Auxin response factor gene transcriptions

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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 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 is 1(C/G/T)-2N-3(G/T)-4G-5T-6C-7(G/T)-8N-9-10N.[1] ARF1 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 UTRs

Main article: UTR promoter gene transcriptions

Negative strand, negative direction: CAGGTTTCTG at 4506, TCGGTCTGCA at 4236, AACCAACCGG at 3948, TACAGACCTC at 3837, TAGGTCGGTA at 3685, TTTGTCTGTA at 2881.

Positive strand, negative direction: CTCCAGCCTG at 4348, CCTGTCTCAA at 4374, CTGAGGCAGG at 4282, CATGCCTGTA at 4122, AGGCAGCATC at 3902, AAGAGGCAGC at 3899, CTCAAGCAAC at 3848, CAGGCTTGAG at 3402, TCTGTCTCAA at 3324, CTCCAGCCTG at 3297, GAGGTTGCTG at 3264, TGGAGACCAG at 3123.

ARF core promoters

Main article: Core promoter gene transcriptions

Negative strand, positive direction: GAGGCCTCCT at 4407.

ARF proximal promoters

Main article: Proximal promoter gene transcriptions

Positive strand, negative direction: CATGCCTGTA at 2673.

Negative strand, positive direction: GAGGCCTCAG at 4194, CTGAGGCCTC at 4192.

Positive strand, positive direction: CCTGTTTGTG at 4257.

ARF distal promoters

Main article: Distal promoter gene transcriptions

Negative strand, negative direction: TTTGTTTGTT at 2488, GAGGCCTCCG at 2358, ATGAGGCCTC at 2356, CACCGACCTC at 2071, CTGAGACAGA at 2031, TACCGACCTC at 1748, TATGTCTGTA at 1570, CTTGCTTCCG at 1557, TTTGTTTGTT at 1392, CTGAGACAGA at 1087, GAGGTCGGAG at 1064, CTGAGACAGA at 921, TTTGTCTGTA at 171, CTGGTCGGTA at 38.

Positive strand, negative direction: CTGAGGCAGG at 2568, CATGCCTGTA at 2539, AACAGGCCAG at 2518, AACAAACAGG at 2514, AACAAACAAA at 2489, AGCAAACAAA at 2485, CTCCAGCCTG at 2434, GAGGTTGCAG at 2401, CTGAGGCAGG at 2367, CATGCTGGTG at 2328, TTGAGACCAG at 2263, TTGAGACCAA at 2147, TGGAGGCCAG at 2076, TCTGTCTCAA at 2034, CTCCAGCCTG at 2008, CTGAGGCAGG at 1941, CTTGCCTGAA at 1624, TGCCAGCAGA at 1614, AACAAACCTA at 1590, ATGAAACAAA at 1586, TACAGACATC at 1571, CAGGCTGGAG at 1466, AACAAACAAA at 1393, GAGGTTGCAG at 1322, AGGAGGCAGA at 1314, CTGAGGCAGG at 1288, TTGCGACCAG at 1193, TCTGTCTCAA at 1090, GAGGTTGCAG at 1031, CTGAGGCAGG at 997, TCTGTCTCAA at 924, CTCCAGCCTG at 898, CTGAGGCAGG at 831, AGCCAGCCTG at 507, AAGAGGCCGG at 374.

