H and ACA box gene transcriptions

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:

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.^[1]

Reals or randoms	Promoters	direction	Numbers	Strands	Occurrences	Averages (± 0.1)
Reals	UTR	negative	3	2	1.5	1.5 ± 1.5 (--3,+-0)
Randoms	UTR	arbitrary negative	2	10	0.2	0.2
Randoms	UTR	alternate negative	2	10	0.2	0.2
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	1	2	0.5	0.5 ± 0.5 (--0,+-1)
Randoms	Proximal	arbitrary negative	0	10	0	0.05
Randoms	Proximal	alternate negative	1	10	0.1	0.05
Reals	Proximal	positive	1	2	0.5	0.5 ± 0.5 (-+0,++1)
Randoms	Proximal	arbitrary positive	1	10	0.1	0.05
Randoms	Proximal	alternate positive	0	10	0	0.05
Reals	Distal	negative	1	2	0.5	0.5 ± 0.5 (--0,+-1)
Randoms	Distal	arbitrary negative	7	10	0.7	0.5
Randoms	Distal	alternate negative	3	10	0.3	0.5
Reals	Distal	positive	6	2	3	3 ± 0 (-+3,++3)
Randoms	Distal	arbitrary positive	5	10	0.5	0.7
Randoms	Distal	alternate positive	9	10	0.9	0.7

Comparison:

The occurrences of real HACA UTRs, proximals and distals are greater than the randoms. This suggests that the real HACAs 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.

References

↑ ^1.0 ^1.1 ^1.2 ^1.3 ^1.4 James R. Mitchell, Jeffrey Cheng, and 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.
↑ 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

Template:Sisterlinks

[Mitchell-1] 1.0 ^1.1 ^1.2 ^1.3 ^1.4 James R. Mitchell, Jeffrey Cheng, and 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.

[Rozhdestvensky-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.

[1]

[2]

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expressions General factor II D gene transcriptions General regulatory factors General transcription factor II A gene transcriptions General transcription factor II B gene transcriptions General transcription factor II D gene transcriptions General transcription factor II F gene transcriptions General transcription factor II H gene transcriptions General transcription factor gene transcriptions Gene transcriptions GGC triplet gene transcriptions Gibberellin responsive element gene transcriptions GLM box gene transcriptions Glucocorticoid response element gene transcriptions Grainy head gene transcriptions Grainy head transcription factor gene transcriptions Growth hormone response element gene transcriptions GT boxes Hac1p gene transcriptions Hair color gene expressions H and ACA box gene transcriptions H box gene transcriptions Heat-responsive element gene transcriptions Heat shock elements Hex sequence gene transcriptions HMG box gene transcriptions HNF gene transcriptions Homeobox gene transcriptions Hsf1p gene transcriptions HY box gene transcriptions Hybrid C, A boxes Hybrid C, G boxes Hybrid C, T boxes Hypoxia-inducible factor gene transcriptions Hypoxia response elements I box gene transcriptions Immunoglobulin like domain containing family Initiator element gene transcriptions Initiator-like element gene transcriptions Inositol/choline-responsive elements Interaction gene transcriptions Interferon regulatory factors Inverse copy gene transcriptions Jasmonic acid-responsive element gene transcriptions K-boxes Kozak sequence gene transcriptions Kruppel-associated box gene transcriptions Krüppel-like factor gene transcriptions L box gene transcriptions Leu3 gene transcriptions M35 box gene transcriptions MADS box gene transcriptions Maf recognition element gene transcriptions M box gene transcriptions Mcm1 regulatory factor gene transcriptions Met3 gene transcriptions Met31p box gene transcriptions Metal responsive element gene transcriptions Middle sporulation element gene transcriptions Mig1p gene transcriptions Model samplings Motif ten element gene transcriptions Msn2,4p gene transcriptions Musashi binding element gene transcriptions MYB recognition element gene transcriptions Myelocytomatosis transcription factor gene transcriptions Myocyte enhancer factor gene transcriptions N-boxes Nanos/Pumilio response element Ndt80p gene transcriptions Nuclear factor 1 Nuclear factor 𝜿B Nuclear factor gene transcriptions Nuclear factor of activated T cell gene transcriptions (NFAT) Nuclear factor Y gene transcriptions Nutrient-sensing response element gene transcriptions Oaf1p gene transcriptions ORE1 binding site gene transcriptions p53 response element gene transcriptions P63 DNA-binding site gene transcriptions P box gene transcriptions Pdr1,3p gene transcriptions Peroxisome proliferator hormone response element gene transcriptions Phosphate starvation-response transcription factor gene transcriptions Pollen1 element gene transcriptions Polycomb response element gene transcriptions Preinitiation complex Preinitiation complex gene transcriptions Pribnow box gene transcriptions Prolamin box gene transcriptions Promoter gene transcriptions Proximal promoter gene transcriptions Promoter occurrence gene transcriptions Pyrimidine box gene transcriptions Q element gene transcriptions Rap1 regulatory factor gene transcriptions Reb1 general regulatory factor gene transcriptions Retinoblastoma control element gene transcriptions Retinoic acid response element gene transcriptions Rgt1p gene transcriptions Rlm1p gene transcriptions RNA polymerase II gene transcriptions RNA polymerase II holoenzyme complex Root specific element gene transcriptions ROR-response element gene transcriptions Rox1p gene transcriptions Rpn4p gene transcriptions R response element gene transcriptions SARE gene transcriptions Seed-specific element gene transcriptions Serum response element gene transcriptions Servenius sequence gene transcriptions Shoot specific element gene transcriptions Sip4p gene transcriptions Smp1p gene transcriptions Sp1 gene transcriptions Spaceflight gene expressions Specificity protein gene transcriptions STAT gene transcriptions Ste12p gene transcriptions Sterol response element gene transcriptions Sucrose box gene transcriptions Synaptic Activity-Responsive Elements TACTAAC box gene transcriptions TAGteam gene transcriptions Tapetum box gene transcriptions TATA binding protein associated factor gene transcriptions TATA binding protein gene transcriptions TATA box actin/cytoskeleton/contractile family TATA box albumin family TATA box aldolase family TATA box alkaline phosphatase family TATA box annexin family TATA box cytochrome superfamily TATA box gene transcriptions TATA box heat shock family TATA box histone family TATA box human genes TATA box keratin family TATA box lipase family TATA box peptidase family TATA box platelet-derived growth factor family TATA box selenium-binding 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control sequence gene transcriptions Tryptophan residue U box gene transcriptions Unfolded protein response element gene transcriptions Upstream response element gene transcriptions Upstream stimulatory factor gene transcriptions UTR promoter gene transcriptions V and P box gene transcriptions V box gene transcriptions Vhr1p gene transcriptions Vitamin D response element gene transcriptions W box gene transcriptions X box gene transcriptions Xbp1p gene transcriptions X core promoter element gene transcriptions Xenobiotic response element gene transcriptions Xenobiotic responsive element gene transcriptions Yap1p,2p gene transcriptions Y box gene transcriptions YY1 gene transcriptions Zap1p gene transcriptions Z box gene transcriptions Zinc responsive element gene transcriptions