Seed-specific element gene transcriptions: Difference between revisions

Revision as of 02:58, 19 September 2024

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

Seed-specific element (CATGCATG).^[1]

Human genes

Consensus sequences

Consensus sequence is CATGCATG.^[1]

SubSEED samplings

Copying the apparent consensus sequence for the seed-specific element (CATG) 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 CATG (starting with SuccessablesSEED.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 CATG, 4, CATG at 2342, CATG at 2213, CATG at 797, CATG at 324.
positive strand, negative direction, looking for CATG, 17, CATG at 4247, CATG at 4116, CATG at 4106, CATG at 2783, CATG at 2751, CATG at 2667, CATG at 2613, CATG at 2533, CATG at 2322, CATG at 2276, CATG at 2151, CATG at 1952, CATG at 1849, CATG at 1206, CATG at 952, CATG at 200, CATG at 123.
positive strand, positive direction, looking for CATG, 0.
negative strand, positive direction, looking for CATG, 0.
complement, negative strand, negative direction, looking for GTAC, 0.
complement, positive strand, negative direction, looking for GTAC, 0.
complement, positive strand, positive direction, looking for GTAC, 0.
complement, negative strand, positive direction, looking for GTAC, 0.
inverse complement, negative strand, negative direction, looking for CATG, 0.
inverse complement, positive strand, negative direction, looking for CATG, 0.
inverse complement, positive strand, positive direction, looking for CATG, 0.
inverse complement, negative strand, positive direction, looking for CATG, 0.
inverse negative strand, negative direction, looking for GTAC, 0.
inverse positive strand, negative direction, looking for GTAC, 0.
inverse positive strand, positive direction, looking for GTAC, 0.
inverse negative strand, positive direction, looking for GTAC, 0.

SEED samplings

Copying the apparent consensus sequence for the seed-specific element (CATGCATG) 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 CATGCATG (starting with SuccessablesSEED.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 CATGCATG, 0.
positive strand, negative direction, looking for CATGCATG, 0.
positive strand, positive direction, looking for CATGCATG, 0.
negative strand, positive direction, looking for CATGCATG, 0.
complement, negative strand, negative direction, looking for GTACGTAC, 0.
complement, positive strand, negative direction, looking for GTACGTAC, 0.
complement, positive strand, positive direction, looking for GTACGTAC, 0.
complement, negative strand, positive direction, looking for GTACGTAC, 0.
inverse complement, negative strand, negative direction, looking for CATGCATG, 0.
inverse complement, positive strand, negative direction, looking for CATGCATG, 0.
inverse complement, positive strand, positive direction, looking for CATGCATG, 0.
inverse complement, negative strand, positive direction, looking for CATGCATG, 0.
inverse negative strand, negative direction, looking for GTACGTAC, 0.
inverse positive strand, negative direction, looking for GTACGTAC, 0.
inverse positive strand, positive direction, looking for GTACGTAC, 0.
inverse negative strand, positive direction, looking for GTACGTAC, 0.

References

↑ ^1.0 ^1.1 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.

External links

[Sharma-1] 1.0 ^1.1 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 28: / Line 28: @@
 For the Basic programs testing consensus sequence CATG (starting with SuccessablesSEED.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 CATG, 4, CATG at 2342, CATG at 2213, CATG at 797, CATG at 324.
-# positive strand, negative direction, looking for CATG, 0.
+# positive strand, negative direction, looking for CATG, 17, CATG at 4247, CATG at 4116, CATG at 4106, CATG at 2783, CATG at 2751, CATG at 2667, CATG at 2613, CATG at 2533, CATG at 2322, CATG at 2276, CATG at 2151, CATG at 1952, CATG at 1849, CATG at 1206, CATG at 952, CATG at 200, CATG at 123.
 # positive strand, positive direction, looking for CATG, 0.
 # negative strand, positive direction, looking for CATG, 0.

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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 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