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Initiator-like element gene transcriptions

From Wikidoc - Reading time: 17 min

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

Consensus sequence for an Inr-like/TCT is TTCTCT.[1]

Inr-like, TCTs (Matsumoto, 9 August 2020) sampling[edit | edit source]

Copying TTCTCT in "⌘F" yields three between ZSCAN22 and A1BG and three between ZNF497 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence TTCTCT (starting with SuccessablesTCT.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 TTCTCT, 3, TTCTCT at 3380, TTCTCT at 2826, TTCTCT at 2809.
  2. positive strand, negative direction, looking for TTCTCT, 1, TTCTCT at 622.
  3. negative strand, positive direction, looking for TTCTCT, 4, TTCTCT at 4386, TTCTCT at 1990, TTCTCT at 139, TTCTCT at 119.
  4. positive strand, positive direction, looking for TTCTCT, 0.
  5. inverse complement, negative strand, negative direction, looking for AGAGAA, 1, AGAGAA at 4527.
  6. inverse complement, positive strand, negative direction, looking for AGAGAA, 3, AGAGAA at 3406, AGAGAA at 2827, AGAGAA at 2810.
  7. inverse complement, negative strand, positive direction, looking for AGAGAA, 0.
  8. inverse complement, positive strand, positive direction, looking for AGAGAA, 2, AGAGAA at 4387, AGAGAA at 3056.

TCT (4560-2846) UTRs[edit | edit source]

  1. Negative strand, negative direction: TTCTCT at 3380.
  2. Negative strand, negative direction: AGAGAA at 4527.
  3. Positive strand, negative direction: AGAGAA at 3406.

TCT negative direction (2846-2811) core promoters[edit | edit source]

  1. Negative strand, negative direction: TTCTCT at 2826.
  2. Positive strand, negative direction: AGAGAA at 2827.

TCT positive direction (4445-4265) core promoters[edit | edit source]

  1. Negative strand, positive direction: TTCTCT at 4386.
  2. Positive strand, positive direction: AGAGAA at 4387.

TCT negative direction (2811-2596) proximal promoters[edit | edit source]

  1. Negative strand, negative direction: TTCTCT at 2809.
  2. Positive strand, negative direction: AGAGAA at 2810.

TCT negative direction (2596-1) distal promoters[edit | edit source]

  1. Positive strand, negative direction: TTCTCT at 622.

TCT positive direction (4050-1) distal promoters[edit | edit source]

  1. Negative strand, positive direction: TTCTCT at 1990, TTCTCT at 139, TTCTCT at 119.
  2. Positive strand, positive direction: AGAGAA at 3056.

Inr-like, TCTs (Matsumoto, 9 August 2020) random dataset samplings[edit | edit source]

  1. TCTr0: 1, TTCTCT at 1974.
  2. TCTr1: 1, TTCTCT at 1566.
  3. TCTr2: 1, TTCTCT at 2740.
  4. TCTr3: 0.
  5. TCTr4: 0.
  6. TCTr5: 0.
  7. TCTr6: 3, TTCTCT at 4004, TTCTCT at 2444, TTCTCT at 1517.
  8. TCTr7: 0.
  9. TCTr8: 0.
  10. TCTr9: 2, TTCTCT at 2753, TTCTCT at 1052.
  11. TCTr0ci: 1, AGAGAA at 1959.
  12. TCTr1ci: 1, AGAGAA at 3267.
  13. TCTr2ci: 0.
  14. TCTr3ci: 2, AGAGAA at 3430, AGAGAA at 2680.
  15. TCTr4ci: 0.
  16. TCTr5ci: 1, AGAGAA at 1329.
  17. TCTr6ci: 0.
  18. TCTr7ci: 0.
  19. TCTr8ci: 2, AGAGAA at 2116, AGAGAA at 1293.
  20. TCTr9ci: 1, AGAGAA at 3489.

