H and ACA box gene transcriptions

# 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)."
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')."
"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."
An H box has a consensus sequence of 3'-ACACCA-5'.
The combined consensus sequence is 5'-ACAGGA-3'.

# 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:
- negative strand, negative direction  is SuccessablesHACA--.bas, looking for 5'-ACAGGA-3', 0.
- positive strand, negative direction is SuccessablesHACA+-.bas, looking for 5'-ACAGGA-3', 1, 5'-ACAGGA-3' at 2690.
- negative strand, positive direction is SuccessablesHACA-+.bas, looking for 5'-ACAGGA-3', 1, 5'-ACAGGA-3' at 3572.
- positive strand, positive direction is SuccessablesHACA++.bas, looking for 5'-ACAGGA-3', 1, 5'-ACAGGA-3' at 3620.
- 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.
- 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.
- inverse complement, positive strand, negative direction is SuccessablesHACAci+-.bas, looking for 5'-TCCTGT-3', 1, 5'-TCCTGT-3' at 1911.
- 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
- Negative strand, negative direction: TCCTGT at 4468, TCCTGT at 3756, TCCTGT at 3389.

## HACA negative direction (2811-2596) proximal promoters
- Positive strand, negative direction: ACAGGA at 2690.

## HACA positive direction (4265-4050) proximal promoters
- Positive strand, positive direction: TCCTGT at 4252.

## HACA negative direction (2596-1) distal promoters
- Positive strand, negative direction: TCCTGT at 1911.

## HACA positive direction (4050-1) distal promoters
- Negative strand, positive direction: TCCTGT at 3622, ACAGGA at 3572, TCCTGT at 144.
- Positive strand, positive direction: ACAGGA at 3620, TCCTGT at 3131, TCCTGT at 2460.

# H and ACA box random dataset samplings
- HACAr0: 0.
- HACAr1: 1, ACAGGA at 3275.
- HACAr2: 0.
- HACAr3: 1, ACAGGA at 1344.
- HACAr4: 0.
- HACAr5: 0.
- HACAr6: 1, ACAGGA at 2593.
- HACAr7: 1, ACAGGA at 2793.
- HACAr8: 0.
- HACAr9: 0.
- HACAr0ci: 3, TCCTGT at 2253, TCCTGT at 1551, TCCTGT at 1009.
- HACAr1ci: 1, TCCTGT at 1802.
- HACAr2ci: 3, TCCTGT at 2879, TCCTGT at 1204, TCCTGT at 725.
- HACAr3ci: 1, TCCTGT at 350.
- HACAr4ci: 1, TCCTGT at 801.
- HACAr5ci: 0.
- HACAr6ci: 0.
- HACAr7ci: 1, TCCTGT at 4129.
- HACAr8ci: 1, TCCTGT at 3449.
- HACAr9ci: 0.

## HACAr arbitrary (evens) (4560-2846) UTRs
- HACAr2ci: TCCTGT at 2879.
- HACAr8ci: TCCTGT at 3449.

## HACAr alternate (odds) (4560-2846) UTRs
- HACAr1: ACAGGA at 3275.
- HACAr7ci: TCCTGT at 4129.

## HACAr alternate negative direction (odds) (2811-2596) proximal promoters
- HACAr7: ACAGGA at 2793.

## HACAr arbitrary positive direction (odds) (4265-4050) proximal promoters
- HACAr7ci: TCCTGT at 4129.

## HACAr arbitrary negative direction (evens) (2596-1) distal promoters
- HACAr6: ACAGGA at 2593.
- HACAr0ci: TCCTGT at 2253, TCCTGT at 1551, TCCTGT at 1009.
- HACAr2ci: TCCTGT at 1204, TCCTGT at 725.
- HACAr4ci: TCCTGT at 801.

## 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
- HACAr1: ACAGGA at 3275.
- HACAr3: ACAGGA at 1344.
- HACAr7: ACAGGA at 2793.
- HACAr1ci: TCCTGT at 1802.
- HACAr3ci: TCCTGT at 350.

## 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
The combined consensus sequence is ACAGGA.
Comparison:
The occurrences of real HACA UTRs, proximals and positive distals are greater than the randoms, negative distals are within the randoms. This suggests that the real HACAs are likely active or activable, negative distals likely random.

# Acknowledgements
The content on this page was first contributed by: Henry A. Hoff.
Initial content for this page in some instances came from Wikiversity.