Cytokinin response regulator gene transcriptions

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

"Cytokinin fulfills its diverse roles in planta through a series of transcriptional responses."[1]

Human genes

Main article: Human genes

Gene expressions

Main article: Gene expressions

"In yeast two-hybrid analyses, the AHPs interact with various Arabidopsis histidine sensor kinases and Arabidopsis response regulators (ARRs) [20,24,25], consistent with their role in mediating phosphotransfer among these elements."[2]

"The 23 ARR genes fall into two main groups on the basis of their sequence similarities, domain structure and transcriptional response to cytokinin [27,28]. The type-A ARRs are comprised of a receiver domain and a short carboxyl terminus and their transcription is rapidly elevated in response to exogenous cytokinin; these are considered to be primary response genes [27,29,30]. The type-B ARRs, in addition to the receiver domain, have a carboxy-terminal output domain that has a DNA-binding GARP domain and a transcriptional activation domain. Transcription of the type-B ARRs is not altered by cytokinin."[2]

"The C-terminal output domain of type-B ARRs contains the 􏰄60-amino-acid GARP motif (so-called after the founding members Golden2, ARR and Psr1; it is also termed B motif or ARRM) [...], which is distantly related to the Myb repeat of transcription factors [33􏰂,37,38]."[3] Some of the ARRs are ARR1 - ARR22.[2][4][3]

Interactions

Main article: Interaction gene transcriptions

"Cytokinin employs a two-component multi-step phosphorelay for its perception and signaling transduction12–14. In Arabidopsis, there are three cytokinin receptors (ARABIDOPSIS HISTIDINE KINASEs; AHK2, 3, 4) and eleven type-B response regulators (ARABIDOSPIS RESPONSE REGULATORs; B-ARRs)8,15."[1]

"The cytokinin transcriptional response centrally affects the family of ARRs. Type-B ARRs (B-ARRs) are transcription factors (TFs) with a GARP-like DNA binding domain at their C-termini and a receiver domain at their N-termini. Type-A ARRs (A-ARRs) are similar to the N-termini receiver domain of B-ARRs but do not possess a DNA binding domain."[1]

Consensus sequences

Main article: Consensus sequence gene transcriptions

ARR1: AGATT(C/T), ARR10: (A/G)GATA(A/C)G, ARR12: (A/G)AGATA.[1]

"Type-B ARRs are transcription factors that localize to the nucleus [9,28,36]. A consensus DNA-binding sequence for type-B ARRs has been delineated (G/A)GGAT(T/C), and this sequence signature is found in the promoters of many of the cytokinin primary response genes [30]."[2]

"We used GeneSpring 5.0 software (Silicon Genetics, Redwood City, CA) to search for common motifs enriched within 1 kb upstream of the translational start site of the 17 genes that are consistently upregulated by cytokinin (those genes induced in six or more of the cytokinin treatments [...]). The sequence GATCTT was identified as a core sequence motif found significantly enriched in the upstream regions of this set of genes. [This] common upstream sequence motif GATCTT [occurs] on the forward strand, and [...] the complement of the motif AAGATC [also occurs]. Upstream regions of the cytokinin-regulated type-A ARRs showed the highest concentration of these motifs, generally clustering in the 500 bp proximal to the coding region. The sequence of this common upstream sequence motif closely matches (G/A)GAT(T/C), the optimal DNA-binding sequence identified in vitro for ARR1 and ARR2, two type-B ARRs (Sakai et al., 2000). Gel shift assays with various derivatives of the optimal type-B ARR-binding site NGAT(T/C) showed a slight preference for A at position 1 and a C at position 5, consistent with part of the common sequence motif we identified (Sakai et al., 2000). The frequency of this common upstream sequence motif in the upstream regions of the type-A ARRs is positively correlated with the level of their induction by cytokinin. The most highly cytokinin-induced genes, ARR5, ARR7, and ARR16, have multiple copies of this motif. Additionally, genes that are either only weakly induced by cytokinin or not expressed at detectable levels, ARR3, ARR4, and ARR17, have one or no motifs [...]. ARR6, which is moderately induced by cytokinin, does not fit this pattern because it has no consensus motif in its upstream region, although two such motifs are found within the fourth intron of this gene. The common upstream sequence motif (GATCTT) should randomly occur approximately 0.32 times per kilobase pair, taking into account the GC content observed in intergenic regions of Arabidopsis (approximately 33%). Our search of all genes present on the Affymetrix GeneChip that are expressed with a raw of at least 500 but not induced by cytokinin (950 genes) revealed that the sequence motif GATCTT is present a total of 358 times in the 1 kb upstream of the translational start site, or approximately 0.38 times per kilobase pair. In contrast, this core sequence motif is present 14 times among the upstream regions of the top 17 cytokinin up-regulated genes and only six times among the upstream regions of the 21 cytokinin down-regulated genes."[4]

Binding site for

Enhancer activity

Main article: Enhancer activity copy gene transcriptions

Promoter occurrences

Main article: Promoter occurrence gene transcriptions

Hypotheses

Main article: Hypotheses
  1. A1BG has no regulatory elements in either promoter.
  2. A1BG is not transcribed by a regulatory element.
  3. No regulatory element participates in the transcription of A1BG.

ARR1 Cytokinin samplings

Copying a responsive elements consensus sequence AGATT(C/T) and putting the sequence in "⌘F" finds one between ZNF497 and A1BG or one between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence AGATT(C/T) (starting with SuccessablesARR1.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 AGATT(C/T), 0.
  2. positive strand, negative direction, looking for AGATT(C/T), 1, AGATTC at 2452.
  3. positive strand, positive direction, looking for AGATT(C/T), 1, AGATTC at 122.
  4. negative strand, positive direction, looking for AGATT(C/T), 1, AGATTT at 2869.
  5. inverse complement, negative strand, negative direction, looking for (A/G)AATCT, 1, AAATCT at 50.
  6. inverse complement, positive strand, negative direction, looking for (A/G)AATCT, 0.
  7. inverse complement, positive strand, positive direction, looking for (A/G)AATCT, 0.
  8. inverse complement, negative strand, positive direction, looking for (A/G)AATCT, 2, GAATCT at 2725, GAATCT at 2243.

ARR1 negative direction (2596-1) distal promoters

  1. Negative strand, negative direction: AAATCT at 50.
  2. Positive strand, negative direction: AGATTC at 2452.

ARR1 positive direction (4050-1) distal promoters

  1. Negative strand, positive direction: AGATTT at 2869, GAATCT at 2725, GAATCT at 2243.
  2. Positive strand, positive direction: AGATTC at 122.

ARR1 random samplings

  1. ARR1r0: 2, AGATTC at 2653, AGATTT at 129.
  2. ARR1r1: 1, AGATTC at 2449.
  3. ARR1r2: 5, AGATTT at 4202, AGATTT at 3002, AGATTC at 2932, AGATTC at 2653, AGATTC at 1691.
  4. ARR1r3: 0.
  5. ARR1r4: 1, AGATTC at 2722.
  6. ARR1r5: 1, AGATTC at 4090.
  7. ARR1r6: 1, AGATTT at 94.
  8. ARR1r7: 1, AGATTT at 708.
  9. ARR1r8: 1, AGATTT at 2243.
  10. ARR1r9: 0.
  11. ARR1r0ci: 0.
  12. ARR1r1ci: 0.
  13. ARR1r2ci: 1, GAATCT at 1168.
  14. ARR1r3ci: 1, AAATCT at 3269.
  15. ARR1r4ci: 2, AAATCT at 2446, GAATCT at 665.
  16. ARR1r5ci: 2, AAATCT at 2374, AAATCT at 2106.
  17. ARR1r6ci: 3, GAATCT at 2335, AAATCT at 728, AAATCT at 364.
  18. ARR1r7ci: 2, AAATCT at 3016, AAATCT at 2284.
  19. ARR1r8ci: 3, AAATCT at 3716, AAATCT at 1301, AAATCT at 285.
  20. ARR1r9ci: 2, GAATCT at 3545, GAATCT at 2835.

ARR1r arbitrary (evens) (4560-2846) UTRs

  1. ARR1r2: AGATTT at 4202, AGATTT at 3002, AGATTC at 2932.
  2. ARR1r8ci: AAATCT at 3716.

ARR1r alternate (odds) (4560-2846) UTRs

  1. ARR1r5: AGATTC at 4090.
  2. ARR1r3ci: AAATCT at 3269.
  3. ARR1r7ci: AAATCT at 3016.
  4. ARR1r9ci: GAATCT at 3545.

ARR1r alternate negative direction (odds) (2846-2811) core promoters

  1. ARR1r9ci: GAATCT at 2835.

ARR1r arbitrary negative direction (evens) (2811-2596) proximal promoters

  1. ARR1r0: AGATTC at 2653.
  2. ARR1r2: AGATTC at 2653.
  3. ARR1r4: AGATTC at 2722.

ARR1r arbitrary positive direction (odds) (4265-4050) proximal promoters

  1. ARR1r5: AGATTC at 4090.

ARR1r alternate positive direction (evens) (4265-4050) proximal promoters

  1. ARR1r2: AGATTT at 4202.

ARR1r arbitrary negative direction (evens) (2596-1) distal promoters

  1. ARR1r0: AGATTT at 129.
  2. ARR1r2: AGATTC at 1691.
  3. ARR1r6: AGATTT at 94.
  4. ARR1r8: AGATTT at 2243.
  5. ARR1r2ci: GAATCT at 1168.
  6. ARR1r4ci: AAATCT at 2446.
  7. ARR1r6ci: GAATCT at 2335.
  8. ARR1r8ci: AAATCT at 1301, AAATCT at 285.

ARR1r alternate negative direction (odds) (2596-1) distal promoters

  1. ARR1r1: AGATTC at 2449.
  2. ARR1r7: AGATTT at 708.
  3. ARR1r5ci: AAATCT at 2374, AAATCT at 2106.
  4. ARR1r7ci: AAATCT at 2284.
  5. ARR1r9ci: GAATCT at 2835.

ARR1r arbitrary positive direction (odds) (4050-1) distal promoters

  1. ARR1r1: AGATTC at 2449.
  2. ARR1r7: AGATTT at 708.
  3. ARR1r3ci: AAATCT at 3269.
  4. ARR1r5ci: AAATCT at 2374, AAATCT at 2106.
  5. ARR1r7ci: AAATCT at 3016, AAATCT at 2284.
  6. ARR1r9ci: GAATCT at 3545, GAATCT at 2835.

ARR1r alternate positive direction (evens) (4050-1) distal promoters

  1. ARR1r0: AGATTC at 2653, AGATTT at 129.
  2. ARR1r2: AGATTT at 3002, AGATTC at 2932, AGATTC at 2653, AGATTC at 1691.
  3. ARR1r4: AGATTC at 2722.
  4. ARR1r6: AGATTT at 94.
  5. ARR1r8: AGATTT at 2243.
  6. ARR1r2ci: GAATCT at 1168.
  7. ARR1r4ci: AAATCT at 2446.
  8. ARR1r6ci: GAATCT at 2335, AAATCT at 728, AAATCT at 364.
  9. ARR1r8ci: AAATCT at 3716, AAATCT at 1301, AAATCT at 285.

ARR1 analysis and results

Main article: Complex locus A1BG and ZNF497 § ARR1s

ARR1: AGATT(C/T).[1]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 0 2 0 0
Randoms UTR arbitrary negative 4 10 0.4 0.4
Randoms UTR alternate negative 4 10 0.4 0.4
Reals Core negative 0 2 0 0
Randoms Core arbitrary negative 0 10 0 0.05
Randoms Core alternate negative 1 10 0.1 0.05
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 3 10 0.3 0.15
Randoms Proximal alternate negative 0 10 0 0.15
Reals Proximal positive 0 2 0 0
Randoms Proximal arbitrary positive 1 10 0.1 0.1
Randoms Proximal alternate positive 1 10 0.1 0.1
Reals Distal negative 2 2 1 1 ± 0 (--1,+-1)
Randoms Distal arbitrary negative 9 10 0.9 0.75
Randoms Distal alternate negative 6 10 0.6 0.75
Reals Distal positive 4 2 2 2 ± 1 (-+3,++1)
Randoms Distal arbitrary positive 9 10 0.9 1.3 ± 0.4
Randoms Distal alternate positive 17 10 1.7 1.3 ± 0.4

Comparison:

The occurrences of real ARR1 negative distals are greater than the randoms, positive direction distals overlap the high randoms. This suggests that the real ARR1s are likely active or activable.

