TACTAAC box gene transcriptions

Editor-In-Chief: Henry A. Hoff

This is a field of Dictyostelium discoideum. Credit: Usman Bashir.

"A consensus sequence TACTAA(C/T) was derived for the branch site of Dictyostelium introns."^[1]

Consensus sequences

"The comparison of the two rp51 genes [...] suggests that this homology might be more extensive if one allows up to 3 bases to differ from a larger consensus sequence, ATTTACTAAC."^[2]

TACT samplings

For the Basic programs (starting with SuccessablesTACT.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 in the negative direction (from ZSCAN22 to A1BG) is SuccessablesTACT--.bas, looking for TACTAA(C/T), 0,
negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesTACT-+.bas, looking for TACTAA(C/T), 0,
positive strand in the negative direction is SuccessablesTACT+-.bas, looking for TACTAA(C/T), 0,
positive strand in the positive direction is SuccessablesTACT++.bas, looking for TACTAA(C/T), 1, TACTAAT at 4157,
inverse complement, negative strand, negative direction is SuccessablesTACTci--.bas, looking for (A/G)TTAGTA, 0,
inverse complement, negative strand, positive direction is SuccessablesTACTci-+.bas, looking for (A/G)TTAGTA, 0,
inverse complement, positive strand, negative direction is SuccessablesTACTci+-.bas, looking for (A/G)TTAGTA, 0,
inverse complement, positive strand, positive direction is SuccessablesTACTci++.bas, looking for (A/G)TTAGTA, 1, ATTAGTA at 4148,

TACT positive direction (4265-4050) proximal promoters

Positive strand, positive direction: TACTAAT at 4157.
Positive strand, positive direction: ATTAGTA at 4148.

TACT random dataset samplings

TACTr0: 0.
TACTr1: 1, TACTAAT at 2375.
TACTr2: 1, TACTAAC at 2375.
TACTr3: 0.
TACTr4: 2, TACTAAT at 3670, TACTAAT at 3217.
TACTr5: 0.
TACTr6: 1, TACTAAC at 2376.
TACTr7: 0.
TACTr8: 1, TACTAAT at 852.
TACTr9: 1, TACTAAT at 3611.
TACTr0ci: 1, ATTAGTA at 3724.
TACTr1ci: 0.
TACTr2ci: 0.
TACTr3ci: 0.
TACTr4ci: 2, GTTAGTA at 3212, ATTAGTA at 2300.
TACTr5ci: 0.
TACTr6ci: 0.
TACTr7ci: 0.
TACTr8ci: 1, ATTAGTA at 2963.
TACTr9ci: 1, GTTAGTA at 4014.

TACTr arbitrary (evens) (4560-2846) UTRs

TACTr4: TACTAAT at 3670, TACTAAT at 3217.
TACTr0ci: ATTAGTA at 3724.
TACTr4ci: GTTAGTA at 3212.
TACTr8ci: ATTAGTA at 2963.

TACTr alternate (odds) (4560-2846) UTRs

TACTr9: TACTAAT at 3611.
TACTr9ci: GTTAGTA at 4014.

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

TACTr2: TACTAAC at 2375.
TACTr6: TACTAAC at 2376.
TACTr8: TACTAAT at 852.
TACTr4ci: ATTAGTA at 2300.

TACTr alternate negative direction (odds) (2596-1) distal promoters

TACTr1: TACTAAT at 2375.

TACTr arbitrary positive direction (odds) (4050-1) distal promoters

TACTr1: TACTAAT at 2375.
TACTr9: TACTAAT at 3611.

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

TACTr2: TACTAAC at 2375.
TACTr4: TACTAAT at 3670, TACTAAT at 3217.
TACTr6: TACTAAC at 2376.
TACTr8: TACTAAT at 852.
TACTr0ci: ATTAGTA at 3724.
TACTr4ci: GTTAGTA at 3212, ATTAGTA at 2300.
TACTr8ci: ATTAGTA at 2963.

TACT analysis and results

"A consensus sequence TACTAA(C/T) was derived for the branch site of Dictyostelium introns."^[1]

Reals or randoms	Promoters	direction	Numbers	Strands	Occurrences	Averages (± 0.1)
Reals	UTR	negative	0	2	0	0
Randoms	UTR	arbitrary negative	5	10	0.5	0.35
Randoms	UTR	alternate negative	2	10	0.2	0.35
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	0	10	0	0
Randoms	Proximal	alternate negative	0	10	0	0
Reals	Proximal	positive	2	2	1	1 ± 1 (-+0,++2)
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	4	10	0.4	0
Randoms	Distal	alternate negative	1	10	0.1	0
Reals	Distal	positive	0	2	0	0
Randoms	Distal	arbitrary positive	2	10	0.2	0.55
Randoms	Distal	alternate positive	9	10	0.9	0.55

Comparison:

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

Acknowledgements

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

Initial content for this page in some instances came from Wikiversity.

References

↑ ^1.0 ^1.1 Francisco Rivero (June 2002). "mRNA processing in Dictyostelium: sequence requirements for termination and splicing" (PDF). Protist. 153 (2): 169–76. doi:10.1078/1434-4610-00095. Retrieved 2017-04-05.
↑ Claudio W. Pikielny, John L. Teem, Michael Rosbash (September 1983). "Evidence for the biochemical role of an internal sequence in yeast nuclear mRNA introns: implications for U1 RNA and metazoan mRNA splicing" (PDF). Cell. 34 (2): 395–403. doi:10.1016/0092-8674(83)90373-2. Retrieved 2017-04-05.

External links

[Rivero-1] 1.0 ^1.1 Francisco Rivero (June 2002). "mRNA processing in Dictyostelium: sequence requirements for termination and splicing" (PDF). Protist. 153 (2): 169–76. doi:10.1078/1434-4610-00095. Retrieved 2017-04-05.

[Pikielny-2] Claudio W. Pikielny, John L. Teem, Michael Rosbash (September 1983). "Evidence for the biochemical role of an internal sequence in yeast nuclear mRNA introns: implications for U1 RNA and metazoan mRNA splicing" (PDF). Cell. 34 (2): 395–403. doi:10.1016/0092-8674(83)90373-2. Retrieved 2017-04-05.

[1]

[2]

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