TACTAAC box gene transcriptions: Difference between revisions

Jump to navigation Jump to search
VisualWikitext
 
(6 intermediate revisions by the same user not shown)
Line 5: Line 5:
|title=mRNA processing in Dictyostelium: sequence requirements for termination and splicing
|title=mRNA processing in Dictyostelium: sequence requirements for termination and splicing
|journal=Protist
|journal=Protist
|month=June
|date=June 2002
|year=2002
|volume=153
|volume=153
|issue=2
|issue=2
Line 24: Line 23:
|title=Evidence for the biochemical role of an internal sequence in yeast nuclear mRNA introns: implications for U1 RNA and metazoan mRNA splicing
|title=Evidence for the biochemical role of an internal sequence in yeast nuclear mRNA introns: implications for U1 RNA and metazoan mRNA splicing
|journal=Cell
|journal=Cell
|month=September
|date=September 1983
|year=1983
|volume=34
|volume=34
|issue=2
|issue=2
Line 36: Line 34:
|accessdate=2017-04-05 }}</ref>
|accessdate=2017-04-05 }}</ref>


==Samplings of the A1BG promoters==
==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:
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 3'-TACTAA(C/T)-5', 0,
# 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 3'-TACTAA(C/T)-5', 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 3'-TACTAA(C/T)-5', 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 3'-TACTAA(C/T)-5', 1, 5'-TACTAAT-3' at 4157,
# positive strand in the positive direction is SuccessablesTACT++.bas, looking for TACTAA(C/T), 1, TACTAAT at 4157,
# complement, negative strand, negative direction is SuccessablesTACTc--.bas, looking for 3'-ATGATT(A/G)-5', 0,
# inverse complement, negative strand, negative direction is SuccessablesTACTci--.bas, looking for (A/G)TTAGTA, 0,
# complement, negative strand, positive direction is SuccessablesTACTc-+.bas, looking for 3'-ATGATT(A/G)-5', 1, 3'-ATGATTA-5', 4157,
# inverse complement, negative strand, positive direction is SuccessablesTACTci-+.bas, looking for (A/G)TTAGTA, 0,
# complement, positive strand, negative direction is SuccessablesTACTc+-.bas, looking for 3'-ATGATT(A/G)-5', 0,
# inverse complement, positive strand, negative direction is SuccessablesTACTci+-.bas, looking for (A/G)TTAGTA, 0,
# complement, positive strand, positive direction is SuccessablesTACTc++.bas, looking for 3'-ATGATT(A/G)-5', 0,
# inverse complement, positive strand, positive direction is SuccessablesTACTci++.bas, looking for (A/G)TTAGTA, 1, ATTAGTA at 4148,
# inverse complement, negative strand, negative direction is SuccessablesTACTci--.bas, looking for 3'-(A/G)TTAGTA-5', 0,
 
# inverse complement, negative strand, positive direction is SuccessablesTACTci-+.bas, looking for 3'-(A/G)TTAGTA-5', 0,
===TACT positive direction (4265-4050) proximal promoters===
# inverse complement, positive strand, negative direction is SuccessablesTACTci+-.bas, looking for 3'-(A/G)TTAGTA-5', 0,
 
# inverse complement, positive strand, positive direction is SuccessablesTACTci++.bas, looking for 3'-(A/G)TTAGTA-5', 1, 3'-ATTAGTA-5', 709,
# Positive strand, positive direction: TACTAAT at 4157.
# inverse, negative strand, negative direction, is SuccessablesTACTi--.bas, looking for 3'-(C/T)AATCAT-5', 0,
# Positive strand, positive direction: ATTAGTA at 4148.
# inverse, negative strand, positive direction, is SuccessablesTACTi-+.bas, looking for 3'-(C/T)AATCAT-5', 1, 3'-TAATCAT-5', 709,
 
# inverse, positive strand, negative direction, is SuccessablesTACTi+-.bas, looking for 3'-(C/T)AATCAT-5', 0,
==TACT random dataset samplings==
# inverse, positive strand, positive direction, is SuccessablesTACTi++.bas, looking for 3'-(C/T)AATCAT-5', 0.
 
