Auxin response factor gene transcriptions: Difference between revisions

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Negative strand, positive direction: 5'-ACCTTTGGTG-3' at 3949, 5'-TCCTCTGGCC-3' at 2985, 5'-GCCTCTGGCT-3' at 2885, 5'-GAGGCTGGTG-3' at 2812, 5'-GCCGCCGGTG-3' at 1761, 5'-GAGGCCGTTC-3' at 1489, 5'-GAGGCCGTTC-3' at 1389, 5'-TCCTTCGGCC-3' at 764, 5'-GTGTCTGGAG-3' at 272, 5'-TTCTTTGTAT-3' at 114, and complements.
Negative strand, positive direction: 5'-ACCTTTGGTG-3' at 3949, 5'-TCCTCTGGCC-3' at 2985, 5'-GCCTCTGGCT-3' at 2885, 5'-GAGGCTGGTG-3' at 2812, 5'-GCCGCCGGTG-3' at 1761, 5'-GAGGCCGTTC-3' at 1489, 5'-GAGGCCGTTC-3' at 1389, 5'-TCCTTCGGCC-3' at 764, 5'-GTGTCTGGAG-3' at 272, 5'-TTCTTTGTAT-3' at 114, and complements.


===TGTCTC (Ulmasov) ARFbs===
===Stigliani random dataset samplings===


====ARF core promoters====
# Stiglianir0: 0.
# Stiglianir1: 0.
# Stiglianir2: 0.
# Stiglianir3: 0.
# Stiglianir4: 0.
# Stiglianir5: 0.
# Stiglianir6: 0.
# Stiglianir7: 0.
# Stiglianir8: 0.
# Stiglianir9: 0.
# Stiglianir0ci: 0.
# Stiglianir1ci: 0.
# Stiglianir2ci: 0.
# Stiglianir3ci: 0.
# Stiglianir4ci: 0.
# Stiglianir5ci: 0.
# Stiglianir6ci: 0.
# Stiglianir7ci: 0.
# Stiglianir8ci: 0.
# Stiglianir9ci: 0.
 
===Stiglianir UTRs===
{{main|UTR promoter gene transcriptions}}
 
===Stiglianir core promoters===
{{main|Core promoter gene transcriptions}}
 
===Stiglianir proximal promoters===
{{main|Proximal promoter gene transcriptions}}
 
===Stiglianir distal promoters===
{{main|Distal promoter gene transcriptions}}
 
==TGTCTC (Ulmasov) ARFbs samplings==
 
===Ulmasov random dataset samplings===
 
# Ulmasovr0: 0.
# Ulmasovr1: 0.
# Ulmasovr2: 0.
# Ulmasovr3: 0.
# Ulmasovr4: 0.
# Ulmasovr5: 0.
# Ulmasovr6: 0.
# Ulmasovr7: 0.
# Ulmasovr8: 0.
# Ulmasovr9: 0.
# Ulmasovr0ci: 0.
# Ulmasovr1ci: 0.
# Ulmasovr2ci: 0.
# Ulmasovr3ci: 0.
# Ulmasovr4ci: 0.
# Ulmasovr5ci: 0.
# Ulmasovr6ci: 0.
# Ulmasovr7ci: 0.
# Ulmasovr8ci: 0.
# Ulmasovr9ci: 0.
 
===Ulmasovr UTRs===
{{main|UTR promoter gene transcriptions}}
 
===Ulmasovr core promoters===
{{main|Core promoter gene transcriptions}}
 
===Ulmasovr proximal promoters===
{{main|Proximal promoter gene transcriptions}}
 
===Ulmasovr distal promoters===
{{main|Distal promoter gene transcriptions}}
 
===ARF core promoters===


Negative strand, negative direction: 5'-TGTCTC-3' at 4519, and complement.
Negative strand, negative direction: 5'-TGTCTC-3' at 4519, and complement.


====ARF proximal promoters====
===ARF proximal promoters===


Positive strand, negative direction: 5'-CC<u>TGTCTC</u>AA-3' at 4374, and complement.
Positive strand, negative direction: 5'-CC<u>TGTCTC</u>AA-3' at 4374, and complement.


====ARF distal promoters====
===ARF distal promoters===


Negative strand, negative direction: 5'-TGTCTC-3' at 3673, 5'-TGTCTC-3' at 2779, 5'-TGTCTC-3' at 2444, 5'-GAGACA-3' at 2029, 5'-TGTCTC-3' at 2018, 5'-GAGACA-3' at 1452, 5'-GAGACA-3' at 1085, 5'-TGTCTC-3' at 1074, 5'-GAGACA-3' at 919, 5'-TGTCTC-3' at 908, and complements.
Negative strand, negative direction: 5'-TGTCTC-3' at 3673, 5'-TGTCTC-3' at 2779, 5'-TGTCTC-3' at 2444, 5'-GAGACA-3' at 2029, 5'-TGTCTC-3' at 2018, 5'-GAGACA-3' at 1452, 5'-GAGACA-3' at 1085, 5'-TGTCTC-3' at 1074, 5'-GAGACA-3' at 919, 5'-TGTCTC-3' at 908, and complements.
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Positive strand, positive direction: 5'-TGTCTC-3' at 3180, 5'-TGTCTC-3' at 3134, 5'-TGTCTC-3' at 2653, 5'-GAGACA-3' at 2308, 5'-GAGACA-3' at 98, and complement.
Positive strand, positive direction: 5'-TGTCTC-3' at 3180, 5'-TGTCTC-3' at 3134, 5'-TGTCTC-3' at 2653, 5'-GAGACA-3' at 2308, 5'-GAGACA-3' at 98, and complement.


