Cell-cycle box gene transcriptions

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

"The 5' non-coding part contains the sequence elements characteristic for eukaryotic promoters such as TATA and CAAT boxes as well as an inverted motif typical for cell-cycle regulated genes named "cell-cycle box" (CCB). The consensus sequence of CCB is CACGAAAA (Nasmyth, 1985), however, more relaxed variants such as CACGAAA, ACGAAA and C-CGAAA were described in budding yeast CLN1 and CLN2 (Ogas et al, 1991)."[1]

## Contents

* 1 Human genes
* 2 Gene expressions
* 3 Interactions
* 4 Consensus sequences
* 5 Binding site for
* 6 Inverse copies
* 7 Enhancer activity
* 8 CACG promoter occurrences
* 9 Hypotheses
* 10 CCB Samplings
* 11 CCB variant samplings
* 11.1 CCB negative direction (2596-1) distal promoters
* 11.2 CCB positive direction (4050-1) distal promoters
* 12 Cell-cycle box variants (CCBV) random dataset samplings
* 12.1 CCBVr arbitrary (evens) (4560-2846) UTRs
* 12.2 CCBVr alternate (odds) (4560-2846) UTRs
* 12.3 CCBVr arbitrary positive direction (odds) (4445-4265) core promoters
* 12.4 CCBVr alternate positive direction (evens) (4445-4265) core promoters
* 12.5 CCBVr arbitrary negative direction (evens) (2811-2596) proximal promoters
* 12.6 CCBVr alternate negative direction (odds) (2811-2596) proximal promoters
* 12.7 CCBVr arbitrary positive direction (odds) (4265-4050) proximal promoters
* 12.8 CCBVr alternate positive direction (evens) (4265-4050) proximal promoters
* 12.9 CCBVr arbitrary negative direction (evens) (2596-1) distal promoters
* 12.10 CCBVr alternate negative direction (odds) (2596-1) distal promoters
* 12.11 CCBVDr arbitrary positive direction (odds) (4050-1) distal promoters
* 12.12 CCBVr alternate positive direction (evens) (4050-1) distal promoters
* 13 Cell-cycle boxes analysis and results
* 14 Acknowledgements
* 15 See also
* 16 References
* 17 External links

## Human genes

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Main article: Human genes

## Gene expressions

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Main article: Gene expressions

## Interactions

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Main article: Interaction gene transcriptions

## Consensus sequences

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Main article: Consensus sequence gene transcriptions

## Binding site for

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## Inverse copies

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Main article: Inverse copy gene transcriptions

"In our soybean genomic clone CCB is represented as an inverted motif TTTTGGTG at the -66 position. (Breeden and Nasmyth (1987) suggested that the "cell cycle box" is functional in either orientation, acting as an enhancer."[1]

## Enhancer activity

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Main article: Enhancer activity copy gene transcriptions

## CACG promoter occurrences

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Main article: Promoter occurrence gene transcriptions

1. Negative strand, negative direction: 16, CACG at 4401, CACG at 3954, CACG at 3880, CACG at 3560, CACG at 3428, CACG at 3196, CACG at 2862, CACG at 2333, CACG at 2195, CACG at 2080, CACG at 1534, CACG at 1469, CACG at 1254, CACG at 446, CACG at 378, CACG at 334.
2. Positive strand, negative direction: 16, CACG at 4470, CACG at 3279, CACG at 3230, CACG at 2523, CACG at 2206, CACG at 1990, CACG at 1771, CACG at 1180, CACG at 962, CACG at 706, CACG at 662, CACG at 652, CACG at 570, CACG at 530, CACG at 433, CACG at 341.
3. Positive strand, positive direction: 33, CACG at 4273, CACG at 3959, CACG at 3882, CACG at 3463, CACG at 3234, CACG at 3150, CACG at 3010, CACG at 2959, CACG at 2799, CACG at 2680, CACG at 2333, CACG at 2325, CACG at 2088, CACG at 2062, CACG at 1785, CACG at 1762, CACG at 1724, CACG at 1588, CACG at 1520, CACG at 1252, CACG at 1243, CACG at 1217, CACG at 1168, CACG at 1159, CACG at 1084, CACG at 1016, CACG at 782, CACG at 664, CACG at 580, CACG at 571, CACG at 545, CACG at 496, CACG at 487.
4. Negative strand, positive direction: 24, CACG at 4258, CACG at 3747, CACG at 3604, CACG at 3253, CACG at 1697, CACG at 1640, CACG at 1558, CACG at 1552, CACG at 1300, CACG at 1222, CACG at 1132, CACG at 1048, CACG at 986, CACG at 978, CACG at 968, CACG at 886, CACG at 878, CACG at 868, CACG at 802, CACG at 796, CACG at 775, CACG at 568, CACG at 298, CACG at 241.

