Krüppel-like factor gene transcriptions: Difference between revisions

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# KRUPr0: 11, GGGCCGTT at 4471, GGGTGTTT at 3708, GGGTATTT at 3513, GGGTTGTG at 3019, GGGGTTGT at 3018, GGGCGGTG at 2998, GGGGCTGG at 2469, GGGGGGGG at 1650, GGGCTGGG at 827, GGGATGTG at 764, GGGTTGTG at 724.
# KRUPr0: 11, GGGCCGTT at 4471, GGGTGTTT at 3708, GGGTATTT at 3513, GGGTTGTG at 3019, GGGGTTGT at 3018, GGGCGGTG at 2998, GGGGCTGG at 2469, GGGGGGGG at 1650, GGGCTGGG at 827, GGGATGTG at 764, GGGTTGTG at 724.
# KRUPr1: 9, GGGCTGGG at 3918, GGGCAGGG at 2653, GGGCCTGT at 2389, GGGCGTTT at 1481, GGGAGGTG at 1172, GGGGAGGT at 1171, GGGCCTTG at 1117, GGGTAGTT at 559, GGGTTTTG at 280.
# KRUPr1: 9, GGGCTGGG at 3918, GGGCAGGG at 2653, GGGCCTGT at 2389, GGGCGTTT at 1481, GGGAGGTG at 1172, GGGGAGGT at 1171, GGGCCTTG at 1117, GGGTAGTT at 559, GGGTTTTG at 280.
# RDr2: 0.
# KRUPr2: 19, GGGGGGTT at 4301, GGGGGGGT at 4300, GGGGGTGG at 4009, GGGACTTG at 3503, GGGCATTT at 3299, GGGTTTTT at 2824, GGGCGGGT at 2820, GGGGCGGG at 2819, GGGAGTGT at 2791, GGGGAGTG at 2790, GGGCCGTT at 2702, GGGGAGGT at 2611, GGGCCTTT at 2286, GGGGAGTG at 2160, GGGTTGGG at 1287, GGGGTTGG at 1286, GGGTATTT at 808, GGGAGTGT at 193, GGGAAGGG at 47.
# RDr3: 0.
# KRUPr3: 19, GGGTTGTT at 4514, GGGTGTTT at 4497, GGGATTTT at 3757, GGGGATTT at 3756, GGGGCTTT at 3638, GGGCAGGG at 3332, GGGCATTT at 2538, GGGAGTTG at 2263, GGGGAGTT at 2262, GGGTGTGG at 2011, GGGCCGGG at 1991, GGGGCTGG at 1925, GGGAGGGT at 1629, GGGGAGGG at 1628, GGGAGGGG at 1624, GGGATTGG at 1231, GGGACGTT at 630, GGGTTGTT at 530, GGGGCGGG at 519.
# RDr4: 0.
# KRUPr4: 15, GGGTCGGT at 4243, GGGCGTGG at 3733, GGGGCGTG at 3732, GGGATTTT at 2768, GGGGATTT at 2767, GGGTTGTT at 2436, GGGTTTTT at 2426, GGGACTGT at 2416, GGGTAGTT at 2397, GGGTATGG at 1830, GGGACGTT at 1606, GGGTTTTG at 1382, GGGCTTTT at 1345, GGGCCGGT at 355, GGGTAGGG at 33.
# RDr5: 0.
# RDr5: 0.
# RDr6: 0.
# RDr6: 0.
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# KRUPr0: GGGCCGTT at 4471, GGGTGTTT at 3708, GGGTATTT at 3513, GGGTTGTG at 3019, GGGGTTGT at 3018, GGGCGGTG at 2998.
# KRUPr0: GGGCCGTT at 4471, GGGTGTTT at 3708, GGGTATTT at 3513, GGGTTGTG at 3019, GGGGTTGT at 3018, GGGCGGTG at 2998.
# KRUPr2: GGGGGGTT at 4301, GGGGGGGT at 4300, GGGGGTGG at 4009, GGGACTTG at 3503, GGGCATTT at 3299.
# KRUPr4: GGGTCGGT at 4243, GGGCGTGG at 3733, GGGGCGTG at 3732.


