V box gene transcriptions

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Editor-In-Chief: Henry A. Hoff

File:Platypus.jpg
Ornithorhynchus anatinus is the platypus. Credit: Stefan Kraft.{{free media}}

"The V boxes encompass a leader exon and first intron of the mature transcript."[1]

"REV-ERBα and RORa are nuclear receptors rather than bZIP transcription factors like VRI [target gene: vrille (VRI)] and PDP1ϵ, and they regulate transcription by binding RORE elements rather than V/P-boxes (Bell-Pedersen et al., 2005)."[2]

"A delayed accumulation of PDP1 leads to a replacement of VRI from P/V (PDP1 and VRI) boxes and restimulates clk transcription."[3]

"For VRI to be a direct repressor of Clk, the 8.0 kb Clk genomic fragment should contain binding sites for VRI. The consensus binding site for VRI has not been determined; however, the basic (DNA binding) domain shares >85% homology with that of mammalian E4BP4, and hence, VRI should bind similar DNA sequences as E4BP4 (George and Terracol, 1997). The optimal binding site for E4BP4 has been determined as 5′-(A/G): (A/G)T(A/C)A(A/T/C)-3′ (Cowell et al., 1992)."[4]

"EMSA confirms that the W and V boxes each binds proteins that also recognize the X box."[5]

Consensus sequences

"As VRI accumulates in the nucleus during the mid to late day, it binds VRI/PDP1ϵ binding sites (V/P-boxes) [consensus A(/G)TTA(/T)T(/C):GTAAT(/C)], to repress Clk and cry transcription (Hardin, 2004)."[2]

Human genes

Gene ID: 3119 is HLA-DQB1 major histocompatibility complex, class II, DQ beta 1. "HLA-DQB1 belongs to the HLA class II beta chain paralogs. This class II molecule is a heterodimer consisting of an alpha (DQA) and a beta chain (DQB), both anchored in the membrane. It plays a central role in the immune system by presenting peptides derived from extracellular proteins. Class II molecules are expressed in antigen presenting cells (APC: B lymphocytes, dendritic cells, macrophages). The beta chain is approximately 26-28 kDa and it contains six exons. Exon 1 encodes the leader peptide, exons 2 and 3 encode the two extracellular domains, exon 4 encodes the transmembrane domain and exon 5 encodes the cytoplasmic tail. Within the DQ molecule both the alpha chain and the beta chain contain the polymorphisms specifying the peptide binding specificities, resulting in up to four different molecules. Typing for these polymorphisms is routinely done for bone marrow transplantation. Alternative splicing results in multiple transcript variants."[6]

  1. NP_002114.3 HLA class II histocompatibility antigen, DQ beta 1 chain isoform 1 precursor (variant 1).
  2. NP_001230890.1 HLA class II histocompatibility antigen, DQ beta 1 chain isoform 2 precursor (variant 2).
  3. NP_001230891.1 HLA class II histocompatibility antigen, DQ beta 1 chain isoform 1 precursor (variant 3).

Gene ID: 3120 is HLA-DQB2 major histocompatibility complex, class II, DQ beta 2. "HLA-DQB2 belongs to the family of HLA class II beta chain paralogs. Class II molecules are heterodimers consisting of an alpha (DQA) and a beta chain (DQB), both anchored in the membrane. They play a central role in the immune system by presenting peptides derived from extracellular proteins. Class II molecules are expressed in antigen presenting cells (APC: B lymphocytes, dendritic cells, macrophages). Polymorphisms in the alpha and beta chains specify the peptide binding specificity, and typing for these polymorphisms is routinely done for bone marrow transplantation. However this gene, HLA-DQB2, is not routinely typed, as it is not thought to have an effect on transplantation. There is conflicting evidence in the literature and public sequence databases for the protein-coding capacity of HLA-DQB2. Because there is evidence of transcription and an intact ORF, HLA-DQB2 is represented in Entrez Gene and in RefSeq as a protein-coding locus."[7]

  1. NP_001287719.1 HLA class II histocompatibility antigen, DQ beta 2 chain isoform 1 precursor (variant 1).
  2. NP_001185787.1 HLA class II histocompatibility antigen, DQ beta 2 chain isoform 2 precursor (variant 2).
  3. XP_005249108.1 HLA class II histocompatibility antigen, DQ beta 2 chain isoform X1.
  4. XP_011512862.1 HLA class II histocompatibility antigen, DQ beta 2 chain isoform X2.
  5. XP_011512863.1 HLA class II histocompatibility antigen, DQ beta 2 chain isoform X3.

Gene ID: 3121 is HLA-DQB3 major histocompatibility complex, class II, DQ beta 3.

"Structural and functional studies indicate that a proximal promoter region exists, extending up to approx. -250 bp upstream of the transcription start site involving a set of conserved cis-acting elements defined as Y, X1/X2, S, W, J and V boxes in addition to the TATA and CAAT box sequences. However, locus-specific differences with respect to the presence and sequence of these elements exist. Although allelic polymorphism is a key feature of HLA class II genes, it was somewhat surprising to learn that the upstream regulatory regions of these genes also harbor allelic variability. This variability affects the array of highly conserved regulatory sequences consisting of the X, Y and W/Z box elements. For the DQB1 proximal promoter, termed QBP1, 10 different alleles have been identified in previous analyses of approx. 600bp immediately upstream of the first exon of the DQB1 gene.6–8 Functional studies indicated that this allelic polymorphism is associated with differences in both transcriptional activity and affinity for DNA-binding proteins.6,9"[8]

"HLA class II expression requires coordinate binding of transcription factors to the W-X-Y box region of the proximal promoter."[8]

Gene ID: 4783 is NFIL3 nuclear factor, interleukin 3 regulated (aka E4BP4; IL3BP1; NFIL3A; NF-IL3A). "The protein encoded by this gene is a transcriptional regulator that binds as a homodimer to activating transcription factor (ATF) sites in many cellular and viral promoters. The encoded protein represses PER1 and PER2 expression and therefore plays a role in the regulation of circadian rhythm. Three transcript variants encoding the same protein have been found for this gene."[9]

  1. NP_001276928.1 nuclear factor interleukin-3-regulated protein (variant 1).
  2. NP_001276929.1 nuclear factor interleukin-3-regulated protein (variant 2).
  3. NP_005375.2 nuclear factor interleukin-3-regulated protein (variant 3).
  4. XP_016870232.1 nuclear factor interleukin-3-regulated protein isoform X1.
  5. XP_016870233.1 nuclear factor interleukin-3-regulated protein isoform X1.

Hypotheses

  1. A1BG has no V boxes in either promoter.

V box samplings

Using the two versions of the consensus sequence and "⌘F" to locate these sequences in the nucleotides for A1BG listed in A1BG gene transcriptions revealed two occurrences (GTTTT) and (ATTTT) on the ZSCAN22 side.

