Musashi binding element gene transcriptions: Difference between revisions

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# MBE1r6ci: 4, ACTAC at 2243, ACTAC at 1584, ACTAT at 1135, ACTAT at 774.
# MBE1r6ci: 4, ACTAC at 2243, ACTAC at 1584, ACTAT at 1135, ACTAT at 774.
# MBE1r7ci: 8, ACTAC at 4117, ACTAC at 3924, ACTAT at 3626, ACTAC at 2338, ACTAT at 1488, ACTAT at 1072, ACTAT at 887, ACTAT at 327.
# MBE1r7ci: 8, ACTAC at 4117, ACTAC at 3924, ACTAT at 3626, ACTAC at 2338, ACTAT at 1488, ACTAT at 1072, ACTAT at 887, ACTAT at 327.
# RDr8ci: 0.
# MBE1r8ci: 5, ACTAC at 4499, ACTAT at 4307, ACTAT at 3741, ACTAT at 825, ACTAT at 201.
# RDr9ci: 0.
# MBE1r9ci: 4, ACTAC at 4089, ACTAT at 3831, ACTAC at 3795, ACTAT at 1603.


===MBE1r arbitrary (evens) (4560-2846) UTRs===
===MBE1r arbitrary (evens) (4560-2846) UTRs===
Line 143: Line 143:
# MBE1r2ci: ACTAT at 4411, ACTAT at 4385, ACTAT at 3820.
# MBE1r2ci: ACTAT at 4411, ACTAT at 4385, ACTAT at 3820.
# MBE1r4ci: ACTAC at 3714, ACTAC at 3080, ACTAC at 3040, ACTAT at 2978.
# MBE1r4ci: ACTAC at 3714, ACTAC at 3080, ACTAC at 3040, ACTAT at 2978.
# MBE1r8ci: ACTAC at 4499, ACTAT at 4307, ACTAT at 3741.


===MBE1r alternate (odds) (4560-2846) UTRs===
===MBE1r alternate (odds) (4560-2846) UTRs===
Line 155: Line 156:
# MBE1r5ci: ACTAC at 4124, ACTAT at 3701, ACTAT at 3515.
# MBE1r5ci: ACTAC at 4124, ACTAT at 3701, ACTAT at 3515.
# MBE1r7ci: ACTAC at 4117, ACTAC at 3924, ACTAT at 3626.
# MBE1r7ci: ACTAC at 4117, ACTAC at 3924, ACTAT at 3626.
 
# MBE1r9ci: ACTAC at 4089, ACTAT at 3831, ACTAC at 3795.
===RDr arbitrary negative direction (evens) (2846-2811) core promoters===
 
===RDr alternate negative direction (odds) (2846-2811) core promoters===


===MBE1r arbitrary positive direction (odds) (4445-4265) core promoters===
===MBE1r arbitrary positive direction (odds) (4445-4265) core promoters===
Line 169: Line 167:


# MBE1r2ci: ACTAT at 4411, ACTAT at 4385.
# MBE1r2ci: ACTAT at 4411, ACTAT at 4385.
# MBE1r8ci: ACTAT at 4307.


===MBE1r arbitrary negative direction (evens) (2811-2596) proximal promoters===
===MBE1r arbitrary negative direction (evens) (2811-2596) proximal promoters===
Line 183: Line 182:
# MBE1r5ci: ACTAC at 4124.
# MBE1r5ci: ACTAC at 4124.
# MBE1r7ci: ACTAC at 4117.
# MBE1r7ci: ACTAC at 4117.
# MBE1r9ci: ACTAC at 4089.


===MBE1r alternate positive direction (evens) (4265-4050) proximal promoters===
===MBE1r alternate positive direction (evens) (4265-4050) proximal promoters===
Line 198: Line 198:
# MBE1r4ci: ACTAC at 2060, ACTAT at 603.
# MBE1r4ci: ACTAC at 2060, ACTAT at 603.
# MBE1r6ci: ACTAC at 2243, ACTAC at 1584, ACTAT at 1135, ACTAT at 774.
# MBE1r6ci: ACTAC at 2243, ACTAC at 1584, ACTAT at 1135, ACTAT at 774.
# MBE1r8ci: ACTAT at 825, ACTAT at 201.