===KRUPr alternate (odds) (4560-2846) UTRs===
===KRUPr alternate (odds) (4560-2846) UTRs===


# KRUPr1: GGGCTGGG at 3918.
# KRUPr1: GGGCTGGG at 3918.
# KRUPr3: GGGTTGTT at 4514, GGGTGTTT at 4497, GGGATTTT at 3757, GGGGATTT at 3756, GGGGCTTT at 3638, GGGCAGGG at 3332.


===RDr arbitrary negative direction (evens) (2846-2811) core promoters===
===KRUPr arbitrary negative direction (evens) (2846-2811) core promoters===
 
# KRUPr2: GGGTTTTT at 2824, GGGCGGGT at 2820, GGGGCGGG at 2819.


===RDr alternate negative direction (odds) (2846-2811) core promoters===
===RDr alternate negative direction (odds) (2846-2811) core promoters===
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===RDr arbitrary positive direction (odds) (4445-4265) core promoters===
===RDr arbitrary positive direction (odds) (4445-4265) core promoters===


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


===KRUPr alternate positive direction (evens) (4445-4265) core promoters===


===RDr arbitrary negative direction (evens) (2811-2596) proximal promoters===
# KRUPr2: GGGGGGTT at 4301, GGGGGGGT at 4300.


===KRUPr arbitrary negative direction (evens) (2811-2596) proximal promoters===
# KRUPr2: GGGAGTGT at 2791, GGGGAGTG at 2790, GGGCCGTT at 2702, GGGGAGGT at 2611.
# KRUPr4: GGGATTTT at 2768, GGGGATTT at 2767.


===KRUPr alternate negative direction (odds) (2811-2596) proximal promoters===
===KRUPr alternate negative direction (odds) (2811-2596) proximal promoters===
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===RDr arbitrary positive direction (odds) (4265-4050) proximal promoters===
===RDr arbitrary positive direction (odds) (4265-4050) proximal promoters===


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


===KRUPr alternate positive direction (evens) (4265-4050) proximal promoters===
# KRUPr4: GGGTCGGT at 4243.


===KRUPr arbitrary negative direction (evens) (2596-1) distal promoters===
===KRUPr arbitrary negative direction (evens) (2596-1) distal promoters===


# KRUPr0: GGGGCTGG at 2469, GGGGGGGG at 1650, GGGCTGGG at 827, GGGATGTG at 764, GGGTTGTG at 724.
# KRUPr0: GGGGCTGG at 2469, GGGGGGGG at 1650, GGGCTGGG at 827, GGGATGTG at 764, GGGTTGTG at 724.
# KRUPr2: GGGCCTTT at 2286, GGGGAGTG at 2160, GGGTTGGG at 1287, GGGGTTGG at 1286, GGGTATTT at 808, GGGAGTGT at 193, GGGAAGGG at 47.
# KRUPr4: GGGTTGTT at 2436, GGGTTTTT at 2426, GGGACTGT at 2416, GGGTAGTT at 2397, GGGTATGG at 1830, GGGACGTT at 1606, GGGTTTTG at 1382, GGGCTTTT at 1345, GGGCCGGT at 355, GGGTAGGG at 33.


===KRUPr alternate negative direction (odds) (2596-1) distal promoters===
===KRUPr alternate negative direction (odds) (2596-1) distal promoters===


# KRUPr1: GGGCCTGT at 2389, GGGCGTTT at 1481, GGGAGGTG at 1172, GGGGAGGT at 1171, GGGCCTTG at 1117, GGGTAGTT at 559, GGGTTTTG at 280.
# KRUPr1: GGGCCTGT at 2389, GGGCGTTT at 1481, GGGAGGTG at 1172, GGGGAGGT at 1171, GGGCCTTG at 1117, GGGTAGTT at 559, GGGTTTTG at 280.
# KRUPr3: GGGCATTT at 2538, GGGAGTTG at 2263, GGGGAGTT at 2262, GGGTGTGG at 2011, GGGCCGGG at 1991, GGGGCTGG at 1925, GGGAGGGT at 1629, GGGGAGGG at 1628, GGGAGGGG at 1624, GGGATTGG at 1231, GGGACGTT at 630, GGGTTGTT at 530, GGGGCGGG at 519.