TCTr arbitrary UTRs[edit | edit source]

  1. TCTr6: TTCTCT at 4004.

TCTr alternate UTRs[edit | edit source]

  1. TCTr3ci: AGAGAA at 3430.
  2. TCTr9ci: AGAGAA at 3489.

TCTr arbitrary negative direction proximal promoters[edit | edit source]

  1. TCTr2: TTCTCT at 2740.

TCTr alternate negative direction proximal promoters[edit | edit source]

  1. TCTr9: TTCTCT at 2753.
  2. TCTr3ci: AGAGAA at 2680.

TCTr arbitrary negative direction distal promoters[edit | edit source]

  1. TCTr0: TTCTCT at 1974.
  2. TCTr6: TTCTCT at 2444, TTCTCT at 1517.
  3. TCTr0ci: AGAGAA at 1959.
  4. TCTr8ci: AGAGAA at 2116, AGAGAA at 1293.

TCTr alternate negative direction distal promoters[edit | edit source]

  1. TCTr1: TTCTCT at 1566.
  2. TCTr9: TTCTCT at 1052.
  3. TCTr5ci: AGAGAA at 1329.

TCTr arbitrary positive direction distal promoters[edit | edit source]

  1. TCTr1: TTCTCT at 1566.
  2. TCTr9: TTCTCT at 2753, TTCTCT at 1052.
  3. TCTr3ci: AGAGAA at 3430, AGAGAA at 2680.
  4. TCTr5ci: AGAGAA at 1329.
  5. TCTr9ci: AGAGAA at 3489.

TCTr alternate positive direction distal promoters[edit | edit source]

  1. TCTr0: TTCTCT at 1974.
  2. TCTr2: TTCTCT at 2740.
  3. TCTr6: TTCTCT at 4004, TTCTCT at 2444, TTCTCT at 1517.
  4. TCTr0ci: AGAGAA at 1959.
  5. TCTr8ci: AGAGAA at 2116, AGAGAA at 1293.

Inr-like, TCTs (Matsumoto, 9 August 2020) analysis and results[edit | edit source]

Main article: Complex locus A1BG and ZNF497 § Inr-like, TCTs

Consensus sequence for an Inr-like/TCT is TTCTCT.[1]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 3 2 1.5 1.5 ± 0.5 (--2,+-1)
Randoms UTR arbitrary negative 1 10 0.1 0.15 ± 0.5
Randoms UTR alternate negative 2 10 0.2 0.15 ± 0.5
Reals Core negative 2 2 1 1 ± 0.5 (--1,+-1)
Randoms Core arbitrary negative 0 10 0 0
Randoms Core alternate negative 0 10 0 0
Reals Core positive 2 2 1 1 ± 0.5 (-+1,++1)
Randoms Core arbitrary positive 0 10 0 0
Randoms Core alternate positive 0 10 0 0
Reals Proximal negative 2 2 1 1 ± 0.5 (--1,+-1)
Randoms Proximal arbitrary negative 1 10 0.1 0.15 ± 0.05
Randoms Proximal alternate negative 2 10 0.2 0.15 ± 0.05
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 1 2 0.5 0.5 ± 0.5 (--0,+-1)
Randoms Distal arbitrary negative 6 10 0.6 0.45 ± 0.15
Randoms Distal alternate negative 3 10 0.3 0.45 ± 0.15
Reals Distal positive 4 2 2 2 ± 1 (-+3,++1)
Randoms Distal arbitrary positive 7 10 0.7 0.75 ± 0.05
Randoms Distal alternate positive 8 10 0.8 0.75 ± 0.05

Comparison:

The occurrences of real Inr-like, TCTs for the distals, proximals, cores and UTRs are greater than the randoms. This suggests that the real responsive element consensus sequences are likely active or activable.