For the Basic programs testing consensus sequence (A/G)TT(A/T)(C/T) (starting with SuccessablesVbox.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: 60, GTTTC at 4504, GTTTT at 4376, GTTTT at 4310, ATTAT at 4223, GTTTT at 4216, ATTAT at 4077, GTTTT at 4066, GTTTT at 3767, ATTAC at 3658, ATTAT at 3538, ATTTT at 3439, ATTTT at 3353, GTTTT at 3326, GTTTT at 3313, ATTTT at 3171, ATTTT at 3163, ATTTT at 3024, ATTTT at 3010, GTTTC at 2891, GTTTT at 2866, ATTTC at 2857, GTTAT at 2849, GTTTT at 2795, GTTTT at 2644, GTTAT at 2497, GTTTT at 2490, GTTTT at 2476, GTTTT at 2307, ATTTT at 2299, GTTTT at 2182, ATTTC at 2174, GTTTT at 2036, GTTTT at 1880, ATTTT at 1872, ATTTT at 1737, ATTAT at 1708, GTTTC at 1638, GTTTT at 1561, ATTTC at 1548, GTTTT at 1394, GTTTT at 1384, GTTTT at 1371, GTTAT at 1362, GTTTT at 1228, GTTTT at 1092, GTTTT at 926, GTTTT at 771, ATTTT at 763, GTTTT at 637, ATTTT at 629, ATTAT at 602, GTTTT at 485, ATTAT at 271, GTTTT at 257, ATTAT at 249, ATTTT at 222, ATTTT at 183, GTTTT at 164, GTTTC at 93, ATTTT at 66.
  2. Positive strand, negative direction: 14, ATTTT at 4511, ATTTC at 3688, ATTAC at 3469, GTTTT at 3349, ATTTC at 2884, ATTTT at 2853, ATTTT at 1727, ATTAT at 1724, ATTTC at 1603, ATTTC at 1380, ATTAC at 1296, GTTTT at 215, ATTTT at 190, ATTTC at 22.
  3. Negative strand, positive direction: 15, ATTAT at 4165, ATTAT at 4158, ATTTT at 4120, GTTTT at 4109, GTTAT at 3382, GTTAT at 3025, GTTTT at 2687, ATTTC at 2645, ATTAT at 2547, ATTTT at 2449, ATTTT at 2441, GTTTC at 2301, GTTTC at 2263, ATTTC at 1978, GTTTT at 147.
  4. Positive strand, positive direction: 11, GTTAT at 3425, GTTAT at 3159, GTTTC at 3064, GTTAC at 2909, GTTTC at 2827, GTTTT at 2707, GTTTC at 2535, GTTTT at 2494, ATTTT at 2445, GTTTT at 2003, GTTAC at 227.
  5. inverse complement, negative strand, negative direction: 38, ATAAT at 4538, AAAAT at 4512, GAAAC at 4462, GAAAC at 3985, ATAAC at 3528, ATAAT at 3468, ATAAT at 3454, GTAAT at 3436, AAAAT at 3350, GTAAC at 3285, GAAAC at 3076, AAAAT at 3021, ATAAT at 2998, ATAAT at 2977, GTAAT at 2951, AAAAT at 2854, GAAAC at 2553, GAAAC at 2217, GAAAC at 2100, GAAAC at 1791, GAAAT at 1734, AAAAT at 1728, GAAAC at 1688, AAAAC at 1433, GTAAC at 1343, GAAAC at 1146, GTAAC at 886, GAAAC at 682, GAAAC at 546, GAAAC at 409, GAAAT at 348, ATAAT at 236, AAAAT at 217, AAAAT at 191, GTAAT at 173, GTAAT at 153, GAAAT at 48, AAAAC at 28.
  6. inverse complement, positive strand, negative direction: 81, AAAAC at 4396, AAAAC at 4311, ATAAT at 4225, ATAAT at 4222, AAAAT at 4219, AAAAT at 4088, ATAAT at 4076, AAAAT at 4069, GTAAT at 3973, AAAAT at 3768, ATAAT at 3657, GAAAC at 3592, ATAAT at 3537, AAAAC at 3510, AAAAT at 3355, AAAAC at 3328, AAAAT at 3314, AAAAT at 3173, AAAAC at 3165, GAAAC at 3147, GTAAT at 3064, AAAAC at 3027, AAAAT at 3011, AAAAC at 2969, GAAAC at 2958, AAAAT at 2930, AAAAT at 2867, AAAAC at 2840, GAAAT at 2747, GTAAT at 2675, AAAAT at 2646, GAAAC at 2620, AAAAC at 2507, AAAAC at 2491, AAAAC at 2310, AAAAT at 2301, GAAAC at 2283, AAAAT at 2185, GAAAT at 2158, GTAAT at 2088, AAAAT at 2061, GTAAT at 1914, AAAAT at 1884, AAAAT at 1874, GAAAC at 1856, GTAAT at 1779, AAAAT at 1738, GTAAT at 1707, GAAAT at 1661, GAAAC at 1643, GAAAT at 1631, GAAAC at 1583, AAAAT at 1562, AAAAC at 1386, AAAAC at 1372, GTAAT at 1261, AAAAT at 1231, GAAAC at 1213, GTAAT at 1134, GTAAT at 804, AAAAT at 774, AAAAT at 765, GTAAT at 670, AAAAT at 640, AAAAT at 631, GTAAC at 613, GTAAT at 534, AAAAT at 496, AAAAT at 488, GAAAC at 474, GTAAT at 397, AAAAC at 359, GAAAC at 313, GAAAC at 304, ATAAT at 270, AAAAC at 258, GTAAT at 248, GAAAC at 227, AAAAC at 165, GAAAC at 127, AAAAC at 67.
  7. inverse complement, negative strand, positive direction: 12, ATAAT at 4168, GAAAT at 4092, GAAAT at 3795, GTAAC at 3732, GAAAT at 3166, GAAAC at 2832, GAAAC at 2630, GAAAT at 2624, AAAAC at 2495, AAAAT at 2446, GAAAC at 2147, AAAAC at 292.
  8. inverse complement, positive strand, positive direction: 15, TAATA at 4165, TAATA at 4158, TAAAA at 4120, CAAAA at 4109, CAATA at 3382, CAATA at 3025, CAAAA at 2687, TAAAG at 2645, TAATA at 2547, TAAAA at 2449, TAAAA at 2441, CAAAG at 2301, CAAAG at 2263, TAAAG at 1978, CAAAA at 147.

Vbox (4560-2846) UTRs

Negative strand

  1. Negative strand, negative direction: GTTTC at 4504, GTTTT at 4376, GTTTT at 4310, ATTAT at 4223, GTTTT at 4216, ATTAT at 4077, GTTTT at 4066, GTTTT at 3767, ATTAC at 3658, ATTAT at 3538, ATTTT at 3439, ATTTT at 3353, GTTTT at 3326, GTTTT at 3313, ATTTT at 3171, ATTTT at 3163, ATTTT at 3024, ATTTT at 3010, GTTTC at 2891, GTTTT at 2866, ATTTC at 2857, GTTAT at 2849
  2. Negative strand, negative direction: ATAAT at 4538, AAAAT at 4512, GAAAC at 4462, GAAAC at 3985, ATAAC at 3528, ATAAT at 3468, ATAAT at 3454, GTAAT at 3436, AAAAT at 3350, GTAAC at 3285, GAAAC at 3076, AAAAT at 3021, ATAAT at 2998, ATAAT at 2977, GTAAT at 2951, AAAAT at 2854.

Positive strand

  1. Positive strand, negative direction: ATTTT at 4511, ATTTC at 3688, ATTAC at 3469, GTTTT at 3349, ATTTC at 2884, ATTTT at 2853.
  2. Positive strand, negative direction: AAAAC at 4396, AAAAC at 4311, ATAAT at 4225, ATAAT at 4222, AAAAT at 4219, AAAAT at 4088, ATAAT at 4076, AAAAT at 4069, GTAAT at 3973, AAAAT at 3768, ATAAT at 3657, GAAAC at 3592, ATAAT at 3537, AAAAC at 3510, AAAAT at 3355, AAAAC at 3328, AAAAT at 3314, AAAAT at 3173, AAAAC at 3165, GAAAC at 3147, GTAAT at 3064, AAAAC at 3027, AAAAT at 3011, AAAAC at 2969, GAAAC at 2958, AAAAT at 2930, AAAAT at 2867.

Vbox negative direction (2846-2811) core promoters

  1. Positive strand, negative direction: AAAAC at 2840.

Vbox negative direction (2811-2596) proximal promoters

  1. Negative strand, negative direction: GTTTT at 2795, GTTTT at 2644.
  2. Positive strand, negative direction: GAAAT at 2747, GTAAT at 2675, AAAAT at 2646, GAAAC at 2620.

Vbox positive direction (4265-4050) proximal promoters

  1. Negative strand, positive direction: ATTAT at 4165, ATTAT at 4158, ATTTT at 4120, GTTTT at 4109.
  2. Negative strand, positive direction: ATAAT at 4168, GAAAT at 4092

Vbox negative direction (2596-1) distal promoters

Negative strand

  1. Negative strand, negative direction: GTTAT at 2497, GTTTT at 2490, GTTTT at 2476, GTTTT at 2307, ATTTT at 2299, GTTTT at 2182, ATTTC at 2174, GTTTT at 2036, GTTTT at 1880, ATTTT at 1872, ATTTT at 1737, ATTAT at 1708, GTTTC at 1638, GTTTT at 1561, ATTTC at 1548, GTTTT at 1394, GTTTT at 1384, GTTTT at 1371, GTTAT at 1362, GTTTT at 1228, GTTTT at 1092, GTTTT at 926, GTTTT at 771, ATTTT at 763, GTTTT at 637, ATTTT at 629, ATTAT at 602, GTTTT at 485, ATTAT at 271, GTTTT at 257, ATTAT at 249, ATTTT at 222, ATTTT at 183, GTTTT at 164, GTTTC at 93, ATTTT at 66.
  2. Negative strand, negative direction: GAAAC at 2553, GAAAC at 2217, GAAAC at 2100, GAAAC at 1791, GAAAT at 1734, AAAAT at 1728, GAAAC at 1688, AAAAC at 1433, GTAAC at 1343, GAAAC at 1146, GTAAC at 886, GAAAC at 682, GAAAC at 546, GAAAC at 409, GAAAT at 348, ATAAT at 236, AAAAT at 217, AAAAT at 191, GTAAT at 173, GTAAT at 153, GAAAT at 48, AAAAC at 28.