===TGTCGG (Boer) ARFbs===
==TGTCGG (Boer) ARFbs samplings==


Negative strand, negative direction: 5'-TGTCGG-3' at 3727, and complement.
Negative strand, negative direction: 5'-TGTCGG-3' at 3727, and complement.
Line 160: Line 230:


Positive strand, positive direction: 5'-TGTCGG-3' at 3896, 5'-CCGACA-3' at 3640, 5'-CCGACA-3' at 3349, 5'-TGTCGG-3' at 3101, 5'-CCGACA-3' at 264, 5'-TGTCGG-3' at 65, and complements.
Positive strand, positive direction: 5'-TGTCGG-3' at 3896, 5'-CCGACA-3' at 3640, 5'-CCGACA-3' at 3349, 5'-TGTCGG-3' at 3101, 5'-CCGACA-3' at 264, 5'-TGTCGG-3' at 65, and complements.
===Boer random dataset samplings===
# Boerr0: 0.
# Boerr1: 0.
# Boerr2: 0.
# Boerr3: 0.
# Boerr4: 0.
# Boerr5: 0.
# Boerr6: 0.
# Boerr7: 0.
# Boerr8: 0.
# Boerr9: 0.
# Boerr0ci: 0.
# Boerr1ci: 0.
# Boerr2ci: 0.
# Boerr3ci: 0.
# Boerr4ci: 0.
# Boerr5ci: 0.
# Boerr6ci: 0.
# Boerr7ci: 0.
# Boerr8ci: 0.
# Boerr9ci: 0.
===Boerr UTRs===
{{main|UTR promoter gene transcriptions}}
===Boerr core promoters===
{{main|Core promoter gene transcriptions}}
===Boerr proximal promoters===
{{main|Proximal promoter gene transcriptions}}
===Boerr distal promoters===
{{main|Distal promoter gene transcriptions}}


==Acknowledgements==
==Acknowledgements==

Revision as of 16:49, 10 May 2021

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

The "genome binding of two [auxin response factors] ARFs (ARF2 and ARF5/Monopteros [MP]) differ largely because these two factors have different preferred ARF binding site (ARFbs) arrangements (orientation and spacing)."[1] "ARFbs were originally defined as TGTCTC (Ulmasov et al., 1995, Guilfoyle et al., 1998), [...]. More recently, protein binding microarray (PBM) experiments suggested that TGTCGG are preferred ARFbs, [...] (Boer et al., 2014, Franco-Zorrilla et al., 2014, Liao et al., 2015)."[1]

Human genes

Main article: Human genes

Gene ID: 84514 is GHDC GH3 domain containing on 17q21.2.

  1. NP_001136095.1 GH3 domain-containing protein isoform 3 precursor: "Transcript Variant: This variant (3) uses an alternate splice site, resulting in a frameshifted and alternate 3' coding region, compared to variant 1. The encoded isoform (3) has a shorter and distinct C-terminus, compared to isoform 1."[2] Conserved Domains (2) summary: cl21606, Location:249 → 410, PLN02247; indole-3-acetic acid-amido synthetase, pfam03321, Location:54 → 420, GH3; GH3 auxin-responsive promoter.[2]
  2. NP_115873.1 GH3 domain-containing protein isoform 1 precursor: "Transcript Variant: This variant (1) encodes the longer isoform (1)."[2] Conserved Domains (2) summary: cl21606, Location:89 → 530, PLN02247; indole-3-acetic acid-amido synthetase, pfam03321, Location:54 → 490, GH3; GH3 auxin-responsive promoter.[2]

Gene ID: 153201 is SLC36A2 solute carrier family 36 member 2 on 5q33.1: "This gene encodes a pH-dependent proton-coupled amino acid transporter that belongs to the amino acid auxin permease 1 protein family. The encoded protein primarily transports small amino acids such as glycine, alanine and proline. Mutations in this gene are associated with iminoglycinuria and hyperglycinuria."[3]

Gene ID: 206358 is SLC36A1 solute carrier family 36 member 1 on 5q33.1: "This gene encodes a member of the eukaryote-specific amino acid/auxin permease (AAAP) 1 transporter family. The encoded protein functions as a proton-dependent, small amino acid transporter. This gene is clustered with related family members on chromosome 5q33.1. Alternative splicing results in multiple transcript variants."[4]

Gene expressions

Main article: Gene expressions

Interactions

Main article: Interaction gene transcriptions

Consensus sequences

Main article: Consensus sequence gene transcriptions

A more general consensus sequence may be 1(C/G/T)-2N-3(G/T)-4G-5(C/T)-6(C/T)-7N-8N-9N-10N, where ARF2[b] is 1(C/G/T)-2(A/C/T)-3(G/T)-4G-5(C/T)-6(C/T)-7(G/T)-8(C/G)-9(A/C/T)-10(A/G/T) and ARF5/MP[b] is 1(C/G/T)-2N-3(G/T)-4G-5T-6C-7(G/T)-8N-9-10N.[1] ARF1[b] has 4G.[1]

Binding site for

Inverse copies

Enhancer activity

Promoter occurrences

Hypotheses

Main article: Hypotheses
  1. A1BG has no Auxin response factors in either promoter.
  2. A1BG is not transcribed by an Auxin response factor.
  3. Auxin response factor does not participate in the transcription of A1BG.