===MBE1r alternate negative direction (odds) (2596-1) distal promoters===
===MBE1r alternate negative direction (odds) (2596-1) distal promoters===
Line 210: Line 211:
# MBE1r5ci: ACTAT at 1894, ACTAT at 1766.
# MBE1r5ci: ACTAT at 1894, ACTAT at 1766.
# MBE1r7ci: ACTAC at 2338, ACTAT at 1488, ACTAT at 1072, ACTAT at 887, ACTAT at 327.
# MBE1r7ci: ACTAC at 2338, ACTAT at 1488, ACTAT at 1072, ACTAT at 887, ACTAT at 327.
# MBE1r9ci: ACTAT at 1603.


===MBE1r arbitrary positive direction (odds) (4050-1) distal promoters===
===MBE1r arbitrary positive direction (odds) (4050-1) distal promoters===
Line 222: Line 224:
# MBE1r5ci: ACTAT at 3701, ACTAT at 3515, ACTAT at 1894, ACTAT at 1766.
# MBE1r5ci: ACTAT at 3701, ACTAT at 3515, ACTAT at 1894, ACTAT at 1766.
# MBE1r7ci: ACTAC at 3924, ACTAT at 3626, ACTAC at 2338, ACTAT at 1488, ACTAT at 1072, ACTAT at 887, ACTAT at 327.
# MBE1r7ci: ACTAC at 3924, ACTAT at 3626, ACTAC at 2338, ACTAT at 1488, ACTAT at 1072, ACTAT at 887, ACTAT at 327.
# MBE1r9ci: ACTAT at 3831, ACTAC at 3795, ACTAT at 1603.


===MBE1r alternate positive direction (evens) (4050-1) distal promoters===
===MBE1r alternate positive direction (evens) (4050-1) distal promoters===
Line 233: Line 236:
# MBE1r4ci: ACTAC at 3714, ACTAC at 3080, ACTAC at 3040, ACTAT at 2978, ACTAC at 2060, ACTAT at 603.
# MBE1r4ci: ACTAC at 3714, ACTAC at 3080, ACTAC at 3040, ACTAT at 2978, ACTAC at 2060, ACTAT at 603.
# MBE1r6ci: ACTAC at 2243, ACTAC at 1584, ACTAT at 1135, ACTAT at 774.
# MBE1r6ci: ACTAC at 2243, ACTAC at 1584, ACTAT at 1135, ACTAT at 774.
# MBE1r8ci: ACTAT at 3741, ACTAT at 825, ACTAT at 201.


==MBE2 samplings==
==MBE2 samplings==

Revision as of 14:59, 10 July 2022

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

"The 24-nt Xenopus Mos [polyadenylation response element] PRE (Charlesworth et al, 2002) contained a match to the SELEX-derived murine Musashi RNA binding consensus sequence (G/AU1−3AGU) (Imai et al, 2001), and included a 3′ U residue essential for PRE function (Charlesworth et al, 2002) [...]."[1]

"Regarding the 3′ UTR cis-regulatory sequences such as AREs (PAS) [110], BRD-Box [111] and MBE [112] mediates negative post-transcriptional regulation by affecting mRNA transcript stability and translational efficiency [110], [140]. In our case, the 3′ cis-regulatory signals, BRD-Box and MBE, located upstream and downstream PAS [...] may regulate tissue-specific alternative polyadenylation which has been detected in approximately 54% of human genes [142]."[2]

Human genes

Main article: Human genes

Gene expressions

Main article: Gene expressions

Interactions

Main article: Interaction gene transcriptions

Consensus sequences

Main article: Consensus sequence gene transcriptions

"The [Musashi-binding element] MBE consensus sequence is (G/A)U1–3AGU."[3]

"Musashi did not form a complex with the Mos UTR when the Musashi binding site was disrupted (AUAGU to AUccU [...])."[1]

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.

MBE1 samplings

Copying a responsive elements consensus sequence (A/G)T1–3AGT and putting the sequenceS in "⌘F" GTAGT, GTTAGT, GTTTAGT finds none or three, or ATTTAGT finds one to three between ZNF497 and A1BG or GTAGT three to six, GTTAGT, GTTTAGT or none between ZSCAN22 and A1BG, or ATAGT none, ATTAGT one, ATTTAGT none as can be found by the computer programs.