===KRUPr arbitrary positive direction (odds) (4050-1) distal promoters===
===KRUPr arbitrary positive direction (odds) (4050-1) distal promoters===


# KRUPr1: GGGCTGGG at 3918, GGGCAGGG at 2653, GGGCCTGT at 2389, GGGCGTTT at 1481, GGGAGGTG at 1172, GGGGAGGT at 1171, GGGCCTTG at 1117, GGGTAGTT at 559, GGGTTTTG at 280.
# KRUPr1: GGGCTGGG at 3918, GGGCAGGG at 2653, GGGCCTGT at 2389, GGGCGTTT at 1481, GGGAGGTG at 1172, GGGGAGGT at 1171, GGGCCTTG at 1117, GGGTAGTT at 559, GGGTTTTG at 280.
# KRUPr3: GGGATTTT at 3757, GGGGATTT at 3756, GGGGCTTT at 3638, GGGCAGGG at 3332, GGGCATTT at 2538, GGGAGTTG at 2263, GGGGAGTT at 2262, GGGTGTGG at 2011, GGGCCGGG at 1991, GGGGCTGG at 1925, GGGAGGGT at 1629, GGGGAGGG at 1628, GGGAGGGG at 1624, GGGATTGG at 1231, GGGACGTT at 630, GGGTTGTT at 530, GGGGCGGG at 519.


===KRUPr alternate positive direction (evens) (4050-1) distal promoters===
===KRUPr alternate positive direction (evens) (4050-1) distal promoters===


# KRUPr0: GGGTGTTT at 3708, GGGTATTT at 3513, GGGTTGTG at 3019, GGGGTTGT at 3018, GGGCGGTG at 2998, GGGGCTGG at 2469, GGGGGGGG at 1650, GGGCTGGG at 827, GGGATGTG at 764, GGGTTGTG at 724.
# KRUPr0: GGGTGTTT at 3708, GGGTATTT at 3513, GGGTTGTG at 3019, GGGGTTGT at 3018, GGGCGGTG at 2998, GGGGCTGG at 2469, GGGGGGGG at 1650, GGGCTGGG at 827, GGGATGTG at 764, GGGTTGTG at 724.
# KRUPr2: GGGGGTGG at 4009, GGGACTTG at 3503, GGGCATTT at 3299, GGGTTTTT at 2824, GGGCGGGT at 2820, GGGGCGGG at 2819, GGGAGTGT at 2791, GGGGAGTG at 2790, GGGCCGTT at 2702, GGGGAGGT at 2611, GGGCCTTT at 2286, GGGGAGTG at 2160, GGGTTGGG at 1287, GGGGTTGG at 1286, GGGTATTT at 808, GGGAGTGT at 193, GGGAAGGG at 47.
# KRUPr4: GGGCGTGG at 3733, GGGGCGTG at 3732, GGGATTTT at 2768, GGGGATTT at 2767, GGGTTGTT at 2436, GGGTTTTT at 2426, GGGACTGT at 2416, GGGTAGTT at 2397, GGGTATGG at 1830, GGGACGTT at 1606, GGGTTTTG at 1382, GGGCTTTT at 1345, GGGCCGGT at 355, GGGTAGGG at 33.


==Response element analysis and results==
==Response element analysis and results==

Revision as of 20:10, 21 June 2022

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

"Krüppel-like factor 1 (KLF1/EKLF) is a transcription factor that globally activates genes involved in erythroid cell development. [...] KLF1 belongs to the KLF family of transcription factors that binds the G-rich strand of so-called CACCC-box motifs located in regulatory regions of numerous erythroid genes."[1]

Human genes

The following human genes encode Kruppel-like factors: KLF1, KLF2, KLF3, KLF4, KLF5, KLF6, KLF7, KLF8, KLF9, KLF10, KLF11, KLF12, KLF13, KLF14, KLF15, KLF16, KLF17.

Interactions

Consensus sequences

"Using the in vitro CASTing method, we identified a new set of sequences bound by [congenital dyserythropoietic anemia] CDA-KLF1, and based on them we defined the consensus binding site as 5′-NGG-GG(T/G)-(T/G)(T/G)(T/G)-3′. It differs from the consensus binding sites for [wild-type] WT-KLF1, 5′-NGG-G(C/T)G-(T/G)GG-3′, and for [neonatal anemia] Nan-KLF1, 5′-NGG-G(C/A)N-(T/G)GG-3′, as well."[1]

An apparent consensus is GGG(A/C/G/T)(A/C/G/T)(G/T)(G/T)(G/T).

