Shoot specific element gene transcriptions: Difference between revisions

Latest revision as of 08:49, 20 September 2024

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

Human genes

Consensus sequences

Shoot specific elements (GATAatGATG).^[1]

GATAAT samplings

Copying the apparent consensus sequence for GATAAT and putting it in "⌘F" finds none located between ZSCAN22 and A1BG or between ZNF497 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence GATAAT (starting with SuccessablesGATAAT.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 GATAAT, 0.
positive strand, negative direction, looking for GATAAT, 0.
positive strand, positive direction, looking for GATAAT, 0.
negative strand, positive direction, looking for GATAAT, 0.
complement, negative strand, negative direction, looking for CTATTA, 0.
complement, positive strand, negative direction, looking for CTATTA, 0.
complement, positive strand, positive direction, looking for CTATTA, 0.
complement, negative strand, positive direction, looking for CTATTA, 0.
inverse complement, negative strand, negative direction, looking for ATTATC, 3, ATTATC at 4078, ATTATC at 1709, ATTATC at 250.
inverse complement, positive strand, negative direction, looking for ATTATC, 0.
inverse complement, positive strand, positive direction, looking for ATTATC, 0.
inverse complement, negative strand, positive direction, looking for ATTATC, 0.
inverse negative strand, negative direction, looking for TAATAG, 0.
inverse positive strand, negative direction, looking for TAATAG, 3, TAATAG at 4078, TAATAG at 1709, TAATAG at 250.
inverse positive strand, positive direction, looking for TAATAG, 0.
inverse negative strand, positive direction, looking for TAATAG, 0.

SHOOT samplings

Copying the apparent consensus sequence for Shoot (GATAATGATG) and putting it in "⌘F" finds none located between ZSCAN22 and A1BG or between ZNF497 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence GATAATGATG (starting with SuccessablesSHOOT.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 GATAATGATG, 0.
positive strand, negative direction, looking for GATAATGATG, 0.
positive strand, positive direction, looking for GATAATGATG, 0.
negative strand, positive direction, looking for GATAATGATG, 0.
complement, negative strand, negative direction, looking for CTATTACTAC, 0.
complement, positive strand, negative direction, looking for CTATTACTAC, 0.
complement, positive strand, positive direction, looking for CTATTACTAC, 0.
complement, negative strand, positive direction, looking for CTATTACTAC, 0.
inverse complement, negative strand, negative direction, looking for CATCATTATC, 0.
inverse complement, positive strand, negative direction, looking for CATCATTATC, 0.
inverse complement, positive strand, positive direction, looking for CATCATTATC, 0.
inverse complement, negative strand, positive direction, looking for CATCATTATC, 0.
inverse negative strand, negative direction, looking for GTAGTAATAG, 0.
inverse positive strand, negative direction, looking for GTAGTAATAG, 0.
inverse positive strand, positive direction, looking for GTAGTAATAG, 0.
inverse negative strand, positive direction, looking for GTAGTAATAG, 0.