ARR10 Cytokinin samplings

Copying a responsive elements consensus sequence (A/G)GATA(A/C)G and putting the sequence in "⌘F" finds none between ZNF497 and A1BG or none between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence (A/G)GATA(A/C)G (starting with SuccessablesARR10.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 (A/G)GATA(A/C)G, 0.
  2. positive strand, negative direction, looking for (A/G)GATA(A/C)G, 0.
  3. positive strand, positive direction, looking for (A/G)GATA(A/C)G, 0.
  4. negative strand, positive direction, looking for (A/G)GATA(A/C)G, 0.
  5. inverse complement, negative strand, negative direction, looking for C(G/T)TATC(C/T), 1, CGTATCC at 3447.
  6. inverse complement, positive strand, negative direction, looking for C(G/T)TATC(C/T), 0.
  7. inverse complement, positive strand, positive direction, looking for C(G/T)TATC(C/T), 0.
  8. inverse complement, negative strand, positive direction, looking for C(G/T)TATC(C/T), 0.

ARR10 (4560-2846) UTRs

  1. Negative strand, negative direction: CGTATCC at 3447.

ARR10 random samplings

  1. ARR10r0: 2, GGATACG at 3220, GGATAAG at 1407.
  2. ARR10r1: 1, GGATACG at 494.
  3. ARR10r2: 1, GGATAAG at 658.
  4. ARR10r3: 0.
  5. ARR10r4: 1, GGATACG at 512.
  6. ARR10r5: 0.
  7. ARR10r6: 1, AGATAAG at 1816.
  8. ARR10r7: 4, AGATAAG at 4077, GGATAAG at 3425, GGATAAG at 2721, AGATAAG at 793.
  9. ARR10r8: 0.
  10. ARR10r9: 0.
  11. ARR10r0ci: 1, CTTATCT at 3618.
  12. ARR10r1ci: 0.
  13. ARR10r2ci: 2, CTTATCC at 2854, CGTATCT at 2323.
  14. ARR10r3ci: 1, CTTATCC at 1874.
  15. ARR10r4ci: 3, CGTATCC at 4507, CTTATCC at 4303, CGTATCT at 4095.
  16. ARR10r5ci: 0.
  17. ARR10r6ci: 0.
  18. ARR10r7ci: 0.
  19. ARR10r8ci: 1, CTTATCC at 2417.
  20. ARR10r9ci: 3, CGTATCT at 3666, CTTATCT at 1991, CGTATCC at 1985.

ARR10r arbitrary (evens) (4560-2846) UTRs

  1. ARR10r0: GGATACG at 3220.
  2. ARR10r0ci: CTTATCT at 3618.
  3. ARR10r2ci: CTTATCC at 2854.
  4. ARR10r4ci: CGTATCC at 4507, CTTATCC at 4303, CGTATCT at 4095.

ARR10r alternate (odds) (4560-2846) UTRs

  1. ARR10r7: AGATAAG at 4077, GGATAAG at 3425.
  2. ARR10r9ci: CGTATCT at 3666.

ARR10r alternate positive direction (evens) (4445-4265) core promoters

  1. ARR10r4ci: CTTATCC at 4303.

ARR10r alternate negative direction (odds) (2811-2596) proximal promoters

  1. ARR10r7: GGATAAG at 2721.

ARR10r arbitrary positive direction (odds) (4265-4050) proximal promoters

  1. ARR10r7: AGATAAG at 4077.

ARR10r alternate positive direction (evens) (4265-4050) proximal promoters

  1. ARR10r4ci: CGTATCT at 4095.

ARR10r arbitrary negative direction (evens) (2596-1) distal promoters

  1. ARR10r0: GGATAAG at 1407.
  2. ARR10r2: GGATAAG at 658.
  3. ARR10r4: GGATACG at 512.
  4. ARR10r6: AGATAAG at 1816.
  5. ARR10r8ci: CTTATCC at 2417.

ARR10r alternate negative direction (odds) (2596-1) distal promoters

  1. ARR10r1: GGATACG at 494.
  2. ARR10r7: AGATAAG at 793.
  3. ARR10r3ci: CTTATCC at 1874.
  4. ARR10r9ci: CTTATCT at 1991, CGTATCC at 1985.

AAR10r arbitrary positive direction (odds) (4050-1) distal promoters

  1. ARR10r1: GGATACG at 494.
  2. ARR10r7: GGATAAG at 3425, GGATAAG at 2721, AGATAAG at 793.
  3. ARR10r3ci: CTTATCC at 1874.
  4. ARR10r9ci: CGTATCT at 3666, CTTATCT at 1991, CGTATCC at 1985.

ARR10r alternate positive direction (evens) (4050-1) distal promoters

  1. ARR10r0: GGATACG at 3220, GGATAAG at 1407.
  2. ARR10r2: GGATAAG at 658.
  3. ARR10r4: GGATACG at 512.
  4. ARR10r6: AGATAAG at 1816.
  5. ARR10r0ci: CTTATCT at 3618.
  6. ARR10r2ci: CTTATCC at 2854, CGTATCT at 2323.
  7. ARR10r8ci: CTTATCC at 2417.

ARR10 analysis and results

Main article: Complex locus A1BG and ZNF497 § ARR10s

ARR10: (A/G)GATA(A/C)G.[1]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 1 2 0.5 0.5 ± 0.5 (--1,+-0)
Randoms UTR arbitrary negative 5 10 0.5 0.4 ± 0.1
Randoms UTR alternate negative 3 10 0.3 0.4 ± 0.1
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 0.05
Randoms Core alternate positive 1 10 0.1 0.05
Reals Proximal negative 0 2 0 0
Randoms Proximal arbitrary negative 0 10 0 0.05
Randoms Proximal alternate negative 1 10 0.1 0.05
Reals Proximal positive 0 2 0 0
Randoms Proximal arbitrary positive 1 10 0.1 0.1
Randoms Proximal alternate positive 1 10 0.1 0.1
Reals Distal negative 0 2 0 0
Randoms Distal arbitrary negative 5 10 0.5 0.5
Randoms Distal alternate negative 5 10 0.5 0.5
Reals Distal positive 0 2 0 0
Randoms Distal arbitrary positive 8 10 0.8 0.85
Randoms Distal alternate positive 9 10 0.9 0.85

Comparison:

The occurrences of real ARR10s are ≥ the randoms. This suggests that the real ARR10s are likely active or activable.

ARR12 Cytokinin samplings

Main article: Model samplings

Copying a responsive elements consensus sequence (A/G)AGATA and putting the sequence in "⌘F" finds none between ZNF497 and A1BG or none between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence (A/G)AGATA (starting with SuccessablesARR1.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 (A/G)AGATA, 1, AAGATA at 1525.
  2. positive strand, negative direction, looking for (A/G)AGATA, 3, AAGATA at 2177, AAGATA at 1595, AAGATA at 57.
  3. positive strand, positive direction, looking for (A/G)AGATA, 0.
  4. negative strand, positive direction, looking for (A/G)AGATA, 0.
  5. inverse complement, negative strand, negative direction, looking for TATCT(C/T), 4, TATCTT at 4080, TATCTC at 1711, TATCTT at 356, TATCTT at 101.
  6. inverse complement, positive strand, negative direction, looking for TATCT(C/T), 1, TATCTT at 1732.
  7. inverse complement, positive strand, positive direction, looking for TATCT(C/T), 1, TATCTT at 2628.
  8. inverse complement, negative strand, positive direction, looking for TATCT(C/T), 0.

ARR12 (4560-2846) UTRs

  1. Negative strand, negative direction: TATCTT at 4080.

ARR12 negative direction (2596-1) distal promoters

  1. Negative strand, negative direction: TATCTC at 1711, AAGATA at 1525, TATCTT at 356, TATCTT at 101.
  2. Positive strand, negative direction: AAGATA at 2177, TATCTT at 1732, AAGATA at 1595, AAGATA at 57.

ARR12 positive direction (4050-1) distal promoters

  1. Positive strand, positive direction: TATCTT at 2628.

ARR12 random samplings

  1. ARR12r0: 0.
  2. ARR12r1: 2, AAGATA at 751, AAGATA at 162.
  3. ARR12r2: 1, GAGATA at 2113.
  4. ARR12r3: 1, GAGATA at 1775.
  5. ARR12r4: 1, GAGATA at 941.
  6. ARR12r5: 2, AAGATA at 3737, AAGATA at 1142.
  7. ARR12r6: 3, AAGATA at 1999, GAGATA at 1814, AAGATA at 1241.
  8. ARR12r7: 2, AAGATA at 4075, GAGATA at 791.
  9. ARR12r8: 4, AAGATA at 4344, AAGATA at 3577, GAGATA at 3467, GAGATA at 2998.
  10. ARR12r9: 3, GAGATA at 4167, AAGATA at 4019, GAGATA at 2993.
  11. ARR12r0ci: 3, TATCTT at 4103, TATCTT at 709, TATCTT at 336.
  12. ARR12r1ci: 0.
  13. ARR12r2ci: 2, TATCTT at 2416, TATCTC at 2324.
  14. ARR12r3ci: 1, TATCTC at 3356.
  15. ARR12r4ci: 4, TATCTT at 4476, TATCTT at 4096, TATCTC at 1680, TATCTT at 168.
  16. ARR12r5ci: 0.
  17. ARR12r6ci: 1, TATCTT at 2039.
  18. ARR12r7ci: 0.
  19. ARR12r8ci: 1, TATCTT at 2327.
  20. ARR12r9ci: 5, TATCTT at 4330, TATCTT at 3834, TATCTT at 3667, TATCTT at 1992, TATCTT at 477.

ARR12r arbitrary (evens) (4560-2846) UTRs

  1. ARR12r8: AAGATA at 4344, AAGATA at 3577, GAGATA at 3467, GAGATA at 2998.
  2. ARR12r0ci: TATCTT at 4103.
  3. ARR12r4ci: TATCTT at 4476, TATCTT at 4096.

ARR12r alternate (odds) (4560-2846) UTRs

  1. ARR12r5: AAGATA at 3737.
  2. ARR12r7: AAGATA at 4075.
  3. ARR12r9: GAGATA at 4167, AAGATA at 4019, GAGATA at 2993.
  4. ARR12r3ci: TATCTC at 3356.
  5. ARR12r9ci: TATCTT at 4330, TATCTT at 3834, TATCTT at 3667.

ARR12r arbitrary positive direction (odds) (4445-4265) core promoters

  1. ARR12r9ci: TATCTT at 4330.

ARR12r alternate positive direction (evens) (4445-4265) core promoters

  1. ARR12r8: AAGATA at 4344.

ARR12r arbitrary positive direction (odds) (4265-4050) proximal promoters

  1. ARR12r7: AAGATA at 4075.
  2. ARR12r9: GAGATA at 4167.

ARR12r alternate positive direction (evens) (4265-4050) proximal promoters

  1. ARR12r0ci: TATCTT at 4103.
  2. ARR12r4ci: TATCTT at 4096.

ARR12r arbitrary negative direction (evens) (2596-1) distal promoters

  1. ARR12r2: GAGATA at 2113.
  2. ARR12r4: GAGATA at 941.
  3. ARR12r6: AAGATA at 1999, GAGATA at 1814, AAGATA at 1241.
  4. ARR12r0ci: TATCTT at 709, TATCTT at 336.
  5. ARR12r2ci: TATCTT at 2416, TATCTC at 2324.
  6. ARR12r4ci: TATCTC at 1680, TATCTT at 168.
  7. ARR12r6ci: TATCTT at 2039.
  8. ARR12r8ci: TATCTT at 2327.

ARR12r alternate negative direction (odds) (2596-1) distal promoters

  1. ARR12r1: AAGATA at 751, AAGATA at 162.
  2. ARR12r3: GAGATA at 1775.
  3. ARR12r5: AAGATA at 1142.
  4. ARR12r7: GAGATA at 791.
  5. ARR12r9ci: TATCTT at 1992, TATCTT at 477.

ARR12r arbitrary positive direction (odds) (4050-1) distal promoters

  1. ARR12r1: AAGATA at 751, AAGATA at 162.
  2. ARR12r3: GAGATA at 1775.
  3. ARR12r5: AAGATA at 3737, AAGATA at 1142.
  4. ARR12r7: GAGATA at 791.
  5. ARR12r9: AAGATA at 4019, GAGATA at 2993.
  6. ARR12r3ci: TATCTC at 3356.
  7. ARR12r9ci: TATCTT at 3834, TATCTT at 3667, TATCTT at 1992, TATCTT at 477.