ARF (Stigliani) samplings

Main article: Model samplings

Copying an auxin response factor consensus sequence 5'-TGTCGG-3' and putting the sequence in "⌘F" finds no location between ZNF497 and A1BG or one location between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence 5'-(C/G/T)(A/C/T)(G/T)G(C/T)(C/T)(G/T)(C/G)(A/C/T)(A/G/T)-3' (starting with SuccessablesARF.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'-(C/G/T)(A/C/T)(G/T)G(C/T)(C/T)(G/T)(C/G)(A/C/T)(A/G/T)-3', 12, 5'-CAGGTTTCTG-3' at 4506, 5'-TCGGTCTGCA-3' at 4236, 5'-TAGGTCGGTA-3' at 3685, 5'-TTTGTCTGTA-3' at 2881, 5'-TTTGTTTGTT-3' at 2488, 5'-GAGGCCTCCG-3' at 2358, 5'-TATGTCTGTA-3' at 1570, 5'-CTTGCTTCCG-3' at 1557, 5'-TTTGTTTGTT-3' at 1392, 5'-GAGGTCGGAG-3' at 1064, 5'-TTTGTCTGTA-3' at 171, 5'-CTGGTCGGTA-3' at 38, and complements.
  2. negative strand, positive direction, looking for 5'-(C/G/T)(A/C/T)(G/T)G(C/T)(C/T)(G/T)(C/G)(A/C/T)(A/G/T)-3', 23, 5'-GAGGCCTCCT-3' at 4407, 5'-GAGGCCTCAG-3' at 4194, 5'-CAGGTCTCAG-3' at 3774, 5'-CTGGCCTCCA-3' at 3685, 5'-CATGTTTGCA-3' at 3341, 5'-CTGGTCTCCT-3' at 3302, 5'-GTTGTCTCTT-3' at 3056, 5'-CAGGCCTCAG-3' at 3040, 5'-CTTGTCTGAG-3' at 3007, 5'-CTGGCTGCCT-3' at 2889, 5'-CAGGCCTCTG-3' at 2882, 5'-GAGGCTGGTG-3' at 2812, 5'-GATGTTGCAG-3' at 2720, 5'-CCTGCCTCAG-3' at 2525, 5'-CATGTTGCCT-3' at 2479, 5'-CAGGCTGGAG-3' at 2322, 5'-TCTGTTTCAT-3' at 2265, 5'-TAGGTCTGTT-3' at 2261, 5'-TCTGTTGGCA-3' at 2187, 5'-GCTGTCTGCT-3' at 1734, 5'-GCGGCCTGAA-3' at 726, 5'-CTTGCTGCAG-3' at 532, 5'-GCTGCCGGTG-3' at 486, and complements.
  3. positive strand, negative direction, looking for 5'-(C/G/T)(A/C/T)(G/T)G(C/T)(C/T)(G/T)(C/G)(A/C/T)(A/G/T)-3', 17, 5'-CCTGTCTCAA-3' at 4374, 5'-CATGCCTGTA-3' at 4122, 5'-CAGGCTTGAG-3' at 3402, 5'-TCTGTCTCAA-3' at 3324, 5'-GAGGTTGCTG-3' at 3264, 5'-CATGCCTGTA-3' at 2673, 5'-CATGCCTGTA-3' at 2539, 5'-GAGGTTGCAG-3' at 2401, 5'-CATGCTGGTG-3' at 2328, 5'-GTGGCTGGAG-3' at 2071, 5'-TCTGTCTCAA-3' at 2034, 5'-CTTGCCTGAA-3' at 1624, 5'-CAGGCTGGAG-3' at 1466, 5'-GAGGTTGCAG-3' at 1322, 5'-TCTGTCTCAA-3' at 1090, 5'-GAGGTTGCAG-3' at 1031, 5'-TCTGTCTCAA-3' at 924, and complements.
  4. positive strand, positive direction, looking for 5'-(C/G/T)(A/C/T)(G/T)G(C/T)(C/T)(G/T)(C/G)(A/C/T)(A/G/T)-3', 5, 5'-CCTGTTTGTG-3' at 4257, 5'-GTGGCCGGTG-3' at 1850, 5'-GAGGTTGGAT-3' at 1282, 5'-GAGGTTGGAG-3' at 610, 5'-CCGGTCGCCG-3' at 332, and complements.
  5. complement, negative strand, negative direction, looking for 5'-(A/C/G)(A/G/T)(A/C)C(A/G)(A/G)(A/C)(C/G)(A/G/T)(A/C/T)-3', 17, 5'-GGACAGAGTT-3' at 4374, 5'-GTACGGACAT-3' at 4122, 5'-GTCCGAACTC-3' at 3402, 5'-AGACAGAGTT-3' at 3324, 5'-CTCCAACGAC-3' at 3264, 5'-GTACGGACAT-3' at 2673, 5'-GTACGGACAT-3' at 2539, 5'-CTCCAACGTC-3' at 2401, 5'-GTACGACCAC-3' at 2328, 5'-CACCGACCTC-3' at 2071, 5'-AGACAGAGTT-3' at 2034, 5'-GAACGGACTT-3' at 1624, 5'-GTCCGACCTC-3' at 1466, 5'-CTCCAACGTC-3' at 1322, 5'-AGACAGAGTT-3' at 1090, 5'-CTCCAACGTC-3' at 1031, 5'-AGACAGAGTT-3' at 924.
  6. complement, negative strand, positive direction, looking for 5'-(A/C/G)(A/G/T)(A/C)C(A/G)(A/G)(A/C)(C/G)(A/G/T)(A/C/T)-3', 5, 5'-GGACAAACAC-3' at 4257, 5'-CACCGGCCAC-3' at 1850, 5'-CTCCAACCTA-3' at 1282, 5'-CTCCAACCTC-3' at 610, 5'-GGCCAGCGGC-3' at 332.
