H and ACA box gene transcriptions: Difference between revisions

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# HACAr8ci: TCCTGT at 3449.
# HACAr8ci: TCCTGT at 3449.


===RDr alternate (odds) (4560-2846) UTRs===
===HACAr alternate (odds) (4560-2846) UTRs===


===RDr arbitrary negative direction (evens) (2846-2811) core promoters===
# HACAr1: ACAGGA at 3275.
# HACAr7ci: TCCTGT at 4129.


===RDr alternate negative direction (odds) (2846-2811) core promoters===
===HACAr alternate negative direction (odds) (2811-2596) proximal promoters===


===RDr arbitrary positive direction (odds) (4445-4265) core promoters===
# HACAr7: ACAGGA at 2793.
 
===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===


===HACAr arbitrary positive direction (odds) (4265-4050) proximal promoters===
===HACAr arbitrary positive direction (odds) (4265-4050) proximal promoters===


# HACAr7ci: TCCTGT at 4129.
# HACAr7ci: TCCTGT at 4129.
===RDr alternate positive direction (evens) (4265-4050) proximal promoters===


===HACAr arbitrary negative direction (evens) (2596-1) distal promoters===
===HACAr arbitrary negative direction (evens) (2596-1) distal promoters===
Line 128: Line 121:
# HACAr4ci: TCCTGT at 801.
# HACAr4ci: TCCTGT at 801.


===RDr alternate negative direction (odds) (2596-1) distal promoters===
===HACAr alternate negative direction (odds) (2596-1) distal promoters===
 
# HACAr3: ACAGGA at 1344.
# HACAr1ci: TCCTGT at 1802.
# HACAr3ci: TCCTGT at 350.


===HACAr arbitrary positive direction (odds) (4050-1) distal promoters===
===HACAr arbitrary positive direction (odds) (4050-1) distal promoters===
Line 138: Line 135:
# HACAr3ci: TCCTGT at 350.
# HACAr3ci: TCCTGT at 350.


===RDr alternate positive direction (evens) (4050-1) distal promoters===
===HACAr alternate positive direction (evens) (4050-1) distal promoters===
 
# HACAr6: ACAGGA at 2593.
# HACAr0ci: TCCTGT at 2253, TCCTGT at 1551, TCCTGT at 1009.
# HACAr2ci: TCCTGT at 2879, TCCTGT at 1204, TCCTGT at 725.
# HACAr4ci: TCCTGT at 801.
# HACAr8ci: TCCTGT at 3449.


==H and ACA boxes analysis and results==
==H and ACA boxes analysis and results==

Revision as of 04:12, 9 January 2023

Editor-In-Chief: Henry A. Hoff

Consensus sequences

"The box H/ACA snoRNAs were most recently recognized as a small RNA family by virtue of an ACA trinucleotide located 3 nt upstream of the mature snoRNA 3' end (41). In addition to this ACA box, they have the consensus H box sequence (5'-ANANNA-3') but have no other primary sequence identity. Despite this lack of primary sequence conservation, the H and ACA boxes are embedded in an evolutionarily conserved hairpin-hinge-hairpin-tail core secondary structure with the H box in the single-stranded hinge region and the ACA box in the single-stranded tail (5, 16)."[1]

The "3' end of mature hTR (45) has an ACA trinucleotide 3 nt upstream of its 3' end. In addition, the 3' region of hTR contains a single H box consensus sequence (5'-AGAGGA-3')."[1]

"Comparison with the murine telomerase RNA (mTR) (7) suggests that the snoRNA-like features of hTR are evolutionarily conserved. The mTR 3' end (nt 169 to 397 as numbered in reference 25) has ~76% sequence identity with the corresponding region of hTR (nt 211 to 451) and includes consensus H (5'-ACAGGA-3') and ACA box sequences."[1]

An H box has a consensus sequence of 3'-ACACCA-5'.[2]

The combined consensus sequence is 5'-ACAGGA-3'.[1]

H and ACA boxes in promoters of A1BG

For the Basic programs (starting with SuccessablesHACA.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 is SuccessablesHACA--.bas, looking for 5'-ACAGGA-3', 0.
  2. positive strand, negative direction is SuccessablesHACA+-.bas, looking for 5'-ACAGGA-3', 1, 5'-ACAGGA-3' at 2690.
  3. negative strand, positive direction is SuccessablesHACA-+.bas, looking for 5'-ACAGGA-3', 1, 5'-ACAGGA-3' at 3572.
  4. positive strand, positive direction is SuccessablesHACA++.bas, looking for 5'-ACAGGA-3', 1, 5'-ACAGGA-3' at 3620.
  5. inverse complement, negative strand, negative direction is SuccessablesHACAci--.bas, looking for 5'-TCCTGT-3', 3, 5'-TCCTGT-3' at 3389, 5'-TCCTGT-3' at 3756, 5'-TCCTGT-3' at 4468.
  6. inverse complement, negative strand, positive direction is SuccessablesHACAci-+.bas, looking for 5'-TCCTGT-3', 2, 5'-TCCTGT-3' at 144, 5'-TCCTGT-3' at 3622.
  7. inverse complement, positive strand, negative direction is SuccessablesHACAci+-.bas, looking for 5'-TCCTGT-3', 1, 5'-TCCTGT-3' at 1911.
  8. inverse complement, positive strand, positive direction is SuccessablesHACAci++.bas, looking for 5'-TCCTGT-3', 3, 5'-TCCTGT-3' at 2460, 5'-TCCTGT-3' at 3131, 5'-TCCTGT-3' at 4252.