Krüppel-like factor Samplings

Copying an apparent consensus sequence for the KLF of GGGTCGTG and putting it in "⌘F" finds six located between ZSCAN22 and A1BG and none between ZNF497 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence GGGNN(G/T)(G/T)(G/T) (starting with SuccessablesKRUP.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 GGGNN(G/T)(G/T)(G/T), 15, GGGTCGGG at 4482, GGGTAGGT at 4457, GGGTCTTG at 4450, GGGTTGTG at 3981, GGGTATGG at 3858, GGGACTTG at 3783, GGGTCGTG at 3733, GGGTTGTT at 3139, GGGTCGTG at 3072, GGGTTGTG at 2549, GGGTCGTG at 1787, GGGCAGTT at 1512, GGGTCGTG at 1142, GGGTCGTG at 678, GGGTCGTG at 405.
  2. negative strand, positive direction, looking for GGGNN(G/T)(G/T)(G/T), 22, GGGGCGGG at 4440, GGGAGGGG at 4435, GGGGCGGG at 4430, GGGTCTGG at 4416, GGGAGGGG at 3981, GGGTGGGG at 3542, GGGCAGGG at 2297, GGGAGGGG at 2291, GGGGAGGG at 2290, GGGACTTT at 2273, GGGTGTGG at 1805, GGGACTGT at 916, GGGACTGT at 816, GGGGAGTG at 495, GGGCGTTG at 448, GGGCTGGG at 418, GGGGCTGG at 417, GGGACGGG at 412, GGGCCTGG at 286, GGGCTGTG at 265, GGGGCTGT at 264, GGGCATTG at 23.
  3. positive strand, negative direction, looking for GGGNN(G/T)(G/T)(G/T), 10, GGGCCTTG at 3570, GGGTGTGG at 3186, GGGCGTGG at 3047, GGGCTGGG at 3042, GGGGCTGG at 3041, GGGAGTTG at 2704, GGGCGTGG at 1897, GGGCGTGG at 1244, GGGCCGGG at 514, GGGAAGTT at 83.
  4. positive strand, positive direction, looking for GGGNN(G/T)(G/T)(G/T), 12, GGGTCTGT at 4332, GGGACGGG at 4233, GGGACTGG at 4216, GGGCCGTG at 4005, GGGAGTGT at 3505, GGGAGTGT at 3209, GGGCAGGG at 3204, GGGTCTTG at 3093, GGGTGGGG at 2019, GGGACTGG at 1662, GGGAAGGG at 1071, GGGTGGGT at 71.
  5. complement, negative strand, negative direction, looking for CCCNN(A/C)(A/C)(A/C), 10, CCCGGAAC at 3570, CCCACACC at 3186, CCCGCACC at 3047, CCCGACCC at 3042, CCCCGACC at 3041, CCCTCAAC at 2704, CCCGCACC at 1897, CCCGCACC at 1244, CCCGGCCC at 514, CCCTTCAA at 83.
  6. complement, negative strand, positive direction, looking for CCCNN(A/C)(A/C)(A/C), 12, CCCAGACA at 4332, CCCTGCCC at 4233, CCCTGACC at 4216, CCCGGCAC at 4005, CCCTCACA at 3505, CCCTCACA at 3209, CCCGTCCC at 3204, CCCAGAAC at 3093, CCCACCCC at 2019, CCCTGACC at 1662, CCCTTCCC at 1071, CCCACCCA at 71.
  7. complement, positive strand, negative direction, looking for CCCNN(A/C)(A/C)(A/C), 15, CCCAGCCC at 4482, CCCATCCA at 4457, CCCAGAAC at 4450, CCCAACAC at 3981, CCCATACC at 3858, CCCTGAAC at 3783, CCCAGCAC at 3733, CCCAACAA at 3139, CCCAGCAC at 3072, CCCAACAC at 2549, CCCAGCAC at 1787, CCCGTCAA at 1512, CCCAGCAC at 1142, CCCAGCAC at 678, CCCAGCAC at 405.
  8. complement, positive strand, positive direction, looking for CCCNN(A/C)(A/C)(A/C), 22, CCCCGCCC at 4440, CCCTCCCC at 4435, CCCCGCCC at 4430, CCCAGACC at 4416, CCCTCCCC at 3981, CCCACCCC at 3542, CCCGTCCC at 2297, CCCTCCCC at 2291, CCCCTCCC at 2290, CCCTGAAA at 2273, CCCACACC at 1805, CCCTGACA at 916, CCCTGACA at 816, CCCCTCAC at 495, CCCGCAAC at 448, CCCGACCC at 418, CCCCGACC at 417, CCCTGCCC at 412, CCCGGACC at 286, CCCGACAC at 265, CCCCGACA at 264, CCCGTAAC at 23.