For the Basic programs testing consensus sequence (A/G)TAGT (starting with SuccessablesMBE1.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: 8, GTAGT at 3616, GTAGT at 3521, GTAGT at 3418, GTAGT at 3415, GTAGT at 3394, GTAGT at 2944, GTAGT at 2941, GTAGT at 2888.
  2. Positive strand, negative direction: 8, GTAGT at 4124, ATAGT at 4047, GTAGT at 2541, ATAGT at 2499, GTAGT at 2340, ATAGT at 1704, ATAGT at 469, ATAGT at 251.
  3. Positive strand, positive direction: 5, GTAGT at 4362, ATAGT at 4124, GTAGT at 4116, GTAGT at 4085, GTAGT at 3251.
  4. Negative strand, positive direction: 1, ATAGT at 1839.
  5. inverse complement, negative strand, negative direction, looking for ACTA(C/T), 9, ACTAC at 3807, ACTAC at 3798, ACTAT at 3544, ACTAT at 3535, ACTAT at 3360, ACTAT at 1702, ACTAT at 1665, ACTAT at 353, ACTAC at 142.
  6. inverse complement, positive strand, negative direction, looking for ACTA(C/T), 4, ACTAC at 3736, ACTAT at 3526, ACTAT at 2975, ACTAT at 210.
  7. inverse complement, positive strand, positive direction, looking for ACTA(C/T), 2, ACTAC at 3845, ACTAC at 2143.
  8. inverse complement, negative strand, positive direction, looking for ACTA(C/T), 1, ACTAC at 2427.

MBE1 (4560-2846) UTRs

  1. Negative strand, negative direction: ACTAC at 3807, ACTAC at 3798, GTAGT at 3616, ACTAT at 3544, ACTAT at 3535, GTAGT at 3521, GTAGT at 3418, GTAGT at 3415, GTAGT at 3394, ACTAT at 3360, GTAGT at 2944, GTAGT at 2941, GTAGT at 2888.
  2. Positive strand, negative direction: GTAGT at 4124, ATAGT at 4047, ACTAC at 3736, ACTAT at 3526, ACTAT at 2975.

MBE1 positive direction (4445-4265) core promoters

  1. Positive strand, positive direction: GTAGT at 4362.

MBE1 positive direction (4265-4050) proximal promoters

  1. Positive strand, positive direction: ATAGT at 4124, GTAGT at 4116, GTAGT at 4085.

MBE1 negative direction (2596-1) distal promoters

  1. Negative strand, negative direction: ACTAT at 1702, ACTAT at 1665, ACTAT at 353, ACTAC at 142.
  2. Positive strand, negative direction: GTAGT at 2541, ATAGT at 2499, GTAGT at 2340, ATAGT at 1704, ATAGT at 469, ATAGT at 251, ACTAT at 210.

MBE1 positive direction (4050-1) distal promoters

  1. Negative strand, positive direction: ACTAC at 2427, ATAGT at 1839.
  2. Positive strand, positive direction: ACTAC at 3845, GTAGT at 3251, ACTAC at 2143.