  7. complement, positive strand, negative direction, looking for 5'-(A/C/G)(A/G/T)(A/C)C(A/G)(A/G)(A/C)(C/G)(A/G/T)(A/C/T)-3', 12, 5'-GTCCAAAGAC-3' at 4506, 5'-AGCCAGACGT-3' at 4236, 5'-ATCCAGCCAT-3' at 3685, 5'-AAACAGACAT-3' at 2881, 5'-AAACAAACAA-3' at 2488, 5'-CTCCGGAGGC-3' at 2358, 5'-ATACAGACAT-3' at 1570, 5'-GAACGAAGGC-3' at 1557, 5'-AAACAAACAA-3' at 1392, 5'-CTCCAGCCTC-3' at 1064, 5'-AAACAGACAT-3' at 171, 5'-GACCAGCCAT-3' at 38.
  8. complement, positive strand, positive direction, looking for 5'-(A/C/G)(A/G/T)(A/C)C(A/G)(A/G)(A/C)(C/G)(A/G/T)(A/C/T)-3', 23, 5'-CTCCGGAGGA-3' at 4407, 5'-CTCCGGAGTC-3' at 4194, 5'-GTCCAGAGTC-3' at 3774, 5'-GACCGGAGGT-3' at 3685, 5'-GTACAAACGT-3' at 3341, 5'-GACCAGAGGA-3' at 3302, 5'-CAACAGAGAA-3' at 3056, 5'-GTCCGGAGTC-3' at 3040, 5'-GAACAGACTC-3' at 3007, 5'-GACCGACGGA-3' at 2889, 5'-GTCCGGAGAC-3' at 2882, 5'-CTCCGACCAC-3' at 2812, 5'-CTACAACGTC-3' at 2720, 5'-GGACGGAGTC-3' at 2525, 5'-GTACAACGGA-3' at 2479, 5'-GTCCGACCTC-3' at 2322, 5'-AGACAAAGTA-3' at 2265, 5'-ATCCAGACAA-3' at 2261, 5'-AGACAACCGT-3' at 2187, 5'-CGACAGACGA-3' at 1734, 5'-CGCCGGACTT-3' at 726, 5'-GAACGACGTC-3' at 532, 5'-CGACGGCCAC-3' at 486.
  9. inverse complement, negative strand, negative direction, looking for 5'-(A/C/T)(A/G/T)(C/G)(A/C)(A/G)(A/G)C(A/C)(A/G/T)(A/C/G)-3', 8, 5'-AACCAACCGG-3' at 3948, 5'-TACAGACCTC-3' at 3837, 5'-ATGAGGCCTC-3' at 2356, 5'-CACCGACCTC-3' at 2071, 5'-CTGAGACAGA-3' at 2031, 5'-TACCGACCTC-3' at 1748, 5'-CTGAGACAGA-3' at 1087, 5'-CTGAGACAGA-3' at 921.
  10. inverse complement, negative strand, positive direction, looking for 5'-(A/C/T)(A/G/T)(C/G)(A/C)(A/G)(A/G)C(A/C)(A/G/T)(A/C/G)-3', 33, 5'-CTGAGGCCTC-3' at 4192, 5'-CACCAGCAGC-3' at 3723, 5'-AGGCAGCAGG-3' at 3694, 5'-CAGAAGCCAG-3' at 3220, 5'-ATGCAGCAGG-3' at 3147, 5'-TTCAGGCCTC-3' at 3038, 5'-TGCAGACCTC-3' at 2863, 5'-TTCAAACAGA-3' at 2652, 5'-TAGAAACCAC-3' at 2633, 5'-TTGCAGCCGC-3' at 2355, 5'-ATGAAACCGC-3' at 2150, 5'-AGGCAACCAC-3' at 2122, 5'-CTCAGGCAAC-3' at 2119, 5'-AAGCAGCCAA-3' at 2011, 5'-CTCCGACAGG-3' at 1966, 5'-CACCGGCCAC-3' at 1850, 5'-TTGCAACCTC-3' at 1618, 5'-CTGCAGCAAG-3' at 1510, 5'-ATGCGGCAAG-3' at 1426, 5'-ATGCGGCAAG-3' at 1326, 5'-CTCCAACCTA-3' at 1282, 5'-CTGCGGCAGC-3' at 1037, 5'-CTGCGGCAAG-3' at 1006, 5'-CTCCAACCTG-3' at 946, 5'-CTCCAACCTG-3' at 846, 5'-CTGCGGCAAG-3' at 754, 5'-CAGCGGCCTG-3' at 724, 5'-CTCCAACCTC-3' at 610, 5'-CTGCAGCATC-3' at 536, 5'-TGCAGACCGG-3' at 442, 5'-AGCAAGCCAC-3' at 342, 5'-CGGCAGCAAG-3' at 338, 5'-CAGCGGCAGC-3' at 335.
  11. inverse complement, positive strand, negative direction, looking for 5'-(A/C/T)(A/G/T)(C/G)(A/C)(A/G)(A/G)C(A/C)(A/G/T)(A/C/G)-3', 33, 5'-CTCCAGCCTG-3' at 4348, 5'-CTGAGGCAGG-3' at 4282, 5'-AGGCAGCATC-3' at 3902, 5'-AAGAGGCAGC-3' at 3899, 5'-CTCAAGCAAC-3' at 3848, 5'-CTCCAGCCTG-3' at 3297, 5'-TGGAGACCAG-3' at 3123, 5'-CTGAGGCAGG-3' at 2568, 5'-AACAGGCCAG-3' at 2518, 5'-AACAAACAGG-3' at 2514, 5'-AACAAACAAA-3' at 2489, 5'-AGCAAACAAA-3' at 2485, 5'-CTCCAGCCTG-3' at 2434, 5'-CTGAGGCAGG-3' at 2367, 5'-TTGAGACCAG-3' at 2263, 5'-TTGAGACCAA-3' at 2147, 5'-TGGAGGCCAG-3' at 2076, 5'-CTCCAGCCTG-3' at 2008, 5'-CTGAGGCAGG-3' at 1941, 5'-TGCCAGCAGA-3' at 1614, 5'-AACAAACCTA-3' at 1590, 5'-ATGAAACAAA-3' at 1586, 5'-TACAGACATC-3' at 1571, 5'-AACAAACAAA-3' at 1393, 5'-AGGAGGCAGA-3' at 1314, 5'-CTGAGGCAGG-3' at 1288, 5'-TTGCGACCAG-3' at 1193, 5'-CTCCAGCCTC-3' at 1064, 5'-CTGAGGCAGG-3' at 997, 5'-CTCCAGCCTG-3' at 898, 5'-CTGAGGCAGG-3' at 831, 5'-AGCCAGCCTG-3' at 507, 5'-AAGAGGCCGG-3' at 374.
