V box gene transcriptions

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."

"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)."

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

"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)."

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

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)."

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."

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."

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"

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

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."

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. RDr4: 0.
6. RDr5: 0.
7. RDr6: 0.
8. RDr7: 0.
9. RDr8: 0.
10. RDr9: 0.
11. RDr0ci: 0.
12. RDr1ci: 0.
13. RDr2ci: 0.
14. RDr3ci: 0.
15. RDr4ci: 0.
16. RDr5ci: 0.
17. RDr6ci: 0.
18. RDr7ci: 0.
19. RDr8ci: 0.
20. RDr9ci: 0.

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.

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.

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.

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.

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.

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

1. Vboxr3: GTTTC at 2784, ATTAC at 2733, ATTTT at 2616.

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.

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.

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.

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.

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.

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.

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)."

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

• P box gene transcriptions
• V and P box gene transcriptions
• W box gene transcriptions
• X box gene transcriptions
• Y box gene transcriptions