TAT box gene transcriptions

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

"Some other cis-acting elements, such as pyrimidine boxes (GGTTTT) and TAT boxes (TATCCAT), are usually present in the vicinity of the GARE sequence of genes regulated by GA in cereal aleurone cells (Gubler and Jacobsen 1992; Cercos et al. 1999; Tsuji et al. 2006)."[1]

"Nucleotide and deduced amino acid of HMW-GS gene 1Bx23 [contains the] putative TAT box [TATAAAA] and CCACC sequence [CCAATT and CCAT] under double lines."[2]

"In Proteobacteria this consensus Tat box is best defined as Ser-Arg-Arg-Xaa-Phe-Leu-Lys where the arginine residues are almost invariant, the other amino acids are found at a frequency in excess of 50% and Xaa is a polar amino acid (Berks, 1996; Stanley et al., 2000). The corresponding sequence for plant chloroplast Tat substrates is Arg-Arg-Xaa-Hyd-Leu/Met where Hyd is a hydrophobic amino acid (Peltier et al., 2000). In both cases this Tat or twin-arginine consensus motif is located at the amino-terminal side of the n-region/h-region boundary [...]."[3]

TAT box (Yang) samplings

Main article: Model samplings

Copying a responsive elements consensus sequence TATAAAA and putting the sequence in "⌘F" finds none between ZNF497 and A1BG or one between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence TATAAAA (starting with SuccessablesTATY.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, negative direction, looking for TATAAAA, 1, TATAAAA at 2853.
  2. positive strand, negative direction, looking for TATAAAA, 2, TATAAAA at 222, TATAAAA at 183.
  3. positive strand, positive direction, looking for TATAAAA, 0.
  4. negative strand, positive direction, looking for TATAAAA, 0.
  5. complement, negative strand, negative direction, looking for ATATTTT, 2, ATATTTT at 222, ATATTTT at 183.
  6. complement, positive strand, negative direction, looking for ATATTTT, 1, ATATTTT at 2853.
  7. complement, positive strand, positive direction, looking for ATATTTT, 0.
  8. complement, negative strand, positive direction, looking for ATATTTT, 0.
  9. inverse complement, negative strand, negative direction, looking for TTTTATA, 2, TTTTATA at 2869, TTTTATA at 1740.
  10. inverse complement, positive strand, negative direction, looking for TTTTATA, 1, TTTTATA at 219.
  11. inverse complement, positive strand, positive direction, looking for TTTTATA, 0.
  12. inverse complement, negative strand, positive direction, looking for TTTTATA, 0.
  13. inverse negative strand, negative direction, looking for AAAATAT, 1, AAAATAT at 219.
  14. inverse positive strand, negative direction, looking for AAAATAT, 2, AAAATAT at 2869, AAAATAT at 1740.
  15. inverse positive strand, positive direction, looking for AAAATAT, 0.
  16. inverse negative strand, positive direction, looking for AAAATAT, 0.

TATY (4560-2846) UTRs

  1. Negative strand, negative direction: TTTTATA at 2869, TATAAAA at 2853.

TATY negative direction (2596-1) distal promoters

  1. Negative strand, negative direction: TTTTATA at 1740.
  2. Positive strand, negative direction: TATAAAA at 222, TTTTATA at 219, TATAAAA at 183.

TAT box (Yang) random dataset samplings

  1. TATYr0: 0.
  2. TATYr1: 0.
  3. TATYr2: 0.
  4. TATYr3: 1, TATAAAA at 4445.
  5. TATYr4: 0.
  6. TATYr5: 0.
  7. TATYr6: 0.
  8. TATYr7: 0.
  9. TATYr8: 1, TATAAAA at 707.
  10. TATYr9: 1, TATAAAA at 2622.
  11. TATYr0ci: 1, TTTTATA at 497.
  12. TATYr1ci: 0.
  13. TATYr2ci: 0.
  14. TATYr3ci: 0.
  15. TATYr4ci: 1, TTTTATA at 4527.
  16. TATYr5ci: 0.
  17. TATYr6ci: 0.
  18. TATYr7ci: 0.
  19. TATYr8ci: 0.
  20. TATYr9ci: 1, TTTTATA at 162.

TATYr arbitrary (evens) (4560-2846) UTRs

  1. TATYr4ci: TTTTATA at 4527.

TATYr alternate (odds) (4560-2846) UTRs

  1. TATYr3: TATAAAA at 4445.

TATYr arbitrary positive direction (odds) (4445-4265) core promoters

  1. TATYr3: TATAAAA at 4445.

TATYr alternate negative direction (odds) (2811-2596) proximal promoters

  1. TATYr9: TATAAAA at 2622.

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

  1. TATYr8: TATAAAA at 707.
  2. TATYr0ci: TTTTATA at 497.

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

  1. TATYr9ci: TTTTATA at 162.

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

  1. TATYr9: TATAAAA at 2622.
  2. TATYr9ci: TTTTATA at 162.

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

  1. TATYr8: TATAAAA at 707.
  2. TATYr0ci: TTTTATA at 497.

TAT box (Yang) analysis and results

Main article: Complex locus A1BG and ZNF497 § TATYs

"Nucleotide and deduced amino acid of HMW-GS gene 1Bx23 [contains the] putative TAT box [TATAAAA]".[2]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 2 2 1 1
Randoms UTR arbitrary negative 1 10 0.1 0.1
Randoms UTR alternate negative 1 10 0.1 0.1
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 1 10 0.1 0.05
Randoms Core alternate positive 0 10 0 0.05
Reals Proximal negative 0 2 0 0
Randoms Proximal arbitrary negative 0 10 0 0.05
Randoms Proximal alternate negative 1 10 0.1 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 4 2 2 2 ± 1 (--1,+-3)
Randoms Distal arbitrary negative 2 10 0.2 0.15
Randoms Distal alternate negative 1 10 0.1 0.15
Reals Distal positive 0 2 0 0
Randoms Distal arbitrary positive 2 10 0.2 0.2
Randoms Distal alternate positive 2 10 0.2 0.2