HACA (4560-2846) UTRs

  1. Negative strand, negative direction: TCCTGT at 4468, TCCTGT at 3756, TCCTGT at 3389.

HACA negative direction (2811-2596) proximal promoters

  1. Positive strand, negative direction: ACAGGA at 2690.

HACA positive direction (4265-4050) proximal promoters

  1. Positive strand, positive direction: TCCTGT at 4252.

HACA negative direction (2596-1) distal promoters

  1. Positive strand, negative direction: TCCTGT at 1911.

HACA positive direction (4050-1) distal promoters

  1. Negative strand, positive direction: TCCTGT at 3622, ACAGGA at 3572, TCCTGT at 144.
  2. Positive strand, positive direction: ACAGGA at 3620, TCCTGT at 3131, TCCTGT at 2460.

H and ACA box random dataset samplings

  1. HACAr0: 0.
  2. HACAr1: 1, ACAGGA at 3275.
  3. HACAr2: 0.
  4. HACAr3: 1, ACAGGA at 1344.
  5. HACAr4: 0.
  6. HACAr5: 0.
  7. HACAr6: 1, ACAGGA at 2593.
  8. HACAr7: 1, ACAGGA at 2793.
  9. HACAr8: 0.
  10. HACAr9: 0.
  11. HACAr0ci: 3, TCCTGT at 2253, TCCTGT at 1551, TCCTGT at 1009.
  12. HACAr1ci: 1, TCCTGT at 1802.
  13. HACAr2ci: 3, TCCTGT at 2879, TCCTGT at 1204, TCCTGT at 725.
  14. HACAr3ci: 1, TCCTGT at 350.
  15. HACAr4ci: 1, TCCTGT at 801.
  16. HACAr5ci: 0.
  17. HACAr6ci: 0.
  18. HACAr7ci: 1, TCCTGT at 4129.
  19. HACAr8ci: 1, TCCTGT at 3449.
  20. HACAr9ci: 0.

HACAr arbitrary (evens) (4560-2846) UTRs

  1. HACAr2ci: TCCTGT at 2879.
  2. HACAr8ci: TCCTGT at 3449.

HACAr alternate (odds) (4560-2846) UTRs

  1. HACAr1: ACAGGA at 3275.
  2. HACAr7ci: TCCTGT at 4129.

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

  1. HACAr7: ACAGGA at 2793.

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

  1. HACAr7ci: TCCTGT at 4129.

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

  1. HACAr6: ACAGGA at 2593.
  2. HACAr0ci: TCCTGT at 2253, TCCTGT at 1551, TCCTGT at 1009.
  3. HACAr2ci: TCCTGT at 1204, TCCTGT at 725.
  4. HACAr4ci: TCCTGT at 801.

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

  1. HACAr3: ACAGGA at 1344.
  2. HACAr1ci: TCCTGT at 1802.
  3. HACAr3ci: TCCTGT at 350.

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

  1. HACAr1: ACAGGA at 3275.
  2. HACAr3: ACAGGA at 1344.
  3. HACAr7: ACAGGA at 2793.
  4. HACAr1ci: TCCTGT at 1802.
  5. HACAr3ci: TCCTGT at 350.

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

  1. HACAr6: ACAGGA at 2593.
  2. HACAr0ci: TCCTGT at 2253, TCCTGT at 1551, TCCTGT at 1009.
  3. HACAr2ci: TCCTGT at 2879, TCCTGT at 1204, TCCTGT at 725.
  4. HACAr4ci: TCCTGT at 801.
  5. HACAr8ci: TCCTGT at 3449.

H and ACA boxes analysis and results

Main article: Complex locus A1BG and ZNF497 § H and ACA boxes

The combined consensus sequence is ACAGGA.[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 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 0 2 0 0
Randoms Distal arbitrary negative 0 10 0 0
Randoms Distal alternate negative 0 10 0 0
Reals Distal positive 0 2 0 0
Randoms Distal arbitrary positive 0 10 0 0
Randoms Distal alternate positive 0 10 0 0

Comparison:

The occurrences of real H and ACA box consensus sequences are greater than the randoms. This suggests that the real H and ACA box consensus sequences 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 1.2 1.3 1.4 James R. Mitchell, Jeffrey Cheng, ang Kathleen Collins (January 1999). "A Box H/ACA Small Nucleolar RNA-Like Domain at the Human Telomerase RNA 3' End" (PDF). Molecular and Cellular Biology. 19 (1): 567–576. Retrieved 5 November 2018.
  2. ↑ Timofey S. Rozhdestvensky, Thean Hock Tang, Inna V. Tchirkova, Jürgen Brosius, Jean‐Pierre Bachellerie and Alexander Hüttenhofer (2003). "Binding of L7Ae protein to the K‐turn of archaeal snoRNAs: a shared RNA binding motif for C/D and H/ACA box snoRNAs in Archaea". Nucleic Acids Research. 31 (3): 869–77. doi:10.1093/nar/gkg175. Retrieved 2014-06-08.

External links

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