ARR12r alternate positive direction (evens) (4050-1) distal promoters

  1. ARR12r2: GAGATA at 2113.
  2. ARR12r4: GAGATA at 941.
  3. ARR12r6: AAGATA at 1999, GAGATA at 1814, AAGATA at 1241.
  4. ARR12r0ci: TATCTT at 709, TATCTT at 336.
  5. ARR12r2ci: TATCTT at 2416, TATCTC at 2324.
  6. ARR12r4ci: TATCTC at 1680, TATCTT at 168.
  7. ARR12r6ci: TATCTT at 2039.
  8. ARR12r8ci: TATCTT at 2327.

ARR12 analysis and results

Main article: Complex locus A1BG and ZNF497 § ARR12s

ARR12: (A/G)AGATA.[1]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 1 2 0.5 0.5 ± 0.5 (--1,+-0)
Randoms UTR arbitrary negative 7 10 0.7 0.8
Randoms UTR alternate negative 9 10 0.9 0.8
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 1 10 0.1 0.1
Randoms Core alternate positive 1 10 0.1 0.1
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 2 10 0.2 0.2
Randoms Proximal alternate positive 2 10 0.2 0.2
Reals Distal negative 8 2 4 4 ± 0 (--4,+-4)
Randoms Distal arbitrary negative 13 10 1.3 1
Randoms Distal alternate negative 7 10 0.7 1
Reals Distal positive 1 2 0.5 0.5 ± 0.5 (-+0,++1)
Randoms Distal arbitrary positive 13 10 1.3 1.3
Randoms Distal alternate positive 13 10 1.3 1.3

Comparison:

The occurrences of real ARR12s are > or < the randoms. This suggests that the real ARR12s are likely active or activable.

ARR (Ferreira) samplings

Copying a responsive elements consensus sequence (G/A)GGAT(T/C) and putting the sequence in "⌘F" finds one between ZNF497 and A1BG or three between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence (G/A)GGAT(T/C) (starting with SuccessablesARRF.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 (G/A)GGAT(T/C), 1, AGGATC at 2093.
  2. positive strand, negative direction, looking for (G/A)GGAT(T/C), 4, AGGATC at 4288, AGGATC at 4157, AGGATC at 4006, GGGATC at 2239.
  3. positive strand, positive direction, looking for (G/A)GGAT(T/C), 1, AGGATT at 2083.
  4. negative strand, positive direction, looking for (G/A)GGAT(T/C), 2, AGGATC at 4080, GGGATT at 2545.
  5. inverse complement, negative strand, negative direction, looking for (A/G)ATCC(C/T), 3, AATCCT at 3457, GATCCT at 1308, AATCCT at 239.
  6. inverse complement, positive strand, negative direction, looking for (A/G)ATCC(C/T), 13, GATCCC at 4477, AATCCC at 3976, AATCCC at 3067, AATCCC at 2678, AATCCT at 2091, AATCCC at 1917, GATCCC at 1814, AATCCC at 1782, AATCCC at 1264, AATCCC at 1137, AATCCC at 807, AATCCC at 673, AATCCC at 400.
  7. inverse complement, positive strand, positive direction, looking for (A/G)ATCC(C/T), 3, GATCCT at 4078, AATCCC at 2766, AATCCC at 2669.
  8. inverse complement, negative strand, positive direction, looking for (A/G)ATCC(C/T), 2, GATCCT at 2515, GATCCT at 2379.

ARRF (4560-2846) UTRs

  1. Negative strand, negative direction: AATCCT at 3457.
  2. Positive strand, negative direction: GATCCC at 4477, AGGATC at 4288, AGGATC at 4157, AGGATC at 4006, AATCCC at 3976, AATCCC at 3067.

ARRF negative direction (2811-2596) proximal promoters

  1. Positive strand, negative direction: AATCCC at 2678.

ARRF positive direction (4265-4050) proximal promoters

  1. Negative strand, positive direction: AGGATC at 4080.
  2. Positive strand, positive direction: GATCCT at 4078.

ARRF negative direction (2596-1) distal promoters

  1. Negative strand, negative direction: AGGATC at 2093, GATCCT at 1308, AATCCT at 239.
  2. Positive strand, negative direction: GGGATC at 2239, AATCCT at 2091, AATCCC at 1917, GATCCC at 1814, AATCCC at 1782, AATCCC at 1264, AATCCC at 1137, AATCCC at 807, AATCCC at 673, AATCCC at 400.

ARRF positive direction (4050-1) distal promoters

  1. Negative strand, positive direction: GGGATT at 2545, GATCCT at 2515, GATCCT at 2379.
  2. Positive strand, positive direction: AATCCC at 2766, AATCCC at 2669, AGGATT at 2083.

ARRF random dataset samplings

  1. ARRFr0: 8, GGGATT at 3973, GGGATT at 3663, AGGATC at 3140, AGGATT at 2354, GGGATT at 1780, GGGATC at 924, GGGATC at 736, GGGATC at 94.
  2. ARRFr1: 5, AGGATT at 3583, AGGATT at 3451, GGGATC at 2724, GGGATC at 2230, GGGATT at 702.
  3. ARRFr2: 3, GGGATC at 157, AGGATT at 134, AGGATT at 127.
  4. ARRFr3: 6, AGGATT at 4294, GGGATT at 3755, GGGATC at 2434, AGGATT at 2410, GGGATT at 1229, AGGATC at 968.
  5. ARRFr4: 4, AGGATC at 3092, GGGATT at 2766, GGGATC at 2690, GGGATC at 1173.
  6. ARRFr5: 7, GGGATT at 4061, AGGATT at 3352, GGGATC at 2884, GGGATC at 2428, AGGATT at 2000, GGGATC at 1812, GGGATT at 1757.
  7. ARRFr6: 4, AGGATT at 3753, AGGATC at 3026, GGGATT at 2539, GGGATC at 2213.
  8. ARRFr7: 5, AGGATC at 4552, AGGATC at 2530, AGGATC at 1921, GGGATC at 501, GGGATT at 241.
  9. ARRFr8: 6, AGGATT at 3481, GGGATT at 1818, AGGATC at 974, AGGATT at 870, AGGATC at 337, GGGATC at 103.
  10. ARRFr9: 3, AGGATC at 3444, GGGATT at 2138, AGGATT at 239.
  11. ARRFr0ci: 9, GATCCC at 4324, AATCCC at 4025, AATCCC at 3917, AATCCT at 3128, AATCCC at 2561, GATCCT at 2251, AATCCT at 1559, GATCCC at 819, AATCCC at 467.
  12. ARRFr1ci: 5, AATCCC at 4342, GATCCT at 4081, AATCCC at 2378, GATCCT at 1800, GATCCT at 1791.
  13. ARRFr2ci: 4, AATCCT at 3232, AATCCT at 2513, GATCCC at 1420, AATCCT at 1202.
  14. ARRFr3ci: 12, GATCCC at 4553, AATCCC at 4234, AATCCC at 3869, GATCCC at 3826, AATCCC at 3517, AATCCT at 2778, AATCCT at 2767, AATCCC at 2519, AATCCC at 2494, AATCCC at 1220, GATCCC at 848, AATCCT at 833.
  15. ARRFr4ci: 4, AATCCT at 4486, AATCCT at 3632, GATCCT at 3049, GATCCC at 1175.
  16. ARRFr5ci: 7, AATCCT at 4159, AATCCT at 3854, AATCCC at 3012, GATCCC at 2886, AATCCT at 2014, GATCCC at 1784, AATCCC at 914.
  17. ARRFr6ci: 3, GATCCT at 4051, AATCCC at 3155, GATCCC at 2876.
  18. ARRFr7ci: 8, AATCCT at 4503, AATCCC at 3861, AATCCT at 3222, AATCCC at 1428, GATCCT at 1164, GATCCT at 1118, GATCCT at 503, AATCCC at 32.
  19. ARRFr8ci: 4, AATCCT at 3428, GATCCC at 3018, AATCCT at 392, GATCCC at 105.
  20. ARRFr9ci: 9, GATCCC at 3584, AATCCC at 3559, GATCCC at 3446, AATCCC at 2961, GATCCC at 2486, GATCCC at 2432, AATCCC at 2395, GATCCT at 2238, AATCCT at 372.

ARRFr arbitrary (evens) (4560-2846) UTRs

  1. ARRFr0: GGGATT at 3973, GGGATT at 3663, AGGATC at 3140.
  2. ARRFr4: AGGATC at 3092.
  3. ARRFr6: AGGATT at 3753, AGGATC at 3026.
  4. ARRFr8: AGGATT at 3481.
  5. ARRFr0ci: GATCCC at 4324, AATCCC at 4025, AATCCC at 3917, AATCCT at 3128.
  6. ARRFr2ci: AATCCT at 3232.
  7. ARRFr4ci: AATCCT at 4486, AATCCT at 3632, GATCCT at 3049.
  8. ARRFr6ci: 3GATCCT at 4051, AATCCC at 3155, GATCCC at 2876.
  9. ARRFr8ci: AATCCT at 3428, GATCCC at 3018.

ARRFr alternate (odds) (4560-2846) UTRs

  1. ARRFr1: AGGATT at 3583, AGGATT at 3451.
  2. ARRFr3: AGGATT at 4294, GGGATT at 3755.
  3. ARRFr5: GGGATT at 4061, AGGATT at 3352, GGGATC at 2884.
  4. ARRFr7: AGGATC at 4552.
  5. ARRFr9: AGGATC at 3444, GGGATT at 2138, AGGATT at 239.
  6. ARRFr1ci: AATCCC at 4342, GATCCT at 4081.
  7. ARRFr3ci: GATCCC at 4553, AATCCC at 4234, AATCCC at 3869, GATCCC at 3826, AATCCC at 3517.
  8. ARRFr5ci: AATCCT at 4159, AATCCT at 3854, AATCCC at 3012, GATCCC at 2886.
  9. ARRFr7ci: AATCCT at 4503, AATCCC at 3861, AATCCT at 3222.
  10. ARRFr9ci: GATCCC at 3584, AATCCC at 3559, GATCCC at 3446, AATCCC at 2961.

ARRFr arbitrary positive direction (odds) (4445-4265) core promoters

  1. ARRFr3: AGGATT at 4294, GGGATT at 3755.
  2. ARRFr1ci: AATCCC at 4342.

ARRFr alternate positive direction (evens) (4445-4265) core promoters

  1. ARRFr0ci: GATCCC at 4324.

ARRFr arbitrary negative direction (evens) (2811-2596) proximal promoters

  1. ARRFr4: GGGATT at 2766, GGGATC at 2690.

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

  1. ARRFr1: GGGATC at 2724.
  2. ARRFr3ci: AATCCT at 2778, AATCCT at 2767.

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

  1. ARRFr5: GGGATT at 4061.
  2. ARRFr1ci: GATCCT at 4081.
  3. ARRFr3ci: AATCCC at 4234.
  4. ARRFr5ci: AATCCT at 4159.

ARRFr alternate positive direction (evens) (4265-4050) proximal promoters

  1. ARRFr6ci: GATCCT at 4051.

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

  1. ARRFr0: AGGATT at 2354, GGGATT at 1780, GGGATC at 924, GGGATC at 736, GGGATC at 94.
  2. ARRFr2: GGGATC at 157, AGGATT at 134, AGGATT at 127.
  3. ARRFr4: GGGATC at 1173.
  4. ARRFr6: GGGATT at 2539, GGGATC at 2213.
  5. ARRFr8: GGGATT at 1818, AGGATC at 974, AGGATT at 870, AGGATC at 337, GGGATC at 103.
  6. ARRFr0ci: AATCCC at 2561, GATCCT at 2251, AATCCT at 1559, GATCCC at 819, AATCCC at 467.
  7. ARRFr2ci: AATCCT at 2513, GATCCC at 1420, AATCCT at 1202.
  8. ARRFr4ci: GATCCC at 1175.
  9. ARRFr8ci: AATCCT at 392, GATCCC at 105.

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

  1. ARRFr1: GGGATC at 2230, GGGATT at 702.
  2. ARRFr3: GGGATC at 2434, AGGATT at 2410, GGGATT at 1229, AGGATC at 968.
  3. ARRFr5: GGGATC at 2428, AGGATT at 2000, GGGATC at 1812, GGGATT at 1757.
  4. ARRFr7: AGGATC at 2530, AGGATC at 1921, GGGATC at 501, GGGATT at 241.
  5. ARRFr9: GGGATT at 2138, AGGATT at 239.
  6. ARRFr1ci: AATCCC at 2378, GATCCT at 1800, GATCCT at 1791.
  7. ARRFr3ci: AATCCC at 2519, AATCCC at 2494, AATCCC at 1220, GATCCC at 848, AATCCT at 833.
  8. ARRFr5ci: AATCCT at 2014, GATCCC at 1784, AATCCC at 914.
  9. ARRFr7ci: AATCCC at 1428, GATCCT at 1164, GATCCT at 1118, GATCCT at 503, AATCCC at 32.
  10. ARRFr9ci: GATCCC at 2486, GATCCC at 2432, AATCCC at 2395, GATCCT at 2238, AATCCT at 372.