Negative strand, positive direction: CAGGTCTCAG at 3774, CACCAGCAGC at 3723, AGGCAGCAGG at 3694, CTGGCCTCCA at 3685, CATGTTTGCA at 3341, CTGGTCTCCT at 3302, CAGAAGCCAG at 3220, ATGCAGCAGG at 3147, GTTGTCTCTT at 3056, CAGGCCTCAG at 3040, TTCAGGCCTC at 3038, CTTGTCTGAG at 3007, CTGGCTGCCT at 2889, CAGGCCTCTG at 2882, TGCAGACCTC at 2863, GAGGCTGGTG at 2812, GATGTTGCAG at 2720, TTCAAACAGA at 2652, TAGAAACCAC at 2633, CCTGCCTCAG at 2525, CATGTTGCCT at 2479, TTGCAGCCGC at 2355, CAGGCTGGAG at 2322, TCTGTTTCAT at 2265, TAGGTCTGTT at 2261, TCTGTTGGCA at 2187, ATGAAACCGC at 2150, AGGCAACCAC at 2122, CTCAGGCAAC at 2119, AAGCAGCCAA at 2011, CTCCGACAGG at 1966, CACCGGCCAC at 1850, GCTGTCTGCT at 1734, TTGCAACCTC at 1618, CTGCAGCAAG at 1510, ATGCGGCAAG at 1426, ATGCGGCAAG at 1326, CTCCAACCTA at 1282, CTGCGGCAGC at 1037, CTGCGGCAAG at 1006, CTCCAACCTG at 946, CTCCAACCTG at 846, CTGCGGCAAG at 754, GCGGCCTGAA at 726, CAGCGGCCTG at 724, CTCCAACCTC at 610, CTGCAGCATC at 536, CTTGCTGCAG at 532, GCTGCCGGTG at 486, TGCAGACCGG at 442, AGCAAGCCAC at 342, CGGCAGCAAG at 338, CAGCGGCAGC at 335.

Positive strand, positive direction: TGGAAACCAC at 3949, AGGAGACCGG at 2985, CGGAGACCGA at 2885, CGGCGGCCAC at 1761, CTCCGGCAAG at 1489, CTCCGGCAAG at 1389, AGGAAGCCGG at 764, CCGGTCGCCG at 332, CACAGACCTC at 272, AAGAAACATA at 114.

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: 7, TACCAACATC at 4415, TTGCGGCATA at 3447, CGCAGGCAAA at 3248, ATCCGACCTG at 2513, CAGAAGCAGG at 1482, CGGAGACCGA at 1317, CGCAAACCGA at 668.
  12. Stiglianir1ci: 18, CACAAGCAAC at 4529, ATCCGGCAGG at 4308, AACAGACATG at 4198, TTGCAGCCAG at 3851, ATGAAACCGC at 3798, AACCAACCTC at 3541, AGGAAACCAA at 3537, TTCCGACAGC at 3040, ATCCAGCAGG at 2841, TTGAAACCAG at 2247, AAGCAGCAAG at 2225, AGCAAGCAGC at 2222, TTCCAACATA at 2099, AACCGACAAC at 1732, AGCCAACATC at 1202, CTGAAGCCTA at 1043, TTCCAGCAAA at 780, CACAGGCCTG at 448.
  13. Stiglianir2ci: 10, TAGCGGCCTG at 3752, AAGAGGCAAG at 3609, AACAAACCAA at 3173, AGCAAACCAA at 2444, TGGAGGCCAA at 2263, CGCAAACCGA at 1747, ATGAAACCAA at 1632, CAGAAACAGC at 949, ATCCGGCCGG at 801, TTCCAACCGA at 122.
  14. Stiglianir3ci: 5, CTGCGGCATC at 2720, TTCCGACCGG at 2366, CTGAAGCCGC at 1451, TTCAAACAGG at 1343, AGCCGGCCGG at 867.
  15. Stiglianir4ci: 7, AAGAGGCAAG at 4403, TGGAGGCATC at 3583, CACCGGCAAG at 3462, TGGAAGCCTG at 1869, TTCAGGCCAA at 790, CTCCAACAAC at 420, ATGAGACAGC at 76.
  16. Stiglianir5ci: 5, AACCGGCAAG at 1436, CAGCGGCAGA at 688, CGGCGGCCAG at 681, TAGCGGCCGC at 596, ATCAAACATG at 141.
  17. Stiglianir6ci: 12, TGGCGGCAAG at 4437, TTCCGACAAA at 4300, TACCGACATG at 3542, TGCCAGCCGA at 3406, TGCCAGCAGG at 3259, TTGCAACCAC at 3073, CAGCGACCGG at 2995, CGCCGACCGC at 2846, CGGAAGCATA at 2583, TAGCGGCAGG at 1564, TTGAAACAGA at 1101, TTCAAACATA at 177.
  18. Stiglianir7ci: 9, AGGCGACCAA at 4431, TTGAAACCAA at 4205, TACAAACAAA at 3788, AACAGACCAA at 3761, CGCCAACCAC at 3690, CTGCGACAGG at 2792, ATCCGGCCGC at 1910, TTCAGGCCTG at 1759, TACCAGCCAA at 482.
  19. Stiglianir8ci: 13, AAGAAGCAAG at 4389, CGCAGACAGA at 4261, TTCAAACCTA at 4003, AGCAGGCCAA at 3897, TGCCAGCCAG at 2790, CGGAAACAAA at 2131, ATCCGACCAC at 1945, CTCAGGCAGG at 1547, CACCAACCAG at 814, TGGCAGCCGC at 760, AAGCGGCCTA at 716, TTCCAACAAA at 619, TGGCGACAAA at 211.
  20. Stiglianir9ci: 15, AACCGACCTG at 4195, AGGAAACCGA at 4191, TGCAAACAGC at 4120, CGCCGACCTG at 4081, CTCAAACCGG at 4043, CGGCGGCAAG at 3899, AACAAACAAG at 3460, CAGAAACCTG at 3195, TACAGACATG at 2919, TGCCAACCTC at 2805, CGGCAGCCTC at 2557, TTGAGGCAGG at 2172, TTGAAACAAA at 1749, AGCCAGCAAC at 1313, AGGAAACCTC at 1282.