  9. inverse complement, negative strand, negative direction, looking for (A/C)(A/C)(A/C)NNCCC, 8, CACTACCC at 3800, ACCAACCC at 3607, CACCACCC at 3193, CCCGACCC at 3042, CACCACCC at 1904, CACCGCCC at 1251, CCCGGCCC at 514, CAACTCCC at 88.
  10. inverse complement, negative strand, positive direction, looking for (A/C)(A/C)(A/C)NNCCC, 10, CACCGCCC at 4292, CCCTGCCC at 4233, ACCTCCCC at 3555, CCCGTCCC at 3204, CACCCCCC at 2021, CCACCCCC at 2020, CCCACCCC at 2019, ACCCACCC at 2018, ACAGTCCC at 1827, CCCTTCCC at 1071.
  11. inverse complement, positive strand, negative direction, looking for (A/C)(A/C)(A/C)NNCCC, 5, CCCAGCCC at 4482, AACTGCCC at 3853, AACAGCCC at 3728, AACAACCC at 2845, AAACCCCC at 2624.
  12. inverse complement, positive strand, positive direction, looking for (A/C)(A/C)(A/C)NNCCC, 30, CCCCGCCC at 4440, CCCTCCCC at 4435, CCCCGCCC at 4430, CCAGACCC at 4417, AACGACCC at 4178, CCCTCCCC at 3981, ACACTCCC at 3906, CACCACCC at 3817, CCCACCCC at 3542, CACGTCCC at 3467, CACAACCC at 2817, CCCGTCCC at 2297, CCCTCCCC at 2291, CCCCTCCC at 2290, AAACCCCC at 2286, AAAACCCC at 2285, AAAAACCC at 2284, ACAGACCC at 1865, CACGTCCC at 1789, CCACGCCC at 1765, AAAAGCCC at 1752, AACGCCCC at 1708, ACCGCCCC at 1027, CACCGCCC at 1026, AACGTCCC at 659, CACGCCCC at 491, CCACGCCC at 490, CCCGACCC at 418, CCCTGCCC at 412, ACCCGCCC at 407.
  13. inverse negative strand, negative direction, looking for (G/T)(G/T)(G/T)NNGGG, 5, GGGTCGGG at 4482, TTGACGGG at 3853, TTGTCGGG at 3728, TTGTTGGG at 2845, TTTGGGGG at 2624.
  14. inverse negative strand, positive direction, looking for (G/T)(G/T)(G/T)NNGGG, 30, GGGGCGGG at 4440, GGGAGGGG at 4435, GGGGCGGG at 4430, GGTCTGGG at 4417, TTGCTGGG at 4178, GGGAGGGG at 3981, TGTGAGGG at 3906, GTGGTGGG at 3817, GGGTGGGG at 3542, GTGCAGGG at 3467, GTGTTGGG at 2817, GGGCAGGG at 2297, GGGAGGGG at 2291, GGGGAGGG at 2290, TTTGGGGG at 2286, TTTTGGGG at 2285, TTTTTGGG at 2284, TGTCTGGG at 1865, GTGCAGGG at 1789, GGTGCGGG at 1765, TTTTCGGG at 1752, TTGCGGGG at 1708, TGGCGGGG at 1027, GTGGCGGG at 1026, TTGCAGGG at 659, GTGCGGGG at 491, GGTGCGGG at 490, GGGCTGGG at 418, GGGACGGG at 412, TGGGCGGG at 407.
  15. inverse positive strand, negative direction, looking for (G/T)(G/T)(G/T)NNGGG, 8, GTGATGGG at 3800, TGGTTGGG at 3607, GTGGTGGG at 3193, GGGCTGGG at 3042, GTGGTGGG at 1904, GTGGCGGG at 1251, GGGCCGGG at 514, GTTGAGGG at 88.
  16. inverse positive strand, positive direction, looking for (G/T)(G/T)(G/T)NNGGG, 10, GTGGCGGG at 4292, GGGACGGG at 4233, TGGAGGGG at 3555, GGGCAGGG at 3204, GTGGGGGG at 2021, GGTGGGGG at 2020, GGGTGGGG at 2019, TGGGTGGG at 2018, TGTCAGGG at 1827, GGGAAGGG at 1071.