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

  1. ARRFr1: AGGATT at 3583, AGGATT at 3451, GGGATC at 2724, GGGATC at 2230, GGGATT at 702.
  2. ARRFr3: GGGATT at 3755, GGGATC at 2434, AGGATT at 2410, GGGATT at 1229, AGGATC at 968.
  3. ARRFr5: AGGATT at 3352, GGGATC at 2884, GGGATC at 2428, AGGATT at 2000, GGGATC at 1812, GGGATT at 1757.
  4. ARRFr7: AGGATC at 2530, AGGATC at 1921, GGGATC at 501, GGGATT at 241.
  5. ARRFr9: AGGATC at 3444, GGGATT at 2138, AGGATT at 239.
  6. ARRFr1ci: AATCCC at 2378, GATCCT at 1800, GATCCT at 1791.
  7. ARRFr3ci: AATCCC at 3869, GATCCC at 3826, AATCCC at 3517, AATCCT at 2778, AATCCT at 2767, AATCCC at 2519, AATCCC at 2494, AATCCC at 1220, GATCCC at 848, AATCCT at 833.
  8. ARRFr5ci: AATCCT at 3854, AATCCC at 3012, GATCCC at 2886, AATCCT at 2014, GATCCC at 1784, AATCCC at 914.
  9. ARRFr7ci: AATCCC at 3861, AATCCT at 3222, AATCCC at 1428, GATCCT at 1164, GATCCT at 1118, GATCCT at 503, AATCCC at 32.
  10. ARRFr9ci: GATCCC at 3584, AATCCC at 3559, GATCCC at 3446, AATCCC at 2961, GATCCC at 2486, GATCCC at 2432, AATCCC at 2395, GATCCT at 2238, AATCCT at 372.

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

  1. ARRFr0: GGGATT at 3973, GGGATT at 3663, AGGATC at 3140, AGGATT at 2354, GGGATT at 1780, GGGATC at 924, GGGATC at 736, GGGATC at 94.
  2. ARRFr2: GGGATC at 157, AGGATT at 134, AGGATT at 127.
  3. ARRFr4: AGGATC at 3092, GGGATT at 2766, GGGATC at 2690, GGGATC at 1173.
  4. ARRFr6: AGGATT at 3753, AGGATC at 3026, GGGATT at 2539, GGGATC at 2213.
  5. ARRFr8: AGGATT at 3481, GGGATT at 1818, AGGATC at 974, AGGATT at 870, AGGATC at 337, GGGATC at 103.
  6. ARRFr0ci: AATCCC at 4025, AATCCC at 3917, AATCCT at 3128, AATCCC at 2561, GATCCT at 2251, AATCCT at 1559, GATCCC at 819, AATCCC at 467.
  7. ARRFr2ci: AATCCT at 3232, AATCCT at 2513, GATCCC at 1420, AATCCT at 1202.
  8. ARRFr4ci: AATCCT at 3632, GATCCT at 3049, GATCCC at 1175.
  9. ARRFr6ci: AATCCC at 3155, GATCCC at 2876.
  10. ARRFr8ci: AATCCT at 3428, GATCCC at 3018, AATCCT at 392, GATCCC at 105.

ARRF analysis and results

Main article: Complex locus A1BG and ZNF497 § ARRFs

"Type-B ARRs are transcription factors that localize to the nucleus [9,28,36]. A consensus DNA-binding sequence for type-B ARRs has been delineated (G/A)GGAT(T/C), and this sequence signature is found in the promoters of many of the cytokinin primary response genes [30]."[2]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 7 2 3.5 3.5 ± 2.5 (--1,+-6)
Randoms UTR arbitrary negative 20 10 2.0 2.45 ± 0.45
Randoms UTR alternate negative 29 10 2.9 2.45 ± 0.45
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 3 10 0.3 0.2
Randoms Core alternate positive 1 10 0.1 0.2
Reals Proximal negative 1 2 0.5 0.5 ± 0.5 (--0,+-1)
Randoms Proximal arbitrary negative 2 10 0.2 0.25
Randoms Proximal alternate negative 3 10 0.3 0.25
Reals Proximal positive 2 2 1 1 ± 0 (-+1,++1)
Randoms Proximal arbitrary positive 4 10 0.4 0.25
Randoms Proximal alternate positive 1 10 0.1 0.25
Reals Distal negative 13 2 6.5 6.5 ± 3.5 (--3,+-10)
Randoms Distal arbitrary negative 27 10 2.7 3.2 ± 0.5
Randoms Distal alternate negative 37 10 3.7 3.2 ± 0.5
Reals Distal positive 6 2 3 3 ± 0 (-+3,++3)
Randoms Distal arbitrary positive 58 10 5.8 5.2 ± 0.6
Randoms Distal alternate positive 46 10 4.6 5.2 ± 0.6

Comparison:

The occurrences of real ARRF UTRs, proximals and positive direction distals are outside the randoms, negative direction distals overlap the high randoms. This suggests that the real ARRFs are likely active or activable.

ARR (Rashotte1) samplings

Copying a responsive elements consensus sequence GATCTT and putting the sequence in "⌘F" finds one between ZNF497 and A1BG or three between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence GATCTT (starting with SuccessablesARRF.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 GATCTT, 0.
  2. positive strand, negative direction, looking for GATCTT, 0.
  3. positive strand, positive direction, looking for GATCTT, 1, GATCTT at 4066.
  4. negative strand, positive direction, looking for GATCTT, 0.
  5. inverse complement, negative strand, negative direction, looking for AAGATC, 0.
  6. inverse complement, positive strand, negative direction, looking for AAGATC, 2, AAGATC at 3276, AAGATC at 877.
  7. inverse complement, positive strand, positive direction, looking for AAGATC, 3, AAGATC at 4076, AAGATC at 4064, AAGATC at 2167.
  8. inverse complement, negative strand, positive direction, looking for AAGATC, 2, AAGATC at 964, AAGATC at 864.

ARRR1 (4560-2846) UTRs

  1. Positive strand, negative direction: AAGATC at 3276.

ARRR1 positive direction (4265-4050) proximal promoters

  1. Positive strand, positive direction: AAGATC at 4076, GATCTT at 4066, AAGATC at 4064.

ARRR1 negative direction (2596-1) distal promoters

  1. Positive strand, negative direction: AAGATC at 877.

ARRR1 positive direction (4050-1) distal promoters

  1. Negative strand, positive direction: AAGATC at 964, AAGATC at 864.
  2. Positive strand, positive direction: AAGATC at 2167.

ARRR1 random samplings

  1. ARRR1r0: 0.
  2. ARRR1r1: 2, GATCTT at 4400, GATCTT at 3862.
  3. ARRR1r2: 2, GATCTT at 1194, GATCTT at 159.
  4. ARRR1r3: 0.
  5. ARRR1r4: 1, GATCTT at 3924.
  6. ARRR1r5: 1, GATCTT at 2430.
  7. ARRR1r6: 1, GATCTT at 2392.
  8. ARRR1r7: 1, GATCTT at 2462.
  9. ARRR1r8: 1, GATCTT at 2194.
  10. ARRR1r9: 0.
  11. ARRR1r0ci: 1, AAGATC at 1852.
  12. ARRR1r1ci: 4, AAGATC at 3860, AAGATC at 2995, AAGATC at 2834, AAGATC at 1779.
  13. ARRR1r2ci: 0.
  14. ARRR1r3ci: 0.
  15. ARRR1r4ci: 2, AAGATC at 3047, AAGATC at 1669.
  16. ARRR1r5ci: 1, AAGATC at 2829.
  17. ARRR1r6ci: 1, AAGATC at 166.
  18. ARRR1r7ci: 0.
  19. ARRR1r8ci: 3, AAGATC at 1872, AAGATC at 1500, AAGATC at 864.
  20. ARRR1r9ci: 0.

ARRR1r arbitrary (evens) (4560-2846) UTRs

  1. ARRR1r4: GATCTT at 3924.
  2. ARRR1r4ci: AAGATC at 3047.

ARRR1r alternate (odds) (4560-2846) UTRs

  1. ARRR1r1: GATCTT at 4400, GATCTT at 3862.
  2. ARRR1r1ci: AAGATC at 3860, AAGATC at 2995.

ARRR1r alternate negative direction (odds) (2846-2811) core promoters

  1. ARRR1r1ci: AAGATC at 2834.
  2. ARRR1r5ci: AAGATC at 2829.

ARRR1r arbitrary positive direction (odds) (4445-4265) core promoters

  1. ARRR1r1: GATCTT at 4400.

ARRR1r arbitrary negative direction (evens) (2596-1) distal promoters

  1. ARRR1r2: GATCTT at 1194, GATCTT at 159.
  2. ARRR1r6: GATCTT at 2392.
  3. ARRR1r8: GATCTT at 2194.
  4. ARRR1r0ci: AAGATC at 1852.
  5. ARRR1r4ci: AAGATC at 3047, AAGATC at 1669.
  6. ARRR1r6ci: AAGATC at 166.
  7. ARRR1r8ci: AAGATC at 1872, AAGATC at 1500, AAGATC at 864.

ARRR1r alternate negative direction (odds) (2596-1) distal promoters

  1. ARRR1r5: GATCTT at 2430.
  2. ARRR1r7: GATCTT at 2462.
  3. ARRR1r1ci: AAGATC at 1779.

ARRR1r arbitrary positive direction (odds) (4050-1) distal promoters

  1. ARRR1r1: GATCTT at 3862.
  2. ARRR1r5: GATCTT at 2430.
  3. ARRR1r7: GATCTT at 2462.
  4. ARRR1r1ci: AAGATC at 3860, AAGATC at 2995, AAGATC at 2834, AAGATC at 1779.
  5. ARRR1r5ci: AAGATC at 2829.

ARRR1r alternate positive direction (evens) (4050-1) distal promoters

  1. ARRR1r2: GATCTT at 1194, GATCTT at 159.
  2. ARRR1r4: GATCTT at 3924.
  3. ARRR1r6: GATCTT at 2392.
  4. ARRR1r8: GATCTT at 2194.
  5. ARRR1r0ci: AAGATC at 1852.
  6. ARRR1r4ci: AAGATC at 3047, AAGATC at 1669.
  7. ARRR1r6ci: AAGATC at 166.
  8. ARRR1r8ci: AAGATC at 1872, AAGATC at 1500, AAGATC at 864.

ARRR1 analysis and results

Main article: Complex locus A1BG and ZNF497 § ARRR1s

"The sequence GATCTT was identified as a core sequence motif found significantly enriched in the upstream regions of this set of genes."[4]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 1 2 0.5 0.5 ± 0.5 (--0,+-1)
Randoms UTR arbitrary negative 2 10 0.2 0.3
Randoms UTR alternate negative 4 10 0.4 0.3
Reals Core negative 0 2 0 0
Randoms Core arbitrary negative 0 10 0 0.1
Randoms Core alternate negative 2 10 0.2 0.1
Reals Core positive 0 2 0 0
Randoms Core arbitrary positive 1 10 0.1 0.05
Randoms Core alternate positive 0 10 0 0.05
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 3 2 1.5 1.5 ± 1.5 (-+0,++3)
Randoms Proximal arbitrary positive 0 10 0 0
Randoms Proximal alternate positive 0 10 0 0
Reals Distal negative 1 2 0.5 0.5 ± 0.5 (--0,+-1)
Randoms Distal arbitrary negative 11 10 1.1 0.7
Randoms Distal alternate negative 3 10 0.3 0.7
Reals Distal positive 3 2 1.5 1.5 ± 0.5 (-+2,++1)
Randoms Distal arbitrary positive 8 10 0.8 1.0
Randoms Distal alternate positive 12 10 1.2 1.0

Comparison:

The occurrences of real ARRR1 UTRs and proximals are greater than the randoms. The distals are ≥ the randoms. The negative direction distals are within the randoms. This suggests that the real ARRR1s are likely active or activable.

