Carbohydrate response element gene transcriptions

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

A high glucose "HG environment promotes [carbohydrate response element-binding protein] ChREBP translocation to the nucleus leading to formation of a heterodimeric complex with MLX (Max-like protein X) and binding to the carbohydrate response elements (ChoRE) of ChREBP target genes in the nucleus (14-16)."[1]

Human genes

Main article: Human genes

Gene ID: 55000 is TUG1 taurine up-regulated 1 on 22q12.2: "This gene produces a long non-coding RNA that interacts with the Polycomb repressor complex and functions in the epigenetic regulation of transcription. This RNA promotes cell proliferation and is upregulated in tumor cells. It may act as a sponge for microRNAs. The homologous mouse gene is required for differentiation of retina. Alternative splicing results in multiple transcript variants."[2]

Gene expressions

Main article: Gene expressions

High "glucose milieu down-regulates Tug1 expression in podocytes."[1]

Interactions

Main article: Interaction gene transcriptions

Consensus sequences

Main article: Consensus sequence gene transcriptions

Binding sites

"The putative ChREBP binding sites ChoRE1 (CACGTGACCGGATCTTG, -324 to -308) and ChoRE2 (TCCGCCCCCATCACGTG, -298 to - 282) were mutated into CACGTGACGGATCTTG and TCCGCCCCATCACGTG respectively, where the 5-nt spacer between the two E-boxes in ChoRE motifs were shortened to 4-nt (underlined) as previously studies showed (10,35)."[1]

"Using a web-based tool, rVista 2.0, we identified several potential binding sites for transcription factors [...]. Notably, we found multiple p53 candidate binding sites, and SP1, YY1, E47, and IRF-3 as well as PPAR-α binding sites."[1]

Inverse copies

Enhancer activity

The E-boxes in ChoRE1 and ChoRE2 are CACGTG and ATCTTG and TCCGCC and CACGTG.[1]

Promoter occurrences

In "response to HG milieu, ChREBP can recruit other members of the ChREBP network, including MLX, MAX (Myc-associated factor), MXD1, (Max dimerization protein 1) and HDAC1 (histone deacetylase 1), to a ChoRE element and neighboring E-box (enhancer box) in the Tug1 promoter, suppressing transcriptional activity."[1]

Hypotheses

Main article: Hypotheses
  1. A1BG has no Carbohydrate response elements in either promoter.
  2. A1BG is not transcribed by a Carbohydrate response element.
  3. Carbohydrate response element does not participate in the transcription of A1BG.

Samplings

Main article: Model samplings

Copying the E-boxes putting these sequences in "⌘F" finds: CACGTG none between ZSCAN22 and A1BG and one between ZNF497 and A1BG, ATCTTG none between ZSCAN22 and A1BG and none between ZNF497 and A1BG, and TCCGCC one between ZSCAN22 and A1BG and none between ZNF497 and A1BG, as can be found by the computer programs.

Copying the ChoRE consensus sequence 5'-ACCGGATCTTG-3' or 5'-TCCGCCCCCAT-3' 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.

Copying the core ChoRE consensus sequence 5'-ACCGG-3' or 5'-CCCAT-3' and putting the sequence in "⌘F" finds one and five between ZSCAN22 and A1BG or six and three between ZNF497 and A1BG as can be found by the computer programs.

ChoRE1 (CACGTGACCGGATCTTG) samplings

For the Basic programs testing consensus sequence 5'-CACGTGACCGGATCTTG-3' (starting with SuccessablesChoRE1.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'-CACGTGACCGGATCTTG-3', 0.
  2. negative strand, positive direction, looking for 5'-CACGTGACCGGATCTTG-3', 0.
  3. positive strand, negative direction, looking for 5'-CACGTGACCGGATCTTG-3', 0.
  4. positive strand, positive direction, looking for 5'-CACGTGACCGGATCTTG-3', 0.
  5. complement, negative strand, negative direction, looking for 5'-GTGCACTGGCCTAGAAC-3', 0.
  6. complement, negative strand, positive direction, looking for 5'-GTGCACTGGCCTAGAAC-3', 0.
  7. complement, positive strand, negative direction, looking for 5'-GTGCACTGGCCTAGAAC-3', 0.
  8. complement, positive strand, positive direction, looking for 5'-GTGCACTGGCCTAGAAC-3', 0.
  9. inverse complement, negative strand, negative direction, looking for 5'-CAAGATCCGGTCACGTG-3', 0.
  10. inverse complement, negative strand, positive direction, looking for 5'-CAAGATCCGGTCACGTG-3', 0.
  11. inverse complement, positive strand, negative direction, looking for 5'-CAAGATCCGGTCACGTG-3', 0.
  12. inverse complement, positive strand, positive direction, looking for 5'-CAAGATCCGGTCACGTG-3', 0.
  13. inverse negative strand, negative direction, looking for 5'-GTTCTAGGCCAGTGCAC-3', 0.
  14. inverse negative strand, positive direction, looking for 5'-GTTCTAGGCCAGTGCAC-3', 0.
  15. inverse positive strand, negative direction, looking for 5'-GTTCTAGGCCAGTGCAC-3', 0.
  16. inverse positive strand, positive direction, looking for 5'-GTTCTAGGCCAGTGCAC-3', 0.

ChoRE2 (TCCGCCCCCATCACGTG) samplings

For the Basic programs testing consensus sequence 5'-TCCGCCCCCATCACGTG-3' (starting with SuccessablesChoRE2.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'-TCCGCCCCCATCACGTG-3', 0.
  2. negative strand, positive direction, looking for 5'-TCCGCCCCCATCACGTG-3', 0.
  3. positive strand, negative direction, looking for 5'-TCCGCCCCCATCACGTG-3', 0.
  4. positive strand, positive direction, looking for 5'-TCCGCCCCCATCACGTG-3', 0.
  5. complement, negative strand, negative direction, looking for 5'-AGGCGGGGGTAGTGCAC-3', 0.
  6. complement, negative strand, positive direction, looking for 5'-AGGCGGGGGTAGTGCAC-3', 0.
  7. complement, positive strand, negative direction, looking for 5'-AGGCGGGGGTAGTGCAC-3', 0.
  8. complement, positive strand, positive direction, looking for 5'-AGGCGGGGGTAGTGCAC-3', 0.
  9. inverse complement, negative strand, negative direction, looking for 5'-CACGTGATGGGGGCGGA-3', 0.
  10. inverse complement, negative strand, positive direction, looking for 5'-CACGTGATGGGGGCGGA-3', 0.
  11. inverse complement, positive strand, negative direction, looking for 5'-CACGTGATGGGGGCGGA-3', 0.
  12. inverse complement, positive strand, positive direction, looking for 5'-CACGTGATGGGGGCGGA-3', 0.
  13. inverse negative strand, negative direction, looking for 5'-GTGCACTACCCCCGCCT-3', 0.
  14. inverse negative strand, positive direction, looking for 5'-GTGCACTACCCCCGCCT-3', 0.
  15. inverse positive strand, negative direction, looking for 5'-GTGCACTACCCCCGCCT-3', 0.
  16. inverse positive strand, positive direction, looking for 5'-GTGCACTACCCCCGCCT-3', 0.

ACCGG (Carb) samplings

UTR promoters

Negative strand, negative direction: CCGGT at 4168, CCGGT at 4100, ACCGG at 4099, CCGGT at 3949, ACCGG at 3948, CCGGT at 3131, ACCGG at 3130.