  12. inverse complement, positive strand, positive direction, looking for 5'-(A/C/T)(A/G/T)(C/G)(A/C)(A/G)(A/G)C(A/C)(A/G/T)(A/C/G)-3', 10, 5'-TGGAAACCAC-3' at 3949, 5'-AGGAGACCGG-3' at 2985, 5'-CGGAGACCGA-3' at 2885, 5'-CTCCGACCAC-3' at 2812, 5'-CGGCGGCCAC-3' at 1761, 5'-CTCCGGCAAG-3' at 1489, 5'-CTCCGGCAAG-3' at 1389, 5'-AGGAAGCCGG-3' at 764, 5'-CACAGACCTC-3' at 272, 5'-AAGAAACATA-3' at 114.
  13. inverse negative strand, negative direction, looking for 5'-(A/G/T)(A/C/T)(C/G)(G/T)(C/T)(C/T)G(G/T)(A/C/T)(C/G/T)-3', 33, 5'-GAGGTCGGAC-3' at 4348, 5'-GACTCCGTCC-3' at 4282, 5'-TCCGTCGTAG-3' at 3902, 5'-TTCTCCGTCG-3' at 3899, 5'-GAGTTCGTTG-3' at 3848, 5'-GAGGTCGGAC-3' at 3297, 5'-ACCTCTGGTC-3' at 3123, 5'-GACTCCGTCC-3' at 2568, 5'-TTGTCCGGTC-3' at 2518, 5'-TTGTTTGTCC-3' at 2514, 5'-TTGTTTGTTT-3' at 2489, 5'-TCGTTTGTTT-3' at 2485, 5'-GAGGTCGGAC-3' at 2434, 5'-GACTCCGTCC-3' at 2367, 5'-AACTCTGGTC-3' at 2263, 5'-AACTCTGGTT-3' at 2147, 5'-ACCTCCGGTC-3' at 2076, 5'-GAGGTCGGAC-3' at 2008, 5'-GACTCCGTCC-3' at 1941, 5'-ACGGTCGTCT-3' at 1614, 5'-TTGTTTGGAT-3' at 1590, 5'-TACTTTGTTT-3' at 1586, 5'-ATGTCTGTAG-3' at 1571, 5'-TTGTTTGTTT-3' at 1393, 5'-TCCTCCGTCT-3' at 1314, 5'-GACTCCGTCC-3' at 1288, 5'-AACGCTGGTC-3' at 1193, 5'-GAGGTCGGAG-3' at 1064, 5'-GACTCCGTCC-3' at 997, 5'-GAGGTCGGAC-3' at 898, 5'-GACTCCGTCC-3' at 831, 5'-TCGGTCGGAC-3' at 507, 5'-TTCTCCGGCC-3' at 374.
  14. inverse negative strand, positive direction, looking for 5'-(A/G/T)(A/C/T)(C/G)(G/T)(C/T)(C/T)G(G/T)(A/C/T)(C/G/T)-3', 10, 5'-ACCTTTGGTG-3' at 3949, 5'-TCCTCTGGCC-3' at 2985, 5'-GCCTCTGGCT-3' at 2885, 5'-GAGGCTGGTG-3' at 2812, 5'-GCCGCCGGTG-3' at 1761, 5'-GAGGCCGTTC-3' at 1489, 5'-GAGGCCGTTC-3' at 1389, 5'-TCCTTCGGCC-3' at 764, 5'-GTGTCTGGAG-3' at 272, 5'-TTCTTTGTAT-3' at 114.
  15. inverse positive strand, negative direction, looking for 5'-(A/G/T)(A/C/T)(C/G)(G/T)(C/T)(C/T)G(G/T)(A/C/T)(C/G/T)-3', 8, 5'-TTGGTTGGCC-3' at 3948, 5'-ATGTCTGGAG-3' at 3837, 5'-TACTCCGGAG-3' at 2356, 5'-GTGGCTGGAG-3' at 2071, 5'-GACTCTGTCT-3' at 2031, 5'-ATGGCTGGAG-3' at 1748, 5'-GACTCTGTCT-3' at 1087, 5'-GACTCTGTCT-3' at 921.
  16. inverse positive strand, positive direction, looking for 5'-(A/G/T)(A/C/T)(C/G)(G/T)(C/T)(C/T)G(G/T)(A/C/T)(C/G/T)-3', 33, 5'-GACTCCGGAG-3' at 4192, 5'-GTGGTCGTCG-3' at 3723, 5'-TCCGTCGTCC-3' at 3694, 5'-GTCTTCGGTC-3' at 3220, 5'-TACGTCGTCC-3' at 3147, 5'-AAGTCCGGAG-3' at 3038, 5'-ACGTCTGGAG-3' at 2863, 5'-AAGTTTGTCT-3' at 2652, 5'-ATCTTTGGTG-3' at 2633, 5'-AACGTCGGCG-3' at 2355, 5'-TACTTTGGCG-3' at 2150, 5'-TCCGTTGGTG-3' at 2122, 5'-GAGTCCGTTG-3' at 2119, 5'-TTCGTCGGTT-3' at 2011, 5'-GAGGCTGTCC-3' at 1966, 5'-GTGGCCGGTG-3' at 1850, 5'-AACGTTGGAG-3' at 1618, 5'-GACGTCGTTC-3' at 1510, 5'-TACGCCGTTC-3' at 1426, 5'-TACGCCGTTC-3' at 1326, 5'-GAGGTTGGAT-3' at 1282, 5'-GACGCCGTCG-3' at 1037, 5'-GACGCCGTTC-3' at 1006, 5'-GAGGTTGGAC-3' at 946, 5'-GAGGTTGGAC-3' at 846, 5'-GACGCCGTTC-3' at 754, 5'-GTCGCCGGAC-3' at 724, 5'-GAGGTTGGAG-3' at 610, 5'-GACGTCGTAG-3' at 536, 5'-ACGTCTGGCC-3' at 442, 5'-TCGTTCGGTG-3' at 342, 5'-GCCGTCGTTC-3' at 338, 5'-GTCGCCGTCG-3' at 335.