ARR (Rashotte2) samplings

Main article: Model samplings

Copying a responsive elements consensus sequence (G/A)GAT(T/C) and putting the sequence in "⌘F" finds one between ZNF497 and A1BG or three between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence (G/A)GAT(T/C) (starting with SuccessablesARRF.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 (G/A)GAT(T/C), 5, GGATC at 2093, GGATT at 1591, GGATC at 1306, GGATT at 64, AGATT at 9.
  2. positive strand, negative direction, looking for (G/A)GAT(T/C), 24, AGATC at 4475, GGATC at 4288, GGATC at 4157, GGATC at 4006, AGATC at 3488, AGATC at 3276, GGATC at 3097, GGATC at 2574, AGATT at 2451, AGATC at 2413, GGATC at 2239, AGATC at 1987, GGATC at 1812, AGATT at 1714, AGATT at 1334, GGATC at 1167, AGATT at 1043, AGATC at 972, AGATC at 877, GGATC at 703, AGATC at 589, AGATT at 583, GGATC at 525, GGATC at 430.
  3. positive strand, positive direction, looking for (G/A)GAT(T/C), 6, AGATC at 4076, AGATC at 4064, GGATC at 2481, AGATC at 2167, GGATT at 2083, AGATT at 121.
  4. negative strand, positive direction, looking for (G/A)GAT(T/C), 6, GGATC at 4080, AGATT at 2868, GGATT at 2545, AGATC at 2230, AGATC at 964, AGATC at 864.
  5. inverse complement, negative strand, negative direction, looking for (A/G)ATC(C/T), 7, GATCT at 3463, AATCC at 3456, AATCT at 3000, AATCT at 2979, GATCC at 1307, AATCC at 238, AATCT at 50.
  6. inverse complement, positive strand, negative direction, looking for (A/G)ATC(C/T), 17, GATCC at 4476, AATCC at 3975, AATCC at 3679, AATCC at 3066, AATCC at 2677, AATCC at 2090, AATCC at 1916, GATCC at 1813, AATCC at 1781, GATCT at 1482, AATCC at 1263, AATCC at 1136, GATCC at 973, AATCC at 806, AATCC at 672, AATCC at 399, AATCT at 232.
  7. inverse complement, positive strand, positive direction, looking for (A/G)ATC(C/T), 10, GATCC at 4077, GATCT at 4065, GATCC at 3522, GATCC at 3484, AATCC at 2765, AATCC at 2668, GATCC at 2639, GATCC at 2482, AATCC at 2366, AATCC at 150.
  8. inverse complement, negative strand, positive direction, looking for (A/G)ATC(C/T), 9, GATCC at 4081, AATCC at 3797, AATCT at 2725, GATCC at 2514, GATCC at 2378, AATCT at 2243, AATCT at 2235, GATCC at 965, GATCC at 865.

ARRR2 (4560-2846) UTRs

  1. Negative strand, negative direction: GATCT at 3463, AATCC at 3456, AATCT at 3000, AATCT at 2979.
  2. Positive strand, negative direction: GATCC at 4476, AGATC at 4475, GGATC at 4288, GGATC at 4157, GGATC at 4006, AATCC at 3975, AATCC at 3679, AGATC at 3488, AGATC at 3276, GGATC at 3097, AATCC at 3066.

ARRR2 negative direction (2811-2596) proximal promoters

  1. Positive strand, negative direction: AATCC at 2677.

ARRR2 positive direction (4265-4050) proximal promoters

  1. Negative strand, positive direction: GATCC at 4081, GGATC at 4080.
  2. Positive strand, positive direction: GATCC at 4077, AGATC at 4076, GATCT at 4065, AGATC at 4064.

ARRR2 negative direction (2596-1) distal promoters

  1. Negative strand, negative direction: GATCT at 3463, AATCC at 3456, AATCT at 3000, AATCT at 2979, GGATC at 2093, GGATT at 1591, GATCC at 1307, GGATC at 1306, AATCC at 238, GGATT at 64, AATCT at 50, AGATT at 9.
  2. Positive strand, negative direction: GGATC at 2574, AGATT at 2451, AGATC at 2413, GGATC at 2239, ATCC at 2090, AGATC at 1987, AATCC at 1916, GATCC at 1813, GGATC at 1812, AATCC at 1781, AGATT at 1714, GATCT at 1482, AGATT at 1334, AATCC at 1263, GGATC at 1167, AATCC at 1136, AGATT at 1043, GATCC at 973, AGATC at 972, AGATC at 877, AATCC at 806, GGATC at 703, AATCC at 672, AGATC at 589, AGATT at 583, GGATC at 525, GGATC at 430, AATCC at 399, AATCT at 232.

ARRR2 positive direction (4050-1) distal promoters

  1. Negative strand, positive direction: AATCC at 3797, AGATT at 2868, AATCT at 2725, GGATT at 2545, GATCC at 2514, GATCC at 2378, AATCT at 2243, AATCT at 2235, AGATC at 2230, GATCC at 965, AGATC at 964, GATCC at 865, AGATC at 864.
  2. Positive strand, positive direction: GATCC at 3522, GATCC at 3484, AATCC at 2765, AATCC at 2668, GATCC at 2639, GATCC at 2482, GGATC at 2481, AATCC at 2366, AGATC at 2167, GGATT at 2083, AATCC at 150, AGATT at 121.

Random results ARRR2

For the Basic programs testing consensus sequence (A/G)GAT(C/T) (starting with SuccessablesARRR2r0.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. ARRR2r0: AGATT at 4462, GGATC at 4322, GGATC at 4271, GGATT at 3973, GGATT at 3663, GGATC at 3140, AGATT at 2856, AGATC at 2761, GGATC at 2667, AGATT at 2652, GGATT at 2354, AGATC at 2249, AGATC at 1949, AGATC at 1852, GGATT at 1780, AGATT at 1774, GGATT at 992, GGATT at 952, GGATC at 924, GGATC at 736, AGATT at 128, GGATC at 94.
  2. ARRR2r1: AGATC at 3860, GGATT at 3583, GGATT at 3451, AGATC at 2995, AGATC at 2834, GGATC at 2724, AGATT at 2448, AGATC at 2250, GGATC at 2230, AGATC at 1798, GGATC at 1789, AGATC at 1779, GGATT at 1259, GGATT at 702, AGATT at 361.
  3. ARRR2r2: AGATT at 4201, AGATT at 3612, AGATT at 3456, GGATC at 3436, AGATT at 3001, AGATT at 2931, AGATT at 2652, AGATT at 1690, GGATT at 1580, GGATC at 1418, GGATT at 559, AGATT at 336, GGATC at 157, GGATT at 134, GGATT at 127.
  4. ARRR2r3: GGATT at 4294, AGATC at 3824, GGATT at 3778, GGATT at 3755, GGATT at 2940, GGATC at 2566, GGATC at 2434, GGATT at 2410, GGATT at 1488, GGATT at 1229, GGATC at 968.
  5. ARRR2r4: GGATC at 3922, AGATC at 3132, GGATC at 3092, AGATC at 3047, AGATC at 2798, GGATT at 2766, AGATT at 2721, GGATC at 2690, AGATC at 1669, GGATC at 1494, GGATC at 1173, AGATT at 945, GGATT at 840, GGATT at 616, GGATT at 558.
  6. ARRR2r5: AGATT at 4089, GGATT at 4061, AGATC at 4030, GGATT at 3352, AGATT at 3170, GGATC at 2884, AGATC at 2829, AGATT at 2437, GGATC at 2428, GGATT at 2000, GGATC at 1812, GGATT at 1757, AGATC at 1746, AGATC at 943, AGATT at 884, AGATT at 690, AGATT at 197.
  7. ARRR2r6: AGATC at 4310, GGATT at 3753, GGATT at 3609, GGATT at 3391, GGATC at 3026, AGATC at 2936, GGATT at 2539, AGATC at 2390, GGATC at 2213, AGATC at 166, AGATT at 93.
  8. ARRR2r7: GGATC at 4552, GGATT at 4515, AGATT at 4197, AGATT at 4178, AGATT at 4146, GGATT at 3595, AGATT at 3374, GGATC at 3367, GGATT at 2764, GGATC at 2530, GGATC at 2460, AGATT at 2402, GGATC at 1921, GGATT at 1297, GGATC at 1285, AGATT at 707, GGATC at 501, GGATT at 241.
  9. ARRR2r8: GGATT at 3481, GGATC at 3016, GGATT at 2432, AGATT at 2242, GGATT at 2089, AGATC at 1872, GGATT at 1818, AGATC at 1500, GGATC at 1057, GGATC at 974, GGATT at 870, AGATC at 864, GGATC at 337, GGATC at 103, AGATC at 26.
  10. ARRR2r9: GGATT at 4276, GGATT at 4234, AGATT at 3720, GGATC at 3444, AGATT at 3313, GGATT at 2628, GGATT at 2603, AGATC at 2430, AGATT at 2327, GGATT at 2138, AGATT at 2060, AGATT at 315, GGATT at 239.
  11. ARRR2r0ci: GATCC at 4323, AATCC at 4024, AATCC at 3916, AATCC at 3127, GATCC at 2762, GATCC at 2668, AATCC at 2560, AATCC at 2507, GATCC at 2250, AATCC at 1558, AATCC at 1160, GATCT at 925, GATCC at 818, GATCT at 737, AATCT at 612, AATCC at 466.
  12. ARRR2r1ci: GATCT at 4399, AATCC at 4341, GATCC at 4080, GATCT at 3861, GATCC at 2835, GATCT at 2627, AATCC at 2377, GATCC at 1799, GATCC at 1790, GATCT at 1336, AATCC at 800.
  13. ARRR2r2ci: AATCC at 4399, AATCT at 3962, GATCT at 3762, AATCC at 3231, AATCC at 2512, GATCC at 1419, AATCC at 1360, AATCC at 1201, GATCT at 1193, AATCT at 1168, AATCT at 828, AATCC at 795, AATCC at 767, AATCC at 568, AATCT at 513, AATCC at 350, GATCT at 158.
  14. ARRR2r3ci: GATCC at 4552, GATCT at 4373, AATCC at 4233, AATCC at 4022, AATCC at 3868, GATCC at 3825, AATCC at 3516, AATCC at 3364, AATCT at 3269, AATCC at 2777, AATCC at 2766, GATCT at 2567, AATCC at 2518, AATCC at 2493, GATCT at 2435, GATCT at 1756, AATCC at 1219, GATCT at 1126, GATCC at 847, AATCC at 832.
  15. ARRR2r4ci: AATCC at 4485, AATCT at 3984, GATCT at 3923, AATCC at 3631, GATCT at 3133, GATCC at 3048, AATCC at 2817, AATCC at 2739, AATCT at 2446, AATCT at 1763, AATCT at 1698, GATCT at 1670, GATCT at 1495, GATCC at 1174, AATCC at 892, AATCC at 777, AATCT at 665, AATCC at 380, GATCT at 66.
  16. ARRR2r5ci: GATCC at 4289, AATCT at 4184, AATCC at 4158, GATCC at 4031, AATCC at 3853, AATCC at 3450, AATCC at 3033, AATCC at 3011, GATCC at 2885, GATCT at 2830, AATCC at 2648, AATCC at 2519, GATCT at 2429, AATCT at 2374, AATCT at 2106, AATCT at 2062, AATCC at 2013, GATCC at 1783, AATCT at 1317, AATCC at 913, AATCC at 778, AATCC at 755, AATCC at 129.
  17. ARRR2r6ci: AATCC at 4378, GATCC at 4050, AATCC at 3337, AATCC at 3154, GATCT at 3048, GATCT at 2937, GATCC at 2875, GATCT at 2391, AATCT at 2335, AATCT at 1741, AATCC at 1187, GATCT at 880, AATCT at 728, GATCT at 702, AATCT at 694, GATCT at 509, AATCT at 364.
  18. ARRR2r7ci: GATCC at 4553, AATCC at 4502, AATCC at 4051, AATCC at 3860, GATCT at 3551, GATCT at 3368, AATCC at 3221, AATCT at 3016, AATCT at 2475, GATCT at 2461, AATCT at 2308, AATCT at 2284, AATCC at 1738, AATCT at 1563, AATCC at 1427, GATCC at 1163, GATCC at 1117, GATCT at 1003, AATCC at 566, GATCC at 502, AATCC at 211, AATCC at 31.
  19. ARRR2r8ci: AATCT at 4175, AATCT at 3940, AATCT at 3716, GATCT at 3703, AATCC at 3427, GATCC at 3017, AATCT at 2927, GATCT at 2193, AATCC at 2009, AATCC at 1939, AATCT at 1301, GATCC at 967, AATCC at 391, AATCT at 285, GATCC at 104, GATCT at 27.
  20. ARRR2r9ci: AATCC at 4501, AATCT at 4295, GATCC at 3583, AATCC at 3558, AATCT at 3545, GATCC at 3445, AATCC at 2960, AATCT at 2835, GATCC at 2485, GATCC at 2431, AATCC at 2394, GATCC at 2237, AATCC at 371.