Core promoters

Negative strand, positive direction: ACCGG at 4345.

Proximal promoters

Negative strand, negative direction: CCGGT at 2608, ACCGG at 2607.

Distal promoters

Negative strand, negative direction: CCGGT at 2517, CCGGT at 2075, CCGGT at 1201, ACCGG at 1200, CCGGT at 690, CCGGT at 646, ACCGG at 645, CCGGT at 554, CCGGT at 417.

Positive strand, negative direction: ACCGG at 2191.

Negative strand, positive direction: ACCGG at 1846, CCGGT at 1760, ACCGG at 1546, ACCGG at 1294, ACCGG at 1210, ACCGG at 1042, CCGGT at 485, ACCGG at 442.

Positive strand, positive direction: ACCGG at 3681, CCGGT at 2991, ACCGG at 2990, ACCGG at 2985, CCGGT at 2572, ACCGG at 2571, CCGGT at 2070, ACCGG at 2069, CCGGT at 1849, ACCGG at 1738, CCGGT at 1173, CCGGT at 982, ACCGG at 949, CCGGT at 882, ACCGG at 849, CCGGT at 327, CCGGT at 213, ACCGG at 199.

Carb random samples

  1. Carbr0: 3, ACCGG at 4060, ACCGG at 3627, ACCGG at 729.
  2. Carbr1: 4, ACCGG at 4519, ACCGG at 3982, ACCGG at 2463, ACCGG at 394.
  3. Carbr2: 3, ACCGG at 1907, ACCGG at 1211, ACCGG at 1131.
  4. Carbr3: 5, ACCGG at 3836, ACCGG at 2366, ACCGG at 2068, ACCGG at 597, ACCGG at 344.
  5. Carbr4: 5, ACCGG at 4237, ACCGG at 3458, ACCGG at 1623, ACCGG at 1219, ACCGG at 108.
  6. Carbr5: 7, ACCGG at 4114, ACCGG at 4047, ACCGG at 2981, ACCGG at 1432, ACCGG at 1069, ACCGG at 661, ACCGG at 604.
  7. Carbr6: 7, ACCGG at 4126, ACCGG at 2995, ACCGG at 2733, ACCGG at 2427, ACCGG at 1919, ACCGG at 1618, ACCGG at 1407.
  8. Carbr7: 2, ACCGG at 3658, ACCGG at 3420.
  9. Carbr8: 7, ACCGG at 3734, ACCGG at 3728, ACCGG at 3722, ACCGG at 3649, ACCGG at 3613, ACCGG at 1970, ACCGG at 1062.
  10. Carbr9: 8, ACCGG at 4043, ACCGG at 3809, ACCGG at 3395, ACCGG at 3060, ACCGG at 3041, ACCGG at 2150, ACCGG at 1707, ACCGG at 596.
  11. Carbr0ci: 4, CCGGT at 4260, CCGGT at 4061, CCGGT at 3628, CCGGT at 1685.
  12. Carbr1ci: 4, CCGGT at 4481, CCGGT at 2668, CCGGT at 1680, CCGGT at 508.
  13. Carbr2ci: 7, CCGGT at 4022, CCGGT at 3398, CCGGT at 1250, CCGGT at 1212, CCGGT at 814, CCGGT at 649, CCGGT at 633.
  14. Carbr3ci: 8, CCGGT at 3476, CCGGT at 2885, CCGGT at 2367, CCGGT at 2069, CCGGT at 2033, CCGGT at 1583, CCGGT at 598, CCGGT at 345.
  15. Carbr4ci: 5, CCGGT at 3394, CCGGT at 755, CCGGT at 355, CCGGT at 143, CCGGT at 109.
  16. Carbr5ci: 7, CCGGT at 4255, CCGGT at 4115, CCGGT at 4038, CCGGT at 3370, CCGGT at 2982, CCGGT at 1070, CCGGT at 605.
  17. Carbr6ci: 4, CCGGT at 2734, CCGGT at 2366, CCGGT at 1619, CCGGT at 493.
  18. Carbr7ci: 3, CCGGT at 1828, CCGGT at 1350, CCGGT at 621.
  19. Carbr8ci: 8, CCGGT at 4472, CCGGT at 3729, CCGGT at 3650, CCGGT at 2692, CCGGT at 513, CCGGT at 365, CCGGT at 120, CCGGT at 50.
  20. Carbr9ci: 6, CCGGT at 4492, CCGGT at 4044, CCGGT at 3983, CCGGT at 3042, CCGGT at 1612, CCGGT at 545.

Carbr arbitrary (evens) (4560-2846) UTRs

  1. Carbr0: ACCGG at 4060, ACCGG at 3627.
  2. Carbr4: ACCGG at 4237, ACCGG at 3458.
  3. Carbr6: ACCGG at 4126, ACCGG at 2995.
  4. Carbr8: ACCGG at 3734, ACCGG at 3728, ACCGG at 3722, ACCGG at 3649, ACCGG at 3613.
  5. Carbr0ci: CCGGT at 4260, CCGGT at 4061, CCGGT at 3628.
  6. Carbr2ci: CCGGT at 4022, CCGGT at 3398.
  7. Carbr4ci: CCGGT at 3394.
  8. Carbr8ci: CCGGT at 4472, CCGGT at 3729, CCGGT at 3650.

Carbr alternate (odds) (4560-2846) UTRs

  1. Carbr1: ACCGG at 4519, ACCGG at 3982.
  2. Carbr3: ACCGG at 3836.
  3. Carbr5: ACCGG at 4114, ACCGG at 4047, ACCGG at 2981.
  4. Carbr7: ACCGG at 3658, ACCGG at 3420.
  5. Carbr9: ACCGG at 4043, ACCGG at 3809, ACCGG at 3395, ACCGG at 3060, ACCGG at 3041.
  6. Carbr1ci: CCGGT at 4481.
  7. Carbr3ci: CCGGT at 3476, CCGGT at 2885.
  8. Carbr5ci: CCGGT at 4255, CCGGT at 4115, CCGGT at 4038, CCGGT at 3370, CCGGT at 2982.
  9. Carbr9ci: CCGGT at 4492, CCGGT at 4044, CCGGT at 3983, CCGGT at 3042.

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

  1. Carbr6: ACCGG at 2733.
  2. Carbr6ci: CCGGT at 2734.
  3. Carbr8ci: CCGGT at 2692.

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

  1. Carbr1ci: CCGGT at 2668.

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

  1. Carbr5: ACCGG at 4114.
  2. Carbr5ci: CCGGT at 4255, CCGGT at 4115.

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

  1. Carbr0: ACCGG at 4060.
  2. Carbr4: ACCGG at 4237.
  3. Carbr6: ACCGG at 4126.
  4. Carbr0ci: CCGGT at 4260, CCGGT at 4061.

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

  1. Carbr0: ACCGG at 729.
  2. Carbr2: ACCGG at 1907, ACCGG at 1211, ACCGG at 1131.
  3. Carbr4: ACCGG at 1623, ACCGG at 1219, ACCGG at 108.
  4. Carbr6: ACCGG at 2427, ACCGG at 1919, ACCGG at 1618, ACCGG at 1407.
  5. Carbr8: ACCGG at 1970, ACCGG at 1062.
  6. Carbr0ci: CCGGT at 1685.
  7. Carbr2ci: CCGGT at 1250, CCGGT at 1212, CCGGT at 814, CCGGT at 649, CCGGT at 633.
  8. Carbr4ci: CCGGT at 755, CCGGT at 355, CCGGT at 143, CCGGT at 109.
  9. Carbr6ci: CCGGT at 2366, CCGGT at 1619, CCGGT at 493.
  10. Carbr8ci: CCGGT at 513, CCGGT at 365, CCGGT at 120, CCGGT at 50.

