C box gene transcriptions: Difference between revisions

Jump to navigation Jump to search
VisualWikitext
mNo edit summary
Line 59: Line 59:
# inverse, positive strand, positive direction, looking for 5'-TCTACCGGAG-3', 0.
# inverse, positive strand, positive direction, looking for 5'-TCTACCGGAG-3', 0.


===Random dataset samplings===
===CJbox random dataset samplings===


# RDr0: 0.
# CJboxr0: 0.
# RDr1: 0.
# CJboxr1: 0.
# RDr2: 0.
# CJboxr2: 0.
# RDr3: 0.
# CJboxr3: 0.
# RDr4: 0.
# CJboxr4: 0.
# RDr5: 0.
# CJboxr5: 0.
# RDr6: 0.
# CJboxr6: 0.
# RDr7: 0.
# CJboxr7: 0.
# RDr8: 0.
# CJboxr8: 0.
# RDr9: 0.
# CJboxr9: 0.
# RDr0ci: 0.
# CJboxr0ci: 0.
# RDr1ci: 0.
# CJboxr1ci: 0.
# RDr2ci: 0.
# CJboxr2ci: 0.
# RDr3ci: 0.
# CJboxr3ci: 0.
# RDr4ci: 0.
# CJboxr4ci: 0.
# RDr5ci: 0.
# CJboxr5ci: 0.
# RDr6ci: 0.
# CJboxr6ci: 0.
# RDr7ci: 0.
# CJboxr7ci: 0.
# RDr8ci: 0.
# CJboxr8ci: 0.
# RDr9ci: 0.
# CJboxr9ci: 0.


===RDr UTRs===
===CJboxr UTRs===
{{main|UTR promoter gene transcriptions}}
{{main|UTR promoter gene transcriptions}}


===RDr core promoters===
===CJboxr core promoters===
{{main|Core promoter gene transcriptions}}
{{main|Core promoter gene transcriptions}}


===RDr proximal promoters===
===CJboxr proximal promoters===
{{main|Proximal promoter gene transcriptions}}
{{main|Proximal promoter gene transcriptions}}


===RDr distal promoters===
===CJboxr distal promoters===
{{main|Distal promoter gene transcriptions}}
{{main|Distal promoter gene transcriptions}}


Revision as of 17:19, 27 June 2021

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

GAGGCCATCT is a C-box, [...].[1]

"Members of the box C/D snoRNA family, which are the subject of the present report, possess characteristic sequence elements known as box C (UGAUGA) and box D (GUCUGA)."[2]

The human ribosomal protein L11 gene (HRPL11) has [...] two potential snRNA-coding sequences in intron 4: the C box beginning at +4131 (GGTGATG), [...] a D box beginning at +4237 (TCCTG), [...].[3]

Analysis "of the recombinant (soybean [Glycine max] TGACG-motif binding factor 1) STF1 protein revealed the C-box (nGACGTCn) to be a high-affinity binding site (Cheong et al., 1998)."[4]

Hypotheses

Main article: Hypotheses
  1. The C boxes are not involved in the transcription of A1BG.

Johnson C-box samplings

For the Basic programs SuccessablesCJbox.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 5'-GAGGCCATCT-3'[1], 0.
  2. negative strand, positive direction, looking for 5'-GAGGCCATCT-3', 0.
  3. positive strand, negative direction, looking for 5'-GAGGCCATCT-3', 0.
  4. positive strand, positive direction, looking for 5'-GAGGCCATCT-3', 0.
  5. complement, negative strand, negative direction, looking for 5'-CTCCGGTAGA-3', 0.
  6. complement, negative strand, positive direction, looking for 5'-CTCCGGTAGA-3', 0.
  7. complement, positive strand, negative direction, looking for 5'-CTCCGGTAGA-3', 0.
  8. complement, positive strand, positive direction, looking for 5'-CTCCGGTAGA-3', 0.
  9. inverse complement, negative strand, negative direction, looking for 5'-AGATGGCCTC-3', 0.
  10. inverse complement, negative strand, positive direction, looking for 5'-AGATGGCCTC-3', 0.
  11. inverse complement, positive strand, negative direction, looking for 5'-AGATGGCCTC-3', 0.
  12. inverse complement, positive strand, positive direction, looking for 5'-AGATGGCCTC-3', 0.
  13. inverse, negative strand, negative direction, looking for 5'-TCTACCGGAG-3', 0.
  14. inverse, negative strand, positive direction, looking for 5'-TCTACCGGAG-3', 0.
  15. inverse, positive strand, negative direction, looking for 5'-TCTACCGGAG-3', 0.
  16. inverse, positive strand, positive direction, looking for 5'-TCTACCGGAG-3', 0.