ARRR2r arbitrary (evens) (4560-2846) UTRs

  1. ARRR2r0: AGATT at 4462, GGATC at 4322, GGATC at 4271, GGATT at 3973, GGATT at 3663, GGATC at 3140, AGATT at 2856.
  2. ARRR2r2.bas: AGATT at 4201, AGATT at 3612, AGATT at 3456, GGATC at 3436, AGATT at 3001, AGATT at 2931.
  3. ARRR2r4.bas: GGATC at 3922, AGATC at 3132, GGATC at 3092, AGATC at 3047.
  4. ARRR2r6: AGATC at 4310, GGATT at 3753, GGATT at 3609, GGATT at 3391, GGATC at 3026, AGATC at 2936.
  5. ARRR2r8: GGATT at 3481, GGATC at 3016.
  6. ARRR2r0ci: GATCC at 4323, AATCC at 4024, AATCC at 3916, AATCC at 3127.
  7. ARRR2r2ci: AATCC at 4399, AATCT at 3962, GATCT at 3762, AATCC at 3231.
  8. ARRR2r4ci: AATCC at 4485, AATCT at 3984, GATCT at 3923, AATCC at 3631, GATCT at 3133, GATCC at 3048.
  9. ARRR2r6ci: AATCC at 4378, GATCC at 4050, AATCC at 3337, AATCC at 3154, GATCT at 3048, GATCT at 2937, GATCC at 2875.
  10. ARRR2r8ci: AATCT at 4175, AATCT at 3940, AATCT at 3716, GATCT at 3703, AATCC at 3427, GATCC at 3017, AATCT at 2927.

ARRR2r alternate (odds) (4560-2846) UTRs

  1. ARRR2r1: AGATC at 3860, GGATT at 3583, GGATT at 3451, AGATC at 2995.
  2. ARRR2r3: GGATT at 4294, AGATC at 3824, GGATT at 3778, GGATT at 3755, GGATT at 2940.
  3. ARRR2r5: AGATT at 4089, GGATT at 4061, AGATC at 4030, GGATT at 3352, AGATT at 3170, GGATC at 2884.
  4. ARRR2r7: GGATC at 4552, GGATT at 4515, AGATT at 4197, AGATT at 4178, AGATT at 4146, GGATT at 3595, AGATT at 3374, GGATC at 3367.
  5. ARRR2r9: GGATT at 4276, GGATT at 4234, AGATT at 3720, GGATC at 3444, AGATT at 3313.
  6. ARRR2r1ci: GATCT at 4399, AATCC at 4341, GATCC at 4080, GATCT at 3861.
  7. ARRR2r3ci: GATCC at 4552, GATCT at 4373, AATCC at 4233, AATCC at 4022, AATCC at 3868, GATCC at 3825, AATCC at 3516, AATCC at 3364, AATCT at 3269.
  8. ARRR2r5ci: GATCC at 4289, AATCT at 4184, AATCC at 4158, GATCC at 4031, AATCC at 3853, AATCC at 3450, AATCC at 3033, AATCC at 3011, GATCC at 2885.
  9. ARRR2r7ci: GATCC at 4553, AATCC at 4502, AATCC at 4051, AATCC at 3860, GATCT at 3551, GATCT at 3368, AATCC at 3221, AATCT at 3016.
  10. ARRR2r9ci: AATCC at 4501, AATCT at 4295, GATCC at 3583, AATCC at 3558, AATCT at 3545, GATCC at 3445, AATCC at 2960.

ARRR2r arbitrary negative direction (evens) (2846-2811) core promoters

  1. ARRR2r4ci: AATCC at 2817.

ARRR2r alternate negative direction (odds) (2846-2811) core promoters

  1. ARRR2r1: AGATC at 2834.
  2. ARRR2r5: AGATC at 2829.
  3. ARRR2r1ci: GATCC at 2835.
  4. ARRR2r5ci: GATCT at 2830.
  5. ARRR2r9ci: AATCT at 2835.

ARRR2r arbitrary positive direction (odds) (4445-4265) core promoters

  1. ARRR2r3: GGATT at 4294.
  2. ARRR2r9: GGATT at 4276.
  3. ARRR2r1ci: GATCT at 4399, AATCC at 4341.
  4. ARRR2r3ci: GATCT at 4373.
  5. ARRR2r5ci: GATCC at 4289.
  6. ARRR2r9ci: AATCT at 4295.

ARRR2r alternate positive direction (evens) (4445-4265) core promoters

  1. ARRR2r0: GGATC at 4322, GGATC at 4271.
  2. ARRR2r6: AGATC at 4310.
  3. ARRR2r0ci: GATCC at 4323.
  4. ARRR2r2ci: AATCC at 4399.
  5. ARRR2r6ci: AATCC at 4378.

ARRR2r arbitrary negative direction (evens) (2811-2596) proximal promoters

  1. ARRR2r0: AGATC at 2761, GGATC at 2667, AGATT at 2652.
  2. ARRR2r2: AGATT at 2652.
  3. ARRR2r4: AGATC at 2798, GGATT at 2766, AGATT at 2721, GGATC at 2690.
  4. ARRR2r0ci: GATCC at 2762, GATCC at 2668.
  5. ARRR2r4ci: AATCC at 2739.

ARRR2r alternate negative direction (odds) (2811-2596) proximal promoters

  1. ARRR2r1: GGATC at 2724.
  2. ARRR2r9: GGATT at 2628, GGATT at 2603.
  3. ARRR2r1ci: GATCT at 2627.
  4. ARRR2r3ci: AATCC at 2777, AATCC at 2766.
  5. ARRR2r5ci: AATCC at 2648.

ARRR2r arbitrary positive direction (odds) (4265-4050) proximal promoters

  1. ARRR2r5: AGATT at 4089, GGATT at 4061.
  2. ARRR2r7: AGATT at 4197, AGATT at 4178, AGATT at 4146.
  3. ARRR2r9: GGATT at 4234.
  4. ARRR2r1ci: GATCC at 4080.
  5. ARRR2r3ci: AATCC at 4233.
  6. ARRR2r5ci: AATCT at 4184, AATCC at 4158.
  7. ARRR2r7ci: AATCC at 4051.

ARRR2r alternate positive direction (evens) (4265-4050) proximal promoters

  1. ARRR2r6ci: GATCC at 4050.
  2. ARRR2r8ci: AATCT at 4175.

ARRR2r arbitrary negative direction (evens) (2596-1) distal promoters

  1. ARRR2r0: GGATT at 2354, AGATC at 2249, AGATC at 1949, AGATC at 1852, GGATT at 1780, AGATT at 1774, GGATT at 992, GGATT at 952, GGATC at 924, GGATC at 736, AGATT at 128, GGATC at 94.
  2. ARRR2r2.bas: AGATT at 1690, GGATT at 1580, GGATC at 1418, GGATT at 559, AGATT at 336, GGATC at 157, GGATT at 134, GGATT at 127.
  3. ARRR2r4: AGATC at 1669, GGATC at 1494, GGATC at 1173, AGATT at 945, GGATT at 840, GGATT at 616, GGATT at 558.
  4. ARRR2r6: GGATT at 2539, AGATC at 2390, GGATC at 2213, AGATC at 166, AGATT at 93.
  5. ARRR2r8: GGATT at 2432, AGATT at 2242, GGATT at 2089, AGATC at 1872, GGATT at 1818, AGATC at 1500, GGATC at 1057, GGATC at 974, GGATT at 870, AGATC at 864, GGATC at 337, GGATC at 103, AGATC at 26.
  6. ARRR2r0ci: AATCC at 2560, AATCC at 2507, GATCC at 2250, AATCC at 1558, AATCC at 1160, GATCT at 925, GATCC at 818, GATCT at 737, AATCT at 612, AATCC at 466.
  7. ARRR2r2ci: AATCC at 2512, GATCC at 1419, AATCC at 1360, AATCC at 1201, GATCT at 1193, AATCT at 1168, AATCT at 828, AATCC at 795, AATCC at 767, AATCC at 568, AATCT at 513, AATCC at 350, GATCT at 158.
  8. ARRR2r4ci: AATCT at 2446, AATCT at 1763, AATCT at 1698, GATCT at 1670, GATCT at 1495, GATCC at 1174, AATCC at 892, AATCC at 777, AATCT at 665, AATCC at 380, GATCT at 66.
  9. ARRR2r6ci: GATCT at 2391, AATCT at 2335, AATCT at 1741, AATCC at 1187, GATCT at 880, AATCT at 728, GATCT at 702, AATCT at 694, GATCT at 509, AATCT at 364.
  10. ARRR2r8ci: GATCT at 2193, AATCC at 2009, AATCC at 1939, AATCT at 1301, GATCC at 967, AATCC at 391, AATCT at 285, GATCC at 104, GATCT at 27.

ARRR2r alternate negative direction (odds) (2596-1) distal promoters

  1. ARRR2r1: AGATT at 2448, AGATC at 2250, GGATC at 2230, AGATC at 1798, GGATC at 1789, AGATC at 1779, GGATT at 1259, GGATT at 702, AGATT at 361.
  2. ARRR2r3.bas: GGATC at 2566, GGATC at 2434, GGATT at 2410, GGATT at 1488, GGATT at 1229, GGATC at 968.
  3. ARRR2r5: AGATT at 2437, GGATC at 2428, GGATT at 2000, GGATC at 1812, GGATT at 1757, AGATC at 1746, AGATC at 943, AGATT at 884, AGATT at 690, AGATT at 197.
  4. ARRR2r7: GGATC at 2530, GGATC at 2460, AGATT at 2402, GGATC at 1921, GGATT at 1297, GGATC at 1285, AGATT at 707, GGATC at 501, GGATT at 241.
  5. ARRR2r9: AGATC at 2430, AGATT at 2327, GGATT at 2138, AGATT at 2060, AGATT at 315, GGATT at 239.
  6. ARRR2r1ci: AATCC at 2377, GATCC at 1799, GATCC at 1790, GATCT at 1336, AATCC at 800.
  7. ARRR2r3ci: GATCT at 2567, AATCC at 2518, AATCC at 2493, GATCT at 2435, GATCT at 1756, AATCC at 1219, GATCT at 1126, GATCC at 847, AATCC at 832.
  8. ARRR2r5ci: AATCC at 2519, GATCT at 2429, AATCT at 2374, AATCT at 2106, AATCT at 2062, AATCC at 2013, GATCC at 1783, AATCT at 1317, AATCC at 913, AATCC at 778, AATCC at 755, AATCC at 129.
  9. ARRR2r7ci: AATCT at 2475, GATCT at 2461, AATCT at 2308, AATCT at 2284, AATCC at 1738, AATCT at 1563, AATCC at 1427, GATCC at 1163, GATCC at 1117, GATCT at 1003, AATCC at 566, GATCC at 502, AATCC at 211, AATCC at 31.
  10. ARRR2r9ci: GATCC at 2485, GATCC at 2431, AATCC at 2394, GATCC at 2237, AATCC at 371.