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

  1. Carbr1: ACCGG at 2463, ACCGG at 394.
  2. Carbr3: ACCGG at 2366, ACCGG at 2068, ACCGG at 597, ACCGG at 344.
  3. Carbr5: ACCGG at 1432, ACCGG at 1069, ACCGG at 661, ACCGG at 604.
  4. Carbr9: ACCGG at 2150, ACCGG at 1707, ACCGG at 596.
  5. Carbr1ci: CCGGT at 1680, CCGGT at 508.
  6. Carbr3ci: CCGGT at 2367, CCGGT at 2069, CCGGT at 2033, CCGGT at 1583, CCGGT at 598, CCGGT at 345.
  7. Carbr5ci: CCGGT at 1070, CCGGT at 605.
  8. Carbr7ci: CCGGT at 1828, CCGGT at 1350, CCGGT at 621.
  9. Carbr9ci: CCGGT at 1612, CCGGT at 545.

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

  1. Carbr1: ACCGG at 3982, ACCGG at 2463, ACCGG at 394.
  2. Carbr3: ACCGG at 3836, ACCGG at 2366, ACCGG at 2068, ACCGG at 597, ACCGG at 344.
  3. Carbr5: ACCGG at 4047, ACCGG at 2981, ACCGG at 1432, ACCGG at 1069, ACCGG at 661, ACCGG at 604.
  4. Carbr7: ACCGG at 3658, ACCGG at 3420.
  5. Carbr9: ACCGG at 4043, ACCGG at 3809, ACCGG at 3395, ACCGG at 3060, ACCGG at 3041, ACCGG at 2150, ACCGG at 1707, ACCGG at 596.
  6. Carbr1ci: CCGGT at 2668, CCGGT at 1680, CCGGT at 508.
  7. Carbr3ci: CCGGT at 3476, CCGGT at 2885, CCGGT at 2367, CCGGT at 2069, CCGGT at 2033, CCGGT at 1583, CCGGT at 598, CCGGT at 345.
  8. Carbr5ci: CCGGT at 4038, CCGGT at 3370, CCGGT at 2982, CCGGT at 1070, CCGGT at 605.
  9. Carbr7ci: CCGGT at 1828, CCGGT at 1350, CCGGT at 621.
  10. Carbr9ci: CCGGT at 4044, CCGGT at 3983, CCGGT at 3042, CCGGT at 1612, CCGGT at 545.

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

  1. Carbr0: ACCGG at 3627, ACCGG at 729.
  2. Carbr2: ACCGG at 1907, ACCGG at 1211, ACCGG at 1131.
  3. Carbr4: ACCGG at 3458, ACCGG at 1623, ACCGG at 1219, ACCGG at 108.
  4. Carbr6: ACCGG at 2995, ACCGG at 2733, ACCGG at 2427, ACCGG at 1919, ACCGG at 1618, ACCGG at 1407.
  5. Carbr8: ACCGG at 3734, ACCGG at 3728, ACCGG at 3722, ACCGG at 3649, ACCGG at 3613, ACCGG at 1970, ACCGG at 1062.
  6. Carbr0ci: CCGGT at 3628, CCGGT at 1685.
  7. Carbr2ci: CCGGT at 4022, CCGGT at 3398, CCGGT at 1250, CCGGT at 1212, CCGGT at 814, CCGGT at 649, CCGGT at 633.
  8. Carbr4ci: CCGGT at 3394, CCGGT at 755, CCGGT at 355, CCGGT at 143, CCGGT at 109.
  9. Carbr6ci: CCGGT at 2734, CCGGT at 2366, CCGGT at 1619, CCGGT at 493.
  10. Carbr8ci: CCGGT at 3729, CCGGT at 3650, CCGGT at 2692, CCGGT at 513, CCGGT at 365, CCGGT at 120, CCGGT at 50.

Carb analysis and results

Main article: Complex locus A1BG and ZNF497 § Carbs

"The putative ChREBP binding sites ChoRE1 [contain the response element here denoted as Carb underlined] (CACGTGACCGGATCTTG, -324 to -308)".[1]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 7 2 3.5 0
Randoms UTR arbitrary negative 20 10 2.0 2.25 ± 0.25
Randoms UTR alternate negative 25 10 2.5 2.25 ± 0.25
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 1 2 0.5 0.5
Randoms Core arbitrary positive 0 10 0 0
Randoms Core alternate positive 0 10 0 0
Reals Proximal negative 2 2 1 1
Randoms Proximal arbitrary negative 3 10 0.3 0.2
Randoms Proximal alternate negative 1 10 0.1 0.2
Reals Proximal positive 0 2 0 0
Randoms Proximal arbitrary positive 3 10 0.3 0.4
Randoms Proximal alternate positive 5 10 0.5 0.4
Reals Distal negative 10 2 5 (--9,+-1)
Randoms Distal arbitrary negative 30 10 3.0 2.9
Randoms Distal alternate negative 28 10 2.8 2.9
Reals Distal positive 25 2 12.5 12.5 ± 4.5(-+8,++17)
Randoms Distal arbitrary positive 48 10 4.8 4.75
Randoms Distal alternate positive 47 10 4.7 4.75

Comparison:

The occurrences of real Carbs are greater than the randoms. This suggests that the real Carbs are likely active or activable.

CCCAT (Carb1) samplings

Positive strand, negative direction: CCCAT at 4454, CCCAT at 3855, ATGGG at 3800, ATGGG at 3660, CCCAT at 3152, CCCAT at 2288, CCCAT at 1861, ATGGG at 202, ATGGG at 78.

Negative strand, positive direction: ATGGG at 4223, CCCAT at 4220, CCCAT at 3899, CCCAT at 3334, ATGGG at 3169, ATGGG at 2911, ATGGG at 2268, ATGGG at 1880, ATGGG at 1188.

Positive strand, positive direction: CCCAT at 3751, ATGGG at 1889.

Carb1 (4560-2846) UTRs

  1. Positive strand, negative direction: CCCAT at 4454, CCCAT at 3855, ATGGG at 3800, ATGGG at 3660, CCCAT at 3152.

Carb1 positive direction (4265-4050) proximal promoters

Negative strand, positive direction: ATGGG at 4223, CCCAT at 4220.

Carb1 negative direction (2596-1) distal promoters

  1. Positive strand, negative direction: CCCAT at 2288, CCCAT at 1861, ATGGG at 202, ATGGG at 78.

Carb1 positive direction (4050-1) distal promoters

  1. Negative strand, positive direction: CCCAT at 3899, CCCAT at 3334, ATGGG at 3169, ATGGG at 2911, ATGGG at 2268, ATGGG at 1880, ATGGG at 1188.