Krup UTR gene transcriptions

Main article: UTR gene transcriptions

Negative strand, negative direction: GGGTCGGG at 4482, GGGTAGGT at 4457, GGGTCTTG at 4450, GGGTTGTG at 3981, GGGTATGG at 3858, CACTACCC at 3800, GGGACTTG at 3783, GGGTCGTG at 3733, ACCAACCC at 3607, CACCACCC at 3193, GGGTTGTT at 3139, GGGTCGTG at 3072, CCCGACCC at 3042.

Positive strand, negative direction: AACTGCCC at 3853, AACAGCCC at 3728, GGGCCTTG at 3570, GGGTGTGG at 3186, GGGCGTGG at 3047, GGGGCTGG at 3041.

Krup core promoters

Main article: Core promoter gene transcriptions

Positive strand, negative direction: AACAACCC at 2845.

Negative strand, positive direction: GGGGCGGG at 4440, GGGAGGGG at 4435, GGGGCGGG at 4430, GGGTCTGG at 4416, CACCGCCC at 4292.

Positive strand, positive direction: CCAGACCC at 4417, GGGTCTGT at 4332.

Krup proximal promoters

Main article: Proximal promoter gene transcriptions

Positive strand, negative direction: GGGAGTTG at 2704, AAACCCCC at 2624.

Negative strand, positive direction: CCCTGCCC at 4233.

Positive strand, positive direction: GGGACTGG at 4216, AACGACCC at 4178.

Krup distal promoters

Main article: Distal promoter gene transcriptions

Negative strand, negative direction: GGGTTGTG at 2549, CACCACCC at 1904, GGGTCGTG at 1787, GGGCAGTT at 1512, CACCGCCC at 1251, GGGTCGTG at 1142, GGGTCGTG at 678, CCCGGCCC at 514, GGGTCGTG at 405, CAACTCCC at 88.

Positive strand, negative direction: GGGCGTGG at 1897, GGGCGTGG at 1244, GGGCCGGG at 514, GGGAAGTT at 83.

Negative strand, positive direction: GGGAGGGG at 3981, ACCTCCCC at 3555, GGGTGGGG at 3542, CCCGTCCC at 3204, GGGCAGGG at 2297, GGGAGGGG at 2291, GGGGAGGG at 2290, GGGACTTT at 2273, CACCCCCC at 2021, CCACCCCC at 2020, CCCACCCC at 2019, ACCCACCC at 2018, ACAGTCCC at 1827, GGGTGTGG at 1805, CCCTTCCC at 1071, GGGACTGT at 916, GGGACTGT at 816, GGGGAGTG at 495, GGGCGTTG at 448, GGGCTGGG at 418, GGGGCTGG at 417, GGGACGGG at 412, GGGCCTGG at 286, GGGCTGTG at 265, GGGGCTGT at 264, GGGCATTG at 23.

Positive strand, positive direction: GGGCCGTG at 4005, ACACTCCC at 3906, CACCACCC at 3817, GGGAGTGT at 3505, CACGTCCC at 3467, GGGAGTGT at 3209, GGGTCTTG at 3093, CACAACCC at 2817, AAACCCCC at 2286, AAAACCCC at 2285, AAAAACCC at 2284, ACAGACCC at 1865, CACGTCCC at 1789, CCACGCCC at 1765, AAAAGCCC at 1752, AACGCCCC at 1708, GGGACTGG at 1662, ACCGCCCC at 1027, CACCGCCC at 1026, AACGTCCC at 659, CACGCCCC at 491, CCACGCCC at 490, ACCCGCCC at 407, GGGTGGGT at 71.