ARRR2r arbitrary positive direction (odds) (4050-1) distal promoters

  1. ARRR2r1: AGATC at 3860, GGATT at 3583, GGATT at 3451, AGATC at 2995, AGATC at 2834, GGATC at 2724, AGATT at 2448, AGATC at 2250, GGATC at 2230, AGATC at 1798, GGATC at 1789, AGATC at 1779, GGATT at 1259, GGATT at 702, AGATT at 361.
  2. ARRR2r3: AGATC at 3824, GGATT at 3778, GGATT at 3755, GGATT at 2940, GGATC at 2566, GGATC at 2434, GGATT at 2410, GGATT at 1488, GGATT at 1229, GGATC at 968.
  3. ARRR2r5: AGATC at 4030, GGATT at 3352, AGATT at 3170, GGATC at 2884, AGATC at 2829, AGATT at 2437, GGATC at 2428, GGATT at 2000, GGATC at 1812, GGATT at 1757, AGATC at 1746, AGATC at 943, AGATT at 884, AGATT at 690, AGATT at 197.
  4. ARRR2r7: GGATT at 3595, AGATT at 3374, GGATC at 3367, GGATT at 2764, GGATC at 2530, GGATC at 2460, AGATT at 2402, GGATC at 1921, GGATT at 1297, GGATC at 1285, AGATT at 707, GGATC at 501, GGATT at 241.
  5. ARRR2r9: AGATT at 3720, GGATC at 3444, AGATT at 3313, GGATT at 2628, GGATT at 2603, AGATC at 2430, AGATT at 2327, GGATT at 2138, AGATT at 2060, AGATT at 315, GGATT at 239.
  6. ARRR2r1ci: GATCT at 3861, GATCC at 2835, GATCT at 2627, AATCC at 2377, GATCC at 1799, GATCC at 1790, GATCT at 1336, AATCC at 800.
  7. ARRR2r3ci: AATCC at 4022, AATCC at 3868, GATCC at 3825, AATCC at 3516, AATCC at 3364, AATCT at 3269, AATCC at 2777, AATCC at 2766, GATCT at 2567, AATCC at 2518, AATCC at 2493, GATCT at 2435, GATCT at 1756, AATCC at 1219, GATCT at 1126, GATCC at 847, AATCC at 832.
  8. ARRR2r5ci: GATCC at 4031, AATCC at 3853, AATCC at 3450, AATCC at 3033, AATCC at 3011, GATCC at 2885, GATCT at 2830, AATCC at 2648, AATCC at 2519, GATCT at 2429, AATCT at 2374, AATCT at 2106, AATCT at 2062, AATCC at 2013, GATCC at 1783, AATCT at 1317, AATCC at 913, AATCC at 778, AATCC at 755, AATCC at 129.
  9. ARRR2r7ci: AATCC at 3860, GATCT at 3551, GATCT at 3368, AATCC at 3221, AATCT at 3016, AATCT at 2475, GATCT at 2461, AATCT at 2308, AATCT at 2284, AATCC at 1738, AATCT at 1563, AATCC at 1427, GATCC at 1163, GATCC at 1117, GATCT at 1003, AATCC at 566, GATCC at 502, AATCC at 211, AATCC at 31.
  10. ARRR2r9ci: GATCC at 3583, AATCC at 3558, AATCT at 3545, GATCC at 3445, AATCC at 2960, AATCT at 2835, GATCC at 2485, GATCC at 2431, AATCC at 2394, GATCC at 2237, AATCC at 371.

ARRR2r alternate positive direction (evens) (4050-1) distal promoters

  1. ARRR2r0: GGATT at 3973, GGATT at 3663, GGATC at 3140, AGATT at 2856, AGATC at 2761, GGATC at 2667, AGATT at 2652, GGATT at 2354, AGATC at 2249, AGATC at 1949, AGATC at 1852, GGATT at 1780, AGATT at 1774, GGATT at 992, GGATT at 952, GGATC at 924, GGATC at 736, AGATT at 128, GGATC at 94.
  2. ARRR2r2.bas: AGATT at 3612, AGATT at 3456, GGATC at 3436, AGATT at 3001, AGATT at 2931, AGATT at 2652, AGATT at 1690, GGATT at 1580, GGATC at 1418, GGATT at 559, AGATT at 336, GGATC at 157, GGATT at 134, GGATT at 127.
  3. ARRR2r4: GGATC at 3922, AGATC at 3132, GGATC at 3092, AGATC at 3047, AGATC at 2798, GGATT at 2766, AGATT at 2721, GGATC at 2690, AGATC at 1669, GGATC at 1494, GGATC at 1173, AGATT at 945, GGATT at 840, GGATT at 616, GGATT at 558.
  4. ARRR2r6: GGATT at 3753, GGATT at 3609, GGATT at 3391, GGATC at 3026, AGATC at 2936, GGATT at 2539, AGATC at 2390, GGATC at 2213, AGATC at 166, AGATT at 93.
  5. ARRR2r8: GGATT at 3481, GGATC at 3016, GGATT at 2432, AGATT at 2242, GGATT at 2089, AGATC at 1872, GGATT at 1818, AGATC at 1500, GGATC at 1057, GGATC at 974, GGATT at 870, AGATC at 864, GGATC at 337, GGATC at 103, AGATC at 26.
  6. ARRR2r0ci: AATCC at 4024, AATCC at 3916, AATCC at 3127, GATCC at 2762, GATCC at 2668, AATCC at 2560, AATCC at 2507, GATCC at 2250, AATCC at 1558, AATCC at 1160, GATCT at 925, GATCC at 818, GATCT at 737, AATCT at 612, AATCC at 466.
  7. ARRR2r2ci: AATCT at 3962, GATCT at 3762, AATCC at 3231, AATCC at 2512, GATCC at 1419, AATCC at 1360, AATCC at 1201, GATCT at 1193, AATCT at 1168, AATCT at 828, AATCC at 795, AATCC at 767, AATCC at 568, AATCT at 513, AATCC at 350, GATCT at 158.
  8. ARRR2r4ci: AATCT at 3984, GATCT at 3923, AATCC at 3631, GATCT at 3133, GATCC at 3048, AATCC at 2817, AATCC at 2739, AATCT at 2446, AATCT at 1763, AATCT at 1698, GATCT at 1670, GATCT at 1495, GATCC at 1174, AATCC at 892, AATCC at 777, AATCT at 665, AATCC at 380, GATCT at 66.
  9. ARRR2r6ci: GATCC at 4050, AATCC at 3337, AATCC at 3154, GATCT at 3048, GATCT at 2937, GATCC at 2875, GATCT at 2391, AATCT at 2335, AATCT at 1741, AATCC at 1187, GATCT at 880, AATCT at 728, GATCT at 702, AATCT at 694, GATCT at 509, AATCT at 364.
  10. ARRR2r8ci: AATCT at 3940, AATCT at 3716, GATCT at 3703, AATCC at 3427, GATCC at 3017, AATCT at 2927, GATCT at 2193, AATCC at 2009, AATCC at 1939, AATCT at 1301, GATCC at 967, AATCC at 391, AATCT at 285, GATCC at 104, GATCT at 27.

ARRR2r proximal promoters

Main article: Proximal promoter gene transcriptions

Negative direction:

  1. ARRR2r0: 3, AGATC at 2761, GGATC at 2667, AGATT at 2652.
  2. ARRR2r1: 1, GGATC at 2724.
  3. ARRR2r2: 1, AGATT at 2652.
  4. ARRR2r4: 4, AGATC at 2798, GGATT at 2766, AGATT at 2721, GGATC at 2690.
  5. ARRR2r7: 1, GGATT at 2764.
  6. ARRR2r9: 2, GGATT at 2628, GGATT at 2603.
  7. ARRR2r0ci: 2, GATCC at 2762, GATCC at 2668.
  8. ARRR2r1ci: 1, GATCT at 2627.
  9. ARRR2r3ci: 2, AATCC at 2777, AATCC at 2766.
  10. ARRR2r4ci: 1, AATCC at 2739.
  11. ARRR2r5ci: 1, AATCC at 2648.

Positive direction:

  1. ARRR2r2: 1, AGATT at 4201.
  2. ARRR2r5: 2, AGATT at 4089, GGATT at 4061.
  3. ARRR2r7: 3, AGATT at 4197, AGATT at 4178, AGATT at 4146.
  4. ARRR2r9: 1, GGATT at 4234.
  5. ARRR2r1ci: 1, GATCC at 4080.
  6. ARRR2r3ci: 1, AATCC at 4233.
  7. ARRR2r5ci: 2, AATCT at 4184, AATCC at 4158.
  8. ARRR2r6ci: 1, GATCC at 4050.
  9. ARRR2r7ci: 1, AATCC at 4051.
  10. ARRR2r8ci: 1, AATCT at 4175.

ARRR2r distal promoters

Main article: Distal promoter gene transcriptions

Negative direction:

  1. ARRR2r0: 12, GGATT at 2354, AGATC at 2249, AGATC at 1949, AGATC at 1852, GGATT at 1780, AGATT at 1774, GGATT at 992, GGATT at 952, GGATC at 924, GGATC at 736, AGATT at 128, GGATC at 94.
  2. ARRR2r1: 9, AGATT at 2448, AGATC at 2250, GGATC at 2230, AGATC at 1798, GGATC at 1789, AGATC at 1779, GGATT at 1259, GGATT at 702, AGATT at 361.
  3. ARRR2r2: 8, AGATT at 1690, GGATT at 1580, GGATC at 1418, GGATT at 559, AGATT at 336, GGATC at 157, GGATT at 134, GGATT at 127.
  4. ARRR2r3: 6, GGATC at 2566, GGATC at 2434, GGATT at 2410, GGATT at 1488, GGATT at 1229, GGATC at 968.
  5. ARRR2r4: 7, AGATC at 1669, GGATC at 1494, GGATC at 1173, AGATT at 945, GGATT at 840, GGATT at 616, GGATT at 558.
  6. ARRR2r5: 10, AGATT at 2437, GGATC at 2428, GGATT at 2000, GGATC at 1812, GGATT at 1757, AGATC at 1746, AGATC at 943, AGATT at 884, AGATT at 690, AGATT at 197.
  7. ARRR2r6: 5, GGATT at 2539, AGATC at 2390, GGATC at 2213, AGATC at 166, AGATT at 93.
  8. ARRR2r7: 9, GGATC at 2530, GGATC at 2460, AGATT at 2402, GGATC at 1921, GGATT at 1297, GGATC at 1285, AGATT at 707, GGATC at 501, GGATT at 241.
  9. ARRR2r8: 13, GGATT at 2432, AGATT at 2242, GGATT at 2089, AGATC at 1872, GGATT at 1818, AGATC at 1500, GGATC at 1057, GGATC at 974, GGATT at 870, AGATC at 864, GGATC at 337, GGATC at 103, AGATC at 26.
  10. ARRR2r9: 6, AGATC at 2430, AGATT at 2327, GGATT at 2138, AGATT at 2060, AGATT at 315, GGATT at 239.
  11. ARRR2r0ci: 10, AATCC at 2560, AATCC at 2507, GATCC at 2250, AATCC at 1558, AATCC at 1160, GATCT at 925, GATCC at 818, GATCT at 737, AATCT at 612, AATCC at 466.
  12. ARRR2r1ci: 5, AATCC at 2377, GATCC at 1799, GATCC at 1790, GATCT at 1336, AATCC at 800.
  13. ARRR2r2ci: 13, AATCC at 2512, GATCC at 1419, AATCC at 1360, AATCC at 1201, GATCT at 1193, AATCT at 1168, AATCT at 828, AATCC at 795, AATCC at 767, AATCC at 568, AATCT at 513, AATCC at 350, GATCT at 158.
  14. ARRR2r3ci: 9, GATCT at 2567, AATCC at 2518, AATCC at 2493, GATCT at 2435, GATCT at 1756, AATCC at 1219, GATCT at 1126, GATCC at 847, AATCC at 832.
  15. ARRR2r4ci: 11, AATCT at 2446, AATCT at 1763, AATCT at 1698, GATCT at 1670, GATCT at 1495, GATCC at 1174, AATCC at 892, AATCC at 777, AATCT at 665, AATCC at 380, GATCT at 66.
  16. ARRR2r5ci: 12, AATCC at 2519, GATCT at 2429, AATCT at 2374, AATCT at 2106, AATCT at 2062, AATCC at 2013, GATCC at 1783, AATCT at 1317, AATCC at 913, AATCC at 778, AATCC at 755, AATCC at 129.
  17. ARRR2r6ci: 10, GATCT at 2391, AATCT at 2335, AATCT at 1741, AATCC at 1187, GATCT at 880, AATCT at 728, GATCT at 702, AATCT at 694, GATCT at 509, AATCT at 364.
  18. ARRR2r7ci: 14, AATCT at 2475, GATCT at 2461, AATCT at 2308, AATCT at 2284, AATCC at 1738, AATCT at 1563, AATCC at 1427, GATCC at 1163, GATCC at 1117, GATCT at 1003, AATCC at 566, GATCC at 502, AATCC at 211, AATCC at 31.
  19. ARRR2r8ci: 9, GATCT at 2193, AATCC at 2009, AATCC at 1939, AATCT at 1301, GATCC at 967, AATCC at 391, AATCT at 285, GATCC at 104, GATCT at 27.
  20. ARRR2r9ci: 5, GATCC at 2485, GATCC at 2431, AATCC at 2394, GATCC at 2237, AATCC at 371.