Comparison:

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

TAT box (Fan) samplings

Copying a responsive elements consensus sequence TATCCAT and putting the sequence in "⌘F" finds none between ZNF497 and A1BG or none between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence TATCCAT (starting with SuccessablesTATF.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, negative direction, looking for TATCCAT, 0.
  2. positive strand, negative direction, looking for TATCCAT, 0.
  3. positive strand, positive direction, looking for TATCCAT, 0.
  4. negative strand, positive direction, looking for TATCCAT, 0.
  5. complement, negative strand, negative direction, looking for ATAGGTA, 0.
  6. complement, positive strand, negative direction, looking for ATAGGTA, 0.
  7. complement, positive strand, positive direction, looking for ATAGGTA, 0.
  8. complement, negative strand, positive direction, looking for ATAGGTA, 0.
  9. inverse complement, negative strand, negative direction, looking for ATGGATA, 1, ATGGATA at 2996.
  10. inverse complement, positive strand, negative direction, looking for ATGGATA, 0.
  11. inverse complement, positive strand, positive direction, looking for ATGGATA, 0.
  12. inverse complement, negative strand, positive direction, looking for ATGGATA, 0.
  13. inverse negative strand, negative direction, looking for TACCTAT, 0.
  14. inverse positive strand, negative direction, looking for TACCTAT, 1, TACCTAT at 2996.
  15. inverse positive strand, positive direction, looking for TACCTAT, 0.
  16. inverse negative strand, positive direction, looking for TACCTAT, 0.

TATF (4560-2846) UTRs

  1. Negative strand, negative direction: ATGGATA at 2996.

TAT box (Fan) random samplings

  1. TATFr0: 0.
  2. TATFr1: 0.
  3. TATFr2: 0.
  4. TATFr3: 0.
  5. TATFr4: 0.
  6. TATFr5: 1, TATCCAT at 652.
  7. TATFr6: 0.
  8. TATFr7: 0.
  9. TATFr8: 0.
  10. TATFr9: 0.
  11. TATFr0ci: 0.
  12. TATFr1ci: 0.
  13. TATFr2ci: 0.
  14. TATFr3ci: 0.
  15. TATFr4ci: 0.
  16. TATFr5ci: 0.
  17. TATFr6ci: 0.
  18. TATFr7ci: 1, ATGGATA at 2719.
  19. TATFr8ci: 0.
  20. TATFr9ci: 0.

TATFr alternate negative direction (odds) (2811-2596) proximal promoters

  1. TATFr7ci: ATGGATA at 2719.

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

  1. TATFr5: TATCCAT at 652.

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

  1. TATFr5: TATCCAT at 652.
  2. TATFr7ci: ATGGATA at 2719.

TAT box (Fan) analysis and results

Main article: Complex locus A1BG and ZNF497 § TATFs

"Some other cis-acting elements, such as pyrimidine boxes (GGTTTT) and TAT boxes (TATCCAT), are usually present in the vicinity of the GARE sequence of genes regulated by GA in cereal aleurone cells (Gubler and Jacobsen 1992; Cercos et al. 1999; Tsuji et al. 2006)."[1]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 1 2 0.5 0.5 ± 0.5 (--1,+-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 0 10 0 0
Randoms Proximal alternate negative 0 10 0 0
Reals Proximal positive 0 2 0 0
Randoms Proximal arbitrary positive 0 10 0 0.05
Randoms Proximal alternate positive 1 10 0.1 0.05
Reals Distal negative 0 2 0 0
Randoms Distal arbitrary negative 0 10 0 0.05
Randoms Distal alternate negative 1 10 0.1 0.05
Reals Distal positive 0 2 0 0
Randoms Distal arbitrary positive 2 10 0.2 0.1
Randoms Distal alternate positive 0 10 0 0.1

Comparison:

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

Acknowledgements

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

See also

References

  1. ↑ 1.0 1.1 Liu-Min Fan, Xiaoyan Feng, Yu Wang and Xing Wang Deng (2007). "Gibberellin Signal Transduction in Rice". Journal of Integrative Plant Biology. 49 (6): 731−741. doi:10.1111/j.1744-7909.2007.00511.x. Retrieved 16 October 2018.
  2. ↑ 2.0 2.1 Zu‐Jun Yang, Guang‐Rong Li, Huan‐Lin Shu, Chang Liu, Juan Feng, Zhi‐Jian Chang and Zheng‐Long Ren (31 August 2006). "Molecular characterization of high molecular weight glutenin subunit allele 1Bx23 in common wheat introduced from hexaploid triticale". Hereditas. 143 (December): 159–166. doi:10.1111/j.2006.0018-0661.01948.x. Retrieved 17 October 2018.
  3. ↑ Ben C. Berks, Tracy Palmer and Frank Sargent (2004). "The Tat protein translocation pathway and its role in microbial physiology" (PDF). Advances in Microbial Physiology. 47: 187–254. doi:10.1016/S0065-2911(03)47004-5. Retrieved 17 October 2018.

External links

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