## Hypotheses

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Main article: Hypotheses

1. A1BG has no regulatory elements in either promoter.
2. A1BG is not transcribed by a regulatory element.
3. No regulatory element participates in the transcription of A1BG.

## CCB Samplings

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Main article: Model samplings

CCB Samplings

Copying a responsive elements consensus sequence CACGAAAA and putting the sequence in "⌘F" finds none between ZNF497 and A1BG or none between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence CACGAAAA (starting with SuccessablesCCB.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 CACGAAAA, 0.
2. positive strand, negative direction, looking for CACGAAAA, 0.
3. positive strand, positive direction, looking for CACGAAAA, 0.
4. negative strand, positive direction, looking for CACGAAAA, 0.
5. complement, negative strand, negative direction, looking for GTGCTTTT, 0.
6. complement, positive strand, negative direction, looking for GTGCTTTT, 0.
7. complement, positive strand, positive direction, looking for GTGCTTTT, 0.
8. complement, negative strand, positive direction, looking for GTGCTTTT, 0.
9. inverse complement, negative strand, negative direction, looking for TTTTCGTG, 0.
10. inverse complement, positive strand, negative direction, looking for TTTTCGTG, 0.
11. inverse complement, positive strand, positive direction, looking for TTTTCGTG, 0.
12. inverse complement, negative strand, positive direction, looking for TTTTCGTG, 0.
13. inverse negative strand, negative direction, looking for AAAAGCAC, 0.
14. inverse positive strand, negative direction, looking for AAAAGCAC, 0.
15. inverse positive strand, positive direction, looking for AAAAGCAC, 0.
16. inverse negative strand, positive direction, looking for AAAAGCAC, 0.

## CCB variant samplings

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Main article: Model samplings

Copying a responsive elements consensus sequence CACGAAA, ACGAAA and C-CGAAA and putting the sequence in "⌘F" finds none between ZNF497 and A1BG or none between ZSCAN22 and A1BG as can be found by the computer programs. Actual consensus sequences to conform should contain CACGAAA, ACGAAA or CCGAAA.

For the Basic programs testing consensus sequence NNCGAAAN (starting with SuccessablesCCBV.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: 0.
2. positive strand, negative direction: 3, GGCGAAAT at 2158, TACGAAAA at 495, GACGAAAC at 313.
3. negative strand, positive direction: 0.
4. positive strand, positive direction: 3, ACCGAAAG at 2164, TCCGAAAG at 1180, TCCGAAAG at 1096.
5. inverse complement, negative strand, negative direction: 6, TTTTCGTT at 2480, TTTTCGTT at 2474, CTTTCGCC at 1680, TTTTCGGT at 946, TTTTCGTA at 187, CTTTCGAC at 139.
6. inverse complement, positive strand, negative direction: 0.
7. inverse complement, negative strand, positive direction: 2, TTTTCGGG at 1752, CTTTCGTC at 1183.
8. inverse complement, positive strand, positive direction: 3, CTTTCGTG at 3600, GTTTCGCA at 2538, TTTTCGTC at 2007.

### CCB negative direction (2596-1) distal promoters

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1. Negative strand, negative direction: TTTTCGTT at 2480, TTTTCGTT at 2474, CTTTCGCC at 1680, TTTTCGGT at 946, TTTTCGTA at 187, CTTTCGAC at 139.
2. Positive strand, negative direction: GGCGAAAT at 2158, TACGAAAA at 495, GACGAAAC at 313.