MBE1 random dataset samplings

  1. MBE1r0: 4, ATAGT at 4388, GTAGT at 2621, ATAGT at 561, ATAGT at 386.
  2. MBE1r1: 3, GTAGT at 3509, ATAGT at 2369, GTAGT at 558.
  3. MBE1r2: 5, ATAGT at 4028, ATAGT at 3688, ATAGT at 3042, GTAGT at 1651, ATAGT at 781.
  4. MBE1r3: 3, ATAGT at 2953, GTAGT at 2202, GTAGT at 1264.
  5. MBE1r4: 4, ATAGT at 4256, ATAGT at 2483, GTAGT at 2396, GTAGT at 1104.
  6. MBE1r5: 7, ATAGT at 4106, GTAGT at 4007, GTAGT at 3259, ATAGT at 3086, ATAGT at 3048, ATAGT at 1260, ATAGT at 316.
  7. MBE1r6: 10, ATAGT at 3869, GTAGT at 3665, GTAGT at 3454, GTAGT at 3451, GTAGT at 3088, ATAGT at 1629, GTAGT at 1393, GTAGT at 1315, GTAGT at 801, GTAGT at 531.
  8. MBE1r7: 5, GTAGT at 4421, GTAGT at 2540, GTAGT at 2116, ATAGT at 1470, GTAGT at 717.
  9. MBE1r8: 6, ATAGT at 4525, GTAGT at 4478, GTAGT at 3473, GTAGT at 3394, ATAGT at 1322, ATAGT at 979.
  10. MBE1r9: 7, ATAGT at 4441, GTAGT at 2933, GTAGT at 2633, GTAGT at 1876, ATAGT at 1563, GTAGT at 914, GTAGT at 16.
  11. MBE1r0ci: 4, ACTAC at 3192, ACTAT at 2726, ACTAT at 1965, ACTAT at 706.
  12. MBE1r1ci: 3, ACTAT at 4252, ACTAT at 376, ACTAC at 373.
  13. MBE1r2ci: 9, ACTAT at 4411, ACTAT at 4385, ACTAT at 3820, ACTAT at 2411, ACTAC at 2150, ACTAT at 1116, ACTAC at 316, ACTAC at 313, ACTAC at 53.
  14. MBE1r3ci: 7, ACTAC at 4271, ACTAC at 3787, ACTAT at 2170, ACTAC at 1854, ACTAC at 1292, ACTAC at 801, ACTAT at 206.
  15. MBE1r4ci: 6, ACTAC at 3714, ACTAC at 3080, ACTAC at 3040, ACTAT at 2978, ACTAC at 2060, ACTAT at 603.
  16. MBE1r5ci: 5, ACTAC at 4124, ACTAT at 3701, ACTAT at 3515, ACTAT at 1894, ACTAT at 1766.
  17. MBE1r6ci: 4, ACTAC at 2243, ACTAC at 1584, ACTAT at 1135, ACTAT at 774.
  18. MBE1r7ci: 8, ACTAC at 4117, ACTAC at 3924, ACTAT at 3626, ACTAC at 2338, ACTAT at 1488, ACTAT at 1072, ACTAT at 887, ACTAT at 327.
  19. MBE1r8ci: 5, ACTAC at 4499, ACTAT at 4307, ACTAT at 3741, ACTAT at 825, ACTAT at 201.
  20. MBE1r9ci: 4, ACTAC at 4089, ACTAT at 3831, ACTAC at 3795, ACTAT at 1603.

MBE1r arbitrary (evens) (4560-2846) UTRs

  1. MBE1r2: ATAGT at 4028, ATAGT at 3688, ATAGT at 3042.
  2. MBE1r4: ATAGT at 4256.
  3. MBE1r6: ATAGT at 3869, GTAGT at 3665, GTAGT at 3454, GTAGT at 3451, GTAGT at 3088.
  4. MBE1r8: ATAGT at 4525, GTAGT at 4478, GTAGT at 3473, GTAGT at 3394.
  5. MBE1r0ci: ACTAC at 3192.
  6. MBE1r2ci: ACTAT at 4411, ACTAT at 4385, ACTAT at 3820.
  7. MBE1r4ci: ACTAC at 3714, ACTAC at 3080, ACTAC at 3040, ACTAT at 2978.
  8. MBE1r8ci: ACTAC at 4499, ACTAT at 4307, ACTAT at 3741.

MBE1r alternate (odds) (4560-2846) UTRs

  1. MBE1r1: GTAGT at 3509.
  2. MBE1r3: ATAGT at 2953.
  3. MBE1r5: ATAGT at 4106, GTAGT at 4007, GTAGT at 3259, ATAGT at 3086, ATAGT at 3048.
  4. MBE1r7: GTAGT at 4421.
  5. MBE1r9: ATAGT at 4441, GTAGT at 2933.
  6. MBE1r1ci: 3ACTAT at 4252.
  7. MBE1r3ci: ACTAC at 4271, ACTAC at 3787.
  8. MBE1r5ci: ACTAC at 4124, ACTAT at 3701, ACTAT at 3515.
  9. MBE1r7ci: ACTAC at 4117, ACTAC at 3924, ACTAT at 3626.
  10. MBE1r9ci: ACTAC at 4089, ACTAT at 3831, ACTAC at 3795.

