Sucrose box gene transcriptions: Difference between revisions

Revision as of 03:51, 2 March 2021

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

Manual "scanning was also done to identify the presence of sugar responsive elements such as sucrose box (NNAATCA) (Chen et al., 2002; Fillion et al., 1999) and pyrimidine box (CCTTTT, TTTTTTCC) (Washio, 2003)."^[1]

Human genes

Gene expressions

Interactions

Consensus sequences

Sucrose box (NNAATCA) (Chen et al., 2002; Fillion et al., 1999).^[1]

Binding site for

Promoter occurrences

Hypotheses

A1BG has no regulatory elements in either promoter.
A1BG is not transcribed by a regulatory element.
No regulatory element participates in the transcription of A1BG.

Sucrose box samplings

Copying a responsive elements consensus sequence NNAATCA 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 NNAATCA (starting with SuccessablesSucrose.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 NNAATCA, 1, GTAATCA at 155.
positive strand, negative direction, looking for NNAATCA, 6, AGAATCA at 3237, GAAATCA at 2749, AAAATCA at 2648, CTAATCA at 982, AGAATCA at 293, AGAATCA at 198.
positive strand, positive direction, looking for NNAATCA, 1, TAAATCA at 4137.
negative strand, positive direction, looking for NNAATCA, 2, TTAATCA at 4147, GCAATCA at 2338.
complement, negative strand, negative direction, looking for NNTTAGT, 6, TCTTAGT at 3237, CTTTAGT at 2749, TTTTAGT at 2648, GATTAGT at 982, TCTTAGT at 293, TCTTAGT at 198.
complement, positive strand, negative direction, looking for NNTTAGT, 1, CATTAGT at 155.
complement, positive strand, positive direction, looking for NNTTAGT, 2, AATTAGT at 4147, CGTTAGT at 2338.
complement, negative strand, positive direction, looking for NNTTAGT, 1, ATTTAGT at 4137.
inverse complement, negative strand, negative direction, looking for TGATTNN, 11, TGATTCC at 3474, TGATTTT at 3163, TGATTCG at 3032, TGATTCG at 2915, TGATTTA at 2636, TGATTTT at 2299, TGATTTC at 2174, TGATTTT at 1872, TGATTCC at 818, TGATTTT at 763, TGATTTT at 629.
inverse complement, positive strand, negative direction, looking for TGATTNN, 0.
inverse complement, positive strand, positive direction, looking for TGATTNN, 0.
inverse complement, negative strand, positive direction, looking for TGATTNN, 4, TGATTAT at 4165, TGATTAT at 4158, TGATTTA at 4135, TGATTGT at 2678.
inverse negative strand, negative direction, looking for ACTAANN, 0.
inverse positive strand, negative direction, looking for ACTAANN, 11, ACTAAGG at 3474, ACTAAAA at 3163, ACTAAGC at 3032, ACTAAGC at 2915, ACTAAAT at 2636, ACTAAAA at 2299, ACTAAAG at 2174, ACTAAAA at 1872, ACTAAGG at 818, ACTAAAA at 763, ACTAAAA at 629.
inverse positive strand, positive direction, looking for ACTAANN, 4, ACTAATA at 4165, ACTAATA at 4158, ACTAAAT at 4135, ACTAACA at 2678.
inverse negative strand, positive direction, looking for ACTAANN, 0.

Sucrose UTRs

Negative strand, negative direction: TGATTCC at 3474, TGATTTT at 3163, TGATTCG at 3032, TGATTCG at 2915.

Positive strand, negative direction: AGAATCA at 3237.

Sucrose proximal promoters

Negative strand, negative direction: TGATTGT at 2678, TGATTTA at 2636.

Positive strand, negative direction: GAAATCA at 2749, AAAATCA at 2648.

Negative strand, positive direction: TGATTAT at 4165, TGATTAT at 4158, TTAATCA at 4147, TGATTTA at 4135.

Positive strand, positive direction: TAAATCA at 4137.

Sucrose distal promoters

Negative strand, negative direction: TGATTTT at 2299, TGATTTC at 2174, TGATTTT at 1872, TGATTCC at 818, TGATTTT at 763, TGATTTT at 629, GTAATCA at 155.

Positive strand, negative direction: CTAATCA at 982, AGAATCA at 293, AGAATCA at 198.