Stiglianir UTRs

Main article: UTR promoter gene transcriptions
  1. Stiglianir0: GAGGTTTCTA at 4222, TTTGTTTGAA at 4182, CATGCTTCAT at 4097, TCTGCCGGCG at 4079, GCGGCTTGCA at 3552, CTGGCCGCCA at 3408, CCTGCTTCAA at 3336.
  2. Stiglianir2: TTGGTCTGTT at 2965, GTTGTTGGTG at 2867.
  3. Stiglianir4: TCGGTTGGCT at 4248, GAGGTTGCAG at 3364.
  4. Stiglianir6: TTTGTTGCTT at 4537, TTGGTTTGTT at 4533, GTGGTTTCTG at 4482, CCTGTTTGTG at 4364, GATGCTTGTT at 4162, TTTGCTTCTA at 3481.
  5. Stiglianir8: GCGGTTGGAA at 3165, TTTGCTTCTA at 3067.
  6. Stiglianir0ci: TACCAACATC at 4415, TTGCGGCATA at 3447, CGCAGGCAAA at 3248.
  7. Stiglianir2ci: TAGCGGCCTG at 3752, AAGAGGCAAG at 3609, AACAAACCAA at 3173.
  8. Stiglianir4ci: AAGAGGCAAG at 4403, TGGAGGCATC at 3583, CACCGGCAAG at 3462.
  9. Stiglianir6ci: TGGCGGCAAG at 4437, TTCCGACAAA at 4300, TACCGACATG at 3542, TGCCAGCCGA at 3406, TGCCAGCAGG at 3259, TTGCAACCAC at 3073, CAGCGACCGG at 2995, CGCCGACCGC at 2846.
  10. Stiglianir8ci: AAGAAGCAAG at 4389, CGCAGACAGA at 4261, TTCAAACCTA at 4003, AGCAGGCCAA at 3897.

Stiglianir core promoters

Main article: Core promoter gene transcriptions
  1. Stiglianir5: CTGGCCGCTT at 4440.
  2. Stiglianir9: GTGGCTGCAG at 4364, GCTGCCGCTA at 4311.
  3. Stiglianir1ci: CACAAGCAAC at 4529, ATCCGGCAGG at 4308.
  4. Stiglianir7ci: AGGCGACCAA at 4431.

Stiglianir proximal promoters

Main article: Proximal promoter gene transcriptions
  1. Stiglianir0: CCTGCCTCTA at 2717.
  2. Stiglianir6ci: CGCCGACCGC at 2846.
  3. Stiglianir8ci: TGCCAGCCAG at 2790.