MBE1r arbitrary positive direction (odds) (4445-4265) core promoters

  1. MBE1r7: GTAGT at 4421.
  2. MBE1r9: ATAGT at 4441.
  3. MBE1r3ci: ACTAC at 4271.

MBE1r alternate positive direction (evens) (4445-4265) core promoters

  1. MBE1r2ci: ACTAT at 4411, ACTAT at 4385.
  2. MBE1r8ci: ACTAT at 4307.

MBE1r arbitrary negative direction (evens) (2811-2596) proximal promoters

  1. MBE1r0ci: ACTAT at 2726.

MBE1r alternate negative direction (odds) (2811-2596) proximal promoters

  1. MBE1r9: GTAGT at 2633.

MBE1r arbitrary positive direction (odds) (4265-4050) proximal promoters

  1. MBE1r5: ATAGT at 4106.
  2. MBE1r5ci: ACTAC at 4124.
  3. MBE1r7ci: ACTAC at 4117.
  4. MBE1r9ci: ACTAC at 4089.

MBE1r alternate positive direction (evens) (4265-4050) proximal promoters

  1. MBE1r4: ATAGT at 4256.

MBE1r arbitrary negative direction (evens) (2596-1) distal promoters

  1. MBE1r2: GTAGT at 1651, ATAGT at 781.
  2. MBE1r4: ATAGT at 2483, GTAGT at 2396, GTAGT at 1104.
  3. MBE1r6: ATAGT at 1629, GTAGT at 1393, GTAGT at 1315, GTAGT at 801, GTAGT at 531.
  4. MBE1r8: ATAGT at 1322, ATAGT at 979.
  5. MBE1r0ci: ACTAT at 1965, ACTAT at 706.
  6. MBE1r2ci: ACTAT at 2411, ACTAC at 2150, ACTAT at 1116, ACTAC at 316, ACTAC at 313, ACTAC at 53.
  7. MBE1r4ci: ACTAC at 2060, ACTAT at 603.
  8. MBE1r6ci: ACTAC at 2243, ACTAC at 1584, ACTAT at 1135, ACTAT at 774.
  9. MBE1r8ci: ACTAT at 825, ACTAT at 201.

MBE1r alternate negative direction (odds) (2596-1) distal promoters

  1. MBE1r1: ATAGT at 2369, GTAGT at 558.
  2. MBE1r3: GTAGT at 2202, GTAGT at 1264.
  3. MBE1r5: ATAGT at 1260, ATAGT at 316.
  4. MBE1r7: GTAGT at 2540, GTAGT at 2116, ATAGT at 1470, GTAGT at 717.
  5. MBE1r9: GTAGT at 1876, ATAGT at 1563, GTAGT at 914, GTAGT at 16.
  6. MBE1r1ci: ACTAT at 376, ACTAC at 373.
  7. MBE1r3ci: ACTAT at 2170, ACTAC at 1854, ACTAC at 1292, ACTAC at 801, ACTAT at 206.
  8. MBE1r5ci: ACTAT at 1894, ACTAT at 1766.
  9. MBE1r7ci: ACTAC at 2338, ACTAT at 1488, ACTAT at 1072, ACTAT at 887, ACTAT at 327.
  10. MBE1r9ci: ACTAT at 1603.