TCT (Parry 2010) samplings[edit | edit source]

The TCT consensus sequence YCTYTYY, where Y is C/T, is (C/T)CT(C/T)T(C/T)(C/T).[2]

For the Basic programs testing consensus sequence (C/T)CT(C/T)T(C/T)(C/T) (starting with SuccessablesTCTP.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: 23, TCTTTTC at 4391, TCTTTTT at 4384, TCTTTTT at 4087, TCTTTCT at 4083, CCTTTCT at 3665, TCTCTTC at 3407, TCTCTCC at 3386, TCTCTCT at 3384, TCTCTCT at 3382, TCTTTCT at 3378, TCTTTTC at 3344, CCTTTTT at 2928, TCTTTTT at 2833, TCTCTTC at 2828, TCTTTTC at 2823, TCTTTTT at 2816, TCTCTTC at 2811, TCTTTTC at 2806, TCTTTCT at 2802, CCTTTTT at 2460, TCTTTTT at 2057, TCTTTTC at 104, TCTTTTC at 54.
  2. Positive strand, negative direction: 5, TCTCTTC at 4528, CCTCTCT at 4526, CCTCTCC at 2629, TCTTTTT at 1420, TCTTTTT at 27.
  3. Negative strand, positive direction: 7, TCTTTCT at 4384, TCTCTTC at 3057, TCTTTTT at 2280, CCTCTCC at 464, CCTCTCT at 253, TCTCTCC at 141, CCTTTTC at 136.
  4. Positive strand, positive direction: 4, CCTCTTC at 3851, CCTCTCC at 3652, CCTTTCC at 1091, CCTCTTC at 48.
  5. inverse complement, negative strand, negative direction: 3, GGAGAGA at 4526, GGAGAGG at 2629, GAAGAGA at 622.
  6. inverse complement, positive strand, negative direction: 27, GAAAAGA at 4392, AAAAAGA at 4387, AAAAAGA at 4380, AAAGAGG at 3926, AAAGAGA at 3380, GAAAAGG at 3345, AAAAAGA at 2836, AAAGAGA at 2826, GAAAAGA at 2824, AAAAAGA at 2819, AAAGAGA at 2809, GAAAAGA at 2807, AAAAAGA at 2798, AAAAAGA at 2053, GAAAAGA at 1628, AAAAAGA at 1400, AAAAAGG at 1107, GAAGAGG at 370, GAAAAGG at 105, GAAAAGA at 55.
  7. inverse complement, negative strand, positive direction: 5, GAAGAGG at 4266, AAAGAGG at 3931, GAAAAGA at 3929, GGAGAGG at 3652, GGAAAGG at 1091.
  8. inverse complement, positive strand, positive direction: 8, AAAGAGA at 4386, AGAAAGA at 4384, GAAAAGA at 2276, AAAGAGA at 139, GAAAAGA at 137.

TCTP (4560-2846) UTRs[edit | edit source]

  1. Negative strand, negative direction: TCTTTTC at 4391, TCTTTTT at 4384, TCTTTTT at 4087, TCTTTCT at 4083, CCTTTCT at 3665, TCTCTTC at 3407, TCTCTCC at 3386, TCTCTCT at 3384, TCTCTCT at 3382, TCTTTCT at 3378, TCTTTTC at 3344, CCTTTTT at 2928.
  2. Negative strand, negative direction: GGAGAGA at 4526.
  3. Positive strand, negative direction: TCTCTTC at 4528, CCTCTCT at 4526.
  4. Positive strand, negative direction: GAAAAGA at 4392, AAAAAGA at 4387, AAAAAGA at 4380, AAAGAGG at 3926, AAAGAGA at 3380, GAAAAGG at 3345.

TCTP negative direction (2846-2811) core promoters[edit | edit source]

  1. Negative strand, negative direction: TCTTTTT at 2833, TCTCTTC at 2828, TCTTTTC at 2823, TCTTTTT at 2816, TCTCTTC at 2811.
  2. Positive strand, negative direction: AAAAAGA at 2836, AAAGAGA at 2826, GAAAAGA at 2824, AAAAAGA at 2819.

TCTP positive direction (4445-4265) core promoters[edit | edit source]

  1. Negative strand, positive direction: TCTTTCT at 4384.
  2. Negative strand, positive direction: GAAGAGG at 4266.
  3. Positive strand, positive direction: AAAGAGA at 4386, AGAAAGA at 4384.