### CCB positive direction (4050-1) distal promoters

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1. Negative strand, positive direction: TTTTCGGG at 1752, CTTTCGTC at 1183.
2. Positive strand, positive direction: ACCGAAAG at 2164, TCCGAAAG at 1180, TCCGAAAG at 1096.
3. Positive strand, positive direction: CTTTCGTG at 3600, GTTTCGCA at 2538, TTTTCGTC at 2007.

## Cell-cycle box variants (CCBV) random dataset samplings

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1. CCBVr0: 4, GCCGAAA at 4295, CCCGAAA at 4138, CCCGAAA at 1527, ACCGAAA at 251.
2. CCBVr1: 4, CCCGAAA at 4438, AACGAAA at 2588, CCCGAAA at 2456, AACGAAA at 1407.
3. CCBVr2: 5, TTCGAAA at 3775, GGCGAAA at 3652, ATCGAAA at 3440, GCCGAAA at 3077, AACGAAA at 2951.
4. CCBVr3: 6, CGCGAAA at 3966, ACCGAAA at 3939, GTCGAAA at 3481, TACGAAA at 2461, CCCGAAA at 1979, AGCGAAA at 1781.
5. CCBVr4: 6, TGCGAAA at 4469, TCCGAAA at 3876, TCCGAAA at 3768, AACGAAA at 3485, GGCGAAA at 528, GGCGAAA at 222.
6. CCBVr5: 6, AGCGAAA at 4334, GGCGAAA at 4283, AACGAAA at 4210, TACGAAA at 2281, GGCGAAA at 1032, CCCGAAA at 992.
7. CCBVr6: 2, CCCGAAA at 1979, GGCGAAA at 1236.
8. CCBVr7: 5, AACGAAA at 4545, CCCGAAA at 4331, CGCGAAA at 3960, CTCGAAA at 3484, CGCGAAA at 864.
9. CCBVr8: 4, ATCGAAA at 3076, GACGAAA at 2977, GCCGAAA at 2522, AACGAAA at 2406.
10. CCBVr9: 6, CCCGAAA at 2490, CACGAAA at 2087, CCCGAAA at 1793, CACGAAA at 1376, TGCGAAA at 882, CCCGAAA at 179.
11. CCBVr0ci: 4, TTTCGGC at 2347, TTTCGGG at 1279, TTTCGCT at 1170, TTTCGCA at 479.
12. CCBVr1ci: 6, TTTCGTA at 3412, TTTCGAC at 2678, TTTCGAC at 2397, TTTCGGT at 1497, TTTCGGC at 477, TTTCGAT at 108.
13. CCBVr2ci: 12, TTTCGGC at 4206, TTTCGAT at 4171, TTTCGCC at 3957, TTTCGCG at 3668, TTTCGAG at 3420, TTTCGTC at 3385, TTTCGCA at 1411, TTTCGCG at 1148, TTTCGTC at 721, TTTCGCG at 589, TTTCGAC at 537, TTTCGAG at 296.
14. CCBVr3ci: 7, TTTCGCC at 4076, TTTCGCT at 4044, TTTCGCA at 3697, TTTCGCT at 3071, TTTCGGC at 3004, TTTCGTA at 2228, TTTCGGG at 1545.
15. CCBVr4ci: 8, TTTCGGA at 4217, TTTCGGC at 3021, TTTCGGA at 2794, TTTCGGC at 2680, TTTCGCG at 2550, TTTCGGG at 1601, TTTCGCG at 1084, TTTCGTT at 369.
16. CCBVr5ci: 2, TTTCGTA at 3659, TTTCGAT at 2501.
17. CCBVr6ci: 5, TTTCGGA at 3298, TTTCGGG at 3018, TTTCGGT at 1475, TTTCGGG at 1263, TTTCGGA at 406.
18. CCBVr7ci: 10, TTTCGGG at 3463, TTTCGTT at 3279, TTTCGGG at 3178, TTTCGGT at 2521, TTTCGGC at 2494, TTTCGCA at 2390, TTTCGTT at 2248, TTTCGTC at 2122, TTTCGGG at 1994, TTTCGCC at 1347.
19. CCBVr8ci: 7, TTTCGAA at 3419, TTTCGGA at 3005, TTTCGAG at 2547, TTTCGAG at 1892, TTTCGGT at 1655, TTTCGGG at 1554, TTTCGTG at 1534.
20. CCBVr9ci: 5, TTTCGGA at 4163, TTTCGCT at 2872, TTTCGAG at 1330, TTTCGCG at 1128, TTTCGCC at 722.