ARF core promoters

Main article: Core promoter gene transcriptions

Negative strand, negative direction: 5'-CAGGTTTCTG-3' at 4506, and complement.

Positive strand, negative direction: 5'-CCTGTCTCAA-3' at 4374, and complement.

Negative strand, positive direction: 5'-GAGGCCTCCT-3' at 4407, and complement.

ARF proximal promoters

Main article: Proximal promoter gene transcriptions

Negative strand, negative direction: 5'-TCGGTCTGCA-3' at 4236, and complement.

Positive strand, negative direction: 5'-CCTGTCTCAA-3' at 4374, 5'-CTCCAGCCTG-3' at 4348, and complements.

Positive strand, negative direction: 5'-CTGAGGCAGG-3' at 4282, and complement.

Negative strand, positive direction: 5'-CTGAGGCCTC-3' at 4192, and complement.

Negative strand, positive direction: 5'-GAGGCCTCAG-3' at 4194, and complement.

Positive strand, positive direction: 5'-CCTGTTTGTG-3' at 4257, and complement.

ARF distal promoters

Main article: Distal promoter gene transcriptions

Negative strand, negative direction: 5'-TAGGTCGGTA-3' at 3685, 5'-TTTGTCTGTA-3' at 2881, 5'-TTTGTTTGTT-3' at 2488, 5'-GAGGCCTCCG-3' at 2358, 5'-TATGTCTGTA-3' at 1570, 5'-CTTGCTTCCG-3' at 1557, 5'-TTTGTTTGTT-3' at 1392, 5'-GAGGTCGGAG-3' at 1064, 5'-TTTGTCTGTA-3' at 171, 5'-CTGGTCGGTA-3' at 38, and complements.

Negative strand, negative direction: 5'-GTACGGACAT-3' at 4122, 5'-GTCCGAACTC-3' at 3402, 5'-AGACAGAGTT-3' at 3324, 5'-CTCCAACGAC-3' at 3264, 5'-GTACGGACAT-3' at 2673, 5'-GTACGGACAT-3' at 2539, 5'-CTCCAACGTC-3' at 2401, 5'-GTACGACCAC-3' at 2328, 5'-CACCGACCTC-3' at 2071, 5'-AGACAGAGTT-3' at 2034, 5'-GAACGGACTT-3' at 1624, 5'-GTCCGACCTC-3' at 1466, 5'-CTCCAACGTC-3' at 1322, 5'-AGACAGAGTT-3' at 1090, 5'-CTCCAACGTC-3' at 1031, 5'-AGACAGAGTT-3' at 924, and complements.

Negative strand, negative direction: 5'-AACCAACCGG-3' at 3948, 5'-TACAGACCTC-3' at 3837, 5'-ATGAGGCCTC-3' at 2356, 5'-CACCGACCTC-3' at 2071, 5'-CTGAGACAGA-3' at 2031, 5'-TACCGACCTC-3' at 1748, 5'-CTGAGACAGA-3' at 1087, 5'-CTGAGACAGA-3' at 921, and complements.