CJbox random dataset samplings

  1. CJboxr0: 0.
  2. CJboxr1: 0.
  3. CJboxr2: 0.
  4. CJboxr3: 0.
  5. CJboxr4: 0.
  6. CJboxr5: 0.
  7. CJboxr6: 0.
  8. CJboxr7: 0.
  9. CJboxr8: 0.
  10. CJboxr9: 0.
  11. CJboxr0ci: 0.
  12. CJboxr1ci: 0.
  13. CJboxr2ci: 0.
  14. CJboxr3ci: 0.
  15. CJboxr4ci: 0.
  16. CJboxr5ci: 0.
  17. CJboxr6ci: 0.
  18. CJboxr7ci: 0.
  19. CJboxr8ci: 0.
  20. CJboxr9ci: 0.

CJboxr UTRs

Main article: UTR promoter gene transcriptions

CJboxr core promoters

Main article: Core promoter gene transcriptions

CJboxr proximal promoters

Main article: Proximal promoter gene transcriptions

CJboxr distal promoters

Main article: Distal promoter gene transcriptions

snoRNA C box

File:RF00071.jpg
This example of a C/D box is a small nucleolar RNA 73 (snoRNA U73). Credit: Rfam database (RF00071).{{free media}}
File:U14 snoRNA.png
This U14 snoRNA from Saccharomyces cerevisiae shows structure and genomic organization. Credit: Dmitry A.Samarsky, Maurille J.Fournier, Robert H.Singer and Edouard Bertrand.{{fairuse}}

For "box C/D snoRNAs, boxes C and D and an adjoining stem form a vital structure, known as the box C/D motif."[2]

"The [C and D] box elements are essential for snoRNA production [transcription] and for snoRNA-directed modification of rRNA nucleotides."[2]

The "motif is necessary and sufficient for nucleolar targeting, both in yeast and mammals. Moreover, in mammalian cells, RNA is targeted to coiled bodies as well. Thus, the box C/D motif is the first intranuclear RNA trafficking signal identified for an RNA family. Remarkably, it also couples snoRNA localization with synthesis and, most likely, function. The distribution of snoRNA precursors in mammalian cells suggests that this coupling is provided by a specific protein(s) which binds the box C/D motif during or rapidly after snoRNA transcription."[2]

In snoRNA U73 on the right, the C box starting from the left side of the stem consists of nucleotides: ARUGAUGA, and from the right side the D box is AGUCY. In 5' to 3' direction, the D box is YCUGA.

Shown in the second image on the right are the C box (3'-AGUAGU-5'). Substituting T for U yields C box = 3'-AGTAGT-5' in the transcription direction on the template strand.

