TAGteam gene transcriptions

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

The "heptamer consensus sequence CAGGTAG (i.e., the TAGteam) is overrepresented in regulatory regions of the earliest expressed zygotic genes [2]."^[1]

Human genes

Consensus sequences

The "heptamer consensus sequence [is] CAGGTAG".^[1]

TAGteam samplings

Copying the consensus TAGteam: CAGGTAG and putting the sequence in "⌘F" finds one location between ZNF497 and A1BG or no locations between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence CAGGTAG (starting with SuccessablesTAG.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 CAGGTAG, 0.
positive strand, negative direction, looking for CAGGTAG, 0.
positive strand, positive direction, looking for CAGGTAG, 0.
negative strand, positive direction, looking for CAGGTAG, 1, CAGGTAG at 4035.
complement, negative strand, negative direction, looking for GTCCATC, 0.
complement, positive strand, negative direction, looking for GTCCATC, 0.
complement, positive strand, positive direction, looking for GTCCATC, 1, GTCCATC at 4035.
complement, negative strand, positive direction, looking for GTCCATC, 0.
inverse complement, negative strand, negative direction, looking for CTACCTG, 0.
inverse complement, positive strand, negative direction, looking for CTACCTG, 0.
inverse complement, positive strand, positive direction, looking for CTACCTG, 0.
inverse complement, negative strand, positive direction, looking for CTACCTG, 1, CTACCTG at 1198.
inverse negative strand, negative direction, looking for GATGGAC, 0.
inverse positive strand, negative direction, looking for GATGGAC, 0.
inverse positive strand, positive direction, looking for GATGGAC, 1, GATGGAC at 1198.
inverse negative strand, positive direction, looking for GATGGAC, 0.

TAG positive direction (4050-1) distal promoters

Negative strand, positive direction: CAGGTAG at 4035.
Negative strand, positive direction: CTACCTG at 1198.

TAGteam random dataset samplings

TAGr0: 0.
TAGr1: 0.
TAGr2: 0.
TAGr3: 0.
TAGr4: 0.
TAGr5: 0.
TAGr6: 0.
TAGr7: 0.
TAGr8: 1, CAGGTAG at 2738.
TAGr9: 0.
TAGr0ci: 0.
TAGr1ci: 0.
TAGr2ci: 0.
TAGr3ci: 0.
TAGr4ci: 0.
TAGr5ci: 0.
TAGr6ci: 0.
TAGr7ci: 0.
TAGr8ci: 1, CTACCTG at 2372.
TAGr9ci: 0.

TAGr arbitrary negative direction (evens) (2811-2596) proximal promoters

TAGr8: CAGGTAG at 2738.

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

TAGr8ci: CTACCTG at 2372.

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

TAGr8: CAGGTAG at 2738.
TAGr8ci: CTACCTG at 2372.

TAGteam analysis and results

The "heptamer consensus sequence [is] CAGGTAG".^[1]

Reals or randoms	Promoters	direction	Numbers	Strands	Occurrences	Averages (± 0.1)
Reals	UTR	negative	0	2	0	0
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	0	2	0	0
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	1	10	0.1	0.05
Randoms	Proximal	alternate negative	0	10	0	0.05
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	0	2	0	0
Randoms	Distal	arbitrary negative	1	10	0.1	0.05
Randoms	Distal	alternate negative	0	10	0	0.05
Reals	Distal	positive	2	2	1	1 ± 1 (-+2,++0)
Randoms	Distal	arbitrary positive	0	10	0	0.1
Randoms	Distal	alternate positive	2	10	0.2	0.1

Comparison:

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

Acknowledgements

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

References

↑ ^1.0 ^1.1 ^1.2 Rodrigo Nunes da Fonseca and Thiago M. Venancio (1 March 2018). "Maternal or zygotic: Unveiling the secrets of the Pancrustacea transcription factor zelda". Plos Genetics. 14 (3): e1007201. doi:10.1371/journal.pgen.1007201. PMID 29494591. Retrieved 5 September 2020.

External links

[Fonseca-1] 1.0 ^1.1 ^1.2 Rodrigo Nunes da Fonseca and Thiago M. Venancio (1 March 2018). "Maternal or zygotic: Unveiling the secrets of the Pancrustacea transcription factor zelda". Plos Genetics. 14 (3): e1007201. doi:10.1371/journal.pgen.1007201. PMID 29494591. Retrieved 5 September 2020.

[1]

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