Response element random dataset samplings

  1. KRUPr0: 11, GGGCCGTT at 4471, GGGTGTTT at 3708, GGGTATTT at 3513, GGGTTGTG at 3019, GGGGTTGT at 3018, GGGCGGTG at 2998, GGGGCTGG at 2469, GGGGGGGG at 1650, GGGCTGGG at 827, GGGATGTG at 764, GGGTTGTG at 724.
  2. KRUPr1: 9, GGGCTGGG at 3918, GGGCAGGG at 2653, GGGCCTGT at 2389, GGGCGTTT at 1481, GGGAGGTG at 1172, GGGGAGGT at 1171, GGGCCTTG at 1117, GGGTAGTT at 559, GGGTTTTG at 280.
  3. KRUPr2: 19, GGGGGGTT at 4301, GGGGGGGT at 4300, GGGGGTGG at 4009, GGGACTTG at 3503, GGGCATTT at 3299, GGGTTTTT at 2824, GGGCGGGT at 2820, GGGGCGGG at 2819, GGGAGTGT at 2791, GGGGAGTG at 2790, GGGCCGTT at 2702, GGGGAGGT at 2611, GGGCCTTT at 2286, GGGGAGTG at 2160, GGGTTGGG at 1287, GGGGTTGG at 1286, GGGTATTT at 808, GGGAGTGT at 193, GGGAAGGG at 47.
  4. KRUPr3: 19, GGGTTGTT at 4514, GGGTGTTT at 4497, GGGATTTT at 3757, GGGGATTT at 3756, GGGGCTTT at 3638, GGGCAGGG at 3332, GGGCATTT at 2538, GGGAGTTG at 2263, GGGGAGTT at 2262, GGGTGTGG at 2011, GGGCCGGG at 1991, GGGGCTGG at 1925, GGGAGGGT at 1629, GGGGAGGG at 1628, GGGAGGGG at 1624, GGGATTGG at 1231, GGGACGTT at 630, GGGTTGTT at 530, GGGGCGGG at 519.
  5. KRUPr4: 15, GGGTCGGT at 4243, GGGCGTGG at 3733, GGGGCGTG at 3732, GGGATTTT at 2768, GGGGATTT at 2767, GGGTTGTT at 2436, GGGTTTTT at 2426, GGGACTGT at 2416, GGGTAGTT at 2397, GGGTATGG at 1830, GGGACGTT at 1606, GGGTTTTG at 1382, GGGCTTTT at 1345, GGGCCGGT at 355, GGGTAGGG at 33.
  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.

KRUPr arbitrary (evens) (4560-2846) UTRs

  1. KRUPr0: GGGCCGTT at 4471, GGGTGTTT at 3708, GGGTATTT at 3513, GGGTTGTG at 3019, GGGGTTGT at 3018, GGGCGGTG at 2998.
  2. KRUPr2: GGGGGGTT at 4301, GGGGGGGT at 4300, GGGGGTGG at 4009, GGGACTTG at 3503, GGGCATTT at 3299.
  3. KRUPr4: GGGTCGGT at 4243, GGGCGTGG at 3733, GGGGCGTG at 3732.

KRUPr alternate (odds) (4560-2846) UTRs

  1. KRUPr1: GGGCTGGG at 3918.
  2. KRUPr3: GGGTTGTT at 4514, GGGTGTTT at 4497, GGGATTTT at 3757, GGGGATTT at 3756, GGGGCTTT at 3638, GGGCAGGG at 3332.

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

  1. KRUPr2: GGGTTTTT at 2824, GGGCGGGT at 2820, GGGGCGGG at 2819.

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

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

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

  1. KRUPr2: GGGGGGTT at 4301, GGGGGGGT at 4300.

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

  1. KRUPr2: GGGAGTGT at 2791, GGGGAGTG at 2790, GGGCCGTT at 2702, GGGGAGGT at 2611.
  2. KRUPr4: GGGATTTT at 2768, GGGGATTT at 2767.

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

  1. KRUPr1: GGGCAGGG at 2653, GGGCCTGT at 2389, GGGCGTTT at 1481, GGGAGGTG at 1172, GGGGAGGT at 1171, GGGCCTTG at 1117, GGGTAGTT at 559, GGGTTTTG at 280.