TCTP negative direction (2811-2596) proximal promoters[edit | edit source]

  1. Negative strand, negative direction: TCTCTTC at 2811, TCTTTTC at 2806, TCTTTCT at 2802.
  2. Positive strand, negative direction: CCTCTCC at 2629.
  3. Positive strand, negative direction: AAAGAGA at 2809, GAAAAGA at 2807, AAAAAGA at 2798.

TCTP negative direction (2596-1) distal promoters[edit | edit source]

  1. Negative strand, negative direction: CCTTTTT at 2460, TCTTTTT at 2057, TCTTTTC at 104, TCTTTTC at 54.
  2. Negative strand, negative direction: GAAGAGA at 622.
  3. Positive strand, negative direction: TCTTTTT at 1420, TCTTTTT at 27.
  4. Positive strand, negative direction: AAAAAGA at 2053, GAAAAGA at 1628, AAAAAGA at 1400, AAAAAGG at 1107, GAAGAGG at 370, GAAAAGG at 105, GAAAAGA at 55.

TCTP positive direction (4050-1) distal promoters[edit | edit source]

  1. Negative strand, positive direction: TCTCTTC at 3057, TCTTTTT at 2280, CCTCTCC at 464, CCTCTCT at 253, TCTCTCC at 141, CCTTTTC at 136.
  2. Negative strand, positive direction: AAAGAGG at 3931, GAAAAGA at 3929, GGAGAGG at 3652, GGAAAGG at 1091.
  3. Positive strand, positive direction: CCTCTTC at 3851, CCTCTCC at 3652, CCTTTCC at 1091, CCTCTTC at 48.
  4. Positive strand, positive direction: GAAAAGA at 2276, AAAGAGA at 139, GAAAAGA at 137.

TCT (Parry 2010) random dataset samplings[edit | edit source]

  1. TCTPr0: 8, TCTTTTT at 3943, CCTCTTT at 3839, TCTCTCC at 1517, CCTTTTC at 1276, CCTCTTT at 1136, CCTTTCC at 1006, TCTTTTT at 655, CCTTTTT at 222.
  2. TCTPr1: 10, TCTTTCT at 3953, CCTTTTC at 3647, TCTTTTT at 2674, CCTTTTT at 2408, TCTTTTC at 2289, CCTCTTT at 2287, CCTCTCC at 1372, CCTTTTT at 1274, CCTTTCT at 1102, CCTTTTC at 655.
  3. TCTPr2: 10, CCTCTTC at 3969, CCTTTTC at 3665, CCTCTCC at 3630, CCTTTTT at 3220, CCTTTCT at 2288, TCTCTCT at 1981, CCTCTCT at 1979, CCTTTCT at 1511, CCTCTTC at 695, CCTTTCC at 225.
  4. TCTPr3: 7, TCTTTCT at 4400, CCTTTTT at 4188, TCTTTTC at 3694, CCTCTCC at 2500, TCTCTTT at 2455, TCTTTTT at 149, CCTTTCC at 114.
  5. TCTPr4: 5, CCTCTTT at 4156, CCTTTTT at 1733, CCTTTTT at 1405, CCTCTCT at 1061, TCTTTTC at 473.
  6. TCTPr5: 6, CCTTTCC at 3829, TCTTTCC at 3696, TCTTTCC at 3224, CCTTTTC at 2356, CCTCTCT at 1408, TCTTTTC at 1266.
  7. TCTPr6: 4, CCTTTTC at 3673, CCTTTTC at 3290, TCTCTTT at 2339, TCTTTCT at 1353.
  8. TCTPr7: 13, TCTTTCC at 4235, CCTTTTC at 3581, CCTTTTC at 3175, TCTTTCT at 3095, TCTTTCC at 2664, CCTTTTC at 1991, CCTCTCC at 1629, CCTTTCC at 1624, TCTCTTC at 1199, CCTCTCT at 1197, CCTTTCC at 928, CCTCTTT at 842, CCTTTCC at 685.
  9. TCTPr8: 2, CCTCTCT at 3786, CCTTTTT at 3415.
  10. TCTPr9: 4, CCTCTCT at 2577, TCTTTTC at 2314, CCTTTTT at 1031, CCTTTTC at 135.
  11. TCTPr0ci: 4, GAAAAGG at 3659, AGAAAGG at 3346, AGAGAGG at 2707, GAAGAGG at 2528.
  12. TCTPr1ci: 4, AAAAAGG at 4013, AAAGAGG at 3826, AAAGAGA at 1411, GGAGAGA at 31.
  13. TCTPr2ci: 11, AAAGAGG at 4294, GAAAAGA at 2341, GGAAAGA at 2230, AGAGAGG at 2033, GAAAAGA at 1846, GAAAAGG at 1440, AAAGAGG at 1178, GGAAAGA at 1176, GAAAAGG at 474, GGAGAGG at 289, AAAAAGG at 252.
  14. TCTPr3ci: 6, GGAGAGA at 3429, AGAGAGA at 2679, GAAGAGA at 2677, AAAAAGG at 2600, GAAAAGG at 2276, AAAGAGG at 396.
  15. TCTPr4ci: 4, AGAGAGA at 3616, AGAAAGG at 2493, GGAAAGG at 1388, GGAAAGG at 38.
  16. TCTPr5ci: 9, GAAAAGA at 4337, AAAGAGG at 4325, GAAAAGA at 4323, GAAGAGA at 1333, AAAGAGA at 1328, GAAAAGA at 1035, GAAAAGG at 637, AAAAAGG at 227, GGAAAGA at 29.
  17. TCTPr6ci: 4, GAAGAGG at 1506, GAAAAGA at 1239, AGAAAGA at 1105, GGAAAGG at 303.
  18. TCTPr7ci: 4, AAAAAGG at 4549, AGAAAGA at 4399, GGAAAGG at 2218, GAAGAGG at 233.
  19. TCTPr8ci: 8, AGAAAGG at 4271, GGAAAGA at 3873, AAAGAGG at 3550, GAAAAGA at 2166, AAAGAGA at 2115, AGAAAGG at 1689, GAAAAGG at 504, AAAAAGA at 311.
  20. TCTPr9ci: 6, AGAAAGG at 4317, AAAAAGA at 3856, GAAGAGA at 3488, AGAGAGG at 1577, GAAAAGG at 588, GGAGAGA at 150.