  1. Stiglianir1: CTGGCTTGAA at 4190, GTGGTCGCTT at 4158, TTTGCTTGCA at 4106.
  2. Stiglianir3: TTGGTTGGCG at 4110.
  3. Stiglianir5: TATGCTTGAT at 4193, TATGTTGGCA at 4175, TTTGCTGGAG at 4144.
  4. Stiglianir7: GATGTTGCAG at 4175, TTTGCTTCCT at 4127.
  5. Stiglianir1ci: AACAGACATG at 4198.
  6. Stiglianir7ci: TTGAAACCAA at 4205.
  7. Stiglianir9ci: AACCGACCTG at 4195, AGGAAACCGA at 4191, TGCAAACAGC at 4120, CGCCGACCTG at 4081.

Stiglianir distal promoters

Main article: Distal promoter gene transcriptions
  1. Stiglianir0: CCGGTTTGAA at 1690, TAGGTCGGCA at 1420.
  2. Stiglianir2: GTTGTCTGCA at 2538, GTGGTTTCTT at 2465, GCTGCTGCCA at 1569, GCTGCTGCTG at 1566, TCTGTCTCCA at 1318, CCTGTTTCCG at 1101, GTGGTTTCAT at 1059.
  3. Stiglianir4: 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.
  4. Stiglianir6: TTTGCCTGCG at 2085, TTTGTTGCCT at 1707, CATGTTGGTG at 1551, TATGTTTGTA at 912.
  5. Stiglianir8: GTTGCCTCCG at 2487, CAGGTTGCCT at 2484, GTTGTTTCTA at 2385, CTTGTCTGCA at 2038, GCTGCCGGAG at 684, CCGGTTTCAG at 370, TAGGCTTCTA at 263, TTTGCCGGTT at 51.
  6. Stiglianir0ci: ATCCGACCTG at 2513, CAGAAGCAGG at 1482, CGGAGACCGA at 1317, CGCAAACCGA at 668.
  7. Stiglianir2ci: AGCAAACCAA at 2444, TGGAGGCCAA at 2263, CGCAAACCGA at 1747, ATGAAACCAA at 1632, CAGAAACAGC at 949, ATCCGGCCGG at 801, TTCCAACCGA at 122.
  8. Stiglianir4ci: TGGAAGCCTG at 1869, TTCAGGCCAA at 790, CTCCAACAAC at 420, ATGAGACAGC at 76.
  9. Stiglianir6ci: CGGAAGCATA at 2583, TAGCGGCAGG at 1564, TTGAAACAGA at 1101, TTCAAACATA at 177.
  10. Stiglianir8ci: CGGAAACAAA at 2131, ATCCGACCAC at 1945, CTCAGGCAGG at 1547, CACCAACCAG at 814, TGGCAGCCGC at 760, AAGCGGCCTA at 716, TTCCAACAAA at 619, TGGCGACAAA at 211.