MBE1r arbitrary positive direction (odds) (4050-1) distal promoters

  1. MBE1r1: GTAGT at 3509, ATAGT at 2369, GTAGT at 558.
  2. MBE1r3: ATAGT at 2953, GTAGT at 2202, GTAGT at 1264.
  3. MBE1r5: GTAGT at 4007, GTAGT at 3259, ATAGT at 3086, ATAGT at 3048, ATAGT at 1260, ATAGT at 316.
  4. MBE1r7: GTAGT at 2540, GTAGT at 2116, ATAGT at 1470, GTAGT at 717.
  5. MBE1r9: GTAGT at 2933, GTAGT at 2633, GTAGT at 1876, ATAGT at 1563, GTAGT at 914, GTAGT at 16.
  6. MBE1r1ci: ACTAT at 376, ACTAC at 373.
  7. MBE1r3ci: ACTAC at 3787, ACTAT at 2170, ACTAC at 1854, ACTAC at 1292, ACTAC at 801, ACTAT at 206.
  8. MBE1r5ci: ACTAT at 3701, ACTAT at 3515, ACTAT at 1894, ACTAT at 1766.
  9. MBE1r7ci: ACTAC at 3924, ACTAT at 3626, ACTAC at 2338, ACTAT at 1488, ACTAT at 1072, ACTAT at 887, ACTAT at 327.
  10. MBE1r9ci: ACTAT at 3831, ACTAC at 3795, ACTAT at 1603.

MBE1r alternate positive direction (evens) (4050-1) distal promoters

  1. MBE1r2: ATAGT at 4028, ATAGT at 3688, ATAGT at 3042, GTAGT at 1651, ATAGT at 781.
  2. MBE1r4: ATAGT at 2483, GTAGT at 2396, GTAGT at 1104.
  3. MBE1r6: ATAGT at 3869, GTAGT at 3665, GTAGT at 3454, GTAGT at 3451, GTAGT at 3088, ATAGT at 1629, GTAGT at 1393, GTAGT at 1315, GTAGT at 801, GTAGT at 531.
  4. MBE1r8: GTAGT at 3473, GTAGT at 3394, ATAGT at 1322, ATAGT at 979.
  5. MBE1r0ci: ACTAC at 3192, ACTAT at 2726, ACTAT at 1965, ACTAT at 706.
  6. MBE1r2ci: ACTAT at 3820, ACTAT at 2411, ACTAC at 2150, ACTAT at 1116, ACTAC at 316, ACTAC at 313, ACTAC at 53.
  7. MBE1r4ci: ACTAC at 3714, ACTAC at 3080, ACTAC at 3040, ACTAT at 2978, ACTAC at 2060, ACTAT at 603.
  8. MBE1r6ci: ACTAC at 2243, ACTAC at 1584, ACTAT at 1135, ACTAT at 774.
  9. MBE1r8ci: ACTAT at 3741, ACTAT at 825, ACTAT at 201.

MBE2 samplings

For the Basic programs testing consensus sequence (A/G)TTAGT (starting with SuccessablesMBE2.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: 1, ATTAGT at 982.
  2. Positive strand, negative direction: 1, ATTAGT at 155.
  3. Positive strand, positive direction: 2, ATTAGT at 4147, GTTAGT at 2338.
  4. Negative strand, positive direction: 0.
  5. inverse complement, negative strand, negative direction, looking for ACTAA(C/T), 0.
  6. inverse complement, positive strand, negative direction, looking for ACTAA(C/T), 0.
  7. inverse complement, positive strand, positive direction, looking for ACTAA(C/T), 3, ACTAAT at 4164, ACTAAT at 4157, ACTAAC at 2677.
  8. inverse complement, negative strand, positive direction, looking for ACTAA(C/T), 0.

MBE2 positive direction (4265-4050) proximal promoters

  1. Positive strand, positive direction: ACTAAT at 4164, ACTAAT at 4157, ATTAGT at 4147.

MBE2 negative direction (2596-1) distal promoters

  1. Negative strand, negative direction: ATTAGT at 982.
  2. Positive strand, negative direction: ATTAGT at 155.

MBE2 positive direction (4050-1) distal promoters

  1. Positive strand, positive direction: ACTAAC at 2677, GTTAGT at 2338.

MBE2 random dataset samplings

  1. RDr0: 0.
  2. RDr1: 0.
  3. RDr2: 0.
  4. RDr3: 0.
  5. RDr4: 0.
  6. RDr5: 0.
  7. RDr6: 0.
  8. RDr7: 0.
  9. RDr8: 0.
  10. RDr9: 0.
  11. RDr0ci: 0.
  12. RDr1ci: 0.
  13. RDr2ci: 0.
  14. RDr3ci: 0.
  15. RDr4ci: 0.
  16. RDr5ci: 0.
  17. RDr6ci: 0.
  18. RDr7ci: 0.
  19. RDr8ci: 0.
  20. RDr9ci: 0.