TCTPr arbitrary (evens) (4560-2846) UTRs[edit | edit source]

  1. TCTPr0: TCTTTTT at 3943, CCTCTTT at 3839.
  2. TCTPr2: CCTCTTC at 3969, CCTTTTC at 3665, CCTCTCC at 3630, CCTTTTT at 3220.
  3. TCTPr4: CCTCTTT at 4156.
  4. TCTPr6: CCTTTTC at 3673, CCTTTTC at 3290.
  5. TCTPr8: CCTCTCT at 3786, CCTTTTT at 3415.
  6. TCTPr0ci: GAAAAGG at 3659, AGAAAGG at 3346.
  7. TCTPr2ci: AAAGAGG at 4294.
  8. TCTPr4ci: AGAGAGA at 3616.
  9. TCTPr8ci: AGAAAGG at 4271, GGAAAGA at 3873, AAAGAGG at 3550.

TCTPr alternate (odds) (4560-2846) UTRs[edit | edit source]

  1. TCTPr1: TCTTTCT at 3953, CCTTTTC at 3647.
  2. TCTPr3: TCTTTCT at 4400, CCTTTTT at 4188, TCTTTTC at 3694.
  3. TCTPr5: CCTTTCC at 3829, TCTTTCC at 3696, TCTTTCC at 3224.
  4. TCTPr7: TCTTTCC at 4235, CCTTTTC at 3581, CCTTTTC at 3175, TCTTTCT at 3095.
  5. TCTPr1ci: AAAAAGG at 4013, AAAGAGG at 3826.
  6. TCTPr3ci: GGAGAGA at 3429.
  7. TCTPr5ci: GAAAAGA at 4337, AAAGAGG at 4325, GAAAAGA at 4323.
  8. TCTPr7ci: AAAAAGG at 4549, AGAAAGA at 4399.
  9. TCTPr9ci: AGAAAGG at 4317, AAAAAGA at 3856, GAAGAGA at 3488.