Carb1 random samplings

  1. Carb1r0: 9, CCCAT at 4496, CCCAT at 4383, CCCAT at 4086, CCCAT at 3953, CCCAT at 3774, CCCAT at 2921, CCCAT at 2820, CCCAT at 2038, CCCAT at 38.
  2. Carb1r1: 6, CCCAT at 3770, CCCAT at 3631, CCCAT at 2827, CCCAT at 2110, CCCAT at 1315, CCCAT at 334.
  3. Carb1r2: 5, CCCAT at 4037, CCCAT at 2892, CCCAT at 2624, CCCAT at 1705, CCCAT at 1624.
  4. Carb1r3: 9, CCCAT at 4456, CCCAT at 3795, CCCAT at 3130, CCCAT at 2796, CCCAT at 2096, CCCAT at 1578, CCCAT at 1464, CCCAT at 1334, CCCAT at 1064.
  5. Carb1r4: 8, CCCAT at 4510, CCCAT at 2915, CCCAT at 2544, CCCAT at 1841, CCCAT at 919, CCCAT at 768, CCCAT at 634, CCCAT at 307.
  6. Carb1r5: 10, CCCAT at 4103, CCCAT at 3210, CCCAT at 3145, CCCAT at 2625, CCCAT at 2607, CCCAT at 2598, CCCAT at 2514, CCCAT at 1776, CCCAT at 837, CCCAT at 808.
  7. Carb1r6: 6, CCCAT at 3347, CCCAT at 3230, CCCAT at 2459, CCCAT at 1544, CCCAT at 623, CCCAT at 309.
  8. Carb1r7: 4, CCCAT at 4219, CCCAT at 2670, CCCAT at 1339, CCCAT at 1174.
  9. Carb1r8: 4, CCCAT at 4141, CCCAT at 3254, CCCAT at 1827, CCCAT at 779.
  10. Carb1r9: 9, CCCAT at 3474, CCCAT at 3406, CCCAT at 2671, CCCAT at 2243, CCCAT at 1782, CCCAT at 615, CCCAT at 423, CCCAT at 83, CCCAT at 56.
  11. Carb1r0ci: 3, ATGGG at 2604, ATGGG at 2280, ATGGG at 936.
  12. Carb1r1ci: 4, ATGGG at 4166, ATGGG at 2983, ATGGG at 1110, ATGGG at 487.
  13. Carb1r2ci: 6, ATGGG at 4388, ATGGG at 2733, ATGGG at 1452, ATGGG at 361, ATGGG at 284, ATGGG at 188.
  14. Carb1r3ci: 5, ATGGG at 4410, ATGGG at 3893, ATGGG at 3327, ATGGG at 2533, ATGGG at 2257.
  15. Carb1r4ci: 7, ATGGG at 4226, ATGGG at 3958, ATGGG at 3220, ATGGG at 2703, ATGGG at 2518, ATGGG at 2500, ATGGG at 1831.
  16. Carb1r5ci: 8, ATGGG at 3871, ATGGG at 3401, ATGGG at 3151, ATGGG at 2581, ATGGG at 2568, ATGGG at 1039, ATGGG at 459, ATGGG at 174.
  17. Carb1r6ci: 3, ATGGG at 4345, ATGGG at 3552, ATGGG at 298.
  18. Carb1r7ci: 4, ATGGG at 3990, ATGGG at 2134, ATGGG at 955, ATGGG at 638.
  19. Carb1r8ci: 8, ATGGG at 3597, ATGGG at 3438, ATGGG at 2950, ATGGG at 2468, ATGGG at 788, ATGGG at 571, ATGGG at 409, ATGGG at 95.
  20. Carb1r9ci: 2, ATGGG at 4529, ATGGG at 3178.

Carb1r arbitrary (evens) (4560-2846) UTRs

  1. Carb1r0: CCCAT at 4496, CCCAT at 4383, CCCAT at 4086, CCCAT at 3953, CCCAT at 3774, CCCAT at 2921.
  2. Carb1r2: CCCAT at 4037, CCCAT at 2892.
  3. Carb1r4: CCCAT at 4510, CCCAT at 2915.
  4. Carb1r6: CCCAT at 3347, CCCAT at 3230.
  5. Carb1r8: CCCAT at 4141, CCCAT at 3254.
  6. Carb1r2ci: ATGGG at 4388.
  7. Carb1r4ci: ATGGG at 4226, ATGGG at 3958, ATGGG at 3220.
  8. Carb1r6ci: ATGGG at 4345, ATGGG at 3552.
  9. Carb1r8ci: ATGGG at 3597, ATGGG at 3438, ATGGG at 2950.

Carb1r alternate (odds) (4560-2846) UTRs

  1. Carb1r1: CCCAT at 3770, CCCAT at 3631.
  2. Carb1r3: CCCAT at 4456, CCCAT at 3795, CCCAT at 3130.
  3. Carb1r5: CCCAT at 4103, CCCAT at 3210, CCCAT at 3145.
  4. Carb1r7: CCCAT at 4219.
  5. Carb1r9: CCCAT at 3474, CCCAT at 3406.
  6. Carb1r1ci: ATGGG at 4166, ATGGG at 2983.
  7. Carb1r3ci: ATGGG at 4410, ATGGG at 3893, ATGGG at 3327.
  8. Carb1r5ci: ATGGG at 3871, ATGGG at 3401, ATGGG at 3151.
  9. Carb1r7ci: ATGGG at 3990.
  10. Carb1r9ci: ATGGG at 4529, ATGGG at 3178.

Carb1r arbitrary negative direction (evens) (2846-2811) core promoters

  1. Carb1r0: CCCAT at 2820.

Carb1r alternate negative direction (odds) (2846-2811) core promoters

  1. Carb1r1: CCCAT at 2827.

Carb1r arbitrary positive direction (odds) (4445-4265) core promoters

  1. Carb1r3ci: ATGGG at 4410.

Carb1r alternate positive direction (evens) (4445-4265) core promoters

  1. Carb1r0: CCCAT at 4383.
  2. Carb1r2ci: ATGGG at 4388.
  3. Carb1r6ci: ATGGG at 4345.

Carb1r arbitrary negative direction (evens) (2811-2596) proximal promoters

  1. Carb1r2: CCCAT at 2624.
  2. Carb1r0ci: ATGGG at 2604.
  3. Carb1r2ci: ATGGG at 2733.
  4. Carb1r4ci: ATGGG at 2703.

Carb1r alternate negative direction (odds) (2811-2596) proximal promoters

  1. Carb1r3: CCCAT at 2796.
  2. Carb1r5: CCCAT at 2625, CCCAT at 2607, CCCAT at 2598.
  3. Carb1r7: CCCAT at 2670.
  4. Carb1r9: CCCAT at 2671.

Carb1r arbitrary positive direction (odds) (4265-4050) proximal promoters

  1. Carb1r5: CCCAT at 4103.
  2. Carb1r7: CCCAT at 4219.
  3. Carb1r1ci: ATGGG at 4166.

Carb1r alternate positive direction (evens) (4265-4050) proximal promoters

  1. Carb1r0: CCCAT at 4086.
  2. Carb1r8: CCCAT at 4141.
  3. Carb1r4ci: ATGGG at 4226.

Carb1r arbitrary negative direction (evens) (2596-1) distal promoters

  1. Carb1r0: CCCAT at 2038, CCCAT at 38.
  2. Carb1r2: CCCAT at 1705, CCCAT at 1624.
  3. Carb1r4: CCCAT at 2544, CCCAT at 1841, CCCAT at 919, CCCAT at 768, CCCAT at 634, CCCAT at 307.
  4. Carb1r6: CCCAT at 2459, CCCAT at 1544, CCCAT at 623, CCCAT at 309.
  5. Carb1r8: CCCAT at 1827, CCCAT at 779.
  6. Carb1r0ci: ATGGG at 2280, ATGGG at 936.
  7. Carb1r2ci: ATGGG at 1452, ATGGG at 361, ATGGG at 284, ATGGG at 188.
  8. Carb1r4ci: ATGGG at 2518, ATGGG at 2500, ATGGG at 1831.
  9. Carb1r6ci: ATGGG at 298.
  10. Carb1r8ci: ATGGG at 2468, ATGGG at 788, ATGGG at 571, ATGGG at 409, ATGGG at 95.

