Auxin response factor gene transcriptions: Difference between revisions

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# Stiglianir2: 9, TTGGTCTGTT at 2965, GTTGTTGGTG at 2867, GTTGTCTGCA at 2538, GTGGTTTCTT at 2465, GCTGCTGCCA at 1569, GCTGCTGCTG at 1566, TCTGTCTCCA at 1318, CCTGTTTCCG at 1101, GTGGTTTCAT at 1059.
# Stiglianir2: 9, TTGGTCTGTT at 2965, GTTGTTGGTG at 2867, GTTGTCTGCA at 2538, GTGGTTTCTT at 2465, GCTGCTGCCA at 1569, GCTGCTGCTG at 1566, TCTGTCTCCA at 1318, CCTGTTTCCG at 1101, GTGGTTTCAT at 1059.
# Stiglianir3: 13, TTGGTTGGCG at 4110, CAGGTTTCCA at 3591, TCTGTTGGTT at 3550, TCGGTCTCAT at 3469, CTTGTTTCAT at 2786, CTGGCTTGAA at 2515, GTTGTTTGTT at 2269, CCGGTTGCTT at 2038, TTTGTTTCCT at 1032, TTTGCCTCCA at 933, CCGGCCTGAA at 873, GTGGTCGGCG at 647, GCGGTCTGTG at 511.
# Stiglianir3: 13, TTGGTTGGCG at 4110, CAGGTTTCCA at 3591, TCTGTTGGTT at 3550, TCGGTCTCAT at 3469, CTTGTTTCAT at 2786, CTGGCTTGAA at 2515, GTTGTTTGTT at 2269, CCGGTTGCTT at 2038, TTTGTTTCCT at 1032, TTTGCCTCCA at 933, CCGGCCTGAA at 873, GTGGTCGGCG at 647, GCGGTCTGTG at 511.
# Stiglianir4: 0.
# Stiglianir4: 11, TCGGTTGGCT at 4248, GAGGTTGCAG at 3364, TTTGTTGGAA at 2262, GCGGTTTCTA at 2123, CCTGTCGGTA at 2030, GCGGCTTCTA at 1587, GATGCTGCCT at 1401, GATGCTGGTG at 1294, GTGGCTTCTG at 964, CCTGTTGCCG at 806, CAGGTTTCCT at 251.
# Stiglianir5: 0.
# Stiglianir5: 11, CTGGCCGCTT at 4440, TATGCTTGAT at 4193, TATGTTGGCA at 4175, TTTGCTGGAG at 4144, TTGGTTTGAA at 3272, CCTGCTTCAA at 2916, GAGGTTTCAA at 1883, CATGCTTCCA at 1669, GTGGTTTCAT at 935, CATGTTTCTA at 147, CCTGTTGGAA at 26.
# Stiglianir6: 0.
# Stiglianir6: 10, TTTGTTGCTT at 4537, TTGGTTTGTT at 4533, GTGGTTTCTG at 4482, CCTGTTTGTG at 4364, GATGCTTGTT at 4162, TTTGCTTCTA at 3481, TTTGCCTGCG at 2085, TTTGTTGCCT at 1707, CATGTTGGTG at 1551, TATGTTTGTA at 912.
# Stiglianir7: 0.
# Stiglianir7: 15, GATGTTGCAG at 4175, TTTGCTTCCT at 4127, GATGTCTGCG at 4007, GTTGCCTCCG at 3838, TTGGTTTGAT at 3730, TATGCCGGCA at 3499, TTGGCCGGAT at 3303, TCTGTTGCCG at 3129, TTGGTCTGTT at 3125, GTTGTTGGAA at 2943, TCGGTTGGAG at 2526, CATGCCTGTT at 2197, GATGCCGCCT at 1771, CAGGCCTGCT at 1761, GTGGCCGCAA at 658.
# Stiglianir8: 0.
# Stiglianir8: 10, GCGGTTGGAA at 3165, TTTGCTTCTA at 3067, GTTGCCTCCG at 2487, CAGGTTGCCT at 2484, GTTGTTTCTA at 2385, CTTGTCTGCA at 2038, GCTGCCGGAG at 684, CCGGTTTCAG at 370, TAGGCTTCTA at 263, TTTGCCGGTT at 51.
# Stiglianir9: 0.
# Stiglianir9: 16, GTGGCTGCAG at 4364, GCTGCCGCTA at 4311, GAGGCCGGTT at 3984, CTGGTTGGAG at 2978, GTGGTTTGCA at 2709, CAGGTCTGCG at 2651, CATGTCGCTT at 1853, GTTGTTTCTG at 1737, TTTGTCGGTA at 1273, CTGGCTGGTA at 1214, TCTGCTGGCG at 1141, TTTGCCTCCG at 1038, TTTGCTTCTG at 713, CTGGCTTGCA at 492, CTGGTTTGTT at 95, TTTGTCTCTT at 27.
