Seed-specific element gene transcriptions

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, 4, CATG at 3114, CATG at 2596, CATG at 565, CATG at 126.
negative strand, positive direction, looking for CATG, 21, CATG at 4370, CATG at 4364, CATG at 4221, CATG at 4153, CATG at 3956, CATG at 3900, CATG at 3827, CATG at 3742, CATG at 3707, CATG at 3580, CATG at 3335, CATG at 3140, CATG at 2473, CATG at 2266, CATG at 2153, CATG at 2140, CATG at 2031, CATG at 1933, CATG at 1871, CATG at 1238, CATG at 1186.
complement, negative strand, negative direction, looking for GTAC, 17, GTAC at 4247, GTAC at 4116, GTAC at 4106, GTAC at 2783, GTAC at 2751, GTAC at 2667, GTAC at 2613, GTAC at 2533, GTAC at 2322, GTAC at 2276, GTAC at 2151, GTAC at 1952, GTAC at 1849, GTAC at 1206, GTAC at 952, GTAC at 200, GTAC at 123.
complement, positive strand, negative direction, looking for GTAC, 4, GTAC at 2342, GTAC at 2213, GTAC at 797, GTAC at 324.
complement, positive strand, positive direction, looking for GTAC, 21, GTAC at 4370, GTAC at 4364, GTAC at 4221, GTAC at 4153, GTAC at 3956, GTAC at 3900, GTAC at 3827, GTAC at 3742, GTAC at 3707, GTAC at 3580, GTAC at 3335, GTAC at 3140, GTAC at 2473, GTAC at 2266, GTAC at 2153, GTAC at 2140, GTAC at 2031, GTAC at 1933, GTAC at 1871, GTAC at 1238, GTAC at 1186.
complement, negative strand, positive direction, looking for GTAC, 4, GTAC at 3114, GTAC at 2596, GTAC at 565, GTAC at 126.
inverse complement, negative strand, negative direction, looking for CATG, 4, CATG at 2342, CATG at 2213, CATG at 797, CATG at 324.
inverse complement, positive strand, negative direction, looking for CATG, 017, 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.
inverse complement, positive strand, positive direction, looking for CATG, 4, CATG at 3114, CATG at 2596, CATG at 565, CATG at 126..
inverse complement, negative strand, positive direction, looking for CATG, 21, CATG at 4370, CATG at 4364, CATG at 4221, CATG at 4153, CATG at 3956, CATG at 3900, CATG at 3827, CATG at 3742, CATG at 3707, CATG at 3580, CATG at 3335, CATG at 3140, CATG at 2473, CATG at 2266, CATG at 2153, CATG at 2140, CATG at 2031, CATG at 1933, CATG at 1871, CATG at 1238, CATG at 1186.
inverse negative strand, negative direction, looking for GTAC, 17, GTAC at 4247, GTAC at 4116, GTAC at 4106, GTAC at 2783, GTAC at 2751, GTAC at 2667, GTAC at 2613, GTAC at 2533, GTAC at 2322, GTAC at 2276, GTAC at 2151, GTAC at 1952, GTAC at 1849, GTAC at 1206, GTAC at 952, GTAC at 200, GTAC at 123.
inverse positive strand, negative direction, looking for GTAC, 4, GTAC at 2342, GTAC at 2213, GTAC at 797, GTAC at 324.
inverse positive strand, positive direction, looking for GTAC, 21, GTAC at 4370, GTAC at 4364, GTAC at 4221, GTAC at 4153, GTAC at 3956, GTAC at 3900, GTAC at 3827, GTAC at 3742, GTAC at 3707, GTAC at 3580, GTAC at 3335, GTAC at 3140, GTAC at 2473, GTAC at 2266, GTAC at 2153, GTAC at 2140, GTAC at 2031, GTAC at 1933, GTAC at 1871, GTAC at 1238, GTAC at 1186.
inverse negative strand, positive direction, looking for GTAC, 4, GTAC at 3114, GTAC at 2596, GTAC at 565, GTAC at 126.

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.

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