Acknowledgements

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

References

↑ 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] 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 19: / Line 19: @@
 |pmid=32533036
 |accessdate=27 August 2020 }}</ref>
+==GATAAT samplings==
+Copying the apparent consensus sequence for GATAAT and putting it in "⌘F" finds none located between ZSCAN22 and A1BG or between ZNF497 and A1BG as can be found by the computer programs.
+For the Basic programs testing consensus sequence GATAAT (starting with SuccessablesGATAAT.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 GATAAT, 0.
+# positive strand, negative direction, looking for GATAAT, 0.
+# positive strand, positive direction, looking for GATAAT, 0.
+# negative strand, positive direction, looking for GATAAT, 0.
+# complement, negative strand, negative direction, looking for CTATTA, 0.
+# complement, positive strand, negative direction, looking for CTATTA, 0.
+# complement, positive strand, positive direction, looking for CTATTA, 0.
+# complement, negative strand, positive direction, looking for CTATTA, 0.
+# inverse complement, negative strand, negative direction, looking for ATTATC, 3, ATTATC at 4078, ATTATC at 1709, ATTATC at 250.
+# inverse complement, positive strand, negative direction, looking for ATTATC, 0.
+# inverse complement, positive strand, positive direction, looking for ATTATC, 0.
+# inverse complement, negative strand, positive direction, looking for ATTATC, 0.
+# inverse negative strand, negative direction, looking for TAATAG, 0.
+# inverse positive strand, negative direction, looking for TAATAG, 3, TAATAG at 4078, TAATAG at 1709, TAATAG at 250.
+# inverse positive strand, positive direction, looking for TAATAG, 0.
+# inverse negative strand, positive direction, looking for TAATAG, 0.
 ==SHOOT samplings==
 {{main|Model samplings}}
-Copying the apparent consensus sequence for Shoot  (GATAATGATG) and putting it in "⌘F" finds none located between ZSCAN22 and A1BG or between ZNF497 and A1BG as can be found by the computer programs.
+Copying the apparent consensus sequence for Shoot (GATAATGATG) and putting it in "⌘F" finds none located between ZSCAN22 and A1BG or between ZNF497 and A1BG as can be found by the computer programs.
 For the Basic programs testing consensus sequence GATAATGATG (starting with SuccessablesSHOOT.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:
@@ Line 29: / Line 51: @@
 # positive strand, positive direction, looking for GATAATGATG, 0.
 # negative strand, positive direction, looking for GATAATGATG, 0.
-# complement, negative strand, negative direction, looking for TTTTTTTT, 0.
+# complement, negative strand, negative direction, looking for CTATTACTAC, 0.
-# complement, positive strand, negative direction, looking for TTTTTTTT, 0.
+# complement, positive strand, negative direction, looking for CTATTACTAC, 0.
-# complement, positive strand, positive direction, looking for TTTTTTTT, 0.
+# complement, positive strand, positive direction, looking for CTATTACTAC, 0.
-# complement, negative strand, positive direction, looking for TTTTTTTT, 0.
+# complement, negative strand, positive direction, looking for CTATTACTAC, 0.
-# inverse complement, negative strand, negative direction, looking for TTTTTTTT, 0.
+# inverse complement, negative strand, negative direction, looking for CATCATTATC, 0.
-# inverse complement, positive strand, negative direction, looking for TTTTTTTT, 0.
+# inverse complement, positive strand, negative direction, looking for CATCATTATC, 0.
-# inverse complement, positive strand, positive direction, looking for TTTTTTTT, 0.
+# inverse complement, positive strand, positive direction, looking for CATCATTATC, 0.
-# inverse complement, negative strand, positive direction, looking for TTTTTTTT, 0.
+# inverse complement, negative strand, positive direction, looking for CATCATTATC, 0.
-# inverse negative strand, negative direction, looking for AAAAAAAA, 0.
+# inverse negative strand, negative direction, looking for GTAGTAATAG, 0.
-# inverse positive strand, negative direction, looking for AAAAAAAA, 0.
+# inverse positive strand, negative direction, looking for GTAGTAATAG, 0.
-# inverse positive strand, positive direction, looking for AAAAAAAA, 0.
+# inverse positive strand, positive direction, looking for GTAGTAATAG, 0.
-# inverse negative strand, positive direction, looking for AAAAAAAA, 0.
+# inverse negative strand, positive direction, looking for GTAGTAATAG, 0.
-===SHOOT UTRs===
-{{main|UTR promoter gene transcriptions}}
-===SHOOT core promoters===
-{{main|Core promoter gene transcriptions}}
-===SHOOT proximal promoters===
+==Acknowledgements==
-{{main|Proximal promoter gene transcriptions}}
-===SHOOT distal promoters===
+The content on this page was first contributed by: Henry A. Hoff.
-{{main|Distal promoter gene transcriptions}}
 ==See also==
 {{div col|colwidth=20em}}
+* [[A1BG gene transcription core promoters]]
+* [[A1BG gene transcriptions]]
+* [[A1BG regulatory elements and regions]]
+* [[A1BG response element negative results]]
+* [[A1BG response element positive results]]
 * [[Complex locus A1BG and ZNF497]]
-* [[Transcription factor]]
 {{Div col end}}
@@ Line 64: / Line 82: @@
 ==External links==
+* [http://www.genome.jp/ GenomeNet KEGG database]
+* [http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene Home - Gene - NCBI]
+* [http://www.ncbi.nlm.nih.gov/sites/gquery NCBI All Databases Search]
+* [http://www.ncbi.nlm.nih.gov/ncbisearch/ NCBI Site Search]
+* [http://www.ncbi.nlm.nih.gov/pccompound PubChem Public Chemical Database]
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@@ Line 69: / Line 92: @@
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-[[Category:Resources last modified in September 2020]]

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gene transcriptions Circadian control element gene transcriptions "Class C" (Leal) samplings 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 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 Heat shock elements 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 M-CAT boxes Mcm1 regulatory factor gene transcriptions Met3 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 Nanos/Pumilio response element 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 Shue boxes Sip4p gene transcriptions Smp1p gene transcriptions Sp1 (Berberich) elements 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 Tryptophan residue 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