Samarsky C box samplings

Main article: Sampling models

For the Basic programs (starting with SuccessablesCbox.bas or SuccessablesDbox.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 in the negative direction (from ZSCAN22 to A1BG) is SuccessablesCbox--.bas, looking for 5'-AGTAGT-3'[2], 4, 5'-AGTAGT-3', 2888, 5'-AGTAGT-3', 2944, 5'-AGTAGT-3', 3418, 5'-AGTAGT-3', 3521,
  2. negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesCbox-+.bas, looking for 5'-AGTAGT-3', 0,
  3. positive strand in the negative direction is SuccessablesCbox+-.bas, looking for 5'-AGTAGT-3', 0,
  4. positive strand in the positive direction is SuccessablesCbox++.bas, looking for 5'-AGTAGT-3', 1, 5'-AGTAGT-3', 3251,
  5. complement, negative strand, negative direction is SuccessablesCboxc--.bas, looking for 5'-TCATCA-3', 0,
  6. complement, negative strand, positive direction is SuccessablesCboxc-+.bas, looking for 5'-TCATCA-3', 1, 5'-TCATCA-3', 3251,
  7. complement, positive strand, negative direction is SuccessablesCboxc+-.bas, looking for 5'-TCATCA-3', 4, 5'-TCATCA-3', 2888, 5'-TCATCA-3', 2944, 5'-TCATCA-3', 3418, 5'-TCATCA-3', 3521,
  8. complement, positive strand, positive direction is SuccessablesCboxc++.bas, looking for 5'-TCATCA-3', 0,
  9. inverse complement, negative strand, negative direction is SuccessablesCboxci--.bas, looking for 5'-ACTACT-3', 0,
  10. inverse complement, negative strand, positive direction is SuccessablesCboxci-+.bas, looking for 5'-ACTACT-3', 0,
  11. inverse complement, positive strand, negative direction is SuccessablesCboxci+-.bas, looking for 5'-ACTACT-3', 0,
  12. inverse complement, positive strand, positive direction is SuccessablesCboxci++.bas, looking for 5'-ACTACT-3', 1, 5'-ACTACT-3' at 2144.
  13. inverse, negative strand, negative direction, is SuccessablesCboxi--.bas, looking for 5'-TGATGA-3', 0,
  14. inverse, negative strand, positive direction, is SuccessablesCboxi-+.bas, looking for 5'-TGATGA-3', 1, 5'-TGATGA-3', 2144,
  15. inverse, positive strand, negative direction, is SuccessablesCboxi+-.bas, looking for 5'-TGATGA-3', 0,
  16. inverse, positive strand, positive direction, is SuccessablesCboxi++.bas, looking for 5'-TGATGA-3', 0.

C box S UTRs

Main article: UTR promoter gene transcriptions

Negative strand, negative direction: AGTAGT at 3521, AGTAGT at 3418, AGTAGT at 2944, AGTAGT at 2888.

C box S distal promoters

Main article: Distal promoter gene transcriptions

Negative strand, positive direction: TGATGA at 2144.

Positive strand, positive direction: AGTAGT at 3251.

Random dataset samplings

  1. RDr0: 0.
  2. RDr1: 0.
  3. RDr2: 0.
  4. RDr3: 0.
  5. RDr4: 0.
  6. RDr5: 0.
  7. RDr6: 0.
  8. RDr7: 0.
  9. RDr8: 0.
  10. RDr9: 0.
  11. RDr0ci: 0.
  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.

RDr UTRs

Main article: UTR promoter gene transcriptions

RDr core promoters

Main article: Core promoter gene transcriptions

RDr proximal promoters

Main article: Proximal promoter gene transcriptions

RDr distal promoters

Main article: Distal promoter gene transcriptions

Voronina C box samplings

For the Basic programs starting with SuccessablesCVbox.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 5'-GGTGATG-3'[3], 0.
  2. negative strand, positive direction, looking for 5'-GGTGATG-3', 0.
  3. positive strand, negative direction, looking for 5'-GGTGATG-3', 1, 5'-GGTGATG-3' at 3798.
  4. positive strand, positive direction, looking for 5'-GGTGATG-3', 0.
  5. complement, negative strand, negative direction, looking for 5'-CCACTAC-3', 1, 5'-CCACTAC-3' at 3798.
  6. complement, negative strand, positive direction, looking for 5'-CCACTAC-3', 0.
  7. complement, positive strand, negative direction, looking for 5'-CCACTAC-3', 0.
  8. complement, positive strand, positive direction, looking for 5'-CCACTAC-3', 0.
  9. inverse complement, negative strand, negative direction, looking for 5'-CATCACC-3', 0.
  10. inverse complement, negative strand, positive direction, looking for 5'-CATCACC-3', 0.
  11. inverse complement, positive strand, negative direction, looking for 5'-CATCACC-3', 0.
  12. inverse complement, positive strand, positive direction, looking for 5'-CATCACC-3', 0.
  13. inverse, negative strand, negative direction, looking for 5'-GTAGTGG-3', 0.
  14. inverse, negative strand, positive direction, looking for 5'-GTAGTGG-3', 0.
  15. inverse, positive strand, negative direction, looking for 5'-GTAGTGG-3', 0.
  16. inverse, positive strand, positive direction, looking for 5'-GTAGTGG-3', 0.