### CCBVr arbitrary (evens) (4560-2846) UTRs

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1. CCBVr0: GCCGAAA at 4295, CCCGAAA at 4138.
2. CCBVr2: TTCGAAA at 3775, GGCGAAA at 3652, ATCGAAA at 3440, GCCGAAA at 3077, AACGAAA at 2951.
3. CCBVr4: TGCGAAA at 4469, TCCGAAA at 3876, TCCGAAA at 3768, AACGAAA at 3485.
4. CCBVr8: ATCGAAA at 3076, GACGAAA at 2977.
5. CCBVr2ci: TTTCGGC at 4206, TTTCGAT at 4171, TTTCGCC at 3957, TTTCGCG at 3668, TTTCGAG at 3420, TTTCGTC at 3385.
6. CCBVr4ci: TTTCGGA at 4217, TTTCGGC at 3021.
7. CCBVr6ci: TTTCGGA at 3298, TTTCGGG at 3018.
8. CCBVr8ci: TTTCGAA at 3419, TTTCGGA at 3005.

### CCBVr alternate (odds) (4560-2846) UTRs

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1. CCBVr1: CCCGAAA at 4438.
2. CCBVr3: CGCGAAA at 3966, ACCGAAA at 3939, GTCGAAA at 3481.
3. CCBVr5: AGCGAAA at 4334, GGCGAAA at 4283, AACGAAA at 4210.
4. CCBVr7: AACGAAA at 4545, CCCGAAA at 4331, CGCGAAA at 3960, CTCGAAA at 3484.
5. CCBVr1ci: TTTCGTA at 3412.
6. CCBVr3ci: TTTCGCC at 4076, TTTCGCT at 4044, TTTCGCA at 3697, TTTCGCT at 3071, TTTCGGC at 3004.
7. CCBVr5ci: TTTCGTA at 3659.
8. CCBVr7ci: TTTCGGG at 3463, TTTCGTT at 3279, TTTCGGG at 3178.
9. CCBVr9ci: TTTCGGA at 4163, TTTCGCT at 2872.

### CCBVr arbitrary positive direction (odds) (4445-4265) core promoters

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1. CCBVr1: CCCGAAA at 4438.
2. CCBVr5: AGCGAAA at 4334, GGCGAAA at 4283.
3. CCBVr7: CCCGAAA at 4331.

### CCBVr alternate positive direction (evens) (4445-4265) core promoters

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1. CCBVr0: GCCGAAA at 4295.

### CCBVr arbitrary negative direction (evens) (2811-2596) proximal promoters

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1. CCBVr4ci: TTTCGGA at 2794, TTTCGGC at 2680.

### CCBVr alternate negative direction (odds) (2811-2596) proximal promoters

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1. CCBVr1ci: TTTCGAC at 2678.

### CCBVr arbitrary positive direction (odds) (4265-4050) proximal promoters

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1. CCBVr5: AACGAAA at 4210.
2. CCBVr3ci: TTTCGCC at 4076.
3. CCBVr9ci: TTTCGGA at 4163.

### CCBVr alternate positive direction (evens) (4265-4050) proximal promoters

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1. CCBVr0: CCCGAAA at 4138.
2. CCBVr2ci: TTTCGGC at 4206, TTTCGAT at 4171.
3. CCBVr4ci: TTTCGGA at 4217.