TCTPr arbitrary positive direction (odds) (4445-4265) core promoters[edit | edit source]

  1. TCTPr3: TCTTTCT at 4400.
  2. TCTPr5ci: GAAAAGA at 4337, AAAGAGG at 4325, GAAAAGA at 4323.
  3. TCTPr7ci: AGAAAGA at 4399.
  4. TCTPr9ci: AGAAAGG at 4317.

TCTPr alternate positive direction (evens) (4445-4265) core promoters[edit | edit source]

  1. TCTPr2ci: AAAGAGG at 4294.
  2. TCTPr8ci: AGAAAGG at 4271.

TCTPr arbitrary negative direction (evens) (2811-2596) proximal promoters[edit | edit source]

  1. TCTPr0ci: AGAGAGG at 2707.

TCTPr alternate negative direction (odds) (2811-2596) proximal promoters[edit | edit source]

  1. TCTPr1: TCTTTTT at 2674.
  2. TCTPr7: TCTTTCC at 2664.
  3. TCTPr3ci: AGAGAGA at 2679, GAAGAGA at 2677, AAAAAGG at 2600.

TCTPr arbitrary positive direction (odds) (4265-4050) proximal promoters[edit | edit source]

  1. TCTPr3: CCTTTTT at 4188.
  2. TCTPr7: TCTTTCC at 4235.

TCTPr alternate positive direction (evens) (4265-4050) proximal promoters[edit | edit source]

  1. TCTPr4: CCTCTTT at 4156.

TCTPr arbitrary negative direction (evens) (2596-1) distal promoters[edit | edit source]

  1. TCTPr0: TCTCTCC at 1517, CCTTTTC at 1276, CCTCTTT at 1136, CCTTTCC at 1006, TCTTTTT at 655, CCTTTTT at 222.
  2. TCTPr2: CCTTTCT at 2288, TCTCTCT at 1981, CCTCTCT at 1979, CCTTTCT at 1511, CCTCTTC at 695, CCTTTCC at 225.
  3. TCTPr4: CCTTTTT at 1733, CCTTTTT at 1405, CCTCTCT at 1061, TCTTTTC at 473.
  4. TCTPr6: TCTCTTT at 2339, TCTTTCT at 1353.
  5. TCTPr0ci: GAAGAGG at 2528.
  6. TCTPr2ci: GAAAAGA at 2341, GGAAAGA at 2230, AGAGAGG at 2033, GAAAAGA at 1846, GAAAAGG at 1440, AAAGAGG at 1178, GGAAAGA at 1176, GAAAAGG at 474, GGAGAGG at 289, AAAAAGG at 252.
  7. TCTPr4ci: AGAAAGG at 2493, GGAAAGG at 1388, GGAAAGG at 38.
  8. TCTPr6ci: GAAGAGG at 1506, GAAAAGA at 1239, AGAAAGA at 1105, GGAAAGG at 303.
  9. TCTPr8ci: GAAAAGA at 2166, AAAGAGA at 2115, AGAAAGG at 1689, GAAAAGG at 504, AAAAAGA at 311.

TCTPr alternate negative direction (odds) (2596-1) distal promoters[edit | edit source]

  1. TCTPr1: CCTTTTT at 2408, TCTTTTC at 2289, CCTCTTT at 2287, CCTCTCC at 1372, CCTTTTT at 1274, CCTTTCT at 1102, CCTTTTC at 655.
  2. TCTPr3: CCTCTCC at 2500, TCTCTTT at 2455, TCTTTTT at 149, CCTTTCC at 114.
  3. TCTPr5: CCTTTTC at 2356, CCTCTCT at 1408, TCTTTTC at 1266.
  4. TCTPr7: CCTTTTC at 1991, CCTCTCC at 1629, CCTTTCC at 1624, TCTCTTC at 1199, CCTCTCT at 1197, CCTTTCC at 928, CCTCTTT at 842, CCTTTCC at 685.
  5. TCTPr9: CCTCTCT at 2577, TCTTTTC at 2314, CCTTTTT at 1031, CCTTTTC at 135.
  6. TCTPr1ci: AAAGAGA at 1411, GGAGAGA at 31.
  7. TCTPr3ci: GAAAAGG at 2276, AAAGAGG at 396.
  8. TCTPr5ci: GAAGAGA at 1333, AAAGAGA at 1328, GAAAAGA at 1035, GAAAAGG at 637, AAAAAGG at 227, GGAAAGA at 29.
  9. TCTPr7ci: GGAAAGG at 2218, GAAGAGG at 233.
  10. TCTPr9ci: AGAGAGG at 1577, GAAAAGG at 588, GGAGAGA at 150.