Negative strand, positive direction: GCAATCA at 2338.

Acknowledgements

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

References

↑ ^1.0 ^1.1 M. Abiramavalli and B. Usha (7 July 2020). "Identification, characterization and expression analysis of sucrose transporters in the model plant Nicotiana tabacum cv.petit havana" (PDF). Journal of Environmental Biology. 41: 803–811. doi:10.22438/jeb/41/4/MRN-1233. Retrieved 7 January 2021.

External links

[Abiramavalli-1] 1.0 ^1.1 M. Abiramavalli and B. Usha (7 July 2020). "Identification, characterization and expression analysis of sucrose transporters in the model plant Nicotiana tabacum cv.petit havana" (PDF). Journal of Environmental Biology. 41: 803–811. doi:10.22438/jeb/41/4/MRN-1233. Retrieved 7 January 2021.

[1]

@@ Line 45: / Line 45: @@
 For the Basic programs testing consensus sequence NNAATCA (starting with SuccessablesSucrose.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 NNAATCA, 0.
+# negative strand, negative direction, looking for NNAATCA, 1, GTAATCA at 155.
-# positive strand, negative direction, looking for AAAAAAAA, 0.
+# positive strand, negative direction, looking for NNAATCA, 6, AGAATCA at 3237, GAAATCA at 2749, AAAATCA at 2648, CTAATCA at 982, AGAATCA at 293, AGAATCA at 198.
-# positive strand, positive direction, looking for AAAAAAAA, 0.
+# positive strand, positive direction, looking for NNAATCA, 1, TAAATCA at 4137.
-# negative strand, positive direction, looking for AAAAAAAA, 0.
+# negative strand, positive direction, looking for NNAATCA, 2, TTAATCA at 4147, GCAATCA at 2338.
-# complement, negative strand, negative direction, looking for NNTTAGT, 0.
+# complement, negative strand, negative direction, looking for NNTTAGT, 6, TCTTAGT at 3237, CTTTAGT at 2749, TTTTAGT at 2648, GATTAGT at 982, TCTTAGT at 293, TCTTAGT at 198.
-# complement, positive strand, negative direction, looking for TTTTTTTT, 0.
+# complement, positive strand, negative direction, looking for NNTTAGT, 1, CATTAGT at 155.
-# complement, positive strand, positive direction, looking for TTTTTTTT, 0.
+# complement, positive strand, positive direction, looking for NNTTAGT, 2, AATTAGT at 4147, CGTTAGT at 2338.
-# complement, negative strand, positive direction, looking for TTTTTTTT, 0.
+# complement, negative strand, positive direction, looking for NNTTAGT, 1, ATTTAGT at 4137.
-# inverse complement, negative strand, negative direction, looking for TGATTNN, 0.
+# inverse complement, negative strand, negative direction, looking for TGATTNN, 11, TGATTCC at 3474, TGATTTT at 3163, TGATTCG at 3032, TGATTCG at 2915, TGATTTA at 2636, TGATTTT at 2299, TGATTTC at 2174, TGATTTT at 1872, TGATTCC at 818, TGATTTT at 763, TGATTTT at 629.
-# inverse complement, positive strand, negative direction, looking for TTTTTTTT, 0.
+# inverse complement, positive strand, negative direction, looking for TGATTNN, 0.
-# inverse complement, positive strand, positive direction, looking for TTTTTTTT, 0.
+# inverse complement, positive strand, positive direction, looking for TGATTNN, 0.
-# inverse complement, negative strand, positive direction, looking for TTTTTTTT, 0.
+# inverse complement, negative strand, positive direction, looking for TGATTNN, 4, TGATTAT at 4165, TGATTAT at 4158, TGATTTA at 4135, TGATTGT at 2678.
 # inverse negative strand, negative direction, looking for ACTAANN, 0.
-# inverse positive strand, negative direction, looking for AAAAAAAA, 0.
+# inverse positive strand, negative direction, looking for ACTAANN, 11, ACTAAGG at 3474, ACTAAAA at 3163, ACTAAGC at 3032, ACTAAGC at 2915, ACTAAAT at 2636, ACTAAAA at 2299, ACTAAAG at 2174, ACTAAAA at 1872, ACTAAGG at 818, ACTAAAA at 763, ACTAAAA at 629.
-# inverse positive strand, positive direction, looking for AAAAAAAA, 0.
+# inverse positive strand, positive direction, looking for ACTAANN, 4, ACTAATA at 4165, ACTAATA at 4158, ACTAAAT at 4135, ACTAACA at 2678.
-# inverse negative strand, positive direction, looking for AAAAAAAA, 0.
+# inverse negative strand, positive direction, looking for ACTAANN, 0.
 ===Sucrose UTRs===
 {{main|UTR promoter gene transcriptions}}
+Negative strand, negative direction: TGATTCC at 3474, TGATTTT at 3163, TGATTCG at 3032, TGATTCG at 2915.
-===Sucrose core promoters===
+Positive strand, negative direction: AGAATCA at 3237.
-{{main|Core promoter gene transcriptions}}
 ===Sucrose proximal promoters===
 {{main|Proximal promoter gene transcriptions}}
+Negative strand, negative direction: TGATTGT at 2678, TGATTTA at 2636.
+Positive strand, negative direction: GAAATCA at 2749, AAAATCA at 2648.
+Negative strand, positive direction: TGATTAT at 4165, TGATTAT at 4158, TTAATCA at 4147, TGATTTA at 4135.
+Positive strand, positive direction: TAAATCA at 4137.
 ===Sucrose distal promoters===
 {{main|Distal promoter gene transcriptions}}
+Negative strand, negative direction: TGATTTT at 2299, TGATTTC at 2174, TGATTTT at 1872, TGATTCC at 818, TGATTTT at 763, TGATTTT at 629, GTAATCA at 155.
+Positive strand, negative direction: CTAATCA at 982, AGAATCA at 293, AGAATCA at 198.
+Negative strand, positive direction: GCAATCA at 2338.
 ==Acknowledgements==