  1. Stiglianir1: 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.
  2. Stiglianir3: 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.
  3. Stiglianir5: TTGGTTTGAA at 3272, CCTGCTTCAA at 2916, GAGGTTTCAA at 1883, CATGCTTCCA at 1669, GTGGTTTCAT at 935, CATGTTTCTA at 147, CCTGTTGGAA at 26.
  4. Stiglianir7: 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.
  5. Stiglianir9: 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.
  6. Stiglianir1ci: TTGCAGCCAG at 3851, ATGAAACCGC at 3798, AACCAACCTC at 3541, AGGAAACCAA at 3537, TTCCGACAGC at 3040, ATCCAGCAGG at 2841, TTGAAACCAG at 2247, AAGCAGCAAG at 2225, AGCAAGCAGC at 2222, TTCCAACATA at 2099, AACCGACAAC at 1732, AGCCAACATC at 1202, CTGAAGCCTA at 1043, TTCCAGCAAA at 780, CACAGGCCTG at 448.
  7. Stiglianir3ci: CTGCGGCATC at 2720, TTCCGACCGG at 2366, CTGAAGCCGC at 1451, TTCAAACAGG at 1343, AGCCGGCCGG at 867.
  8. Stiglianir5ci: AACCGGCAAG at 1436, CAGCGGCAGA at 688, CGGCGGCCAG at 681, TAGCGGCCGC at 596, ATCAAACATG at 141.
  9. Stiglianir7ci: TACAAACAAA at 3788, AACAGACCAA at 3761, CGCCAACCAC at 3690, CTGCGACAGG at 2792, ATCCGGCCGC at 1910, TTCAGGCCTG at 1759, TACCAGCCAA at 482.
  10. Stiglianir9ci: CTCAAACCGG at 4043, CGGCGGCAAG at 3899, AACAAACAAG at 3460, CAGAAACCTG at 3195, TACAGACATG at 2919, TGCCAACCTC at 2805, CGGCAGCCTC at 2557, TTGAGGCAGG at 2172, TTGAAACAAA at 1749, AGCCAGCAAC at 1313, AGGAAACCTC at 1282.

TGTCTC (Ulmasov) ARFbs samplings

ARF (Ulmasov) UTRs

Negative strand, negative direction: TGTCTC at 4519, TGTCTC at 3673.

Positive strand, negative direction: TGTCTC at 4372, TGTCTC at 3322.

ARF (Ulmasov) proximal promoters

Negative strand, negative direction: TGTCTC at 2779.

ARF (Ulmasov) distal promoters

Negative strand, negative direction: TGTCTC at 2444, GAGACA at 2029, TGTCTC at 2018, GAGACA at 1452, GAGACA at 1085, TGTCTC at 1074, GAGACA at 919, TGTCTC at 908.

Positive strand, negative direction: TGTCTC at 2166, TGTCTC at 2032, TGTCTC at 1088, TGTCTC at 922.

Negative strand, positive direction: TGTCTC at 3054, TGTCTC at 2467, TGTCTC at 2173, TGTCTC at 2079, GAGACA at 712.

Positive strand, positive direction: TGTCTC at 3180, TGTCTC at 3134, TGTCTC at 2653, GAGACA at 2308, GAGACA at 98.

Ulmasov random dataset samplings

  1. Ulmasovr0: 0.
  2. Ulmasovr1: 0.
  3. Ulmasovr2: 2, TGTCTC at 1316, TGTCTC at 599.
  4. Ulmasovr3: 0.
  5. Ulmasovr4: 1, TGTCTC at 3995.
  6. Ulmasovr5: 0.
  7. Ulmasovr6: 1, TGTCTC at 1292.
  8. Ulmasovr7: 0.
  9. Ulmasovr8: 0.
  10. Ulmasovr9: 1, TGTCTC at 25.
  11. Ulmasovr0ci: 2, GAGACA at 4234, GAGACA at 2330.
  12. Ulmasovr1ci: 2, GAGACA at 3256, GAGACA at 33.
  13. Ulmasovr2ci: 0.
  14. Ulmasovr3ci: 0.
  15. Ulmasovr4ci: 1, GAGACA at 74.
  16. Ulmasovr5ci: 1, GAGACA at 923.
  17. Ulmasovr6ci: 0.
  18. Ulmasovr7ci: 0.
  19. Ulmasovr8ci: 0.
  20. Ulmasovr9ci: 0.

Ulmasovr UTRs

Main article: UTR promoter gene transcriptions
  1. Ulmasovr4: TGTCTC at 3995.
  2. Ulmasovr0ci: GAGACA at 4234.

Ulmasovr distal promoters

Main article: Distal promoter gene transcriptions
  1. Ulmasovr2: 2, TGTCTC at 1316, TGTCTC at 599.
  2. Ulmasovr6: TGTCTC at 1292.
  3. Ulmasovr0ci: GAGACA at 2330.
  4. Ulmasovr4ci: GAGACA at 74.