# 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==
{{main|Complex locus A1BG and ZNF497#TACTs}}
"A consensus sequence TACTAA(C/T) was derived for the branch site of ''Dictyostelium'' introns."<ref name=Rivero/>
 
{|class="wikitable"
|-
! 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==
==Acknowledgements==
Line 74: Line 185:


<!-- footer templates -->
<!-- footer templates -->
{{Gene project}}{{Sisterlinks|TACTAAC boxes}}
{{Gene project}}


<!-- footer categories -->
<!-- footer categories -->
[[Category:Gene project/Lectures]]
[[Category:Gene project lectures]]
[[Category:Genes/Lectures]]
[[Category:Gene lectures]]
[[Category:Genetics/Lectures]]
[[Category:Genetics lectures]]
[[Category:Gene transcriptions/Lectures]]
[[Category:Gene transcription lectures]]
[[Category:Phosphates/Lectures]]
[[Category:Phosphate lectures]]
[[Category:Resources last modified in October 2019]]
[[Category:Resources last modified in December 2020]]

Latest revision as of 06:05, 12 February 2023

Editor-In-Chief: Henry A. Hoff

File:Dictyostelium discoideum 43.jpg
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:

  1. negative strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesTACT--.bas, looking for TACTAA(C/T), 0,
  2. negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesTACT-+.bas, looking for TACTAA(C/T), 0,
  3. positive strand in the negative direction is SuccessablesTACT+-.bas, looking for TACTAA(C/T), 0,
  4. positive strand in the positive direction is SuccessablesTACT++.bas, looking for TACTAA(C/T), 1, TACTAAT at 4157,
  5. inverse complement, negative strand, negative direction is SuccessablesTACTci--.bas, looking for (A/G)TTAGTA, 0,
  6. inverse complement, negative strand, positive direction is SuccessablesTACTci-+.bas, looking for (A/G)TTAGTA, 0,
  7. inverse complement, positive strand, negative direction is SuccessablesTACTci+-.bas, looking for (A/G)TTAGTA, 0,
  8. 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

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

TACT random dataset samplings

  1. TACTr0: 0.
  2. TACTr1: 1, TACTAAT at 2375.
  3. TACTr2: 1, TACTAAC at 2375.
  4. TACTr3: 0.
  5. TACTr4: 2, TACTAAT at 3670, TACTAAT at 3217.
  6. TACTr5: 0.
  7. TACTr6: 1, TACTAAC at 2376.
  8. TACTr7: 0.
  9. TACTr8: 1, TACTAAT at 852.
  10. TACTr9: 1, TACTAAT at 3611.
  11. TACTr0ci: 1, ATTAGTA at 3724.
  12. TACTr1ci: 0.
  13. TACTr2ci: 0.
  14. TACTr3ci: 0.
  15. TACTr4ci: 2, GTTAGTA at 3212, ATTAGTA at 2300.
  16. TACTr5ci: 0.
  17. TACTr6ci: 0.
  18. TACTr7ci: 0.
  19. TACTr8ci: 1, ATTAGTA at 2963.
  20. TACTr9ci: 1, GTTAGTA at 4014.

TACTr arbitrary (evens) (4560-2846) UTRs

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

TACTr alternate (odds) (4560-2846) UTRs

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

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

  1. TACTr2: TACTAAC at 2375.
  2. TACTr6: TACTAAC at 2376.
  3. TACTr8: TACTAAT at 852.
  4. TACTr4ci: ATTAGTA at 2300.

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

  1. TACTr1: TACTAAT at 2375.

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

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

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

  1. TACTr2: TACTAAC at 2375.
  2. TACTr4: TACTAAT at 3670, TACTAAT at 3217.
  3. TACTr6: TACTAAC at 2376.
  4. TACTr8: TACTAAT at 852.
  5. TACTr0ci: ATTAGTA at 3724.
  6. TACTr4ci: GTTAGTA at 3212, ATTAGTA at 2300.
  7. TACTr8ci: ATTAGTA at 2963.

TACT analysis and results

Main article: Complex locus A1BG and ZNF497 § TACTs

"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.

See also

References

  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.
  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.

External links

Retrieved from "https://www.wikidoc.org/index.php?title=TACTAAC_box_gene_transcriptions&oldid=1733105"