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

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

  1. KRUPr4: GGGTCGGT at 4243.

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

  1. KRUPr0: GGGGCTGG at 2469, GGGGGGGG at 1650, GGGCTGGG at 827, GGGATGTG at 764, GGGTTGTG at 724.
  2. KRUPr2: GGGCCTTT at 2286, GGGGAGTG at 2160, GGGTTGGG at 1287, GGGGTTGG at 1286, GGGTATTT at 808, GGGAGTGT at 193, GGGAAGGG at 47.
  3. KRUPr4: GGGTTGTT at 2436, GGGTTTTT at 2426, GGGACTGT at 2416, GGGTAGTT at 2397, GGGTATGG at 1830, GGGACGTT at 1606, GGGTTTTG at 1382, GGGCTTTT at 1345, GGGCCGGT at 355, GGGTAGGG at 33.

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

  1. KRUPr1: GGGCCTGT at 2389, GGGCGTTT at 1481, GGGAGGTG at 1172, GGGGAGGT at 1171, GGGCCTTG at 1117, GGGTAGTT at 559, GGGTTTTG at 280.
  2. KRUPr3: GGGCATTT at 2538, GGGAGTTG at 2263, GGGGAGTT at 2262, GGGTGTGG at 2011, GGGCCGGG at 1991, GGGGCTGG at 1925, GGGAGGGT at 1629, GGGGAGGG at 1628, GGGAGGGG at 1624, GGGATTGG at 1231, GGGACGTT at 630, GGGTTGTT at 530, GGGGCGGG at 519.

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

  1. KRUPr1: GGGCTGGG at 3918, GGGCAGGG at 2653, GGGCCTGT at 2389, GGGCGTTT at 1481, GGGAGGTG at 1172, GGGGAGGT at 1171, GGGCCTTG at 1117, GGGTAGTT at 559, GGGTTTTG at 280.
  2. KRUPr3: GGGATTTT at 3757, GGGGATTT at 3756, GGGGCTTT at 3638, GGGCAGGG at 3332, GGGCATTT at 2538, GGGAGTTG at 2263, GGGGAGTT at 2262, GGGTGTGG at 2011, GGGCCGGG at 1991, GGGGCTGG at 1925, GGGAGGGT at 1629, GGGGAGGG at 1628, GGGAGGGG at 1624, GGGATTGG at 1231, GGGACGTT at 630, GGGTTGTT at 530, GGGGCGGG at 519.

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

  1. KRUPr0: GGGTGTTT at 3708, GGGTATTT at 3513, GGGTTGTG at 3019, GGGGTTGT at 3018, GGGCGGTG at 2998, GGGGCTGG at 2469, GGGGGGGG at 1650, GGGCTGGG at 827, GGGATGTG at 764, GGGTTGTG at 724.
  2. KRUPr2: GGGGGTGG at 4009, GGGACTTG at 3503, GGGCATTT at 3299, GGGTTTTT at 2824, GGGCGGGT at 2820, GGGGCGGG at 2819, GGGAGTGT at 2791, GGGGAGTG at 2790, GGGCCGTT at 2702, GGGGAGGT at 2611, GGGCCTTT at 2286, GGGGAGTG at 2160, GGGTTGGG at 1287, GGGGTTGG at 1286, GGGTATTT at 808, GGGAGTGT at 193, GGGAAGGG at 47.
  3. KRUPr4: GGGCGTGG at 3733, GGGGCGTG at 3732, GGGATTTT at 2768, GGGGATTT at 2767, GGGTTGTT at 2436, GGGTTTTT at 2426, GGGACTGT at 2416, GGGTAGTT at 2397, GGGTATGG at 1830, GGGACGTT at 1606, GGGTTTTG at 1382, GGGCTTTT at 1345, GGGCCGGT at 355, GGGTAGGG at 33.

Response element analysis and results

Main article: Complex locus A1BG and ZNF497 § KRUPs

The Pax-4 homeodomain [HD] was shown to preferentially dimerize on DNA sequences consisting of an inverted TAAT motif, separated by 4-nucleotide spacing."[2]

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.

See also

References

  1. ↑ 1.0 1.1 Klaudia Kulczynska, James J. Bieker, Miroslawa Siatecka (12 February 2020). "A Krüppel-like factor 1 (KLF1) Mutation Associated with Severe Congenital Dyserythropoietic Anemia Alters Its DNA-Binding Specificity". Molecular and Cellular Biology. 40 (5): e00444–19. doi:10.1128/MCB.00444-19. PMID 31818881. |access-date= requires |url= (help)
  2. ↑

External links

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