H and ACA box gene transcriptions: Difference between revisions

Revision as of 06:08, 30 April 2022

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.
negative strand, positive direction is SuccessablesHACA-+.bas, looking for 5'-ACAGGA-3', 1, 5'-ACAGGA-3' at 3572.
positive strand, negative direction is SuccessablesHACA+-.bas, looking for 5'-ACAGGA-3', 1, 5'-ACAGGA-3' at 2690.
positive strand, positive direction is SuccessablesHACA++.bas, looking for 5'-ACAGGA-3', 1, 5'-ACAGGA-3' at 3620.
complement, negative strand, negative direction is SuccessablesHACAc--.bas, looking for 5'-TGTCCT-3', 1, 5'-TGTCCT-3' at 2690.
complement, negative strand, positive direction is SuccessablesHACAc-+.bas, looking for 5'-TGTCCT-3', 1, 5'-TGTCCT-3' at 3620.
complement, positive strand, negative direction is SuccessablesHACAc+-.bas, looking for 5'-TGTCCT-3', 0.
complement, positive strand, positive direction is SuccessablesHACAc++.bas, looking for 5'-TGTCCT-3', 1, 5'-TGTCCT-3' at 3572.
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.
inverse, negative strand, negative direction, is SuccessablesHACAi--.bas, looking for 5'-AGGACA-3', 1, 5'-AGGACA-3' at 1911.
inverse, negative strand, positive direction, is SuccessablesHACAi-+.bas, looking for 5'-AGGACA-3', 3, 3'-AGGACA-3' at 2460, 3'-AGGACA-3' at 3131, 3'-AGGACA-3' at 4252.
inverse, positive strand, negative direction, is SuccessablesHACAi+-.bas, looking for 5'-AGGACA-3', 3, 5'-AGGACA-3' at 3389, 5'-AGGACA-3' at 3756, 5'-AGGACA-3' at 4468.
inverse, positive strand, positive direction, is SuccessablesHACAi++.bas, looking for 5'-AGGACA-3', 2, 5'-AGGACA-3' at 144, 5'-AGGACA-3' at 3622.

AAA UTRs

AAA core promoters

AAA proximal promoters

AAA distal promoters

Random dataset samplings

RDr0: 0.
RDr1: 0.
RDr2: 0.
RDr3: 0.
RDr4: 0.
RDr5: 0.
RDr6: 0.
RDr7: 0.
RDr8: 0.
RDr9: 0.
RDr0ci: 0.
RDr1ci: 0.
RDr2ci: 0.
RDr3ci: 0.
RDr4ci: 0.
RDr5ci: 0.
RDr6ci: 0.
RDr7ci: 0.
RDr8ci: 0.
RDr9ci: 0.

RDr UTRs

RDr core promoters

RDr proximal promoters

RDr distal promoters

Response element analysis and results

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

Reals or randoms	Promoters	direction	Strands
Reals	UTR	negative	2
Randoms	UTR	arbitrary negative	10
Randoms	UTR	alternate negative	10
Reals	Core	negative	2
Randoms	Core	negative	10
Reals	Core	positive	2
Randoms	Core	positive	10
Reals	Proximal	negative	2
Randoms	Proximal	negative	10
Reals	Proximal	positive	2
Randoms	Proximal	positive	10
Reals	Distal	negative	2
Randoms	Distal	negative	10
Reals	Distal	positive	2
Randoms	Distal	positive	10

Comparison:

The occurrences of real responsive element consensus sequences are larger than the randoms. This suggests that the real responsive element 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.

References

↑ ^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.
↑ 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, 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.

[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]

@@ Line 59: / Line 59: @@
 # inverse, positive strand, negative direction, is SuccessablesHACAi+-.bas, looking for 5'-AGGACA-3', 3, 5'-AGGACA-3' at 3389, 5'-AGGACA-3' at 3756, 5'-AGGACA-3' at 4468.
 # inverse, positive strand, positive direction, is SuccessablesHACAi++.bas, looking for 5'-AGGACA-3', 2, 5'-AGGACA-3' at 144, 5'-AGGACA-3' at 3622.
+===AAA UTRs===
+{{main|UTR promoter gene transcriptions}}
+===AAA core promoters===
+{{main|Core promoter gene transcriptions}}
+===AAA proximal promoters===
+{{main|Proximal promoter gene transcriptions}}
+===AAA distal promoters===
+{{main|Distal promoter gene transcriptions}}
+==Random dataset samplings==
+# RDr0: 0.
+# RDr1: 0.
+# RDr2: 0.
+# RDr3: 0.
+# RDr4: 0.
+# RDr5: 0.
+# RDr6: 0.
+# RDr7: 0.
+# RDr8: 0.
+# RDr9: 0.
+# RDr0ci: 0.
+# RDr1ci: 0.
+# RDr2ci: 0.
+# RDr3ci: 0.
+# RDr4ci: 0.
+# RDr5ci: 0.
+# RDr6ci: 0.
+# RDr7ci: 0.
+# RDr8ci: 0.
+# RDr9ci: 0.
+===RDr UTRs===
+===RDr core promoters===
+===RDr proximal promoters===
+===RDr distal promoters===
+==Response element analysis and results==
+{{main|Complex locus A1BG and ZNF497#H and ACA boxes}}
+The combined consensus sequence is 5'-ACAGGA-3'.<ref name=Mitchell/>
+{|class="wikitable"
+|-
+! 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 || negative || 0 || 10 || 0 || 0
+|-
+| Reals || Core || positive || 0 || 2 || 0 || 0
+|-
+| Randoms || Core || positive || 0 || 10 || 0 || 0
+|-
+| Reals || Proximal || negative || 0 || 2 || 0 || 0
+|-
+| Randoms || Proximal || negative || 0 || 10 || 0 || 0
+|-
+| Reals || Proximal || positive || 0 || 2 || 0 || 0
+|-
+| Randoms || Proximal || positive || 0 || 10 || 0 || 0
+|-
+| Reals || Distal || negative || 0 || 2 || 0 || 0
+|-
+| Randoms || Distal || negative || 0 || 10 || 0 || 0
+|-
+| Reals || Distal || positive || 0 || 2 || 0 || 0
+|-
+| Randoms || Distal || positive || 0 || 10 || 0 || 0
+|}
+Comparison:
+The occurrences of real responsive element consensus sequences are larger than the randoms. This suggests that the real responsive element consensus sequences are likely active or activable.
 ==Acknowledgements==