Voronina C box UTRs

Main article: UTR promoter gene transcriptions
  1. Positive strand, negative direction: GGTGATG at 3798.

Random dataset samplings

  1. RDr0: 0.
  2. RDr1: 0.
  3. RDr2: 0.
  4. RDr3: 0.
  5. RDr4: 0.
  6. RDr5: 0.
  7. RDr6: 0.
  8. RDr7: 0.
  9. RDr8: 0.
  10. RDr9: 0.
  11. RDr0ci: 0.
  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.

RDr UTRs

Main article: UTR promoter gene transcriptions

RDr core promoters

Main article: Core promoter gene transcriptions

RDr proximal promoters

Main article: Proximal promoter gene transcriptions

RDr distal promoters

Main article: Distal promoter gene transcriptions

Song C-boxes

Analysis "of the recombinant (soybean [Glycine max] TGACG-motif binding factor 1) STF1 protein revealed the C-box (nGACGTCn) to be a high-affinity binding site (Cheong et al., 1998). The HY5 protein interacts with both the G- (CACGTG) and Z- (ATACGTGT) boxes of the light-regulated promoter of RbcS1A (ribulose bisphosphate carboxylase small subunit) and the CHS (chalcone synthase) genes (Ang et al., 1998; Chattopadhyay et al., 1998; Yadav et al., 2002). To test whether STF1 and HY5 have similar DNA-binding properties, the binding properties of each were compared with eight different DNA sequences that represent G-, C-, and C/G-box motifs [TGACGTGT]. C-box sequences carrying the mammalian cAMP responsive element (CRE; TGACGTCA) motif and the Hex sequence (TGACGTGGC), a hybrid C/G-box (Cheong et al., 1998), were high-affinity binding sites for both proteins [...]. No binding or limited binding was observed to as-1 (Lam et al., 1989), nos-1 (Lam et al., 1990), or the AP-1 site (TGACTCA; Kim et al., 1993). Binding to the palindromic G-box (PA G-box, GCCACGTGGC) was moderate. However, binding activity to the G-box of the light-responsive unit 1 (U1) region of the parsley (Petroselinum crispum) CHS promoter (CHS-U1: TCCACGTGGC; Schulze-Lefert et al., 1989) or the G-box of GmAux28 (TCCACGTGTC) was much weaker than to the PA G-box [...]."[4]

The "binding affinities of both bZIP proteins were similar to CREA/T (ATGACGTCAT), a CRE sequence with flanking adenine and thymine (A/T) at positions -4 and +4. [The] bZIP domains of both STF1 and HY5 have similar binding properties for recognizing ACGT-containing elements (ACEs). [Although] the G-box is a known target site for the HY5 protein, the C-box sequences are the preferred binding sites for both STF1 and HY5."[4]

"When analyzed by type of ACE, these sequences can be grouped into four subclasses [...]: C-box, where the C residue comes at the 12 position; a hybrid C/G- box (C/G-box), with G at the 12 position; C/A-box [TGACGTAT], with A at the 12 position; and C/T-box, with T at the 12 position. The C-box subclass contains the largest number of selected binding sites for STF1 (38% at 50 mM KCl and 48% at 150 mM), followed by the C/G- (25.3%) and the C/A-boxes (26%). Only a small number of C/T-boxes [TGACGTTA] (4/100) and non-TGACGT sequences (4/100) were selected."[4]

C-boxes are TCTTACGTCATC, AATGACGTCGAA, TCTCACGTGTGG, TTTGACGTGTGA, GATGACGTCATC, and AGAGACGTCAAC for an apparent consensus sequence of (A/G/T)(A/C/G/T)(A/T)(C/G/T)ACGT(C/G)(A/G/T)(A/G/T)(A/C/G).[4]