### CCBVr arbitrary negative direction (evens) (2596-1) distal promoters

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1. CCBVr0: CCCGAAA at 1527, ACCGAAA at 251.
2. CCBVr4: GGCGAAA at 528, GGCGAAA at 222.
3. CCBVr6: CCCGAAA at 1979, GGCGAAA at 1236.
4. CCBVr8: GCCGAAA at 2522, AACGAAA at 2406.
5. CCBVr0ci: TTTCGGC at 2347, TTTCGGG at 1279, TTTCGCT at 1170, TTTCGCA at 479.
6. CCBVr2ci: TTTCGCA at 1411, TTTCGCG at 1148, TTTCGTC at 721, TTTCGCG at 589, TTTCGAC at 537, TTTCGAG at 296.
7. CCBVr4ci: TTTCGCG at 2550, TTTCGGG at 1601, TTTCGCG at 1084, TTTCGTT at 369.
8. CCBVr6ci: TTTCGGT at 1475, TTTCGGG at 1263, TTTCGGA at 406.
9. CCBVr8ci: TTTCGAG at 2547, TTTCGAG at 1892, TTTCGGT at 1655, TTTCGGG at 1554, TTTCGTG at 1534.

### CCBVr alternate negative direction (odds) (2596-1) distal promoters

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1. CCBVr1: AACGAAA at 2588, CCCGAAA at 2456, AACGAAA at 1407.
2. CCBVr3: TACGAAA at 2461, CCCGAAA at 1979, AGCGAAA at 1781.
3. CCBVr5: TACGAAA at 2281, GGCGAAA at 1032, CCCGAAA at 992.
4. CCBVr7: CGCGAAA at 864.
5. CCBVr9: CCCGAAA at 2490, CACGAAA at 2087, CCCGAAA at 1793, CACGAAA at 1376, TGCGAAA at 882, CCCGAAA at 179.
6. CCBVr1ci: TTTCGAC at 2397, TTTCGGT at 1497, TTTCGGC at 477, TTTCGAT at 108.
7. CCBVr3ci: TTTCGTA at 2228, TTTCGGG at 1545.
8. CCBVr5ci: TTTCGAT at 2501.
9. CCBVr7ci: TTTCGGT at 2521, TTTCGGC at 2494, TTTCGCA at 2390, TTTCGTT at 2248, TTTCGTC at 2122, TTTCGGG at 1994, TTTCGCC at 1347.
10. CCBVr9ci: TTTCGAG at 1330, TTTCGCG at 1128, TTTCGCC at 722.

### CCBVDr arbitrary positive direction (odds) (4050-1) distal promoters

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1. CCBVr1: AACGAAA at 2588, CCCGAAA at 2456, AACGAAA at 1407.
2. CCBVr3: CGCGAAA at 3966, ACCGAAA at 3939, GTCGAAA at 3481, TACGAAA at 2461, CCCGAAA at 1979, AGCGAAA at 1781.
3. CCBVr5: TACGAAA at 2281, GGCGAAA at 1032, CCCGAAA at 992.
4. CCBVr7: CGCGAAA at 3960, CTCGAAA at 3484, CGCGAAA at 864.
5. CCBVr9: CCCGAAA at 2490, CACGAAA at 2087, CCCGAAA at 1793, CACGAAA at 1376, TGCGAAA at 882, CCCGAAA at 179.
6. CCBVr1ci: TTTCGTA at 3412, TTTCGAC at 2678, TTTCGAC at 2397, TTTCGGT at 1497, TTTCGGC at 477, TTTCGAT at 108.
7. CCBVr3ci: TTTCGCT at 4044, TTTCGCA at 3697, TTTCGCT at 3071, TTTCGGC at 3004, TTTCGTA at 2228, TTTCGGG at 1545.
8. CCBVr5ci: TTTCGTA at 3659, TTTCGAT at 2501.
9. CCBVr7ci: TTTCGGG at 3463, TTTCGTT at 3279, TTTCGGG at 3178, TTTCGGT at 2521, TTTCGGC at 2494, TTTCGCA at 2390, TTTCGTT at 2248, TTTCGTC at 2122, TTTCGGG at 1994, TTTCGCC at 1347.
10. CCBVr9ci: TTTCGCT at 2872, TTTCGAG at 1330, TTTCGCG at 1128, TTTCGCC at 722.