Carb1r alternate negative direction (odds) (2596-1) distal promoters

  1. Carb1r1: CCCAT at 2110, CCCAT at 1315, CCCAT at 334.
  2. Carb1r3: CCCAT at 2096, CCCAT at 1578, CCCAT at 1464, CCCAT at 1334, CCCAT at 1064.
  3. Carb1r5: CCCAT at 2514, CCCAT at 1776, CCCAT at 837, CCCAT at 808.
  4. Carb1r7: CCCAT at 1339, CCCAT at 1174.
  5. Carb1r9: CCCAT at 2243, CCCAT at 1782, CCCAT at 615, CCCAT at 423, CCCAT at 83, CCCAT at 56.
  6. Carb1r1ci: ATGGG at 1110, ATGGG at 487.
  7. Carb1r3ci: ATGGG at 2533, ATGGG at 2257.
  8. Carb1r5ci: ATGGG at 2581, ATGGG at 2568, ATGGG at 1039, ATGGG at 459, ATGGG at 174.
  9. Carb1r7ci: ATGGG at 2134, ATGGG at 955, ATGGG at 638.

Carb1r arbitrary positive direction (odds) (4050-1) distal promoters

  1. Carb1r1: CCCAT at 3770, CCCAT at 3631, CCCAT at 2827, CCCAT at 2110, CCCAT at 1315, CCCAT at 334.
  2. Carb1r3: CCCAT at 3795, CCCAT at 3130, CCCAT at 2796, CCCAT at 2096, CCCAT at 1578, CCCAT at 1464, CCCAT at 1334, CCCAT at 1064.
  3. Carb1r5: CCCAT at 3210, CCCAT at 3145, CCCAT at 2625, CCCAT at 2607, CCCAT at 2598, CCCAT at 2514, CCCAT at 1776, CCCAT at 837, CCCAT at 808.
  4. Carb1r7: CCCAT at 2670, CCCAT at 1339, CCCAT at 1174.
  5. Carb1r9: CCCAT at 3474, CCCAT at 3406, CCCAT at 2671, CCCAT at 2243, CCCAT at 1782, CCCAT at 615, CCCAT at 423, CCCAT at 83, CCCAT at 56.
  6. Carb1r1ci: ATGGG at 2983, ATGGG at 1110, ATGGG at 487.
  7. Carb1r3ci: ATGGG at 3893, ATGGG at 3327, ATGGG at 2533, ATGGG at 2257.
  8. Carb1r5ci: ATGGG at 3871, ATGGG at 3401, ATGGG at 3151, ATGGG at 2581, ATGGG at 2568, ATGGG at 1039, ATGGG at 459, ATGGG at 174.
  9. Carb1r7ci: ATGGG at 3990, ATGGG at 2134, ATGGG at 955, ATGGG at 638.
  10. Carb1r9ci: ATGGG at 3178.

Carb1r alternate positive direction (evens) (4050-1) distal promoters

  1. Carb1r0: CCCAT at 3953, CCCAT at 3774, CCCAT at 2921, CCCAT at 2820, CCCAT at 2038, CCCAT at 38.
  2. Carb1r2: CCCAT at 4037, CCCAT at 2892, CCCAT at 2624, CCCAT at 1705, CCCAT at 1624.
  3. Carb1r4: CCCAT at 2915, CCCAT at 2544, CCCAT at 1841, CCCAT at 919, CCCAT at 768, CCCAT at 634, CCCAT at 307.
  4. Carb1r6: CCCAT at 3347, CCCAT at 3230, CCCAT at 2459, CCCAT at 1544, CCCAT at 623, CCCAT at 309.
  5. Carb1r8: CCCAT at 3254, CCCAT at 1827, CCCAT at 779.
  6. Carb1r0ci: ATGGG at 2604, ATGGG at 2280, ATGGG at 936.
  7. Carb1r2ci: ATGGG at 2733, ATGGG at 1452, ATGGG at 361, ATGGG at 284, ATGGG at 188.
  8. Carb1r4ci: ATGGG at 3958, ATGGG at 3220, ATGGG at 2703, ATGGG at 2518, ATGGG at 2500, ATGGG at 1831.
  9. Carb1r6ci: ATGGG at 3552, ATGGG at 298.
  10. Carb1r8ci: ATGGG at 3597, ATGGG at 3438, ATGGG at 2950, ATGGG at 2468, ATGGG at 788, ATGGG at 571, ATGGG at 409, ATGGG at 95.

Carb1 analysis and results

Main article: Complex locus A1BG and ZNF497 § Carb1s

"The putative ChREBP binding sites [contain the response element here denoted as Carb1 underlined] ChoRE2 (TCCGCCCCCATCACGTG, -298 to - 282)".[1]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 5 2 2.5 2.5
Randoms UTR arbitrary negative 23 10 2.3 2.3
Randoms UTR alternate negative 23 10 2.3 2.3
Reals Core negative 0 2 0 0
Randoms Core arbitrary negative 1 10 0.1 0.1
Randoms Core alternate negative 1 10 0.1 0.1
Reals Core positive 0 2 0 0
Randoms Core arbitrary positive 1 10 0.1 0.2
Randoms Core alternate positive 3 10 0.3 0.2
Reals Proximal negative 0 2 0 0
Randoms Proximal arbitrary negative 4 10 0.4 0.5
Randoms Proximal alternate negative 6 10 0.6 0.5
Reals Proximal positive 2 2 1 1
Randoms Proximal arbitrary positive 3 10 0.3 0.3
Randoms Proximal alternate positive 3 10 0.3 0.3
Reals Distal negative 4 2 2 2
Randoms Distal arbitrary negative 31 10 3.1 3.15
Randoms Distal alternate negative 32 10 3.2 3.15
Reals Distal positive 7 2 3.5 3.5
Randoms Distal arbitrary positive 55 10 5.5 5.1
Randoms Distal alternate positive 47 10 4.7 5.1

Comparison:

The occurrences of real Carb1 UTRs and proximals are greater than the randoms and distals are less than the randoms. This suggests that the real Carb1s are likely active or activable.

Enhancer boxes

Main article: Enhancer box gene transcriptions

The consensus sequence for the E-box element is CANNTG, with a palindromic canonical sequence of CACGTG.[3]

ATCTTG (CarbE1) samplings

  1. Negative strand, negative direction: 1, ATCTTG at 286.
  2. Positive strand, negative direction: 0.
  3. Negative strand, positive direction: 0.
  4. Positive strand, positive direction: 1, ATCTTG at 4067.
  5. Negative strand, negative direction, complement inverse: 0.
  6. Positive strand, negative direction, complement inverse: 2, CAAGAT at 3275, CAAGAT at 876.
  7. Negative strand, positive direction, complement inverse: 0.
  8. Positive strand, positive direction, complement inverse: 1, CAAGAT at 4075.