TCTPr arbitrary positive direction (odds) (4050-1) distal promoters[edit | edit source]

  1. TCTPr1: TCTTTCT at 3953, CCTTTTC at 3647, TCTTTTT at 2674, CCTTTTT at 2408, TCTTTTC at 2289, CCTCTTT at 2287, CCTCTCC at 1372, CCTTTTT at 1274, CCTTTCT at 1102, CCTTTTC at 655.
  2. TCTPr3: TCTTTTC at 3694, CCTCTCC at 2500, TCTCTTT at 2455, TCTTTTT at 149, CCTTTCC at 114.
  3. TCTPr5: CCTTTCC at 3829, TCTTTCC at 3696, TCTTTCC at 3224, CCTTTTC at 2356, CCTCTCT at 1408, TCTTTTC at 1266.
  4. TCTPr7: CCTTTTC at 3581, CCTTTTC at 3175, TCTTTCT at 3095, TCTTTCC at 2664, CCTTTTC at 1991, CCTCTCC at 1629, CCTTTCC at 1624, TCTCTTC at 1199, CCTCTCT at 1197, CCTTTCC at 928, CCTCTTT at 842, CCTTTCC at 685.
  5. TCTPr9: CCTCTCT at 2577, TCTTTTC at 2314, CCTTTTT at 1031, CCTTTTC at 135.
  6. TCTPr1ci: AAAAAGG at 4013, AAAGAGG at 3826, AAAGAGA at 1411, GGAGAGA at 31.
  7. TCTPr3ci: GGAGAGA at 3429, AGAGAGA at 2679, GAAGAGA at 2677, AAAAAGG at 2600, GAAAAGG at 2276, AAAGAGG at 396.
  8. TCTPr5ci: GAAGAGA at 1333, AAAGAGA at 1328, GAAAAGA at 1035, GAAAAGG at 637, AAAAAGG at 227, GGAAAGA at 29.
  9. TCTPr7ci: GGAAAGG at 2218, GAAGAGG at 233.
  10. TCTPr9ci: AAAAAGA at 3856, GAAGAGA at 3488, AGAGAGG at 1577, GAAAAGG at 588, GGAGAGA at 150.

TCTPr alternate positive direction (evens) (4050-1) distal promoters[edit | edit source]

  1. TCTPr0: TCTTTTT at 3943, CCTCTTT at 3839, TCTCTCC at 1517, CCTTTTC at 1276, CCTCTTT at 1136, CCTTTCC at 1006, TCTTTTT at 655, CCTTTTT at 222.
  2. TCTPr2: CCTCTTC at 3969, CCTTTTC at 3665, CCTCTCC at 3630, CCTTTTT at 3220, CCTTTCT at 2288, TCTCTCT at 1981, CCTCTCT at 1979, CCTTTCT at 1511, CCTCTTC at 695, CCTTTCC at 225.
  3. TCTPr4: CCTTTTT at 1733, CCTTTTT at 1405, CCTCTCT at 1061, TCTTTTC at 473.
  4. TCTPr6: CCTTTTC at 3673, CCTTTTC at 3290, TCTCTTT at 2339, TCTTTCT at 1353.
  5. TCTPr8: CCTCTCT at 3786, CCTTTTT at 3415.
  6. TCTPr0ci: GAAAAGG at 3659, AGAAAGG at 3346, AGAGAGG at 2707, GAAGAGG at 2528.
  7. TCTPr2ci: GAAAAGA at 2341, GGAAAGA at 2230, AGAGAGG at 2033, GAAAAGA at 1846, GAAAAGG at 1440, AAAGAGG at 1178, GGAAAGA at 1176, GAAAAGG at 474, GGAGAGG at 289, AAAAAGG at 252.
  8. TCTPr4ci: AGAGAGA at 3616, AGAAAGG at 2493, GGAAAGG at 1388, GGAAAGG at 38.
  9. TCTPr6ci: GAAGAGG at 1506, GAAAAGA at 1239, AGAAAGA at 1105, GGAAAGG at 303.
  10. TCTPr8ci: GGAAAGA at 3873, AAAGAGG at 3550, GAAAAGA at 2166, AAAGAGA at 2115, AGAAAGG at 1689, GAAAAGG at 504, AAAAAGA at 311.