Song C-box samplings

For the Basic programs starting with SuccessablesC-box.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 GACGTC[4], 1, GACGTC at 4316.
  2. negative strand, positive direction, looking for GACGTC, 0.
  3. positive strand, negative direction, looking for GACGTC, 0,
  4. positive strand, positive direction, looking for GACGTC, 9, GACGTC at 4316, GACGTC at 3280, GACGTC at 3231, GACGTC at 2858, GACGTC at 1506, GACGTC at 1120, GACGTC at 532, GACGTC at 437, GACGTC at 193.
  5. inverse complement is the same as the direct consensus sequence.
  6. complement, negative strand, negative direction, looking for 5'-CTGCAG-3', 0,
  7. complement, negative strand, positive direction, looking for 5'-CTGCAG-3', 9, 5'-CTGCAG-3' at 193, 5'-CTGCAG-3' at 437, 5'-CTGCAG-3' at 532, 5'-CTGCAG-3' at 1120, 5'-CTGCAG-3' at 1506, 5'-CTGCAG-3' at 2858, 5'-CTGCAG-3' at 3231, 5'-CTGCAG-3' at 3280, 5'-CTGCAG-3' at 4316.
  8. complement, positive strand, negative direction, looking for 5'-CTGCAG-3', 1, 5'-CTGCAG-3' at 4316.
  9. complement, positive strand, positive direction, looking for 5'-CTGCAG-3', 0.

Song C-box UTRs

Main article: UTR promoter gene transcriptions

Negative strand, negative direction: GACGTC at 4316.

Song C-box core promoters

Main article: Core promoter gene transcriptions

Positive strand, positive direction: GACGTC at 4316.

Song C-box distal promoters

Main article: Distal promoter gene transcriptions

Positive strand, positive direction: GACGTC at 3280, GACGTC at 3231, GACGTC at 2858, GACGTC at 1506, GACGTC at 1120, GACGTC at 532, GACGTC at 437, GACGTC at 193.

Random dataset samplings

  1. RDr0: 0.
  2. RDr1: 0.
  3. RDr2: 0.
  4. RDr3: 0.
  5. RDr4: 0.
  6. RDr5: 0.
  7. RDr6: 0.
  8. RDr7: 0.
  9. RDr8: 0.
  10. RDr9: 0.
  11. RDr0ci: 0.
  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.

RDr UTRs

Main article: UTR promoter gene transcriptions

RDr core promoters

Main article: Core promoter gene transcriptions

RDr proximal promoters

Main article: Proximal promoter gene transcriptions

RDr distal promoters

Main article: Distal promoter gene transcriptions

Song C box hybrids

Hybrid C, A boxes

"When analyzed by type of ACE, these sequences can be grouped into four subclasses [...]: C-box, where the C residue comes at the 12 position; a hybrid C/G- box (C/G-box), with G at the 12 position; C/A-box [TGACGTAT], with A at the 12 position; and C/T-box, with T at the 12 position."[4]

Hybrid C, G boxes

"To test whether STF1 and HY5 have similar DNA-binding properties, the binding properties of each were compared with eight different DNA sequences that represent G-, C-, and C/G-box motifs [TGACGTGT]. C-box sequences carrying the mammalian cAMP responsive element (CRE; TGACGTCA) motif and the Hex sequence (TGACGTGGC), a hybrid C/G-box (Cheong et al., 1998), were high-affinity binding sites for both proteins [...]."[4]

Hybrid C, T boxes

"Only a small number of C/T-boxes [TGACGTTA] (4/100) and non-TGACGT sequences (4/100) were selected."[4]

Song hybrid C box samplings

Hybrid C, A box samplings

Copying a portion of the consensus sequence for the hybrid C, A box of TGACGTAT and putting it in "⌘F" finds none located between ZSCAN22 and A1BG and none between ZNF497 and A1BG as can be found by the computer programs.