### CCBVr alternate positive direction (evens) (4050-1) distal promoters

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1. CCBVr0: CCCGAAA at 1527, ACCGAAA at 251.
2. CCBVr2: TTCGAAA at 3775, GGCGAAA at 3652, ATCGAAA at 3440, GCCGAAA at 3077, AACGAAA at 2951.
3. CCBVr4: TCCGAAA at 3876, TCCGAAA at 3768, AACGAAA at 3485, GGCGAAA at 528, GGCGAAA at 222.
4. CCBVr6: CCCGAAA at 1979, GGCGAAA at 1236.
5. CCBVr8: ATCGAAA at 3076, GACGAAA at 2977, GCCGAAA at 2522, AACGAAA at 2406.
6. CCBVr0ci: TTTCGGC at 2347, TTTCGGG at 1279, TTTCGCT at 1170, TTTCGCA at 479.
7. CCBVr2ci: TTTCGCC at 3957, TTTCGCG at 3668, TTTCGAG at 3420, TTTCGTC at 3385, TTTCGCA at 1411, TTTCGCG at 1148, TTTCGTC at 721, TTTCGCG at 589, TTTCGAC at 537, TTTCGAG at 296.
8. CCBVr6ci: TTTCGGA at 3298, TTTCGGG at 3018, TTTCGGT at 1475, TTTCGGG at 1263, TTTCGGA at 406.
9. CCBVr8ci: TTTCGAA at 3419, TTTCGGA at 3005, TTTCGAG at 2547, TTTCGAG at 1892, TTTCGGT at 1655, TTTCGGG at 1554, TTTCGTG at 1534.

## Cell-cycle boxes analysis and results

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Main article: Complex locus A1BG and ZNF497 § Cell-cycle box variants

Cell-cycle boxes analysis and results

The real promoters have been examined for the CCB variants: CACGAAA, ACGAAA and C-CGAAA, where C-C indicates CC with the likely A being absent (CCGAAA). The inverse complements are TTTCGTG, TTTCGT and TTTCG-G (TTTCGG). The possibility of finding these CCB variants has been performed using a general consensus sequence of NNCGAAA, the expected variants should occur if present. The real promoters have CCB variants only in the distal promoters. In the negative direction, the variants occur ACGAAA at 494 and ACGAAA at 312. The actual general consensus sequence occurrences are GGCGAAA at 2157, TACGAAA at 494, and GACGAAA at 312. CACGAAA or CCGAAA never occurred. The inverse complements occur in the negative and positive direction: TTTCGT at 2479, TTTCGT at 2473 and TTTCGT at 186, and TTTCGGG at 1752, negative strand, positive strand: TTTCGTG at 3600, TTTCGT at 2006, respectively. The occurrences are 2.5 and 1.5 per direction.

The random datasets had twenty-three UTR general consensus sequences for an occurrence of 2.3. Of these the CCB variants had the following frequencies: CACGAAA (0), ACGAAA (2) and CCGAAA (5). The inverse complements had TTTCGTG (0), TTTCGT (1) and TTTCGG (6). The remaining nine were of the general consensus sequence of NNCGAAA or TTTCGNN.

The random datasets had three general consensus sequences in arbitrary positive direction core promoter only for an occurrence of 0.3 (two strands, one direction) or 0.15 (four strands, both directions). The proximal general consensus sequences (five) had occurrences of 0.2 and 0.3.

The distal promoters for the random datasets had twenty-six in the arbitrary negative direction for an occurrence of 2.6 and forty-two in the positive direction for an occurrence of 4.2.

As the choices for direction are arbitrary for the random datasets an average occurrence would be 3.25. Even separately the real occurrences are lower than the random ones albeit not by much for the real negative direction (2.5) vs. the arbitrarily chosen negative direction (2.6) for the randoms. The randoms also had UTR, core and proximal promoter occurrences where the reals have none.