CarbE1 (4560-2846) UTRs

  1. Positive strand, negative direction: CAAGAT at 3275.

CarbE1 positive direction (4265-4050) proximal promoters

  1. Positive strand, positive direction: ATCTTG at 4067.
  2. Positive strand, positive direction, complement inverse: CAAGAT at 4075.

CarbE1 negative direction (2596-1) distal promoters

  1. Negative strand, negative direction: ATCTTG at 286.
  2. Positive strand, negative direction: CAAGAT at 876.

Carb E1 random samplings

  1. CarbE1r0: 1, ATCTTG at 4104.
  2. CarbE1r1: 1, ATCTTG at 3863.
  3. CarbE1r2: 2, ATCTTG at 1063, ATCTTG at 211.
  4. CarbE1r3: 0.
  5. CarbE1r4: 1, ATCTTG at 1765.
  6. CarbE1r5: 2, ATCTTG at 2431, ATCTTG at 2064.
  7. CarbE1r6: 3, ATCTTG at 2040, ATCTTG at 1743, ATCTTG at 366.
  8. CarbE1r7: 2, ATCTTG at 2477, ATCTTG at 2463.
  9. CarbE1r8: 2, ATCTTG at 2929, ATCTTG at 2195.
  10. CarbE1r9: 3, ATCTTG at 3835, ATCTTG at 3668, ATCTTG at 3410.
  11. CarbE1r0ci: 2, CAAGAT at 1851, CAAGAT at 1124.
  12. CarbE1r1ci: 1, CAAGAT at 2994.
  13. CarbE1r2ci: 2, CAAGAT at 4200, CAAGAT at 3611.
  14. CarbE1r3ci: 0.
  15. CarbE1r4ci: 1, CAAGAT at 3046.
  16. CarbE1r5ci: 0.
  17. CarbE1r6ci: 1, CAAGAT at 165.
  18. CarbE1r7ci: 1, CAAGAT at 706.
  19. CarbE1r8ci: 1, CAAGAT at 863.
  20. CarbE1r9ci: 1, CAAGAT at 1422.

CarbE1r arbitrary (evens) (4560-2846) UTRs

  1. CarbE1r0: ATCTTG at 4104.
  2. CarbE1r8: ATCTTG at 2929.
  3. CarbE1r2ci: CAAGAT at 4200, CAAGAT at 3611.
  4. CarbE1r4ci: CAAGAT at 3046.

CarbE1r alternate (odds) (4560-2846) UTRs

  1. CarbE1r1: ATCTTG at 3863.
  2. CarbE1r9: ATCTTG at 3835, ATCTTG at 3668, ATCTTG at 3410.
  3. CarbE1r1ci: CAAGAT at 2994.

CarbE1r alternate positive direction (evens) (4265-4050) proximal promoters

  1. CarbE1r0: ATCTTG at 4104.
  2. CarbE1r2ci: CAAGAT at 4200.

CarbE1r arbitrary negative direction (evens) (2596-1) distal promoters

  1. CarbE1r2: ATCTTG at 1063, ATCTTG at 211.
  2. CarbE1r4: ATCTTG at 1765.
  3. CarbE1r6: ATCTTG at 2040, ATCTTG at 1743, ATCTTG at 366.
  4. CarbE1r8: ATCTTG at 2195.
  5. CarbE1r0ci: CAAGAT at 1851, CAAGAT at 1124.
  6. CarbE1r6ci: CAAGAT at 165.
  7. CarbE1r8ci: CAAGAT at 863.

CarbE1r alternate negative direction (odds) (2596-1) distal promoters

  1. CarbE1r5: ATCTTG at 2431, ATCTTG at 2064.
  2. CarbE1r7: ATCTTG at 2477, ATCTTG at 2463.
  3. CarbE1r7ci: CAAGAT at 706.
  4. CarbE1r9ci: CAAGAT at 1422.

CarbE1r arbitrary positive direction (odds) (4050-1) distal promoters

  1. CarbE1r1: ATCTTG at 3863.
  2. CarbE1r5: ATCTTG at 2431, ATCTTG at 2064.
  3. CarbE1r7: ATCTTG at 2477, ATCTTG at 2463.
  4. CarbE1r9: ATCTTG at 3835, ATCTTG at 3668, ATCTTG at 3410.
  5. CarbE1r1ci: CAAGAT at 2994.
  6. CarbE1r7ci: CAAGAT at 706.
  7. CarbE1r9ci: CAAGAT at 1422.

CarbE1r alternate positive direction (evens) (4050-1) distal promoters

  1. CarbE1r2: ATCTTG at 1063, ATCTTG at 211.
  2. CarbE1r4: ATCTTG at 1765.
  3. CarbE1r6: ATCTTG at 2040, ATCTTG at 1743, ATCTTG at 366.
  4. CarbE1r8: ATCTTG at 2929, ATCTTG at 2195.
  5. CarbE1r0ci: CAAGAT at 1851, CAAGAT at 1124.
  6. CarbE1r2ci: CAAGAT at 3611.
  7. CarbE1r4ci: CAAGAT at 3046.
  8. CarbE1r6ci: CAAGAT at 165.
  9. CarbE1r8ci: CAAGAT at 863.

CarbE1 analysis and results

Main article: Complex locus A1BG and ZNF497 § CarbE1s

ATCTTG and TCCGCC are the two E-boxes in ChoRE motifs.[1]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 1 2 0.5 0.5 ± 0.1
Randoms UTR arbitrary negative 5 10 0.5 0.5 ± 0.1
Randoms UTR alternate negative 5 10 0.5 0.5 ± 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
Randoms Core alternate positive 0 10 0 0
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 2 2 1 1 ± 0.1
Randoms Proximal arbitrary positive 0 10 0 0.1 ± 0.1
Randoms Proximal alternate positive 2 10 0.2 0.1 ± 0.1
Reals Distal negative 2 2 1 1 ± 0.1
Randoms Distal arbitrary negative 11 10 1.1 0.85 ± 0.1
Randoms Distal alternate negative 6 10 0.6 0.85 ± 0.1
Reals Distal positive 0 2 0 0
Randoms Distal arbitrary positive 11 10 1.1 1.25 ± 0.1
Randoms Distal alternate positive 14 10 1.4 1.25 ± 0.1

Comparison:

The occurrences of real CarbE1 UTRs are the same as the randoms, proximals are greater than the randoms, the distals overlap the high randoms. This suggests that the real CarbE1 proximals are likely active or activable.

CACGTG (CarbE2) samplings

  1. Negative strand, positive direction: CACGTG at 570.
  2. Positive strand, positive direction: CACGTG at 3884, CACGTG at 2961, CACGTG at 1219, CACGTG at 547.

CarbE2 positive direction (4050-1) distal promoters

  1. Negative strand, positive direction: CACGTG at 570.
  2. Positive strand, positive direction: CACGTG at 3884, CACGTG at 2961, CACGTG at 1219, CACGTG at 547.

Carb E2 random samplings

Main article: Phosphate starvation-response transcription factor gene transcriptions § Phop random dataset samplings
  1. Phopr0: 1, CACGTG at 4343.
  2. Phopr1: 0.
  3. Phopr2: 0.
  4. Phopr3: 1, CACGTG at 3769.
  5. Phopr4: 1, CACGTG at 2287.
  6. Phopr5: 1, CACGTG at 59.
  7. Phopr6: 2, CACGTG at 2905, CACGTG at 654.
  8. Phopr7: 1, CACGTG at 1856.
  9. Phopr8: 0.
  10. Phopr9: 1, CACGTG at 1187.

