Servenius sequence gene transcriptions: Difference between revisions

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# SERVr3: 0.
# SERVr3: 0.
# SERVr4: 0.
# SERVr4: 0.
# RDr5: 0.
# SERVr5: 0.
# RDr6: 0.
# SERVr6: 1, GGACCCT at 2271.
# RDr7: 0.
# SERVr7: 0.
# RDr8: 0.
# SERVr8: 0.
# RDr9: 0.
# SERVr9: 0.
# RDr0ci: 0.
# SERVr0ci: 1, AGGGTCC at 3950.
# RDr1ci: 0.
# RDr1ci: 0.
# RDr2ci: 0.
# RDr2ci: 0.
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# RDr9ci: 0.
# RDr9ci: 0.


===RDr arbitrary (evens) (4560-2846) UTRs===
===SERVr arbitrary (evens) (4560-2846) UTRs===
 
# SERVr0ci: AGGGTCC at 3950.


===RDr alternate (odds) (4560-2846) UTRs===
===RDr alternate (odds) (4560-2846) UTRs===
Line 103: Line 105:


# SERVr0: GGACCCT at 680.
# SERVr0: GGACCCT at 680.
# SERVr6: GGACCCT at 2271.


===SERVr alternate negative direction (odds) (2596-1) distal promoters===
===SERVr alternate negative direction (odds) (2596-1) distal promoters===
Line 115: Line 118:


# SERVr0: GGACCCT at 680.
# SERVr0: GGACCCT at 680.
# SERVr6: GGACCCT at 2271.
# SERVr0ci: AGGGTCC at 3950.


==Response element analysis and results==
==Response element analysis and results==

Revision as of 21:09, 26 January 2023

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

The "positive effect of W element may result from cooperative interactions between Z and other downstream elements such as the Servenius sequence, GGACCCT, located from -131 to -125 bp(28,38)."[1]

Human genes

Consensus sequences

The consensus sequence for the Servenius sequence is5'-GGACCCT-3'.[1]

Servenius samplings

Copying the apparent consensus sequence for Servenius (GGACCCT) and putting it in "⌘F" finds three located between ZSCAN22 and A1BG and one between ZNF497 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence GGACCCT (starting with SuccessablesSERV.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 GGACCCT, 5, GGACCCT at 4548, GGACCCT at 4496, GGACCCT at 4302, GGACCCT at 1961, GGACCCT at 1017.
  2. positive strand, negative direction, looking for GGACCCT, 0.
  3. positive strand, positive direction, looking for GGACCCT, 2, GGACCCT at 3760, GGACCCT at 288.
  4. negative strand, positive direction, looking for GGACCCT, 1, GGACCCT at 189.
  5. complement, negative strand, negative direction, looking for CCTGGGA, 0.
  6. complement, positive strand, negative direction, looking for CCTGGGA, 5, CCTGGGA at 4548, CCTGGGA at 4496, CCTGGGA at 4302, CCTGGGA at 1961, CCTGGGA at 1017.
  7. complement, positive strand, positive direction, looking for CCTGGGA, 1, CCTGGGA at 189.
  8. complement, negative strand, positive direction, looking for CCTGGGA, 2, CCTGGGA at 3760, CCTGGGA at 288.
  9. inverse complement, negative strand, negative direction, looking for AGGGTCC, 0.
  10. inverse complement, positive strand, negative direction, looking for AGGGTCC, 0.
  11. inverse complement, positive strand, positive direction, looking for AGGGTCC, 0.
  12. inverse complement, negative strand, positive direction, looking for AGGGTCC, 0.
  13. inverse negative strand, negative direction, looking for TCCCAGG, 0.
  14. inverse positive strand, negative direction, looking for TCCCAGG, 0.
  15. inverse positive strand, positive direction, looking for TCCCAGG, 0.
  16. inverse negative strand, positive direction, looking for TCCCAGG, 0.

SERV (4560-2846) UTRs

  1. Negative strand, negative direction: GGACCCT at 4548, GGACCCT at 4496, GGACCCT at 4302.

SERV negative direction (2596-1) distal promoters

  1. Negative strand, negative direction: GGACCCT at 1961, GGACCCT at 1017.

SERV positive direction (4050-1) distal promoters

  1. Negative strand, positive direction: GGACCCT at 189.
  2. Positive strand, positive direction: GGACCCT at 3760, GGACCCT at 288.

SERV random dataset samplings

  1. SERVr0: 1, GGACCCT at 680.
  2. SERVr1: 1, GGACCCT at 216.
  3. SERVr2: 0.
  4. SERVr3: 0.
  5. SERVr4: 0.
  6. SERVr5: 0.
  7. SERVr6: 1, GGACCCT at 2271.
  8. SERVr7: 0.
  9. SERVr8: 0.
  10. SERVr9: 0.
  11. SERVr0ci: 1, AGGGTCC at 3950.
  12. RDr1ci: 0.
  13. RDr2ci: 0.
  14. RDr3ci: 0.
  15. RDr4ci: 0.
  16. RDr5ci: 0.
  17. RDr6ci: 0.
  18. RDr7ci: 0.
  19. RDr8ci: 0.
  20. RDr9ci: 0.

SERVr arbitrary (evens) (4560-2846) UTRs

  1. SERVr0ci: AGGGTCC at 3950.

RDr alternate (odds) (4560-2846) UTRs

RDr arbitrary negative direction (evens) (2846-2811) core promoters

RDr alternate negative direction (odds) (2846-2811) core promoters

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

RDr alternate positive direction (evens) (4445-4265) core promoters

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

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

RDr arbitrary positive direction (odds) (4265-4050) proximal promoters

RDr alternate positive direction (evens) (4265-4050) proximal promoters

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

  1. SERVr0: GGACCCT at 680.
  2. SERVr6: GGACCCT at 2271.

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

  1. SERVr1: GGACCCT at 216.

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

  1. SERVr1: GGACCCT at 216.

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

  1. SERVr0: GGACCCT at 680.
  2. SERVr6: GGACCCT at 2271.
  3. SERVr0ci: AGGGTCC at 3950.

Response element analysis and results

Main article: Complex locus A1BG and ZNF497 § SERVs

The "positive effect of W element may result from cooperative interactions between Z and other downstream elements such as the Servenius sequence, GGACCCT, located from -131 to -125 bp(28,38)."[1]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 3 2 1.5 1.5
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
Randoms Proximal alternate positive 0 10 0 0
Reals Distal negative 2 2 1 1
Randoms Distal arbitrary negative 0 10 0 0
Randoms Distal alternate negative 0 10 0 0
Reals Distal positive 3 2 1.5 1.5 ± 0.5 (-+1,++2)
Randoms Distal arbitrary positive 0 10 0 0
Randoms Distal alternate positive 0 10 0 0

Comparison:

The occurrences of real responsive element consensus sequences are greater than the randoms. This suggests that the real responsive element consensus sequences are likely active or activable.

See also

References

  1. ↑ 1.0 1.1 1.2 John P. Cogswell, Patricia V. Basta, and Jenny P.-Y. Ting (October 1990). "X-box-binding proteins positively and negatively regulate transcription of the HLA-DRA gene through interaction with discrete upstream W and V elements" (PDF). Proceedings of the National Academy of Sciences USA. 87 (19): 7703–7707. doi:10.1073/pnas.87.19.7703. PMID 2120707. Retrieved 20 August 2020.

External links


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