  1. Ulmasovr9: TGTCTC at 25.
  2. Ulmasovr1ci: 2, GAGACA at 3256, GAGACA at 33.
  3. Ulmasovr5ci: GAGACA at 923.

TGTCGG (Boer) ARFbs samplings

ARF (Boer) UTRs

Negative strand, negative direction: TGTCGG at 3727.

ARF (Boer) distal promoters

Negative strand, positive direction: CCGACA at 1964.

Positive strand, positive direction: TGTCGG at 3896, CCGACA at 3640, CCGACA at 3349, TGTCGG at 3101, CCGACA at 264, TGTCGG at 65.

Boer random dataset samplings

  1. Boerr0: 1, TGTCGG at 867.
  2. Boerr1: 0.
  3. Boerr2: 0.
  4. Boerr3: 0.
  5. Boerr4: 1, TGTCGG at 2028.
  6. Boerr5: 1, TGTCGG at 2902.
  7. Boerr6: 1, TGTCGG at 475.
  8. Boerr7: 1, TGTCGG at 3352.
  9. Boerr8: 1, TGTCGG at 3903.
  10. Boerr9: 1, TGTCGG at 1271.
  11. Boerr0ci: 1, CCGACA at 1319.
  12. Boerr1ci: 3, CCGACA at 3038, CCGACA at 1730, CCGACA at 959.
  13. Boerr2ci: 1, CCGACA at 1719.
  14. Boerr3ci: 0.
  15. Boerr4ci: 2, CCGACA at 4357, CCGACA at 399.
  16. Boerr5ci: 0.
  17. Boerr6ci: 2, CCGACA at 4298, CCGACA at 3540.
  18. Boerr7ci: 1, CCGACA at 2420.
  19. Boerr8ci: 1, CCGACA at 431.
  20. Boerr9ci: 2, CCGACA at 2521, CCGACA at 392.

Boerr UTRs

Main article: UTR promoter gene transcriptions
  1. Boerr8: 1, TGTCGG at 3903.
  2. Boerr4ci: 2, CCGACA at 4357.
  3. Boerr6ci: 2, CCGACA at 4298, CCGACA at 3540.

Boerr distal promoters

Main article: Distal promoter gene transcriptions
  1. Boerr0: 1, TGTCGG at 867.
  2. Boerr4: 1, TGTCGG at 2028.
  3. Boerr6: 1, TGTCGG at 475.
  4. Boerr0ci: 1, CCGACA at 1319.
  5. Boerr2ci: 1, CCGACA at 1719.
  6. Boerr8ci: 1, CCGACA at 431.
  7. Boerr4ci: CCGACA at 399.


  1. Boerr5: 1, TGTCGG at 2902.
  2. Boerr7: 1, TGTCGG at 3352.
  3. Boerr9: 1, TGTCGG at 1271.
  4. Boerr1ci: 3, CCGACA at 3038, CCGACA at 1730, CCGACA at 959.
  5. Boerr7ci: 1, CCGACA at 2420.
  6. Boerr9ci: 2, CCGACA at 2521, CCGACA at 392.