Positive strand

  1. Positive strand, negative direction: ATTTT at 1727, ATTAT at 1724, ATTTC at 1603, ATTTC at 1380, ATTAC at 1296, GTTTT at 215, ATTTT at 190, ATTTC at 22.
  2. Positive strand, negative direction: AAAAC at 2507, AAAAC at 2491, AAAAC at 2310, AAAAT at 2301, GAAAC at 2283, AAAAT at 2185, GAAAT at 2158, GTAAT at 2088, AAAAT at 2061, GTAAT at 1914, AAAAT at 1884, AAAAT at 1874, GAAAC at 1856, GTAAT at 1779, AAAAT at 1738, GTAAT at 1707, GAAAT at 1661, GAAAC at 1643, GAAAT at 1631, GAAAC at 1583, AAAAT at 1562, AAAAC at 1386, AAAAC at 1372, GTAAT at 1261, AAAAT at 1231, GAAAC at 1213, GTAAT at 1134, GTAAT at 804, AAAAT at 774, AAAAT at 765, GTAAT at 670, AAAAT at 640, AAAAT at 631, GTAAC at 613, GTAAT at 534, AAAAT at 496, AAAAT at 488, GAAAC at 474, GTAAT at 397, AAAAC at 359, GAAAC at 313, GAAAC at 304, ATAAT at 270, AAAAC at 258, GTAAT at 248, GAAAC at 227, AAAAC at 165, GAAAC at 127, AAAAC at 67.

Vbox positive direction (4050-1) distal promoters

Negative strand

  1. Negative strand, positive direction: GTTAT at 3382, GTTAT at 3025, GTTTT at 2687, ATTTC at 2645, ATTAT at 2547, ATTTT at 2449, ATTTT at 2441, GTTTC at 2301, GTTTC at 2263, ATTTC at 1978, GTTTT at 147.
  2. Negative strand, positive direction: GAAAT at 3795, GTAAC at 3732, GAAAT at 3166, GAAAC at 2832, GAAAC at 2630, GAAAT at 2624, AAAAC at 2495, AAAAT at 2446, GAAAC at 2147, AAAAC at 292.

Positive strand

  1. Positive strand, positive direction: GTTAT at 3425, GTTAT at 3159, GTTTC at 3064, GTTAC at 2909, GTTTC at 2827, GTTTT at 2707, GTTTC at 2535, GTTTT at 2494, ATTTT at 2445, GTTTT at 2003, GTTAC at 227.