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Transcription resources	A1BG gene transcription core promoters A1BG gene transcriptions A1BG regulatory elements and regions A1BG response element gene transcriptions A1BG response element negative results A1BG response element positive results ABA-response element gene transcriptions Abf1 regulatory factor gene transcriptions A box gene transcriptions ACGT-containing element gene transcriptions Activating protein gene transcriptions Activating transcription factor gene transcriptions Adenylate–uridylate rich element gene transcriptions Adr1p gene transcriptions Aft1p gene transcriptions AGC box gene transcriptions AGCE gene transcriptions Alpha-amylase conserved element gene transcriptions Amino acid response element gene transcriptions AARE-like Androgen response element gene transcriptions Angiotensinogen core promoter element gene transcriptions Antioxidant-electrophile responsive element gene transcriptions ATA box gene transcriptions Auxin response factor gene transcriptions B box gene transcriptions Bioinformatics tool gene transcriptions Box gene transcriptions B recognition element upstream Bridge gene transcriptions CAAT box gene transcriptions CACA elements CadC binding domain gene transcriptions Calcineurin-responsive transcription factor gene transcriptions Calcium-response element gene transcriptions cAMP response element gene transcriptions C and D boxes gene transcriptions Carbohydrate response element gene transcriptions Carbon source-responsive element gene transcriptions Carcinoembryonic antigen gene family CARE gene transcriptions CArG box gene transcriptions CAT box gene transcriptions Cat8p gene transcriptions Cbf1 regulatory factor gene transcriptions C box gene transcriptions CCCTC-binding factor gene transcriptions C-EBP box gene transcriptions Cell-cycle box gene transcriptions Cell cycle regulation gene transcriptions CENP-B box gene transcriptions CGCG box gene transcriptions Circadian control element gene transcriptions Cold-responsive element gene transcriptions Complement copy gene transcriptions Complement-inverse copy gene transcriptions Consensus sequence gene transcriptions Copper response element gene transcriptions Core promoter gene transcriptions Coupling element gene transcriptions CRE box gene transcriptions Cytokinin response regulator gene transcriptions Cytoplasmic polyadenylation element gene transcriptions DAF-16-associated element gene transcriptions DAF-16 binding element gene transcriptions D box gene transcriptions Defense and stress-responsive element gene transcriptions Degenerate nucleotide gene transcriptions Dispersed promoter gene transcriptions Distal promoter gene transcriptions DNA melting gene transcriptions DNA damage response element gene transcriptions DNA replication-related element gene transcriptions Downstream core element gene transcriptions Downstream promoter element gene transcriptions Downstream TFIIB recognition element gene transcriptions DREB box gene transcriptions E2 box gene transcriptions EIF4E basal element gene transcriptions EIN3 binding site gene transcriptions Enhancer activity copy gene transcriptions E box gene transcriptions Element gene transcriptions Endoplasmic reticulum stress response element gene transcriptions Endosperm expression gene transcriptions Enhancer box gene transcriptions Estrogen response element gene transcriptions Ethylene responsive element gene transcriptions Families of TATA box genes F box gene transcriptions Focused promoter gene transcriptions Forkhead box gene transcriptions Fur box gene transcriptions GAAC element gene transcriptions Gal4p gene transcriptions Γ-interferon activated sequence gene transcriptions GARE gene transcriptions GA responsive complex gene transcriptions GATA gene transcriptions G box gene transcriptions GC box gene transcriptions GCC box gene transcriptions Gcn4p gene transcriptions Gcr1p gene transcriptions Gene 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 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 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 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 family TATA box serine protease family TATA box serpin superfamily TATA box transforming growth factor superfamily TATA box trefoil family TATA box tumor necrosis factor superfamily TATA box zinc metalloenzyme family TAT box gene transcriptions TATC box gene transcriptions Tbf1 regulatory factor gene transcriptions T box gene transcriptions TCCACCATA element gene transcriptions TC element gene transcriptions TCT gene transcriptions TEA consensus sequence gene transcriptions Tec1p gene transcriptions Telomeric repeat DNA-binding factor gene transcriptions Tetradecanoylphorbol-13-acetate response element gene transcriptions TGF-β control elements (TCEs) TGF-β inhibitory elements (TIEs) Thyroid hormone response element gene transcriptions Transcriptional regulation Transcription bubble gene transcriptions Transcription factor gene transcriptions Transcription factor 3 gene transcriptions Transcription factory gene transcriptions Transcription start site gene transcriptions Translational control sequence gene transcriptions 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