TCT (Parry 2010) analysis and results[edit | edit source]

Main article: Complex locus A1BG and ZNF497 § TCTPs

The TCT consensus sequence is (C/T)CT(C/T)T(C/T)(C/T).[2]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 21 2 10.5 10.5 ± 2.5 (--13,+-8)
Randoms UTR arbitrary negative 18 10 1.8 2.05 ± 0.25
Randoms UTR alternate negative 23 10 2.3 2.05 ± 0.25
Reals Core negative 9 2 4.5 4.5 ± 0.5 (--5,+-4)
Randoms Core arbitrary negative 0 10 0 0
Randoms Core alternate negative 0 10 0 0
Reals Core positive 4 2 2 2 ± 0 (-+2,++2)
Randoms Core arbitrary positive 6 10 0.6 0.4 ± 0.2
Randoms Core alternate positive 2 10 0.2 0.4 ± 0.2
Reals Proximal negative 7 2 3.5 3.5 ± 0.5 (--3,+-4)
Randoms Proximal arbitrary negative 1 10 0.1 0.3 ± 0.2
Randoms Proximal alternate negative 5 10 0.5 0.3 ± 0.2
Reals Proximal positive 0 2 0 0
Randoms Proximal arbitrary positive 2 10 0.2 0.15 ± 0.05
Randoms Proximal alternate positive 1 10 0.1 0.15 ± 0.05
Reals Distal negative 14 2 7 7 ± 2 (--5,+-9)
Randoms Distal arbitrary negative 41 10 4.1 4.1
Randoms Distal alternate negative 41 10 4.1 4.1
Reals Distal positive 17 2 8.5 8.5 ± 1.5 (-+10,++7)
Randoms Distal arbitrary positive 60 10 6.0 5.85 ± 0.15
Randoms Distal alternate positive 57 10 5.7 5.85 ± 0.15

Comparison:

The occurrences of real TCT UTRs (Parry), cores, proximals, and distals are greater than the randoms. This suggests that the real TCTs (Parry) are likely active or activable.

Acknowledgements[edit | edit source]

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

Initial content for this page in some instances came from Wikiversity.

See also[edit | edit source]

References[edit | edit source]

  1. ↑ 1.0 1.1 Takuya Matsumoto, Saemi Kitajima, Chisato Yamamoto, Mitsuru Aoyagi, Yoshiharu Mitoma, Hiroyuki Harada and Yuji Nagashima (9 August 2020). "Cloning and tissue distribution of the ATP-binding cassette subfamily G member 2 gene in the marine pufferfish Takifugu rubripes" (PDF). Fisheries Science. 86: 873–887. doi:10.1007/s12562-020-01451-z. Retrieved 27 September 2020.
  2. ↑ 2.0 2.1 Trevor J. Parry, Joshua W. M. Theisen, Jer-Yuan Hsu, Yuan-Liang Wang, David L. Corcoran, Moriah Eustice, Uwe Ohler, and James T. Kadonaga (27 August 2010) The TCT motif, a key component of an RNA polymerase II transcription system for the translational machinery. Genes & Development 24:2013–2018. doi:10.1101/gad.1951110. https://genesdev.cshlp.org/content/24/18/2013.full.html.

External links[edit | edit source]

{{Phosphate biochemistry}}


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