V box random dataset samplings

  1. Vboxr0: 56, GTTTT at 4376, GTTTT at 4351, ATTAT at 4226, GTTTC at 4220, ATTTT at 4202, ATTTT at 4129, ATTAT at 4100, ATTTT at 4003, ATTAC at 3777, GTTTC at 3709, ATTTT at 3695, GTTTC at 3686, GTTAC at 3681, ATTTC at 3665, ATTAC at 3606, ATTTC at 3514, GTTAT at 3471, GTTTT at 3182, GTTTT at 3080, GTTTC at 3031, ATTTT at 3024, GTTTC at 2917, GTTAT at 2894, ATTTC at 2826, GTTTT at 2566, GTTTC at 2344, GTTAT at 2177, ATTTT at 2145, GTTAT at 2140, GTTAC at 2097, GTTTT at 1970, GTTTC at 1921, ATTTC at 1911, ATTTT at 1820, GTTTT at 1671, ATTTT at 1569, ATTTT at 1460, ATTTT at 1451, GTTTT at 1411, ATTTT at 1193, ATTTC at 1167, GTTAC at 1053, GTTTC at 1038, GTTAC at 1012, ATTAT at 813, GTTTT at 605, GTTTT at 570, GTTAT at 558, ATTAC at 547, ATTTT at 494, ATTAT at 483, ATTTT at 475, GTTTT at 301, ATTAT at 276, GTTAC at 189, ATTTC at 130.
  2. Vboxr1: 46, GTTTT at 4492, GTTAC at 4413, GTTAC at 4385, ATTTT at 4220, GTTAT at 4123, ATTTC at 4035, GTTTT at 3837, GTTAC at 3718, GTTTC at 3689, ATTTT at 3606, ATTTC at 3585, ATTTT at 3453, ATTTC at 3409, GTTAT at 3376, ATTAT at 3145, GTTTT at 3030, GTTAC at 2962, GTTTC at 2812, ATTTT at 2566, GTTTC at 2394, GTTAC at 2344, GTTTC at 2163, ATTTT at 2141, GTTTT at 1663, GTTTC at 1656, ATTAT at 1542, ATTTC at 1494, GTTTT at 1482, GTTAT at 1472, ATTTC at 1292, ATTAT at 1264, ATTAT at 1261, ATTAT at 1232, ATTAT at 1027, GTTTT at 1020, ATTTT at 828, ATTTT at 789, ATTTT at 767, GTTTC at 549, ATTAC at 368, ATTAT at 363, ATTAT at 337, ATTTT at 307, GTTTT at 279, ATTAT at 251, GTTTC at 200.
  3. Vboxr2: 54, ATTTT at 4484, GTTAC at 4332, GTTAC at 4303, GTTAT at 4216, ATTTC at 4203, GTTTT at 4113, ATTAT at 4070, ATTAC at 4033, ATTTT at 3952, GTTTC at 3711, ATTAT at 3614, ATTTT at 3558, GTTTC at 3493, ATTTC at 3405, ATTTT at 3381, ATTTT at 3300, GTTTC at 3272, ATTTT at 3116, ATTTC at 2922, GTTTT at 2823, GTTAC at 2591, GTTTT at 2528, GTTTC at 2463, GTTTT at 2369, GTTTC at 2349, GTTAC at 2310, GTTTT at 2269, GTTAC at 2248, ATTAT at 2178, ATTAT at 1780, GTTTC at 1654, ATTAT at 1582, GTTTC at 1408, ATTTT at 1374, ATTTC at 1246, GTTTC at 1145, GTTTC at 1099, GTTTC at 1057, GTTTT at 1027, GTTTC at 1010, ATTAT at 848, ATTTC at 809, GTTTC at 739, GTTTC at 718, GTTTT at 585, GTTTC at 534, GTTAC at 481, GTTTT at 446, GTTTT at 408, GTTTC at 293, ATTTT at 262, GTTTT at 245, GTTTC at 66, ATTTT at 34.
  4. Vboxr3: 41, GTTAT at 4487, GTTAT at 4414, ATTTT at 4350, ATTTC at 4296, ATTTT at 4195, GTTTT at 4101, ATTTC at 4094, ATTTC at 4051, GTTTC at 4005, ATTAC at 3919, ATTAT at 3916, ATTAT at 3890, ATTTT at 3757, ATTTC at 3689, GTTTC at 3589, GTTAC at 3297, GTTTC at 3249, GTTAC at 3202, ATTTT at 3165, GTTTT at 3065, GTTTT at 3022, ATTAC at 2974, GTTTT at 2956, GTTTC at 2784, ATTAC at 2733, ATTTT at 2616, ATTTT at 2539, ATTTC at 2505, GTTTT at 2184, GTTTC at 2092, ATTTC at 2019, GTTAC at 1380, GTTTT at 1111, GTTTC at 1030, ATTTT at 925, ATTTC at 920, GTTAC at 454, ATTTC at 409, ATTTT at 403, GTTAT at 258, ATTTT at 170.
  5. Vboxr4: 45, GTTTT at 4536, GTTAC at 4520, GTTTT at 4424, GTTTC at 4214, GTTTC at 3869, ATTAC at 3753, ATTTC at 3673, ATTTT at 3664, GTTTT at 3533, ATTTT at 3515, ATTTT at 3354, ATTTC at 3018, ATTTT at 2887, GTTTC at 2791, ATTTT at 2768, GTTTC at 2732, GTTTC at 2677, ATTAC at 2647, GTTTT at 2633, ATTTC at 2547, GTTTT at 2425, ATTAT at 2328, GTTAT at 2293, ATTTT at 2255, ATTAT at 2252, ATTAC at 2235, GTTTC at 2121, GTTTT at 2074, GTTAC at 1935, GTTTC at 1598, GTTTT at 1381, GTTTC at 1187, ATTAC at 951, GTTAC at 887, ATTTT at 842, ATTAC at 621, ATTAT at 618, ATTTC at 540, GTTTC at 411, GTTTT at 361, GTTTC at 280, GTTTC at 249, ATTTT at 241, ATTAT at 165, GTTTT at 42.
  6. Vboxr5: 52, ATTTC at 4469, ATTTC at 4196, GTTTC at 4109, ATTAC at 4063, ATTAT at 3784, ATTTT at 3704, ATTTC at 3656, ATTAT at 3626, ATTTT at 3493, ATTTC at 3460, GTTTT at 3437, ATTTT at 3354, GTTTC at 3328, GTTAC at 3292, GTTAT at 3233, GTTTC at 3191, ATTAT at 3148, GTTTT at 2976, GTTTT at 2952, ATTTT at 2705, ATTTT at 2601, GTTTC at 2544, ATTAC at 2510, GTTTC at 2498, GTTTT at 2074, GTTTC at 1881, GTTTC at 1660, ATTTC at 1609, ATTAT at 1560, ATTTT at 1448, GTTTT at 1414, GTTTT at 1297, ATTAT at 1273, ATTTC at 1175, GTTTT at 1149, GTTTT at 1094, ATTAC at 1066, ATTTC at 996, GTTTC at 933, ATTAC at 893, ATTTT at 860, ATTAT at 853, GTTTT at 846, GTTTT at 831, ATTAC at 692, ATTAT at 648, GTTTT at 319, ATTTC at 294, ATTTT at 273, GTTTT at 268, GTTTC at 145, ATTTT at 111.
  7. Vboxr6: 43, ATTAC at 4495, GTTTC at 4480, GTTTC at 4293, ATTTC at 4266, ATTAT at 4263, ATTAT at 3866, ATTAT at 3755, ATTAC at 3684, ATTTC at 3265, GTTTT at 3014, GTTTC at 2965, GTTAT at 2806, ATTTT at 2799, GTTTT at 2777, ATTTC at 2742, ATTTT at 2650, ATTAC at 2526, GTTAT at 2523, ATTAC at 2462, GTTTT at 2415, GTTTC at 2345, ATTAC at 2294, ATTTT at 2231, GTTAC at 2117, GTTTT at 2078, GTTAC at 1889, ATTTC at 1879, ATTAC at 1784, GTTAT at 1749, GTTTT at 1700, ATTTT at 1655, ATTTT at 1649, GTTAC at 1420, GTTAT at 1414, GTTTC at 1318, ATTTT at 1306, GTTTT at 1118, GTTTC at 1000, ATTTC at 816, GTTTT at 567, ATTAT at 470, ATTTC at 403, ATTAT at 184.
  8. Vboxr7: 33, GTTAT at 4522, ATTAT at 4517, GTTTT at 4268, GTTAT at 4081, GTTAT at 3773, ATTAT at 3597, ATTTT at 3453, ATTAC at 3376, ATTTC at 3242, GTTTT at 2821, ATTTT at 2517, ATTAC at 2404, ATTAC at 2335, ATTTT at 2243, GTTAC at 2199, GTTTT at 2180, GTTTC at 2119, GTTAC at 2033, ATTTT at 1894, GTTAT at 1806, ATTAT at 1651, ATTAC at 1572, GTTAC at 1394, ATTTT at 1342, GTTTC at 1089, GTTTC at 767, ATTTT at 709, GTTTC at 609, ATTTT at 489, GTTTT at 460, GTTTT at 347, ATTAT at 309, GTTTC at 24.
  9. Vboxr8: 54, ATTTC at 4542, GTTTT at 4398, GTTAC at 4369, ATTTC at 4355, GTTTT at 4242, ATTAC at 3967, GTTTC at 3776, GTTTT at 3604, GTTTT at 3570, ATTAT at 3507, GTTTT at 3375, ATTTT at 3335, GTTAC at 3229, GTTTT at 3173, ATTTC at 3002, ATTTT at 2541, GTTTT at 2394, GTTTC at 2383, ATTTT at 2289, ATTTC at 2222, ATTAT at 2186, GTTTT at 2153, ATTTT at 2120, ATTAC at 2091, ATTAT at 2084, ATTAT at 1960, GTTTC at 1889, GTTTT at 1851, GTTTT at 1833, ATTAC at 1820, ATTTT at 1812, ATTTC at 1802, GTTTC at 1786, ATTAC at 1723, GTTTC at 1551, GTTTC at 1531, ATTTC at 1480, ATTAT at 1364, GTTAT at 1335, GTTTC at 1314, GTTAT at 1169, ATTTC at 1158, ATTAT at 1075, GTTTC at 982, GTTTT at 952, ATTTC at 931, ATTTC at 872, ATTTT at 740, GTTAT at 552, ATTTT at 483, GTTTC at 368, ATTAC at 228, ATTTT at 166, GTTAT at 92.
  10. Vboxr9: 44, ATTTT at 4271, GTTAC at 4247, GTTAT at 4176, GTTTC at 4160, ATTTT at 3802, GTTAC at 3731, GTTAC at 3685, GTTTT at 3385, GTTTT at 3208, GTTTC at 3028, ATTTC at 2927, GTTTC at 2899, GTTAT at 2893, ATTTC at 2783, ATTTT at 2525, ATTTT at 2511, GTTAC at 2357, ATTTT at 2342, ATTTT at 2140, ATTTC at 2126, GTTAT at 2121, GTTAC at 2010, GTTTC at 1735, GTTAC at 1704, ATTTC at 1653, ATTTT at 1351, GTTTC at 1327, GTTTT at 1247, GTTTC at 1238, ATTAC at 1168, ATTAT at 1158, GTTTT at 1124, GTTTT at 1078, GTTAC at 917, ATTTT at 834, ATTAT at 806, GTTTT at 717, GTTTT at 706, GTTAC at 548, ATTTT at 467, GTTTT at 348, GTTAC at 172, ATTTT at 159, GTTTC at 97.
  11. Vboxr0ci: 55, AAAAC at 4431, AAAAC at 4297, GAAAC at 4194, GTAAT at 4151, GAAAT at 4126, GAAAT at 4022, GAAAT at 3914, ATAAT at 3603, ATAAT at 3579, ATAAC at 3539, GAAAC at 3417, AAAAT at 3172, ATAAT at 3125, AAAAC at 2738, AAAAT at 2696, GTAAC at 2624, GTAAC at 2608, GTAAC at 2410, AAAAC at 2396, AAAAT at 2334, ATAAT at 2262, AAAAT at 2259, GTAAC at 2221, GAAAC at 2200, GAAAT at 2156, GTAAC at 2131, AAAAC at 2085, AAAAC at 2009, GAAAC at 1932, AAAAT at 1812, ATAAC at 1791, AAAAT at 1556, AAAAC at 1500, ATAAT at 1491, GAAAT at 1448, ATAAC at 1141, GAAAC at 902, GAAAC at 831, AAAAT at 797, AAAAT at 770, GAAAT at 749, AAAAC at 635, GAAAT at 544, AAAAC at 436, ATAAC at 430, GAAAC at 252, AAAAC at 237, GAAAC at 216, AAAAC at 201, AAAAT at 195, GTAAC at 183, AAAAC at 170, ATAAT at 148, ATAAT at 145, GAAAT at 114.
  12. Vboxr1ci: 44, AAAAC at 4454, GAAAC at 4439, AAAAC at 4432, ATAAT at 4335, GTAAC at 4317, GTAAC at 4172, GTAAC at 4027, GAAAT at 3970, ATAAT at 3937, AAAAT at 3883, GAAAC at 3873, GAAAC at 3795, AAAAC at 3601, AAAAT at 3591, GAAAC at 3534, AAAAT at 3489, ATAAC at 3474, AAAAT at 3363, GTAAT at 3330, AAAAC at 3271, ATAAT at 3083, AAAAT at 3072, AAAAC at 2856, AAAAC at 2715, GTAAC at 2491, GAAAT at 2423, GAAAC at 2244, ATAAC at 2156, GAAAT at 1941, AAAAT at 1933, AAAAC at 1883, AAAAT at 1869, AAAAC at 1819, GTAAC at 1725, AAAAC at 1708, ATAAC at 1592, GAAAT at 1422, AAAAC at 1052, AAAAT at 1001, GTAAT at 805, AAAAC at 782, GTAAT at 538, GAAAC at 384, AAAAT at 166.
  13. Vboxr2ci: 42, ATAAC at 4472, AAAAC at 4323, GTAAT at 4025, ATAAT at 3983, GTAAT at 3980, ATAAT at 3945, ATAAC at 3823, AAAAT at 3798, GTAAT at 3447, GAAAT at 3441, AAAAC at 3208, GTAAT at 3113, GTAAC at 3018, GAAAC at 2952, GTAAC at 2947, AAAAT at 2919, AAAAC at 2781, AAAAT at 2665, ATAAT at 2510, AAAAT at 2382, AAAAC at 2189, GAAAT at 2128, AAAAT at 2083, AAAAC at 2069, GAAAC at 1991, AAAAC at 1850, ATAAT at 1838, GAAAC at 1629, GAAAT at 1332, ATAAC at 1139, ATAAT at 989, GAAAC at 946, AAAAC at 940, GTAAT at 845, GTAAT at 826, ATAAT at 793, GAAAC at 579, AAAAT at 369, AAAAT at 348, AAAAC at 310, ATAAT at 240, AAAAT at 185.
  14. RDr3ci: 0.
  15. RDr4ci: 0.
  16. RDr5ci: 0.
  17. RDr6ci: 0.
  18. RDr7ci: 0.
  19. RDr8ci: 0.
  20. RDr9ci: 0.