Positive direction:

  1. ARRR2r0: 19, GGATT at 3973, GGATT at 3663, GGATC at 3140, AGATT at 2856, AGATC at 2761, GGATC at 2667, AGATT at 2652, GGATT at 2354, AGATC at 2249, AGATC at 1949, AGATC at 1852, GGATT at 1780, AGATT at 1774, GGATT at 992, GGATT at 952, GGATC at 924, GGATC at 736, AGATT at 128, GGATC at 94.
  2. ARRR2r1: 15, AGATC at 3860, GGATT at 3583, GGATT at 3451, AGATC at 2995, AGATC at 2834, GGATC at 2724, AGATT at 2448, AGATC at 2250, GGATC at 2230, AGATC at 1798, GGATC at 1789, AGATC at 1779, GGATT at 1259, GGATT at 702, AGATT at 361.
  3. ARRR2r2: 14, AGATT at 3612, AGATT at 3456, GGATC at 3436, AGATT at 3001, AGATT at 2931, AGATT at 2652, AGATT at 1690, GGATT at 1580, GGATC at 1418, GGATT at 559, AGATT at 336, GGATC at 157, GGATT at 134, GGATT at 127.
  4. ARRR2r3: 10, AGATC at 3824, GGATT at 3778, GGATT at 3755, GGATT at 2940, GGATC at 2566, GGATC at 2434, GGATT at 2410, GGATT at 1488, GGATT at 1229, GGATC at 968.
  5. ARRR2r4: 15, GGATC at 3922, AGATC at 3132, GGATC at 3092, AGATC at 3047, AGATC at 2798, GGATT at 2766, AGATT at 2721, GGATC at 2690, AGATC at 1669, GGATC at 1494, GGATC at 1173, AGATT at 945, GGATT at 840, GGATT at 616, GGATT at 558.
  6. ARRR2r5: 15, AGATC at 4030, GGATT at 3352, AGATT at 3170, GGATC at 2884, AGATC at 2829, AGATT at 2437, GGATC at 2428, GGATT at 2000, GGATC at 1812, GGATT at 1757, AGATC at 1746, AGATC at 943, AGATT at 884, AGATT at 690, AGATT at 197.
  7. ARRR2r6: 10, GGATT at 3753, GGATT at 3609, GGATT at 3391, GGATC at 3026, AGATC at 2936, GGATT at 2539, AGATC at 2390, GGATC at 2213, AGATC at 166, AGATT at 93.
  8. ARRR2r7: 13, GGATT at 3595, AGATT at 3374, GGATC at 3367, GGATT at 2764, GGATC at 2530, GGATC at 2460, AGATT at 2402, GGATC at 1921, GGATT at 1297, GGATC at 1285, AGATT at 707, GGATC at 501, GGATT at 241.
  9. ARRR2r8: 15, GGATT at 3481, GGATC at 3016, GGATT at 2432, AGATT at 2242, GGATT at 2089, AGATC at 1872, GGATT at 1818, AGATC at 1500, GGATC at 1057, GGATC at 974, GGATT at 870, AGATC at 864, GGATC at 337, GGATC at 103, AGATC at 26.
  10. ARRR2r9: 11, AGATT at 3720, GGATC at 3444, AGATT at 3313, GGATT at 2628, GGATT at 2603, AGATC at 2430, AGATT at 2327, GGATT at 2138, AGATT at 2060, AGATT at 315, GGATT at 239.
  11. ARRR2r0ci: 15, AATCC at 4024, AATCC at 3916, AATCC at 3127, GATCC at 2762, GATCC at 2668, AATCC at 2560, AATCC at 2507, GATCC at 2250, AATCC at 1558, AATCC at 1160, GATCT at 925, GATCC at 818, GATCT at 737, AATCT at 612, AATCC at 466.
  12. ARRR2r1ci: 8, GATCT at 3861, GATCC at 2835, GATCT at 2627, AATCC at 2377, GATCC at 1799, GATCC at 1790, GATCT at 1336, AATCC at 800.
  13. ARRR2r2ci: 16, AATCT at 3962, GATCT at 3762, AATCC at 3231, AATCC at 2512, GATCC at 1419, AATCC at 1360, AATCC at 1201, GATCT at 1193, AATCT at 1168, AATCT at 828, AATCC at 795, AATCC at 767, AATCC at 568, AATCT at 513, AATCC at 350, GATCT at 158.
  14. ARRR2r3ci: 17, AATCC at 4022, AATCC at 3868, GATCC at 3825, AATCC at 3516, AATCC at 3364, AATCT at 3269, AATCC at 2777, AATCC at 2766, GATCT at 2567, AATCC at 2518, AATCC at 2493, GATCT at 2435, GATCT at 1756, AATCC at 1219, GATCT at 1126, GATCC at 847, AATCC at 832.
  15. ARRR2r4ci: 18, AATCT at 3984, GATCT at 3923, AATCC at 3631, GATCT at 3133, GATCC at 3048, AATCC at 2817, AATCC at 2739, AATCT at 2446, AATCT at 1763, AATCT at 1698, GATCT at 1670, GATCT at 1495, GATCC at 1174, AATCC at 892, AATCC at 777, AATCT at 665, AATCC at 380, GATCT at 66.
  16. ARRR2r5ci: 20, GATCC at 4031, AATCC at 3853, AATCC at 3450, AATCC at 3033, AATCC at 3011, GATCC at 2885, GATCT at 2830, AATCC at 2648, AATCC at 2519, GATCT at 2429, AATCT at 2374, AATCT at 2106, AATCT at 2062, AATCC at 2013, GATCC at 1783, AATCT at 1317, AATCC at 913, AATCC at 778, AATCC at 755, AATCC at 129.
  17. ARRR2r6ci: 16, GATCC at 4050, AATCC at 3337, AATCC at 3154, GATCT at 3048, GATCT at 2937, GATCC at 2875, GATCT at 2391, AATCT at 2335, AATCT at 1741, AATCC at 1187, GATCT at 880, AATCT at 728, GATCT at 702, AATCT at 694, GATCT at 509, AATCT at 364.
  18. ARRR2r7ci: 19, AATCC at 3860, GATCT at 3551, GATCT at 3368, AATCC at 3221, AATCT at 3016, AATCT at 2475, GATCT at 2461, AATCT at 2308, AATCT at 2284, AATCC at 1738, AATCT at 1563, AATCC at 1427, GATCC at 1163, GATCC at 1117, GATCT at 1003, AATCC at 566, GATCC at 502, AATCC at 211, AATCC at 31.
  19. ARRR2r8ci: 15, AATCT at 3940, AATCT at 3716, GATCT at 3703, AATCC at 3427, GATCC at 3017, AATCT at 2927, GATCT at 2193, AATCC at 2009, AATCC at 1939, AATCT at 1301, GATCC at 967, AATCC at 391, AATCT at 285, GATCC at 104, GATCT at 27.
  20. ARRR2r9ci: 11, GATCC at 3583, AATCC at 3558, AATCT at 3545, GATCC at 3445, AATCC at 2960, AATCT at 2835, GATCC at 2485, GATCC at 2431, AATCC at 2394, GATCC at 2237, AATCC at 371.

ARRR2 analysis and results

Main article: Complex locus A1BG and ZNF497 § ARRR2s

"The sequence of this common upstream sequence motif closely matches (G/A)GAT(T/C), the optimal DNA-binding sequence identified in vitro for ARR1 and ARR2, two type-B ARRs (Sakai et al., 2000)."[4]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 15 2 7.5 7.5 ± 3.5 (--4,+-11)
Randoms UTR arbitrary negative 53 10 5.3 5.9 ± 0.6
Randoms UTR alternate negative 65 10 6.5 5.9 ± 0.6
Reals Core negative 0 2 0 0
Randoms Core arbitrary negative 1 10 0.1 0.3 ± 0.2
Randoms Core alternate negative 5 10 0.5 0.3 ± 0.2
Reals Core positive 0 2 0 0
Randoms Core arbitrary positive 7 10 0.7 0.65
Randoms Core alternate positive 6 10 0.6 0.65
Reals Proximal negative 1 2 0.5 0.5 ± 0.5 (--0,+-1)
Randoms Proximal arbitrary negative 11 10 1.1 0.9
Randoms Proximal alternate negative 7 10 0.7 0.9
Reals Proximal positive 6 2 3 3 ± 1 (-+2,++4)
Randoms Proximal arbitrary positive 11 10 1.1 0.65
Randoms Proximal alternate positive 2 10 0.2 0.65
Reals Distal negative 41 2 20.5 20.5 ± 8.5 (--12,+-29)
Randoms Distal arbitrary negative 98 10 9.8 9.15
Randoms Distal alternate negative 85 10 8.5 9.15
Reals Distal positive 25 2 12.5 12.5 ± 0.5(-+13,++12)
Randoms Distal arbitrary positive 139 10 13.9 14.6
Randoms Distal alternate positive 153 10 15.3 14.6

Comparison:

The occurrences of real ARRR2 UTRs, positive direction proximals and distals are outside the randoms, negative direction proximals are within the randoms. This suggests that the real ARRR2s are likely active or activable.

Discussion

Several of the cytokinin response regulators: ARR10s, ARR12s, and those of Rashotte et al. (2003) have occurrences in the UTR of A1BG from the ZSCAN22 side and in the proximal promoters of A1BG from the ZNF497 side.

Any of the randomly generated nucleotide data sets (0 through 9) can be used to represent any of the real data for the response element of interest.

ARR1

Every response element ARR1 has 6 in the distal promoter (2 negative direction and 4 positive direction). Random samplings ranges from 0-3. For the proximal promoter there is one for two datasets out of 20. No random in the core promoter. And, four for two datasets in the UTR out of 20.

ARR10

ARR10 has only one element in the negative direction in the UTR. Four of the 10 random datasets had 1.25 response elements in the UTR. No sequences in the core promoters, but one sequence in the proximal promoter and many in the distal promoters. The only response element in the A1BG promoters is an inverse complement and five of the six random UTR response elements are inverse complements.

ARR12

For ARR12, the random samples have about 2.5 UTR elements, but ARR12 has only one in the UTR. The A1BG has no core promoters on either side but one random sample out of ten has one on the positive direction from ZNF497. The ARR12 in A1BG proximal promoters have none while two out of ten random datasets have one each. In the distal promoters the negative directions averaged four while the random datasets average 1.3. The positive direction has only one and the random datasets averaged 1.3.

ARR (Ferreira)

Rashotte 1

The Rashotte1 ARR (ARRR1) results differ from random datasets: one in the UTR on the ZSCAN22 side versus two (random). No core promoter elements versus one in two of ten (random). Three proximal promoters versus none (random). Distal promoters: one in the negative direction and three in the positive and one to three (random).

Rashotte 2

For (G/A)GAT(T/C) in ARRR2 (Rashotte2) UTRs, there are none for the negative strand, negative direction, but each random data set finds 2-8. For the positive strand, negative direction, there are seven versus 2-8 from the randomly generated nucleotide data sets (0 through 9).

For (A/G)ATC(C/T) in ARRR2 (Rashotte2) UTRs, all four of the negative strand, negative direction results are inverse complements, where the random data sets have (4-9). For the positive strand, negative direction there are eleven, but the random datasets have 2-9.

Neither direction for ARRR2 (Rashotte2) has core promoter elements, while the random results have an average of (1 per data set, 0-1, negative direction, 0-3, positive direction).

For the negative direction and the proximal promoter, ARRR2 (Rashotte2) produced only one. And, the random datasets have an average of (1 per data set, 0-4).

The positive direction, ARRR2 (Rashotte2) has six. The random datasets have about 1 per dataset (0-3).

The distal promoters, negative direction, ARRR2 (Rashotte2) has 37 and the positive direction 25. The random datasets cover 8-20.

Acknowledgements

The content on this page was first contributed by: Henry A. Hoff.

See also

References

  1. ↑ 1.0 1.1 1.2 1.3 1.4 1.5 1.6 Mingtang Xie, Hongyu Chen, Ling Huang, Ryan C. O’Neil, Maxim N. Shokhirev & Joseph R. Ecker (23 April 2018). "A B-ARR-mediated cytokinin transcriptional network directs hormone cross-regulation and shoot development" (PDF). Nature Communications. 9 (1604): 1–13. doi:10.1038/s41467-018-03921-6. Retrieved 26 April 2021.
  2. ↑ 2.0 2.1 2.2 2.3 2.4 Fernando J Ferreira and Joseph J Kieber (October 2005). "Cytokinin signaling" (PDF). Current Opinion in Plant Biology. 8 (5): 518–525. doi:10.1016/j.pbi.2005.07.013. Retrieved 28 April 2021.
  3. ↑ 3.0 3.1 Cytokinin signal perception and transduction (2003). "Alexander Heyl and Thomas Schmülling" (PDF). Current Opinion in Plant Biology. 6: 480–488. doi:10.1016/S1369-5266(03)00087-6. Retrieved 28 April 2021.
  4. ↑ 4.0 4.1 4.2 4.3 Aaron M. Rashotte, Susan D.B. Carson, Jennifer P.C. To, and Joseph J. Kieber (August 2003). "Expression Profiling of Cytokinin Action in Arabidopsis" (PDF). Plant Physiology. 132 (4): 1998–2011. doi:10.1104/pp.103.021436. Retrieved 28 April 2021.

External links

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