CarbE2r arbitrary (evens) (4560-2846) UTRs

  1. Phopr0: CACGTG at 4343.
  2. Phopr6: CACGTG at 2905.

CarbE2r alternate (odds) (4560-2846) UTRs

  1. Phopr3: CACGTG at 3769.

CarbE2r alternate positive direction (evens) (4445-4265) core promoters

  1. Phopr0: CACGTG at 4343.

CarbE2r arbitrary negative direction (evens) (2596-1) distal promoters

  1. Phopr4: CACGTG at 2287.
  2. Phopr6: CACGTG at 654.

CarbE2r alternate negative direction (odds) (2596-1) distal promoters

  1. Phopr5: CACGTG at 59.
  2. Phopr7: CACGTG at 1856.
  3. Phopr9: CACGTG at 1187.

CarbE2r arbitrary positive direction (odds) (4050-1) distal promoters

  1. Phopr3: CACGTG at 3769.
  2. Phopr5: CACGTG at 59.
  3. Phopr7: CACGTG at 1856.

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

  1. Phopr4: CACGTG at 2287.
  2. Phopr6: CACGTG at 2905, CACGTG at 654.

CarbE2 results and analysis

Main article: Complex locus A1BG and ZNF497 § CarbE2s

Consensus sequences: CACGTG.[3]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 0 2 0 0
Randoms UTR arbitrary negative 2 10 0.2 0.15 ± 0.05
Randoms UTR alternate negative 1 10 0.1 0.15 ± 0.05
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
Randoms Proximal alternate negative 0 10 0 0
Reals Proximal positive 0 2 0 0
Randoms Proximal arbitrary positive 0 10 0 0
Randoms Proximal alternate positive 0 10 0 0
Reals Distal negative 0 2 0 0
Randoms Distal arbitrary negative 2 10 0.2 0.25 ± 0.05
Randoms Distal alternate negative 3 10 0.3 0.25 ± 0.05
Reals Distal positive 5 2 2.5 2.5 ± 0.1
Randoms Distal arbitrary positive 3 10 0.3 0.3 ± 0.1
Randoms Distal alternate positive 3 10 0.3 0.3 ± 0.1

Comparison:

The occurrences of real CarbE2s are greater than the randoms. This suggests that the real CarbE2s are likely active or activable.

TCCGCC (CarbE3) samplings

  1. Negative strand, negative direction: TCCGCC at 3999, TCCGCC at 3090, TCCGCC at 2392, TCCGCC at 2231, TCCGCC at 1752, GGCGGA at 1504, TCCGCC at 856, TCCGCC at 700, TCCGCC at 427.
  2. Positive strand, negative direction: GGCGGA at 2728, GGCGGA at 2393, GGCGGA at 1810, TCCGCC at 1503, GGCGGA at 857, GGCGGA at 701, GGCGGA at 428.
  3. Negative strand, positive direction: GGCGGA at 1203, GGCGGA at 357.
  4. Positive strand, positive direction: GGCGGA at 4239, TCCGCC at 3487, TCCGCC at 2485, GGCGGA at 905.

CarbE3 (4560-2846) UTRs

  1. Negative strand, negative direction: TCCGCC at 3999, TCCGCC at 3090.

CarbE3 negative direction (2811-2596) proximal promoters

  1. Positive strand, negative direction: GGCGGA at 2728.

CarbE3 positive direction (4265-4050) proximal promoters

  1. Positive strand, positive direction: GGCGGA at 4239.

CarbE3 negative direction (2596-1) distal promoters

  1. Negative strand, negative direction: TCCGCC at 2392, TCCGCC at 2231, TCCGCC at 1752, GGCGGA at 1504, TCCGCC at 856, TCCGCC at 700, TCCGCC at 427.
  2. Positive strand, negative direction: GGCGGA at 2393, GGCGGA at 1810, TCCGCC at 1503, GGCGGA at 857, GGCGGA at 701, GGCGGA at 428.

CarbE3 positive direction (4050-1) distal promoters

  1. Negative strand, positive direction: GGCGGA at 1203, GGCGGA at 357.
  2. Positive strand, positive direction: TCCGCC at 3487, TCCGCC at 2485, GGCGGA at 905.

CarbE3 random samplings

  1. Carb E3r0: 1, TCCGCC at 368.
  2. Carb E3r1: 1, TCCGCC at 1645.
  3. Carb E3r2: 1, TCCGCC at 639.
  4. Carb E3r3: 3, TCCGCC at 3376, TCCGCC at 484, TCCGCC at 117.
  5. Carb E3r4: 2, TCCGCC at 3492, TCCGCC at 14.
  6. Carb E3r5: 2, TCCGCC at 1159, TCCGCC at 7.
  7. Carb E3r6: 0.
  8. Carb E3r7: 2, TCCGCC at 2742, TCCGCC at 2667.
  9. Carb E3r8: 1, TCCGCC at 2012.
  10. Carb E3r9: 3, TCCGCC at 4446, TCCGCC at 2809, TCCGCC at 1558.
  11. Carb E3r0ci: 1, GGCGGA at 2033.
  12. Carb E3r1ci: 2, GGCGGA at 3214, GGCGGA at 1153.
  13. Carb E3r2ci: 0.
  14. Carb E3r3ci: 2, GGCGGA at 3926, GGCGGA at 3147.
  15. Carb E3r4ci: 1, GGCGGA at 4497.
  16. Carb E3r5ci: 1, GGCGGA at 3182.
  17. Carb E3r6ci: 1, GGCGGA at 2577.
  18. Carb E3r7ci: 3, GGCGGA at 3880, GGCGGA at 1221, GGCGGA at 787.
  19. Carb E3r8ci: 0.
  20. Carb E3r9ci: 2, GGCGGA at 3631, GGCGGA at 1143.

CarbEr arbitrary (evens) (4560-2846) UTRs

  1. Carb E3r4: TCCGCC at 3492.
  2. Carb E3r4ci: GGCGGA at 4497.

CarbEr alternate (odds) (4560-2846) UTRs

  1. Carb E3r3: TCCGCC at 3376.
  2. Carb E3r9: TCCGCC at 4446.
  3. Carb E3r1ci: GGCGGA at 3214.
  4. Carb E3r3ci: GGCGGA at 3926, GGCGGA at 3147.
  5. Carb E3r5ci: GGCGGA at 3182.
  6. Carb E3r7ci: GGCGGA at 3880.
  7. Carb E3r9ci: GGCGGA at 3631.

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

  1. Carb E3r7: TCCGCC at 2742, TCCGCC at 2667.
  2. Carb E3r9: TCCGCC at 2809.

CarbE3r arbitrary negative direction (evens) (2596-1) distal promoters

  1. Carb E3r0: TCCGCC at 368.
  2. Carb E3r2: TCCGCC at 639.
  3. Carb E3r4: TCCGCC at 14.
  4. Carb E3r8: TCCGCC at 2012.
  5. Carb E3r0ci: GGCGGA at 2033.
  6. Carb E3r6ci: GGCGGA at 2577.