Vboxr arbitrary (evens) (4560-2846) UTRs

  1. Vboxr0: GTTTT at 4376, GTTTT at 4351, ATTAT at 4226, GTTTC at 4220, ATTTT at 4202, ATTTT at 4129, ATTAT at 4100, ATTTT at 4003, ATTAC at 3777, GTTTC at 3709, ATTTT at 3695, GTTTC at 3686, GTTAC at 3681, ATTTC at 3665, ATTAC at 3606, ATTTC at 3514, GTTAT at 3471, GTTTT at 3182, GTTTT at 3080, GTTTC at 3031, ATTTT at 3024, GTTTC at 2917, GTTAT at 2894.
  2. Vboxr2: ATTTT at 4484, GTTAC at 4332, GTTAC at 4303, GTTAT at 4216, ATTTC at 4203, GTTTT at 4113, ATTAT at 4070, ATTAC at 4033, ATTTT at 3952, GTTTC at 3711, ATTAT at 3614, ATTTT at 3558, GTTTC at 3493, ATTTC at 3405, ATTTT at 3381, ATTTT at 3300, GTTTC at 3272, ATTTT at 3116, ATTTC at 2922.
  3. Vboxr4: GTTTT at 4536, GTTAC at 4520, GTTTT at 4424, GTTTC at 4214, GTTTC at 3869, ATTAC at 3753, ATTTC at 3673, ATTTT at 3664, GTTTT at 3533, ATTTT at 3515, ATTTT at 3354, ATTTC at 3018, ATTTT at 2887.
  4. Vboxr6: ATTAC at 4495, GTTTC at 4480, GTTTC at 4293, ATTTC at 4266, ATTAT at 4263, ATTAT at 3866, ATTAT at 3755, ATTAC at 3684, ATTTC at 3265, GTTTT at 3014, GTTTC at 2965.
  5. Vboxr8: ATTTC at 4542, GTTTT at 4398, GTTAC at 4369, ATTTC at 4355, GTTTT at 4242, ATTAC at 3967, GTTTC at 3776, GTTTT at 3604, GTTTT at 3570, ATTAT at 3507, GTTTT at 3375, ATTTT at 3335, GTTAC at 3229, GTTTT at 3173, ATTTC at 3002.
  6. Vboxr0ci: AAAAC at 4431, AAAAC at 4297, GAAAC at 4194, GTAAT at 4151, GAAAT at 4126, GAAAT at 4022, GAAAT at 3914, ATAAT at 3603, ATAAT at 3579, ATAAC at 3539, GAAAC at 3417, AAAAT at 3172, ATAAT at 3125.
  7. Vboxr2ci: ATAAC at 4472, AAAAC at 4323, GTAAT at 4025, ATAAT at 3983, GTAAT at 3980, ATAAT at 3945, ATAAC at 3823, AAAAT at 3798, GTAAT at 3447, GAAAT at 3441, AAAAC at 3208, GTAAT at 3113, GTAAC at 3018, GAAAC at 2952, GTAAC at 2947, AAAAT at 2919.

Vboxr alternate (odds) (4560-2846) UTRs

  1. Vboxr1: GTTTT at 4492, GTTAC at 4413, GTTAC at 4385, ATTTT at 4220, GTTAT at 4123, ATTTC at 4035, GTTTT at 3837, GTTAC at 3718, GTTTC at 3689, ATTTT at 3606, ATTTC at 3585, ATTTT at 3453, ATTTC at 3409, GTTAT at 3376, ATTAT at 3145, GTTTT at 3030, GTTAC at 2962.
  2. Vboxr3: GTTAT at 4487, GTTAT at 4414, ATTTT at 4350, ATTTC at 4296, ATTTT at 4195, GTTTT at 4101, ATTTC at 4094, ATTTC at 4051, GTTTC at 4005, ATTAC at 3919, ATTAT at 3916, ATTAT at 3890, ATTTT at 3757, ATTTC at 3689, GTTTC at 3589, GTTAC at 3297, GTTTC at 3249, GTTAC at 3202, ATTTT at 3165, GTTTT at 3065, GTTTT at 3022, ATTAC at 2974, GTTTT at 2956.
  3. Vboxr5: ATTTC at 4469, ATTTC at 4196, GTTTC at 4109, ATTAC at 4063, ATTAT at 3784, ATTTT at 3704, ATTTC at 3656, ATTAT at 3626, ATTTT at 3493, ATTTC at 3460, GTTTT at 3437, ATTTT at 3354, GTTTC at 3328, GTTAC at 3292, GTTAT at 3233, GTTTC at 3191, ATTAT at 3148, GTTTT at 2976, GTTTT at 2952.
  4. Vboxr7: GTTAT at 4522, ATTAT at 4517, GTTTT at 4268, GTTAT at 4081, GTTAT at 3773, ATTAT at 3597, ATTTT at 3453, ATTAC at 3376, ATTTC at 3242.
  5. Vboxr9: ATTTT at 4271, GTTAC at 4247, GTTAT at 4176, GTTTC at 4160, ATTTT at 3802, GTTAC at 3731, GTTAC at 3685, GTTTT at 3385, GTTTT at 3208, GTTTC at 3028, ATTTC at 2927, GTTTC at 2899, GTTAT at 2893.
  6. Vboxr1ci: AAAAC at 4454, GAAAC at 4439, AAAAC at 4432, ATAAT at 4335, GTAAC at 4317, GTAAC at 4172, GTAAC at 4027, GAAAT at 3970, ATAAT at 3937, AAAAT at 3883, GAAAC at 3873, GAAAC at 3795, AAAAC at 3601, AAAAT at 3591, GAAAC at 3534, AAAAT at 3489, ATAAC at 3474, AAAAT at 3363, GTAAT at 3330, AAAAC at 3271, ATAAT at 3083, AAAAT at 3072, AAAAC at 2856.

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

  1. Vboxr0: ATTTC at 2826.
  2. Vboxr2: GTTTT at 2823.

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

  1. Vboxr1: GTTTC at 2812.
  2. Vboxr7: GTTTT at 2821.

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

  1. Vboxr1: GTTAC at 4413, GTTAC at 4385.
  2. Vboxr3: GTTAT at 4414, ATTTT at 4350, ATTTC at 4296.
  3. Vboxr7: GTTTT at 4268.
  4. Vboxr9: ATTTT at 4271.
  5. Vboxr1ci: GAAAC at 4439, AAAAC at 4432, ATAAT at 4335, GTAAC at 4317.

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

  1. Vboxr0: GTTTT at 4376, GTTTT at 4351.
  2. Vboxr2: GTTAC at 4332, GTTAC at 4303.
  3. Vboxr4: GTTTT at 4424.
  4. Vboxr6: GTTTC at 4293, ATTTC at 4266.
  5. Vboxr8: GTTTT at 4398, GTTAC at 4369, ATTTC at 4355.
  6. Vboxr0ci: AAAAC at 4431, AAAAC at 4297.
  7. Vboxr2ci: AAAAC at 4323.

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

  1. Vboxr4: GTTTC at 2791, ATTTT at 2768, GTTTC at 2732, GTTTC at 2677, ATTAC at 2647, GTTTT at 2633.
  2. Vboxr6: GTTAT at 2806, ATTTT at 2799, GTTTT at 2777, ATTTC at 2742, ATTTT at 2650.
  3. Vboxr0ci: AAAAC at 2738, AAAAT at 2696, GTAAC at 2624, GTAAC at 2608.
  4. Vboxr2ci: AAAAC at 2781, AAAAT at 2665.

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

  1. Vboxr3: GTTTC at 2784, ATTAC at 2733, ATTTT at 2616.
  2. Vboxr5: ATTTT at 2705, ATTTT at 2601.
  3. Vboxr9: ATTTC at 2783.
  4. Vboxr1ci: AAAAC at 2715.

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

  1. Vboxr1: ATTTT at 4220, GTTAT at 4123.
  2. Vboxr3: ATTTT at 4195, GTTTT at 4101, ATTTC at 4094, ATTTC at 4051.
  3. Vboxr5: ATTTC at 4196, GTTTC at 4109, ATTAC at 4063.
  4. Vboxr7: GTTAT at 4081.
  5. Vboxr9: GTTAC at 4247, GTTAT at 4176, GTTTC at 4160.
  6. Vboxr1ci: GTAAC at 4172.