For the Basic programs SuccessablesCAbox.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 5'-TGACGTAT-3'[4], 0.
  2. negative strand, positive direction, looking for 5'-TGACGTAT-3', 0.
  3. positive strand, negative direction, looking for 5'-TGACGTAT-3', 0.
  4. positive strand, positive direction, looking for 5'-TGACGTAT-3', 0.
  5. complement, negative strand, negative direction, looking for 5'-ACTGCATA-3', 0.
  6. complement, negative strand, positive direction, looking for 5'-ACTGCATA-3', 0.
  7. complement, positive strand, negative direction, looking for 5'-ACTGCATA-3', 0.
  8. complement, positive strand, positive direction, looking for 5'-ACTGCATA-3', 0.
  9. inverse complement, negative strand, negative direction, looking for 5'-ATACGTCA-3', 0.
  10. inverse complement, negative strand, positive direction, looking for 5'-ATACGTCA-3', 0.
  11. inverse complement, positive strand, negative direction, looking for 5'-ATACGTCA-3', 0.
  12. inverse complement, positive strand, positive direction, looking for 5'-ATACGTCA-3', 0.
  13. inverse, negative strand, negative direction, looking for 5'-TATGCAGT-3', 0.
  14. inverse, negative strand, positive direction, looking for 5'-TATGCAGT-3', 0.
  15. inverse, positive strand, negative direction, looking for 5'-TATGCAGT-3', 0.
  16. inverse, positive strand, positive direction, looking for 5'-TATGCAGT-3', 0.

Random dataset samplings

  1. RDr0: 0.
  2. RDr1: 0.
  3. RDr2: 0.
  4. RDr3: 0.
  5. RDr4: 0.
  6. RDr5: 0.
  7. RDr6: 0.
  8. RDr7: 0.
  9. RDr8: 0.
  10. RDr9: 0.
  11. RDr0ci: 0.
  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.

RDr UTRs

Main article: UTR promoter gene transcriptions

RDr core promoters

Main article: Core promoter gene transcriptions

RDr proximal promoters

Main article: Proximal promoter gene transcriptions

RDr distal promoters

Main article: Distal promoter gene transcriptions

Hybrid C, G box samplings

Copying a portion of the consensus sequence for the hybrid C, G box of TGACGTGT and putting it in "⌘F" finds none located between ZSCAN22 and A1BG and none between ZNF497 and A1BG as can be found by the computer programs.

For the Basic programs SuccessablesCGbox.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 5'-TGACGTGT-3'[4], 0.
  2. negative strand, positive direction, looking for 5'-TGACGTGT-3', 0.
  3. positive strand, negative direction, looking for 5'-TGACGTGT-3', 0.
  4. positive strand, positive direction, looking for 5'-TGACGTGT-3', 0.
  5. complement, negative strand, negative direction, looking for 5'-ACTGCACA-3', 0.
  6. complement, negative strand, positive direction, looking for 5'-ACTGCACA-3', 0.
  7. complement, positive strand, negative direction, looking for 5'-ACTGCACA-3', 0.
  8. complement, positive strand, positive direction, looking for 5'-ACTGCACA-3', 0.
  9. inverse complement, negative strand, negative direction, looking for 5'-ACACGTCA-3', 0.
  10. inverse complement, negative strand, positive direction, looking for 5'-ACACGTCA-3', 0.
  11. inverse complement, positive strand, negative direction, looking for 5'-ACACGTCA-3', 0.
  12. inverse complement, positive strand, positive direction, looking for 5'-ACACGTCA-3', 1, 5'-ACACGTCA-3' at 3962.
  13. inverse, negative strand, negative direction, looking for 5'-TGTGCAGT-3', 0.
  14. inverse, negative strand, positive direction, looking for 5'-TGTGCAGT-3', 1, 5'-TGTGCAGT-3' at 3962.
  15. inverse, positive strand, negative direction, looking for 5'-TGTGCAGT-3', 0.
  16. inverse, positive strand, positive direction, looking for 5'-TGTGCAGT-3', 0.

Random dataset samplings

  1. RDr0: 0.
  2. RDr1: 0.
  3. RDr2: 0.
  4. RDr3: 0.
  5. RDr4: 0.
  6. RDr5: 0.
  7. RDr6: 0.
  8. RDr7: 0.
  9. RDr8: 0.
  10. RDr9: 0.
  11. RDr0ci: 0.
  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.

RDr UTRs

Main article: UTR promoter gene transcriptions

RDr core promoters

Main article: Core promoter gene transcriptions

RDr proximal promoters

Main article: Proximal promoter gene transcriptions

RDr distal promoters

Main article: Distal promoter gene transcriptions

Hybrid C, T box samplings

Copying a portion of the consensus sequence for the hybrid C, T box of TGACGTTA and putting it in "⌘F" finds none located between ZSCAN22 and A1BG and none between ZNF497 and A1BG as can be found by the computer programs.