Negative strand, negative direction: 5'-TCCGTCGTAG-3' at 3902, 5'-TTCTCCGTCG-3' at 3899, 5'-GAGTTCGTTG-3' at 3848, 5'-GAGGTCGGAC-3' at 3297, 5'-ACCTCTGGTC-3' at 3123, 5'-GACTCCGTCC-3' at 2568, 5'-TTGTCCGGTC-3' at 2518, 5'-TTGTTTGTCC-3' at 2514, 5'-TTGTTTGTTT-3' at 2489, 5'-TCGTTTGTTT-3' at 2485, 5'-GAGGTCGGAC-3' at 2434, 5'-GACTCCGTCC-3' at 2367, 5'-AACTCTGGTC-3' at 2263, 5'-AACTCTGGTT-3' at 2147, 5'-ACCTCCGGTC-3' at 2076, 5'-GAGGTCGGAC-3' at 2008, 5'-GACTCCGTCC-3' at 1941, 5'-ACGGTCGTCT-3' at 1614, 5'-TTGTTTGGAT-3' at 1590, 5'-TACTTTGTTT-3' at 1586, 5'-ATGTCTGTAG-3' at 1571, 5'-TTGTTTGTTT-3' at 1393, 5'-TCCTCCGTCT-3' at 1314, 5'-GACTCCGTCC-3' at 1288, 5'-AACGCTGGTC-3' at 1193, 5'-GAGGTCGGAG-3' at 1064, 5'-GACTCCGTCC-3' at 997, 5'-GAGGTCGGAC-3' at 898, 5'-GACTCCGTCC-3' at 831, 5'-TCGGTCGGAC-3' at 507, 5'-TTCTCCGGCC-3' at 374, and complements.

Negative strand, positive direction: 5'-CAGGTCTCAG-3' at 3774, 5'-CTGGCCTCCA-3' at 3685, 5'-CATGTTTGCA-3' at 3341, 5'-CTGGTCTCCT-3' at 3302, 5'-GTTGTCTCTT-3' at 3056, 5'-CAGGCCTCAG-3' at 3040, 5'-CTTGTCTGAG-3' at 3007, 5'-CTGGCTGCCT-3' at 2889, 5'-CAGGCCTCTG-3' at 2882, 5'-GAGGCTGGTG-3' at 2812, 5'-GATGTTGCAG-3' at 2720, 5'-CCTGCCTCAG-3' at 2525, 5'-CATGTTGCCT-3' at 2479, 5'-CAGGCTGGAG-3' at 2322, 5'-TCTGTTTCAT-3' at 2265, 5'-TAGGTCTGTT-3' at 2261, 5'-TCTGTTGGCA-3' at 2187, 5'-GCTGTCTGCT-3' at 1734, 5'-GCGGCCTGAA-3' at 726, 5'-CTTGCTGCAG-3' at 532, 5'-GCTGCCGGTG-3' at 486, and complements.

Negative strand, positive direction: 5'-CACCGGCCAC-3' at 1850, 5'-CTCCAACCTA-3' at 1282, 5'-CTCCAACCTC-3' at 610, 5'-GGCCAGCGGC-3' at 332.

Negative strand, positive direction: 5'-CACCAGCAGC-3' at 3723, 5'-AGGCAGCAGG-3' at 3694, 5'-CAGAAGCCAG-3' at 3220, 5'-ATGCAGCAGG-3' at 3147, 5'-TTCAGGCCTC-3' at 3038, 5'-TGCAGACCTC-3' at 2863, 5'-TTCAAACAGA-3' at 2652, 5'-TAGAAACCAC-3' at 2633, 5'-TTGCAGCCGC-3' at 2355, 5'-ATGAAACCGC-3' at 2150, 5'-AGGCAACCAC-3' at 2122, 5'-CTCAGGCAAC-3' at 2119, 5'-AAGCAGCCAA-3' at 2011, 5'-CTCCGACAGG-3' at 1966, 5'-CACCGGCCAC-3' at 1850, 5'-TTGCAACCTC-3' at 1618, 5'-CTGCAGCAAG-3' at 1510, 5'-ATGCGGCAAG-3' at 1426, 5'-ATGCGGCAAG-3' at 1326, 5'-CTCCAACCTA-3' at 1282, 5'-CTGCGGCAGC-3' at 1037, 5'-CTGCGGCAAG-3' at 1006, 5'-CTCCAACCTG-3' at 946, 5'-CTCCAACCTG-3' at 846, 5'-CTGCGGCAAG-3' at 754, 5'-CAGCGGCCTG-3' at 724, 5'-CTCCAACCTC-3' at 610, 5'-CTGCAGCATC-3' at 536, 5'-TGCAGACCGG-3' at 442, 5'-AGCAAGCCAC-3' at 342, 5'-CGGCAGCAAG-3' at 338, 5'-CAGCGGCAGC-3' at 335, and complements.

Negative strand, positive direction: 5'-ACCTTTGGTG-3' at 3949, 5'-TCCTCTGGCC-3' at 2985, 5'-GCCTCTGGCT-3' at 2885, 5'-GAGGCTGGTG-3' at 2812, 5'-GCCGCCGGTG-3' at 1761, 5'-GAGGCCGTTC-3' at 1489, 5'-GAGGCCGTTC-3' at 1389, 5'-TCCTTCGGCC-3' at 764, 5'-GTGTCTGGAG-3' at 272, 5'-TTCTTTGTAT-3' at 114, and complements.

Stigliani random dataset samplings

  1. Stiglianir0: 0.
  2. Stiglianir1: 0.
  3. Stiglianir2: 0.
  4. Stiglianir3: 0.
  5. Stiglianir4: 0.
  6. Stiglianir5: 0.
  7. Stiglianir6: 0.
  8. Stiglianir7: 0.
  9. Stiglianir8: 0.
  10. Stiglianir9: 0.
  11. Stiglianir0ci: 0.
  12. Stiglianir1ci: 0.
  13. Stiglianir2ci: 0.
  14. Stiglianir3ci: 0.
  15. Stiglianir4ci: 0.
  16. Stiglianir5ci: 0.
  17. Stiglianir6ci: 0.
  18. Stiglianir7ci: 0.
  19. Stiglianir8ci: 0.
  20. Stiglianir9ci: 0.