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

  1. Vboxr0: ATTAT at 4226, GTTTC at 4220, ATTTT at 4202, ATTTT at 4129, ATTAT at 4100.
  2. Vboxr2: GTTAT at 4216, ATTTC at 4203, GTTTT at 4113, ATTAT at 4070.
  3. Vboxr4: GTTTC at 4214.
  4. Vboxr6: ATTAT at 4263.
  5. Vboxr8: GTTTT at 4242.
  6. Vboxr0ci: GAAAC at 4194, GTAAT at 4151, GAAAT at 4126.

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

  1. Vboxr0: GTTTT at 2566, GTTTC at 2344, GTTAT at 2177, ATTTT at 2145, GTTAT at 2140, GTTAC at 2097, GTTTT at 1970, GTTTC at 1921, ATTTC at 1911, ATTTT at 1820, GTTTT at 1671, ATTTT at 1569, ATTTT at 1460, ATTTT at 1451, GTTTT at 1411, ATTTT at 1193, ATTTC at 1167, GTTAC at 1053, GTTTC at 1038, GTTAC at 1012, ATTAT at 813, GTTTT at 605, GTTTT at 570, GTTAT at 558, ATTAC at 547, ATTTT at 494, ATTAT at 483, ATTTT at 475, GTTTT at 301, ATTAT at 276, GTTAC at 189, ATTTC at 130.
  2. Vboxr2: GTTAC at 2591, GTTTT at 2528, GTTTC at 2463, GTTTT at 2369, GTTTC at 2349, GTTAC at 2310, GTTTT at 2269, GTTAC at 2248, ATTAT at 2178, ATTAT at 1780, GTTTC at 1654, ATTAT at 1582, GTTTC at 1408, ATTTT at 1374, ATTTC at 1246, GTTTC at 1145, GTTTC at 1099, GTTTC at 1057, GTTTT at 1027, GTTTC at 1010, ATTAT at 848, ATTTC at 809, GTTTC at 739, GTTTC at 718, GTTTT at 585, GTTTC at 534, GTTAC at 481, GTTTT at 446, GTTTT at 408, GTTTC at 293, ATTTT at 262, GTTTT at 245, GTTTC at 66, ATTTT at 34.
  3. Vboxr4: ATTTC at 2547, GTTTT at 2425, ATTAT at 2328, GTTAT at 2293, ATTTT at 2255, ATTAT at 2252, ATTAC at 2235, GTTTC at 2121, GTTTT at 2074, GTTAC at 1935, GTTTC at 1598, GTTTT at 1381, GTTTC at 1187, ATTAC at 951, GTTAC at 887, ATTTT at 842, ATTAC at 621, ATTAT at 618, ATTTC at 540, GTTTC at 411, GTTTT at 361, GTTTC at 280, GTTTC at 249, ATTTT at 241, ATTAT at 165, GTTTT at 42.
  4. Vboxr6: ATTAC at 2526, GTTAT at 2523, ATTAC at 2462, GTTTT at 2415, GTTTC at 2345, ATTAC at 2294, ATTTT at 2231, GTTAC at 2117, GTTTT at 2078, GTTAC at 1889, ATTTC at 1879, ATTAC at 1784, GTTAT at 1749, GTTTT at 1700, ATTTT at 1655, ATTTT at 1649, GTTAC at 1420, GTTAT at 1414, GTTTC at 1318, ATTTT at 1306, GTTTT at 1118, GTTTC at 1000, ATTTC at 816, GTTTT at 567, ATTAT at 470, ATTTC at 403, ATTAT at 184.
  5. Vboxr8: ATTTT at 2541, GTTTT at 2394, GTTTC at 2383, ATTTT at 2289, ATTTC at 2222, ATTAT at 2186, GTTTT at 2153, ATTTT at 2120, ATTAC at 2091, ATTAT at 2084, ATTAT at 1960, GTTTC at 1889, GTTTT at 1851, GTTTT at 1833, ATTAC at 1820, ATTTT at 1812, ATTTC at 1802, GTTTC at 1786, ATTAC at 1723, GTTTC at 1551, GTTTC at 1531, ATTTC at 1480, ATTAT at 1364, GTTAT at 1335, GTTTC at 1314, GTTAT at 1169, ATTTC at 1158, ATTAT at 1075, GTTTC at 982, GTTTT at 952, ATTTC at 931, ATTTC at 872, ATTTT at 740, GTTAT at 552, ATTTT at 483, GTTTC at 368, ATTAC at 228, ATTTT at 166, GTTAT at 92.
  6. Vboxr0ci: GTAAC at 2410, AAAAC at 2396, AAAAT at 2334, ATAAT at 2262, AAAAT at 2259, GTAAC at 2221, GAAAC at 2200, GAAAT at 2156, GTAAC at 2131, AAAAC at 2085, AAAAC at 2009, GAAAC at 1932, AAAAT at 1812, ATAAC at 1791, AAAAT at 1556, AAAAC at 1500, ATAAT at 1491, GAAAT at 1448, ATAAC at 1141, GAAAC at 902, GAAAC at 831, AAAAT at 797, AAAAT at 770, GAAAT at 749, AAAAC at 635, GAAAT at 544, AAAAC at 436, ATAAC at 430, GAAAC at 252, AAAAC at 237, GAAAC at 216, AAAAC at 201, AAAAT at 195, GTAAC at 183, AAAAC at 170, ATAAT at 148, ATAAT at 145, GAAAT at 114.
  7. Vboxr2ci: ATAAT at 2510, AAAAT at 2382, AAAAC at 2189, GAAAT at 2128, AAAAT at 2083, AAAAC at 2069, GAAAC at 1991, AAAAC at 1850, ATAAT at 1838, GAAAC at 1629, GAAAT at 1332, ATAAC at 1139, ATAAT at 989, GAAAC at 946, AAAAC at 940, GTAAT at 845, GTAAT at 826, ATAAT at 793, GAAAC at 579, AAAAT at 369, AAAAT at 348, AAAAC at 310, ATAAT at 240, AAAAT at 185.

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

  1. Vboxr1: ATTTT at 2566, GTTTC at 2394, GTTAC at 2344, GTTTC at 2163, ATTTT at 2141, GTTTT at 1663, GTTTC at 1656, ATTAT at 1542, ATTTC at 1494, GTTTT at 1482, GTTAT at 1472, ATTTC at 1292, ATTAT at 1264, ATTAT at 1261, ATTAT at 1232, ATTAT at 1027, GTTTT at 1020, ATTTT at 828, ATTTT at 789, ATTTT at 767, GTTTC at 549, ATTAC at 368, ATTAT at 363, ATTAT at 337, ATTTT at 307, GTTTT at 279, ATTAT at 251, GTTTC at 200.
  2. Vboxr3: ATTTT at 2539, ATTTC at 2505, GTTTT at 2184, GTTTC at 2092, ATTTC at 2019, GTTAC at 1380, GTTTT at 1111, GTTTC at 1030, ATTTT at 925, ATTTC at 920, GTTAC at 454, ATTTC at 409, ATTTT at 403, GTTAT at 258, ATTTT at 170.
  3. Vboxr5: GTTTC at 2544, ATTAC at 2510, GTTTC at 2498, GTTTT at 2074, GTTTC at 1881, GTTTC at 1660, ATTTC at 1609, ATTAT at 1560, ATTTT at 1448, GTTTT at 1414, GTTTT at 1297, ATTAT at 1273, ATTTC at 1175, GTTTT at 1149, GTTTT at 1094, ATTAC at 1066, ATTTC at 996, GTTTC at 933, ATTAC at 893, ATTTT at 860, ATTAT at 853, GTTTT at 846, GTTTT at 831, ATTAC at 692, ATTAT at 648, GTTTT at 319, ATTTC at 294, ATTTT at 273, GTTTT at 268, GTTTC at 145, ATTTT at 111.
  4. Vboxr7: ATTTT at 2517, ATTAC at 2404, ATTAC at 2335, ATTTT at 2243, GTTAC at 2199, GTTTT at 2180, GTTTC at 2119, GTTAC at 2033, ATTTT at 1894, GTTAT at 1806, ATTAT at 1651, ATTAC at 1572, GTTAC at 1394, ATTTT at 1342, GTTTC at 1089, GTTTC at 767, ATTTT at 709, GTTTC at 609, ATTTT at 489, GTTTT at 460, GTTTT at 347, ATTAT at 309, GTTTC at 24.
  5. Vboxr9: ATTTT at 2525, ATTTT at 2511, GTTAC at 2357, ATTTT at 2342, ATTTT at 2140, ATTTC at 2126, GTTAT at 2121, GTTAC at 2010, GTTTC at 1735, GTTAC at 1704, ATTTC at 1653, ATTTT at 1351, GTTTC at 1327, GTTTT at 1247, GTTTC at 1238, ATTAC at 1168, ATTAT at 1158, GTTTT at 1124, GTTTT at 1078, GTTAC at 917, ATTTT at 834, ATTAT at 806, GTTTT at 717, GTTTT at 706, GTTAC at 548, ATTTT at 467, GTTTT at 348, GTTAC at 172, ATTTT at 159, GTTTC at 97.
  6. Vboxr1ci: GTAAC at 2491, GAAAT at 2423, GAAAC at 2244, ATAAC at 2156, GAAAT at 1941, AAAAT at 1933, AAAAC at 1883, AAAAT at 1869, AAAAC at 1819, GTAAC at 1725, AAAAC at 1708, ATAAC at 1592, GAAAT at 1422, AAAAC at 1052, AAAAT at 1001, GTAAT at 805, AAAAC at 782, GTAAT at 538, GAAAC at 384, AAAAT at 166.