# Stiglianir0ci: 0.
# Stiglianir0ci: 0.
# Stiglianir1ci: 0.
# Stiglianir1ci: 0.

Revision as of 03:23, 11 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: 10, GAGGTTTCTA at 4222, TTTGTTTGAA at 4182, CATGCTTCAT at 4097, TCTGCCGGCG at 4079, GCGGCTTGCA at 3552, CTGGCCGCCA at 3408, CCTGCTTCAA at 3336, CCTGCCTCTA at 2717, CCGGTTTGAA at 1690, TAGGTCGGCA at 1420.
  2. Stiglianir1: 13, CTGGCTTGAA at 4190, GTGGTCGCTT at 4158, TTTGCTTGCA at 4106, CTGGCCGGCA at 3710, GTGGTCGGTG at 3006, CAGGTTTCCG at 2814, CTTGTTTCCT at 2165, TCGGTTTGCA at 1979, GATGTCGCAA at 1454, GTGGTCGCAA at 581, TCGGCCTCCA at 517, CAGGCCTGAT at 450, TTTGTCTGCG at 10.
  3. Stiglianir2: 9, TTGGTCTGTT at 2965, GTTGTTGGTG at 2867, GTTGTCTGCA at 2538, GTGGTTTCTT at 2465, GCTGCTGCCA at 1569, GCTGCTGCTG at 1566, TCTGTCTCCA at 1318, CCTGTTTCCG at 1101, GTGGTTTCAT at 1059.
  4. Stiglianir3: 13, TTGGTTGGCG at 4110, CAGGTTTCCA at 3591, TCTGTTGGTT at 3550, TCGGTCTCAT at 3469, CTTGTTTCAT at 2786, CTGGCTTGAA at 2515, GTTGTTTGTT at 2269, CCGGTTGCTT at 2038, TTTGTTTCCT at 1032, TTTGCCTCCA at 933, CCGGCCTGAA at 873, GTGGTCGGCG at 647, GCGGTCTGTG at 511.
  5. Stiglianir4: 11, TCGGTTGGCT at 4248, GAGGTTGCAG at 3364, TTTGTTGGAA at 2262, GCGGTTTCTA at 2123, CCTGTCGGTA at 2030, GCGGCTTCTA at 1587, GATGCTGCCT at 1401, GATGCTGGTG at 1294, GTGGCTTCTG at 964, CCTGTTGCCG at 806, CAGGTTTCCT at 251.
  6. Stiglianir5: 11, CTGGCCGCTT at 4440, TATGCTTGAT at 4193, TATGTTGGCA at 4175, TTTGCTGGAG at 4144, TTGGTTTGAA at 3272, CCTGCTTCAA at 2916, GAGGTTTCAA at 1883, CATGCTTCCA at 1669, GTGGTTTCAT at 935, CATGTTTCTA at 147, CCTGTTGGAA at 26.
  7. Stiglianir6: 10, TTTGTTGCTT at 4537, TTGGTTTGTT at 4533, GTGGTTTCTG at 4482, CCTGTTTGTG at 4364, GATGCTTGTT at 4162, TTTGCTTCTA at 3481, TTTGCCTGCG at 2085, TTTGTTGCCT at 1707, CATGTTGGTG at 1551, TATGTTTGTA at 912.
  8. Stiglianir7: 15, GATGTTGCAG at 4175, TTTGCTTCCT at 4127, GATGTCTGCG at 4007, GTTGCCTCCG at 3838, TTGGTTTGAT at 3730, TATGCCGGCA at 3499, TTGGCCGGAT at 3303, TCTGTTGCCG at 3129, TTGGTCTGTT at 3125, GTTGTTGGAA at 2943, TCGGTTGGAG at 2526, CATGCCTGTT at 2197, GATGCCGCCT at 1771, CAGGCCTGCT at 1761, GTGGCCGCAA at 658.
  9. Stiglianir8: 10, GCGGTTGGAA at 3165, TTTGCTTCTA at 3067, GTTGCCTCCG at 2487, CAGGTTGCCT at 2484, GTTGTTTCTA at 2385, CTTGTCTGCA at 2038, GCTGCCGGAG at 684, CCGGTTTCAG at 370, TAGGCTTCTA at 263, TTTGCCGGTT at 51.
  10. Stiglianir9: 16, GTGGCTGCAG at 4364, GCTGCCGCTA at 4311, GAGGCCGGTT at 3984, CTGGTTGGAG at 2978, GTGGTTTGCA at 2709, CAGGTCTGCG at 2651, CATGTCGCTT at 1853, GTTGTTTCTG at 1737, TTTGTCGGTA at 1273, CTGGCTGGTA at 1214, TCTGCTGGCG at 1141, TTTGCCTCCG at 1038, TTTGCTTCTG at 713, CTGGCTTGCA at 492, CTGGTTTGTT at 95, TTTGTCTCTT at 27.
  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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