RDr arbitrary (evens) (4560-2846) UTRs

RDr alternate (odds) (4560-2846) UTRs

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

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

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

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

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

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

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

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

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

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

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

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

MBE3 samplings

For the Basic programs testing consensus sequence (A/G)TTTAGT (starting with SuccessablesMBE3.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: 0.
  2. Positive strand, negative direction: 0.
  3. Positive strand, positive direction: 0.
  4. Negative strand, positive direction: 1, ATTTAGT at 4137.
  5. inverse complement, negative strand, negative direction, looking for ACTAAA(C/T), 0.
  6. inverse complement, positive strand, negative direction, looking for ACTAAA(C/T), 1, ACTAAAT at 2636.
  7. inverse complement, positive strand, positive direction, looking for ACTAAA(C/T), 1, ACTAAAT at 4135.
  8. inverse complement, negative strand, positive direction, looking for ACTAAA(C/T), 0.

MBE3 negative direction (2811-2596) proximal promoters

  1. Positive strand, negative direction: ACTAAAT at 2636.

MBE3 positive direction (4265-4050) proximal promoters

  1. Negative strand, positive direction: ATTTAGT at 4137.
  2. Positive strand, positive direction: ACTAAAT at 4135.

MBE3 random dataset samplings

  1. RDr0: 0.
  2. RDr1: 0.
  3. RDr2: 0.
  4. RDr3: 0.
  5. RDr4: 0.
  6. RDr5: 0.
  7. RDr6: 0.
  8. RDr7: 0.
  9. RDr8: 0.
  10. RDr9: 0.
  11. RDr0ci: 0.
  12. RDr1ci: 0.
  13. RDr2ci: 0.
  14. RDr3ci: 0.
  15. RDr4ci: 0.
  16. RDr5ci: 0.
  17. RDr6ci: 0.
  18. RDr7ci: 0.
  19. RDr8ci: 0.
  20. RDr9ci: 0.

RDr arbitrary (evens) (4560-2846) UTRs

RDr alternate (odds) (4560-2846) UTRs

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

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

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

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

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

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

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

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

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

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

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

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

Musashi binding element analysis and results

Main article: Complex locus A1BG and ZNF497 § MBEs

"The [Musashi-binding element] MBE consensus sequence is (G/A)U1–3AGU."[3]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 0 2 0 0
Randoms UTR arbitrary negative 0 10 0 0
Randoms UTR alternate negative 0 10 0 0
Reals Core negative 0 2 0 0
Randoms Core 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 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 0 10 0 0
Randoms Distal alternate negative 0 10 0 0
Reals Distal positive 0 2 0 0
Randoms Distal arbitrary positive 0 10 0 0
Randoms Distal alternate positive 0 10 0 0

Comparison:

The occurrences of real responsive element consensus sequences are greater than the randoms. This suggests that the real responsive element consensus sequences are likely active or activable.

Acknowledgements

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

See also

References

  1. ↑ 1.0 1.1 Amanda Charlesworth, Anna Wilczynska, Prajitha Thampi, Linda L Cox, and Angus M MacNicol (21 June 2006). "Musashi regulates the temporal order of mRNA translation during Xenopus oocyte maturation". The EMBO Journal. 25 (12): 2792–2801. doi:10.1038/sj.emboj.7601159. PMID 16763568. Retrieved 17 April 2021.
  2. ↑ Siva Arumugam Saravanaperuma, Dario Pediconi, Carlo Renieri, Antonietta La Terza (15 June 2012). "Skipping of Exons by Premature Termination of Transcription and Alternative Splicing within Intron-5 of the Sheep SCF Gene: A Novel Splice Variant". PLOS ONE. 7 (6): e38657. doi:10.1371/journal.pone.0038657. Retrieved 17 April 2021.
  3. ↑ 3.0 3.1 Tomoya Kotani, Kaori Maehata, Natsumi Takei (2017). "Regulation of Translationally Repressed mRNAs in Zebrafish and Mouse Oocytes, In: Oocytes. Results and Problems in Cell Differentiation". 63. Cham: Springer: 297–324. doi:10.1007/978-3-319-60855-6_13. Retrieved 17 April 2021.

External links

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