ARF5 samplings

Copying an ARF5 consensus sequence CAGGTCT and putting the sequence in "⌘F" finds two locations between ZNF497 and A1BG or TCTGTCT found no location between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence (C/G/T)N(G/T)GTC(G/T) (starting with SuccessablesARF5.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 (C/G/T)N(G/T)GTC(G/T), 41, TTTGTCT at 4518, GGGGTCT at 4448, GAGGTCG at 4345, TCGGTCT at 4233, CTGGTCG at 4033, CGTGTCT at 3917, CGGGTCG at 3731, CTTGTCG at 3726, CAGGTCG at 3701, GGTGTCG at 3694, TAGGTCG at 3682, TGTGTCT at 3672, TTGGTCT at 3486, GAGGTCG at 3294, CGGGTCG at 3209, CTGGTCG at 3124, TTTGTCT at 2878, GTTGTCT at 2778, GGGGTCG at 2766, GTTGTCT at 2443, GAGGTCG at 2431, CCTGTCG at 2273, CTGGTCG at 2264, CCTGTCT at 2119, GCTGTCT at 2017, GAGGTCG at 2005, TATGTCT at 1567, TGGGTCT at 1518, TGGGTCT at 1411, CTGGTCG at 1194, GTTGTCT at 1073, GAGGTCG at 1061, TAGGTCG at 976, GTTGTCT at 907, GAGGTCG at 895, CTGGTCG at 737, CTGGTCG at 728, TCGGTCG at 504, CTTGTCT at 289, TTTGTCT at 168, CTGGTCG at 35.
  2. positive strand, negative direction, looking for (C/G/T)N(G/T)GTC(G/T), 10, CCTGTCT at 4371, CCTGTCT at 4210, TATGTCT at 3833, GTGGTCG at 3813, TCTGTCT at 3321, TATGTCT at 2986, TCTGTCT at 2031, CGTGTCT at 1222, TCTGTCT at 1087, TCTGTCT at 921.
  3. positive strand, positive direction, looking for (C/G/T)N(G/T)GTC(G/T), 34, GGGGTCT at 4330, TCTGTCG at 3895, GAGGTCT at 3891, GAGGTCT at 3806, GTGGTCG at 3720, CTGGTCT at 3548, CGGGTCG at 3239, TCGGTCT at 3221, GGTGTCG at 3194, TTTGTCT at 3179, CCTGTCT at 3133, TGTGTCG at 3100, TGGGTCT at 3091, TGTGTCT at 2837, TTTGTCT at 2652, TTGGTCT at 2228, CGGGTCT at 1742, GTGGTCT at 1631, GTGGTCG at 1463, GCGGTCG at 1457, GTGGTCG at 1363, GCGGTCG at 1357, TCGGTCG at 1271, GTGGTCG at 1127, CGTGTCG at 1054, TCGGTCT at 935, TCGGTCT at 835, TGTGTCG at 718, GGTGTCG at 634, GTGGTCG at 623, TCGGTCG at 617, CCGGTCG at 329, GGGGTCT at 204, GAGGTCT at 15.
  4. negative strand, positive direction, looking for (C/G/T)N(G/T)GTC(G/T), 19, GGGGTCT at 4414, GTGGTCT at 4380, CAGGTCT at 3771, CTGGTCT at 3299, CTGGTCT at 3245, GTTGTCT at 3053, CAGGTCT at 3019, CTTGTCT at 3004, GTGGTCT at 2941, CGGGTCT at 2489, TAGGTCT at 2258, TGTGTCT at 2078, GGGGTCT at 1958, CCTGTCT at 1862, GCTGTCT at 1731, GGGGTCT at 1711, GAGGTCG at 1687, TGTGTCT at 268, TCTGTCT at 100.
  5. inverse complement, negative strand, negative direction, looking for (A/C)GAC(A/C)N(A/C/G), 21, CGACACC at 3959, AGACCTC at 3837, CGACACC at 3711, AGACACA at 3558, AGACAGA at 3321, CGACCCA at 3182, CGACCCG at 3043, CGACCCC at 3037, CGACCAC at 2328, CGACCTC at 2071, AGACAGA at 2031, CGACCCG at 1893, CGACCCG at 1758, CGACCTC at 1748, CGACCTC at 1466, AGACAAC at 1454, AGACCCG at 1358, CGACCCG at 1113, AGACAGA at 1087, AGACAGA at 921, CGACCTA at 783.
  6. inverse complement, positive strand, negative direction, looking for (A/C)GAC(A/C)N(A/C/G), 15, AGACAAG at 4183, AGACCAG at 4032, AGACCAC at 3763, AGACCAG at 3123, AGACCAG at 2600, AGACCAG at 2263, AGACCAA at 2147, AGACCAC at 2123, CGACAGA at 2017, AGACATC at 1571, CGACCAG at 1193, CGACAAC at 1070, AGACCAG at 727, AGACAGG at 561, AGACAGG at 424.
  7. inverse complement, positive strand, positive direction, looking for (A/C)GAC(A/C)N(A/C/G), 30, AGACCCA at 4418, CGACACC at 4394, CGACCCG at 4179, CGACCCG at 3991, CGACACC at 3642, CGACAAG at 3351, CGACCAG at 3244, AGACCAA at 3023, AGACCGG at 2985, AGACACG at 2959, AGACCGA at 2885, CGACCAC at 2812, CGACCTC at 2772, CGACCTA at 2736, CGACCTC at 2322, AGACAAA at 2262, AGACAAC at 2184, AGACCCC at 1866, CGACCGG at 1738, CGACAGA at 1731, AGACCGC at 1478, AGACCGC at 1378, CGACCAC at 781, CGACCCG at 419, CGACCCG at 388, CGACCCC at 279, AGACCTC at 272, CGACACA at 266, AGACCAC at 104, AGACAGA at 100.
  8. inverse complement, negative strand, positive direction, looking for (A/C)GAC(A/C)N(A/C/G), 6, AGACAGC at 3895, AGACCTC at 3552, AGACCTC at 2863, CGACAGG at 1966, AGACACA at 714, AGACCGG at 442.

