) (4445-4265) core promoters

QEr5: AGGTCA at 4296.

RDr alternate positive direction (evens) (4445-4265) core promoters

QEr2: AGGTCA at 4381.

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

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

QEr0: AGGTCA at 699.

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

QEr1: AGGTCA at 1750.
QEr3: AGGTCA at 2303.

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

QEr1: AGGTCA at 1750.
QEr3: AGGTCA at 2303.

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

QEr0: AGGTCA at 699.
QEr2: AGGTCA at 3163.

QE analysis and results

The consensus sequence for a Q element is AGGTCA.^[1]

Reals or randoms	Promoters	direction	Numbers	Strands	Occurrences	Averages (± 0.1)
Reals	UTR	negative	1	2	0.5	0.5
Randoms	UTR	arbitrary negative	0	10	0	0
Randoms	UTR	alternate negative	0	10	0	0
Reals	Core	negative	0	2	0	0
Randoms	Core	arbitrary negative	0	10	0	0
Randoms	Core	alternate negative	0	10	0	0
Reals	Core	positive	1	2	0.5	0.5
Randoms	Core	arbitrary positive	0	10	0	0
Randoms	Core	alternate positive	0	10	0	0
Reals	Proximal	negative	0	2	0	0
Randoms	Proximal	arbitrary negative	0	10	0	0
Randoms	Proximal	alternate negative	0	10	0	0
Reals	Proximal	positive	0	2	0	0
Randoms	Proximal	arbitrary positive	0	10	0	0
Randoms	Proximal	alternate positive	0	10	0	0
Reals	Distal	negative	8	2	4	4 ± 2 (—2,+-6)
Randoms	Distal	arbitrary negative	0	10	0	0
Randoms	Distal	alternate negative	0	10	0	0
Reals	Distal	positive	4	2	2	2 ± 2 (-+4,++0)
Randoms	Distal	arbitrary positive	0	10	0	0
Randoms	Distal	alternate positive	0	10	0	0

Comparison: The occurrences of real QEs are greater than the randoms. This suggests that the real QEs are likely active or activable.

References

↑ ^1.0 ^1.1 ^1.2 Zi-Wei Ye, Jie Xu, Jianxin Shi, Dabing Zhang and Mee-Len Chye (January 2017). "Kelch-motif containing acyl-CoA binding proteins AtACBP4 and AtACBP5 are differentially expressed and function in floral lipid metabolism" (PDF). Plant Molecular Biology. 93: 209–225. doi:10.1007/s11103-016-0557-5. PMID 27826761. Retrieved 7 May 2020.

External links

[Ye-1] 1.0 ^1.1 ^1.2 Zi-Wei Ye, Jie Xu, Jianxin Shi, Dabing Zhang and Mee-Len Chye (January 2017). "Kelch-motif containing acyl-CoA binding proteins AtACBP4 and AtACBP5 are differentially expressed and function in floral lipid metabolism" (PDF). Plant Molecular Biology. 93: 209–225. doi:10.1007/s11103-016-0557-5. PMID 27826761. Retrieved 7 May 2020.

[1]

@@ Line 66: / Line 66: @@
 # QEr1: 1, AGGTCA at 1750.
 # QEr2: 2, AGGTCA at 4381, AGGTCA at 3163.
-# RDr3: 0.
+# QEr3: 1, AGGTCA at 2303.
-# RDr4: 0.
+# QEr4: 0.
-# RDr5: 0.
+# QEr5: 1, AGGTCA at 4296.
 # RDr6: 0.
 # RDr7: 0.
@@ Line 88: / Line 88: @@
 # QEr2: AGGTCA at 4381, AGGTCA at 3163.
-===RDr alternate (odds) (4560-2846) UTRs===
+===QEr alternate (odds) (4560-2846) UTRs===
+# QEr5: AGGTCA at 4296.
 ===RDr arbitrary negative direction (evens) (2846-2811) core promoters===
-===RDr alternate negative direction (odds) (2846-2811) core promoters===
+===QEr alternate negative direction (odds) (2846-2811) core promoters===
+===QEr arbitrary positive direction (odds) (4445-4265) core promoters===
-===RDr arbitrary positive direction (odds) (4445-4265) core promoters===
+# QEr5: AGGTCA at 4296.
 ===RDr alternate positive direction (evens) (4445-4265) core promoters===
@@ Line 115: / Line 119: @@
 # QEr1: AGGTCA at 1750.
+# QEr3: AGGTCA at 2303.
 ===RDr arbitrary positive direction (odds) (4050-1) distal promoters===
 # QEr1: AGGTCA at 1750.
+# QEr3: AGGTCA at 2303.
 ===QEr alternate positive direction (evens) (4050-1) distal promoters===

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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