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Transcription resources	A1BG gene transcription core promoters A1BG gene transcriptions A1BG regulatory elements and regions A1BG response element gene transcriptions A1BG response element negative results A1BG response element positive results ABA-response element gene transcriptions Abf1 regulatory factor gene transcriptions A box gene transcriptions ACGT-containing element gene transcriptions Activating protein gene transcriptions Activating transcription factor gene transcriptions Adenylate–uridylate rich element gene transcriptions Adr1p gene transcriptions Aft1p gene transcriptions AGC box gene transcriptions AGCE gene transcriptions Alpha-amylase conserved element gene transcriptions Amino acid response element gene transcriptions AARE-like Androgen response element gene transcriptions Angiotensinogen core promoter element gene transcriptions Antioxidant-electrophile responsive element gene transcriptions ATA box gene transcriptions Auxin response factor gene transcriptions B box gene transcriptions Bioinformatics tool gene transcriptions Box gene transcriptions Bridge gene transcriptions CAAT box gene transcriptions CadC binding domain gene transcriptions Calcineurin-responsive transcription factor gene transcriptions Calcium-response element gene transcriptions cAMP response element gene transcriptions C and D boxes gene transcriptions Carbohydrate response element gene transcriptions Carbon source-responsive element gene transcriptions Carcinoembryonic antigen gene family CARE gene transcriptions CArG box gene transcriptions CAT box gene transcriptions Cat8p gene transcriptions Cbf1 regulatory factor gene transcriptions C box gene transcriptions CCCTC-binding factor gene transcriptions C-EBP box gene transcriptions Cell-cycle box gene transcriptions Cell cycle regulation gene transcriptions CENP-B box gene transcriptions CGCG box gene transcriptions Circadian control element gene transcriptions Cold-responsive element gene transcriptions Complement copy gene transcriptions Complement-inverse copy gene transcriptions Consensus sequence gene transcriptions Copper response element gene transcriptions Core promoter gene transcriptions Coupling element gene transcriptions CRE box gene transcriptions Cytokinin response regulator gene transcriptions Cytoplasmic polyadenylation element gene transcriptions DAF-16-associated element gene transcriptions DAF-16 binding element gene transcriptions D box gene transcriptions Defense and stress-responsive element gene transcriptions Degenerate nucleotide gene transcriptions Dispersed promoter gene transcriptions Distal promoter gene transcriptions DNA melting gene transcriptions DNA damage response element gene transcriptions DNA replication-related element gene transcriptions Downstream core element gene transcriptions Downstream promoter element gene transcriptions Downstream TFIIB recognition element gene transcriptions DREB box gene transcriptions E2 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 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