ARF5 UTRs

Main article: UTR promoter gene transcriptions
  1. Negative strand, negative direction: TTTGTCT at 4518, GGGGTCT at 4448, GAGGTCG at 4345, TCGGTCT at 4233, CTGGTCG at 4033, CGACACC at 3959, CGTGTCT at 3917, AGACCTC at 3837, CGGGTCG at 3731, CTTGTCG at 3726, CGACACC at 3711, CAGGTCG at 3701, GGTGTCG at 3694, TAGGTCG at 3682, TGTGTCT at 3672, AGACACA at 3558, TTGGTCT at 3486, AGACAGA at 3321, GAGGTCG at 3294, CGGGTCG at 3209, CGACCCA at 3182, CTGGTCG at 3124, CGACCCG at 3043, CGACCCC at 3037, TTTGTCT at 2878.
  2. Positive strand, negative direction: CCTGTCT at 4371, CCTGTCT at 4210, AGACAAG at 4183, AGACCAG at 4032, TATGTCT at 3833, GTGGTCG at 3813, AGACCAC at 3763, TCTGTCT at 3321, AGACCAG at 3123, TATGTCT at 2986.

ARF5 core promoters

Main article: Core promoter gene transcriptions
  1. Negative strand, positive direction: GGGGTCT at 4414, GTGGTCT at 4380.
  2. Positive strand, positive direction: AGACCCA at 4418, CGACACC at 4394, GGGGTCT at 4330.

ARF5 proximal promoters

Main article: Proximal promoter gene transcriptions
  1. Negative strand, negative direction: GTTGTCT at 2778, GGGGTCG at 2766.
  2. Positive strand, negative direction: AGACCAG at 2600.
  3. Positive strand, positive direction: CGACCCG at 4179.

ARF5 distal promoters

Main article: Distal promoter gene transcriptions

ARF5 random dataset samplings

  1. ARF5r0: 0.
  2. ARF5r1: 0.
  3. ARF5r2: 0.
  4. ARF5r3: 0.
  5. ARF5r4: 0.
  6. ARF5r5: 0.
  7. ARF5r6: 0.
  8. ARF5r7: 0.
  9. ARF5r8: 0.
  10. ARF5r9: 0.
  11. ARF5r0ci: 0.
  12. ARF5r1ci: 0.
  13. ARF5r2ci: 0.
  14. ARF5r3ci: 0.
  15. ARF5r4ci: 0.
  16. ARF5r5ci: 0.
  17. ARF5r6ci: 0.
  18. ARF5r7ci: 0.
  19. ARF5r8ci: 0.
  20. ARF5r9ci: 0.

ARF5r UTRs

Main article: UTR promoter gene transcriptions

ARF5r core promoters

Main article: Core promoter gene transcriptions

ARF5r proximal promoters

Main article: Proximal promoter gene transcriptions

ARF5r 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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