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

  1. Vboxr1: ATTTC at 4035, GTTTT at 3837, GTTAC at 3718, GTTTC at 3689, ATTTT at 3606, ATTTC at 3585, ATTTT at 3453, ATTTC at 3409, GTTAT at 3376, ATTAT at 3145, GTTTT at 3030, GTTAC at 2962, GTTTC at 2812, ATTTT at 2566, GTTTC at 2394, GTTAC at 2344, GTTTC at 2163, ATTTT at 2141, GTTTT at 1663, GTTTC at 1656, ATTAT at 1542, ATTTC at 1494, GTTTT at 1482, GTTAT at 1472, ATTTC at 1292, ATTAT at 1264, ATTAT at 1261, ATTAT at 1232, ATTAT at 1027, GTTTT at 1020, ATTTT at 828, ATTTT at 789, ATTTT at 767, GTTTC at 549, ATTAC at 368, ATTAT at 363, ATTAT at 337, ATTTT at 307, GTTTT at 279, ATTAT at 251, GTTTC at 200.
  2. Vboxr3: GTTTC at 4005, ATTAC at 3919, ATTAT at 3916, ATTAT at 3890, ATTTT at 3757, ATTTC at 3689, GTTTC at 3589, GTTAC at 3297, GTTTC at 3249, GTTAC at 3202, ATTTT at 3165, GTTTT at 3065, GTTTT at 3022, ATTAC at 2974, GTTTT at 2956, GTTTC at 2784, ATTAC at 2733, ATTTT at 2616, ATTTT at 2539, ATTTC at 2505, GTTTT at 2184, GTTTC at 2092, ATTTC at 2019, GTTAC at 1380, GTTTT at 1111, GTTTC at 1030, ATTTT at 925, ATTTC at 920, GTTAC at 454, ATTTC at 409, ATTTT at 403, GTTAT at 258, ATTTT at 170.
  3. Vboxr5: ATTAT at 3784, ATTTT at 3704, ATTTC at 3656, ATTAT at 3626, ATTTT at 3493, ATTTC at 3460, GTTTT at 3437, ATTTT at 3354, GTTTC at 3328, GTTAC at 3292, GTTAT at 3233, GTTTC at 3191, ATTAT at 3148, GTTTT at 2976, GTTTT at 2952, ATTTT at 2705, ATTTT at 2601, GTTTC at 2544, ATTAC at 2510, GTTTC at 2498, GTTTT at 2074, GTTTC at 1881, GTTTC at 1660, ATTTC at 1609, ATTAT at 1560, ATTTT at 1448, GTTTT at 1414, GTTTT at 1297, ATTAT at 1273, ATTTC at 1175, GTTTT at 1149, GTTTT at 1094, ATTAC at 1066, ATTTC at 996, GTTTC at 933, ATTAC at 893, ATTTT at 860, ATTAT at 853, GTTTT at 846, GTTTT at 831, ATTAC at 692, ATTAT at 648, GTTTT at 319, ATTTC at 294, ATTTT at 273, GTTTT at 268, GTTTC at 145, ATTTT at 111.
  4. Vboxr7: GTTAT at 3773, ATTAT at 3597, ATTTT at 3453, ATTAC at 3376, ATTTC at 3242, GTTTT at 2821, ATTTT at 2517, ATTAC at 2404, ATTAC at 2335, ATTTT at 2243, GTTAC at 2199, GTTTT at 2180, GTTTC at 2119, GTTAC at 2033, ATTTT at 1894, GTTAT at 1806, ATTAT at 1651, ATTAC at 1572, GTTAC at 1394, ATTTT at 1342, GTTTC at 1089, GTTTC at 767, ATTTT at 709, GTTTC at 609, ATTTT at 489, GTTTT at 460, GTTTT at 347, ATTAT at 309, GTTTC at 24.
  5. Vboxr9: ATTTT at 3802, GTTAC at 3731, GTTAC at 3685, GTTTT at 3385, GTTTT at 3208, GTTTC at 3028, ATTTC at 2927, GTTTC at 2899, GTTAT at 2893, ATTTC at 2783, ATTTT at 2525, ATTTT at 2511, GTTAC at 2357, ATTTT at 2342, ATTTT at 2140, ATTTC at 2126, GTTAT at 2121, GTTAC at 2010, GTTTC at 1735, GTTAC at 1704, ATTTC at 1653, ATTTT at 1351, GTTTC at 1327, GTTTT at 1247, GTTTC at 1238, ATTAC at 1168, ATTAT at 1158, GTTTT at 1124, GTTTT at 1078, GTTAC at 917, ATTTT at 834, ATTAT at 806, GTTTT at 717, GTTTT at 706, GTTAC at 548, ATTTT at 467, GTTTT at 348, GTTAC at 172, ATTTT at 159, GTTTC at 97.
  6. Vboxr1ci: GTAAC at 4027, GAAAT at 3970, ATAAT at 3937, AAAAT at 3883, GAAAC at 3873, GAAAC at 3795, AAAAC at 3601, AAAAT at 3591, GAAAC at 3534, AAAAT at 3489, ATAAC at 3474, AAAAT at 3363, GTAAT at 3330, AAAAC at 3271, ATAAT at 3083, AAAAT at 3072, AAAAC at 2856, AAAAC at 2715, GTAAC at 2491, GAAAT at 2423, GAAAC at 2244, ATAAC at 2156, GAAAT at 1941, AAAAT at 1933, AAAAC at 1883, AAAAT at 1869, AAAAC at 1819, GTAAC at 1725, AAAAC at 1708, ATAAC at 1592, GAAAT at 1422, AAAAC at 1052, AAAAT at 1001, GTAAT at 805, AAAAC at 782, GTAAT at 538, GAAAC at 384, AAAAT at 166.