Stiglianir UTRs

Main article: UTR promoter gene transcriptions

Stiglianir core promoters

Main article: Core promoter gene transcriptions

Stiglianir proximal promoters

Main article: Proximal promoter gene transcriptions

Stiglianir distal promoters

Main article: Distal promoter gene transcriptions

TGTCTC (Ulmasov) ARFbs samplings

Ulmasov random dataset samplings

  1. Ulmasovr0: 0.
  2. Ulmasovr1: 0.
  3. Ulmasovr2: 0.
  4. Ulmasovr3: 0.
  5. Ulmasovr4: 0.
  6. Ulmasovr5: 0.
  7. Ulmasovr6: 0.
  8. Ulmasovr7: 0.
  9. Ulmasovr8: 0.
  10. Ulmasovr9: 0.
  11. Ulmasovr0ci: 0.
  12. Ulmasovr1ci: 0.
  13. Ulmasovr2ci: 0.
  14. Ulmasovr3ci: 0.
  15. Ulmasovr4ci: 0.
  16. Ulmasovr5ci: 0.
  17. Ulmasovr6ci: 0.
  18. Ulmasovr7ci: 0.
  19. Ulmasovr8ci: 0.
  20. Ulmasovr9ci: 0.

Ulmasovr UTRs

Main article: UTR promoter gene transcriptions

Ulmasovr core promoters

Main article: Core promoter gene transcriptions

Ulmasovr proximal promoters

Main article: Proximal promoter gene transcriptions

Ulmasovr distal promoters

Main article: Distal promoter gene transcriptions

ARF core promoters

Negative strand, negative direction: 5'-TGTCTC-3' at 4519, and complement.

ARF proximal promoters

Positive strand, negative direction: 5'-CCTGTCTCAA-3' at 4374, and complement.

ARF distal promoters

Negative strand, negative direction: 5'-TGTCTC-3' at 3673, 5'-TGTCTC-3' at 2779, 5'-TGTCTC-3' at 2444, 5'-GAGACA-3' at 2029, 5'-TGTCTC-3' at 2018, 5'-GAGACA-3' at 1452, 5'-GAGACA-3' at 1085, 5'-TGTCTC-3' at 1074, 5'-GAGACA-3' at 919, 5'-TGTCTC-3' at 908, and complements.

Positive strand, negative direction: 5'-TCTGTCTCAA-3' at 3324, 5'-TGTCTC-3' at 2166, 5'-TCTGTCTCAA-3' at 2034, 5'-TCTGTCTCAA-3' at 1090, 5'-TCTGTCTCAA-3' at 924, and complements.

Negative strand, positive direction: 5'-GTTGTCTCTT-3' at 3056, 5'-TGTCTC-3' at 2467, 5'-TGTCTC-3' at 2173, 5'-TGTCTC-3' at 2079, 5'-GAGACA-3' at 712, and complements.

Positive strand, positive direction: 5'-TGTCTC-3' at 3180, 5'-TGTCTC-3' at 3134, 5'-TGTCTC-3' at 2653, 5'-GAGACA-3' at 2308, 5'-GAGACA-3' at 98, and complement.

TGTCGG (Boer) ARFbs samplings

Negative strand, negative direction: 5'-TGTCGG-3' at 3727, and complement.

Negative strand, positive direction: 5'-CCGACA-3' at 1964, and complement.

Positive strand, positive direction: 5'-TGTCGG-3' at 3896, 5'-CCGACA-3' at 3640, 5'-CCGACA-3' at 3349, 5'-TGTCGG-3' at 3101, 5'-CCGACA-3' at 264, 5'-TGTCGG-3' at 65, and complements.

Boer random dataset samplings

  1. Boerr0: 0.
  2. Boerr1: 0.
  3. Boerr2: 0.
  4. Boerr3: 0.
  5. Boerr4: 0.
  6. Boerr5: 0.
  7. Boerr6: 0.
  8. Boerr7: 0.
  9. Boerr8: 0.
  10. Boerr9: 0.
  11. Boerr0ci: 0.
  12. Boerr1ci: 0.
  13. Boerr2ci: 0.
  14. Boerr3ci: 0.
  15. Boerr4ci: 0.
  16. Boerr5ci: 0.
  17. Boerr6ci: 0.
  18. Boerr7ci: 0.
  19. Boerr8ci: 0.
  20. Boerr9ci: 0.

Boerr UTRs

Main article: UTR promoter gene transcriptions

Boerr core promoters

Main article: Core promoter gene transcriptions

Boerr proximal promoters

Main article: Proximal promoter gene transcriptions

Boerr distal promoters

Main article: Distal promoter gene transcriptions

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 Arnaud Stigliani, Raquel Martin-Arevalillo, Jérémy Lucas, Adrien Bessy, Thomas Vinos-Poyo, Victoria Mironova, Teva Vernoux, Renaud Dumas and François Parcy (3 June 2019). "Capturing Auxin Response Factors Syntax Using DNA Binding Models". Molecular Plant. 12 (6): 822–832. doi:10.1016/j.molp.2018.09.010. PMID 30336329. Retrieved 29 August 2020.
  2. ↑ 2.0 2.1 2.2 2.3 HGNC (8 November 2020). "GHDC GH3 domain containing [ Homo sapiens (human) ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 11 November 2020.
  3. ↑ RefSeq (September 2010). "SLC36A1 solute carrier family 36 member 1 [ Homo sapiens (human) ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 11 November 2020.
  4. ↑ RefSeq (April 2015). "SLC36A1 solute carrier family 36 member 1 [ Homo sapiens (human) ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 11 November 2020.

External links

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