CarbE3r alternate negative direction (odds) (2596-1) distal promoters

  1. Carb E3r1: TCCGCC at 1645.
  2. Carb E3r3: TCCGCC at 484, TCCGCC at 117.
  3. Carb E3r5: TCCGCC at 1159, TCCGCC at 7.
  4. Carb E3r9: TCCGCC at 1558.
  5. Carb E3r1ci: GGCGGA at 1153.
  6. Carb E3r7ci: GGCGGA at 1221, GGCGGA at 787.
  7. Carb E3r9ci: GGCGGA at 1143.

CarbE3r arbitrary positive direction (odds) (4050-1) distal promoters

  1. Carb E3r1: TCCGCC at 1645.
  2. Carb E3r3: TCCGCC at 3376, TCCGCC at 484, TCCGCC at 117.
  3. Carb E3r5: TCCGCC at 1159, TCCGCC at 7.
  4. Carb E3r7: TCCGCC at 2742, TCCGCC at 2667.
  5. Carb E3r9: TCCGCC at 2809, TCCGCC at 1558.
  6. Carb E3r1ci: GGCGGA at 3214, GGCGGA at 1153.
  7. Carb E3r3ci: GGCGGA at 3926, GGCGGA at 3147.
  8. Carb E3r5ci: GGCGGA at 3182.
  9. Carb E3r7ci: GGCGGA at 3880, GGCGGA at 1221, GGCGGA at 787.
  10. Carb E3r9ci: GGCGGA at 3631, GGCGGA at 1143.

CarbE3r alternate positive direction (evens) (4050-1) distal promoters

  1. Carb E3r0: TCCGCC at 368.
  2. Carb E3r2: TCCGCC at 639.
  3. Carb E3r4: TCCGCC at 3492, TCCGCC at 14.
  4. Carb E3r8: TCCGCC at 2012.
  5. Carb E3r0ci: GGCGGA at 2033.
  6. Carb E3r6ci: GGCGGA at 2577.

CarbE3 analysis and results

Main article: Complex locus A1BG and ZNF497 § CarbE3s

The E-boxes in ChoRE1 and ChoRE2 are CACGTG and ATCTTG and TCCGCC and CACGTG.[1]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 2 2 1 1
Randoms UTR arbitrary negative 2 10 0.2 0.5 ± 0.3
Randoms UTR alternate negative 8 10 0.8 0.5 ± 0.3
Reals Core negative 0 2 0 0
Randoms Core arbitrary negative 0 10 0 0
Randoms Core alternate negative 0 10 0 0
Reals Core positive 0 2 0 0
Randoms Core arbitrary positive 0 10 0 0
Randoms Core alternate positive 0 10 0 0
Reals Proximal negative 1 2 0.5 0.5
Randoms Proximal arbitrary negative 0 10 0 0.15 ± 0.15
Randoms Proximal alternate negative 3 10 0.3 0.15 ± 0.15
Reals Proximal positive 1 2 0.5 0.5
Randoms Proximal arbitrary positive 0 10 0 0
Randoms Proximal alternate positive 0 10 0 0
Reals Distal negative 13 2 6.5 6.5 ± 0.5 (--7,+-6)
Randoms Distal arbitrary negative 6 10 0.6 0.8 ± 0.2
Randoms Distal alternate negative 10 10 1.0 0.8 ± 0.2
Reals Distal positive 5 2 2.5 2.5 ± 0.5 (-+2,++3)
Randoms Distal arbitrary positive 20 10 2.0 1.35 ± 0.65
Randoms Distal alternate positive 7 10 0.7 1.35 ± 0.65

Comparison:

The occurrences of real CarbE3 UTRs, proximals and negative direction distals are greater than the randoms, low positive direction distals overlap high randoms. This suggests that the real CarbE3s are likely active or activable.

A1BG core promoters

Main article: Core promoter gene transcriptions

Negative strand, positive direction: ACCGG at 4345 (Carb).

Positive strand, negative direction: CCCAT at 4454 (Carb1).

A1BG proximal promoters

Main article: Proximal promoter gene transcriptions

Negative strand, positive direction: CCCAT at 4220 (Carb1).

Negative strand, positive direction: GTTCTA at 4075 (CarbE1).

Positive strand, positive direction: ATCTTG at 4067 (CarbE1).

Positive strand, positive direction: GGCGGA at 4239 (CarbE3).

A1BG distal promoters

Main article: Distal promoter gene transcriptions

Negative strand, negative direction: ACCGG at 4099, ACCGG at 3948, ACCGG at 3130, ACCGG at 2607, ACCGG at 1200, ACCGG at 645 (Carb).

Negative strand, negative direction: GTTCTA at 3275, GTTCTA at 876, ATCTTG at 286 (CarbE1).

Negative strand, negative direction: TCCGCC at 3999, TCCGCC at 3090, TCCGCC at 2392, TCCGCC at 2231, TCCGCC at 1752, GGCGGA at 1504, TCCGCC at 856, TCCGCC at 700, TCCGCC at 427 (CarbE3).

Positive strand, negative direction: CCCAT at 3855, CCCAT at 3152, CCCAT at 2288, CCCAT at 1861 (Carb1).

Positive strand, negative direction: ACCGG at 2191 (Carb).

Positive strand, negative direction: GGCGGA at 2728,GGCGGA at 2393, GGCGGA at 1810, TCCGCC at 1503, GGCGGA at 857, GGCGGA at 701, GGCGGA at 428 (CarbE3).

Negative strand, positive direction: ACCGG at 1846, ACCGG at 1546, ACCGG at 1294, ACCGG at 1210, ACCGG at 1042, ACCGG at 442 (Carb).

Negative strand, positive direction: CCCAT at 3899, CCCAT at 3334 (Carb1).

Negative strand, positive direction: CACGTG at 570 (CarbE2).

Negative strand, positive direction: GGCGGA at 1203, GGCGGA at 357 (CarbE3).

Positive strand, positive direction: ACCGG at 3681, ACCGG at 2990, ACCGG at 2985, ACCGG at 2571, ACCGG at 2069, ACCGG at 1738, ACCGG at 949, ACCGG at 849, ACCGG at 199 (Carb).

Positive strand, positive direction: CCCAT at 3751 (Carb1).

Positive strand, positive direction: CACGTG at 3884, CACGTG at 2961, CACGTG at 1219, CACGTG at 547 (CarbE2).

Positive strand, positive direction: TCCGCC at 3487, TCCGCC at 2485, GGCGGA at 905 (CarbE3).

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 1.7 1.8 1.9 Jianyin Long, Daniel L. Galvan, Koki Mise, Yashpal S. Kanwar, Li Li, Naravat Poungavrin, Paul A. Overbeek, Benny H. Chang, and Farhad R. Danesh (28 May 2020). "Role for carbohydrate response element-binding protein (ChREBP) in high glucose-mediated repression of long noncoding RNA Tug1" (PDF). Journal of Biological Chemistry. 5 (28). doi:10.1074/jbc.RA120.013228. Retrieved 6 October 2020.
  2. ↑ RefSeq (December 2017). "TUG1 taurine up-regulated 1 [ Homo sapiens (human) ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 7 November 2020.
  3. ↑ 3.0 3.1 Jaideep Chaudhary and Michael K. Skinner (May 1999). "Basic Helix-Loop-Helix Proteins Can Act at the E-Box within the Serum Response Element of the c-fos Promoter to Influence Hormone-Induced Promoter Activation in Sertoli Cells". Molecular Endocrinology. 13 (5): 774–86. doi:10.1210/me.13.5.774. PMID 10319327. Retrieved 2013-06-14.

External links


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