For the Basic programs SuccessablesCTbox.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 5'-TGACGTTA-3'[4], 0.
  2. negative strand, positive direction, looking for 5'-TGACGTTA-3', 0.
  3. positive strand, negative direction, looking for 5'-TGACGTTA-3', 0.
  4. positive strand, positive direction, looking for 5'-TGACGTTA-3', 0.
  5. complement, negative strand, negative direction, looking for 5'-ACTGCAAT-3', 0.
  6. complement, negative strand, positive direction, looking for 5'-ACTGCAAT-3', 0.
  7. complement, positive strand, negative direction, looking for 5'-ACTGCAAT-3', 0.
  8. complement, positive strand, positive direction, looking for 5'-ACTGCAAT-3', 0.
  9. inverse complement, negative strand, negative direction, looking for 5'-TAACGTCA-3', 0.
  10. inverse complement, negative strand, positive direction, looking for 5'-TAACGTCA-3', 0.
  11. inverse complement, positive strand, negative direction, looking for 5'-TAACGTCA-3', 0.
  12. inverse complement, positive strand, positive direction, looking for 5'-TAACGTCA-3', 0.
  13. inverse, negative strand, negative direction, looking for 5'-ATTGCAGT-3', 0.
  14. inverse, negative strand, positive direction, looking for 5'-ATTGCAGT-3', 0.
  15. inverse, positive strand, negative direction, looking for 5'-ATTGCAGT-3', 0.
  16. inverse, positive strand, positive direction, looking for 5'-ATTGCAGT-3', 0.

Random dataset samplings

  1. RDr0: 0.
  2. RDr1: 0.
  3. RDr2: 0.
  4. RDr3: 0.
  5. RDr4: 0.
  6. RDr5: 0.
  7. RDr6: 0.
  8. RDr7: 0.
  9. RDr8: 0.
  10. RDr9: 0.
  11. RDr0ci: 0.
  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.

RDr UTRs

Main article: UTR promoter gene transcriptions

RDr core promoters

Main article: Core promoter gene transcriptions

RDr proximal promoters

Main article: Proximal promoter gene transcriptions

RDr distal promoters

Main article: Distal promoter gene transcriptions

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 PA Johnson, D Bunick, NB Hecht (1991). "Protein Binding Regions in the Mouse and Rat Protamine-2 Genes" (PDF). Biology of Reproduction. 44 (1): 127–134. Retrieved 6 April 2019.
  2. ↑ 2.0 2.1 2.2 2.3 2.4 Dmitry A. Samarsky, Maurille J.Fournier, Robert H.Singer and Edouard Bertrand (1 July 1998). "The snoRNA box C/D motif directs nucleolar targeting and also couples snoRNA synthesis and localization" (PDF). The European Molecular Biology Organization (EMBO) Journal. 17 (13): 3747–3757. doi:10.1093/emboj/17.13.3747. PMID 9649444. Retrieved 2017-02-04.
  3. ↑ 3.0 3.1 E. N. Voronina, T. D. Kolokol’tsova, E. A. Nechaeva, and M. L. Filipenko (2003). "Structural–Functional Analysis of the Human Gene for Ribosomal Protein L11" (PDF). Molecular Biology. 37 (3): 362–371. Retrieved 11 April 2019.
  4. ↑ 4.00 4.01 4.02 4.03 4.04 4.05 4.06 4.07 4.08 4.09 4.10 4.11 Young Hun Song, Cheol Min Yoo, An Pio Hong, Seong Hee Kim, Hee Jeong Jeong, Su Young Shin, Hye Jin Kim, Dae-Jin Yun, Chae Oh Lim, Jeong Dong Bahk, Sang Yeol Lee, Ron T. Nagao, Joe L. Key, and Jong Chan Hong (April 2008). "DNA-Binding Study Identifies C-Box and Hybrid C/G-Box or C/A-Box Motifs as High-Affinity Binding Sites for STF1 and LONG HYPOCOTYL5 Proteins" (PDF). Plant Physiology. 146 (4): 1862–1877. doi:10.1104/pp.107.113217. Retrieved 26 March 2019.

External links

Retrieved from "https://www.wikidoc.org/index.php?title=C_box_gene_transcriptions&oldid=1705289"