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

  1. Vboxr0: ATTTT at 4003, ATTAC at 3777, GTTTC at 3709, ATTTT at 3695, GTTTC at 3686, GTTAC at 3681, ATTTC at 3665, ATTAC at 3606, ATTTC at 3514, GTTAT at 3471, GTTTT at 3182, GTTTT at 3080, GTTTC at 3031, ATTTT at 3024, GTTTC at 2917, GTTAT at 2894, ATTTC at 2826, GTTTT at 2566, GTTTC at 2344, GTTAT at 2177, ATTTT at 2145, GTTAT at 2140, GTTAC at 2097, GTTTT at 1970, GTTTC at 1921, ATTTC at 1911, ATTTT at 1820, GTTTT at 1671, ATTTT at 1569, ATTTT at 1460, ATTTT at 1451, GTTTT at 1411, ATTTT at 1193, ATTTC at 1167, GTTAC at 1053, GTTTC at 1038, GTTAC at 1012, ATTAT at 813, GTTTT at 605, GTTTT at 570, GTTAT at 558, ATTAC at 547, ATTTT at 494, ATTAT at 483, ATTTT at 475, GTTTT at 301, ATTAT at 276, GTTAC at 189, ATTTC at 130.
  2. Vboxr2: ATTAC at 4033, ATTTT at 3952, GTTTC at 3711, ATTAT at 3614, ATTTT at 3558, GTTTC at 3493, ATTTC at 3405, ATTTT at 3381, ATTTT at 3300, GTTTC at 3272, ATTTT at 3116, ATTTC at 2922, GTTTT at 2823, GTTAC at 2591, GTTTT at 2528, GTTTC at 2463, GTTTT at 2369, GTTTC at 2349, GTTAC at 2310, GTTTT at 2269, GTTAC at 2248, ATTAT at 2178, ATTAT at 1780, GTTTC at 1654, ATTAT at 1582, GTTTC at 1408, ATTTT at 1374, ATTTC at 1246, GTTTC at 1145, GTTTC at 1099, GTTTC at 1057, GTTTT at 1027, GTTTC at 1010, ATTAT at 848, ATTTC at 809, GTTTC at 739, GTTTC at 718, GTTTT at 585, GTTTC at 534, GTTAC at 481, GTTTT at 446, GTTTT at 408, GTTTC at 293, ATTTT at 262, GTTTT at 245, GTTTC at 66, ATTTT at 34.
  3. Vboxr4: GTTTC at 3869, ATTAC at 3753, ATTTC at 3673, ATTTT at 3664, GTTTT at 3533, ATTTT at 3515, ATTTT at 3354, ATTTC at 3018, ATTTT at 2887, GTTTC at 2791, ATTTT at 2768, GTTTC at 2732, GTTTC at 2677, ATTAC at 2647, GTTTT at 2633, ATTTC at 2547, GTTTT at 2425, ATTAT at 2328, GTTAT at 2293, ATTTT at 2255, ATTAT at 2252, ATTAC at 2235, GTTTC at 2121, GTTTT at 2074, GTTAC at 1935, GTTTC at 1598, GTTTT at 1381, GTTTC at 1187, ATTAC at 951, GTTAC at 887, ATTTT at 842, ATTAC at 621, ATTAT at 618, ATTTC at 540, GTTTC at 411, GTTTT at 361, GTTTC at 280, GTTTC at 249, ATTTT at 241, ATTAT at 165, GTTTT at 42.
  4. Vboxr6: ATTAT at 3866, ATTAT at 3755, ATTAC at 3684, ATTTC at 3265, GTTTT at 3014, GTTTC at 2965, GTTAT at 2806, ATTTT at 2799, GTTTT at 2777, ATTTC at 2742, ATTTT at 2650, ATTAC at 2526, GTTAT at 2523, ATTAC at 2462, GTTTT at 2415, GTTTC at 2345, ATTAC at 2294, ATTTT at 2231, GTTAC at 2117, GTTTT at 2078, GTTAC at 1889, ATTTC at 1879, ATTAC at 1784, GTTAT at 1749, GTTTT at 1700, ATTTT at 1655, ATTTT at 1649, GTTAC at 1420, GTTAT at 1414, GTTTC at 1318, ATTTT at 1306, GTTTT at 1118, GTTTC at 1000, ATTTC at 816, GTTTT at 567, ATTAT at 470, ATTTC at 403, ATTAT at 184.
  5. Vboxr8: ATTAC at 3967, GTTTC at 3776, GTTTT at 3604, GTTTT at 3570, ATTAT at 3507, GTTTT at 3375, ATTTT at 3335, GTTAC at 3229, GTTTT at 3173, ATTTC at 3002, ATTTT at 2541, GTTTT at 2394, GTTTC at 2383, ATTTT at 2289, ATTTC at 2222, ATTAT at 2186, GTTTT at 2153, ATTTT at 2120, ATTAC at 2091, ATTAT at 2084, ATTAT at 1960, GTTTC at 1889, GTTTT at 1851, GTTTT at 1833, ATTAC at 1820, ATTTT at 1812, ATTTC at 1802, GTTTC at 1786, ATTAC at 1723, GTTTC at 1551, GTTTC at 1531, ATTTC at 1480, ATTAT at 1364, GTTAT at 1335, GTTTC at 1314, GTTAT at 1169, ATTTC at 1158, ATTAT at 1075, GTTTC at 982, GTTTT at 952, ATTTC at 931, ATTTC at 872, ATTTT at 740, GTTAT at 552, ATTTT at 483, GTTTC at 368, ATTAC at 228, ATTTT at 166, GTTAT at 92.
  6. Vboxr0ci: GAAAT at 4022, GAAAT at 3914, ATAAT at 3603, ATAAT at 3579, ATAAC at 3539, GAAAC at 3417, AAAAT at 3172, ATAAT at 3125, AAAAC at 2738, AAAAT at 2696, GTAAC at 2624, GTAAC at 2608, GTAAC at 2410, AAAAC at 2396, AAAAT at 2334, ATAAT at 2262, AAAAT at 2259, GTAAC at 2221, GAAAC at 2200, GAAAT at 2156, GTAAC at 2131, AAAAC at 2085, AAAAC at 2009, GAAAC at 1932, AAAAT at 1812, ATAAC at 1791, AAAAT at 1556, AAAAC at 1500, ATAAT at 1491, GAAAT at 1448, ATAAC at 1141, GAAAC at 902, GAAAC at 831, AAAAT at 797, AAAAT at 770, GAAAT at 749, AAAAC at 635, GAAAT at 544, AAAAC at 436, ATAAC at 430, GAAAC at 252, AAAAC at 237, GAAAC at 216, AAAAC at 201, AAAAT at 195, GTAAC at 183, AAAAC at 170, ATAAT at 148, ATAAT at 145, GAAAT at 114.
  7. Vboxr2ci: GTAAT at 4025, ATAAT at 3983, GTAAT at 3980, ATAAT at 3945, ATAAC at 3823, AAAAT at 3798, GTAAT at 3447, GAAAT at 3441, AAAAC at 3208, GTAAT at 3113, GTAAC at 3018, GAAAC at 2952, GTAAC at 2947, AAAAT at 2919, AAAAC at 2781, AAAAT at 2665, ATAAT at 2510, AAAAT at 2382, AAAAC at 2189, GAAAT at 2128, AAAAT at 2083, AAAAC at 2069, GAAAC at 1991, AAAAC at 1850, ATAAT at 1838, GAAAC at 1629, GAAAT at 1332, ATAAC at 1139, ATAAT at 989, GAAAC at 946, AAAAC at 940, GTAAT at 845, GTAAT at 826, ATAAT at 793, GAAAC at 579, AAAAT at 369, AAAAT at 348, AAAAC at 310, ATAAT at 240, AAAAT at 185.

V box analysis and results

Main article: Complex locus A1BG and ZNF497 § Vboxes

"As VRI accumulates in the nucleus during the mid to late day, it binds VRI/PDP1ϵ binding sites (V/P-boxes) [consensus A(/G)TTA(/T)T(/C):GTAAT(/C)], to repress Clk and cry transcription (Hardin, 2004)."[2]

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

Comparison:

The occurrences of real V boxes are greater than the randoms. This suggests that the real V boxes are likely active or activable.

Acknowledgements

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

Initial content for this page in some instances came from Wikiversity.

See also

References

  1. ↑ Louis M Staudt and Michael J Lenardo (April 1991). "Immunoglobulin gene transcription". Annual Review of Immunology. 9: 373–98. doi:10.1146/annurev.iy.09.040191.002105. Retrieved 20 November 2018.
  2. ↑ 2.0 2.1 2.2 Wangjie Yu and Paul E. Hardin (2006). "Circadian oscillators of Drosophila and mammals". Journal of Cell Science. 119: 4793–5. doi:10.1242/jcs.03174. Retrieved 2017-02-19.
  3. ↑ Alexandra Schoenle (August 7, 2015). Time to (dia)pause - Clock gene expression patterns in the calanoid copepod Calanus finmarchicus during early and late diapause (PDF). Leobener Str., 28358 Bremen: University Bremen. p. 49. Retrieved 28 November 2018.
  4. ↑ Nicholas R. J. Glossop, Jerry H. Houl, Hao Zheng, Fanny S. Ng, Scott M. Dudek, Paul E. Hardin (23 January 2003). "VRILLE Feeds Back to Control Circadian Transcription of Clock in the Drosophila Circadian Oscillator". Neuron. 37 (2): 249–261. Retrieved 28 November 2018.
  5. ↑ Y. Koide and T. O. Yoshida (May 1995). "Dissection of positive regulatory elements in the upstream region of the HLA–DBP1 gene". Tissue Antigens. 45 (5): 309–316. doi:10.1111/j.1399-0039.1995.tb02459.x. Retrieved 20 November 2018.
  6. ↑ RefSeq (September 2011). HLA-DQB1 major histocompatibility complex, class II, DQ beta 1 [ Homo sapiens (human) ]. 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 20 November 2018.
  7. ↑ RefSeq (October 2010). HLA-DQB1 major histocompatibility complex, class II, DQ beta 1 [ Homo sapiens (human) ]. 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 20 November 2018.
  8. ↑ 8.0 8.1 B. Ferstl, T. Zacher, B. Lauer, N. Blagitko-Dorfs, A. Carl and R. Wassmuth (2004). "Allele-specific quantification of HLA-DQB1 gene expression by real-time reverse transcriptase-polymerase chain reaction" (PDF). Genes and Immunity. 5: 405–416. doi:10.1038/sj.gene.6364108. Retrieved 20 November 2018.
  9. ↑ RefSeq (February 2014). NFIL3 nuclear factor, interleukin 3 regulated [ Homo sapiens (human) ]. 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 29 November 2018.

External links

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