These results suggest that the real variants ACGAAA (2), TTTCGT (5) and TTTCGG (1), are likely active or activable.

"The consensus sequence of CCB is CACGAAAA (Nasmyth, 1985), however, more relaxed variants such as CACGAAA, ACGAAA and C-CGAAA were described in budding yeast CLN1 and CLN2 (Ogas et al, 1991)."[1] The specific relaxed variant tested for in A1BG is ACGAAA.

Reals or randoms | Promoters | direction | Numbers | Strands | Occurrences | Averages (± 0.1)

|
|
|
|
|
|

Reals | UTR | negative | 0 | 2 | 0 | 0
Randoms | UTR | arbitrary negative | 25 | 10 | 2.5 | 2.4
Randoms | UTR | alternate negative | 23 | 10 | 2.3 | 2.4
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 | 4 | 10 | 0.4 | 0.25
Randoms | Core | alternate positive | 1 | 10 | 0.1 | 0.25
Reals | Proximal | negative | 0 | 2 | 0 | 0
Randoms | Proximal | arbitrary negative | 2 | 10 | 0.2 | 0.15
Randoms | Proximal | alternate negative | 1 | 10 | 0.1 | 0.15
Reals | Proximal | positive | 0 | 2 | 0 | 0
Randoms | Proximal | arbitrary positive | 3 | 10 | 0.3 | 0.35
Randoms | Proximal | alternate positive | 4 | 10 | 0.4 | 0.35
Reals | Distal | negative | 9 | 2 | 4.5 | 4.5 ± 1.5 (--6,+-3)
Randoms | Distal | arbitrary negative | 30 | 10 | 3 | 3.15
Randoms | Distal | alternate negative | 33 | 10 | 3.3 | 3.15
Reals | Distal | positive | 8 | 2 | 4 | 4 ± (-+2,++6)
Randoms | Distal | arbitrary positive | 49 | 10 | 4.9 | 4.65
Randoms | Distal | alternate positive | 44 | 10 | 4.4 | 4.65

Comparison:

The occurrences of real CCB distals are outside than the randoms or overlap at the low end in the negative distals. This suggests that the real CCBs are likely active or activable.

## Acknowledgements

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

## See also

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* A1BG gene transcription core promoters
* A1BG gene transcriptions
* A1BG regulatory elements and regions
* A1BG response element gene transcriptions
* A1BG response element negative results
* A1BG response element positive results
* Complex locus A1BG and ZNF497

## References

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1. ↑ 1.0 1.1 1.2 Joanna Deckert, Natasha Taranenko, and Peter M. Gresshoff (1994). Peter M. Gresshoff, ed. Cell Cycle Genes and Their Plant Homologues, In: Plant Genome Analysis: Current Topics in Plant Molecular Biology. 2000 Corporate Blvd., N.W., Boca Raton, Florida 33431: CRC Press, Inc. pp. 169–194. ISBN 0-8493-8264-5. Retrieved 19 April 2021.CS1 maint: Multiple names: authors list (link)

## External links

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* CArG box gene transcription laboratory
* CGCG box gene transcription laboratory
* CRE box gene transcription laboratory
* E2 box gene transcription laboratory
* Enhancer box gene transcription laboratory
* Factor II B recognition element gene transcription laboratory
* GA responsive complex gene transcription laboratory
* GC box gene transcription laboratory
* H box gene transcription laboratory
* HNF6 gene transcription laboratory
* HY box gene transcription laboratory
* Initiator element gene transcription laboratory
* Metal responsive element gene transcription laboratory
* STAT5 gene transcription laboratory
* TATA box gene transcription laboratory

Lessons|

* A1BG gene transcription programming
* Amino Acids
* Enzymes
* Enzyme catalysis
* Enzyme structure and function
* Eukaryotic transcription
* Gene regulation in prokaryotes

Lists|

* Biomolecules

Modules|

* Module:Infobox gene
* Module:InfoboxImage

Original research|

* Gene project

Projects|

* Biochemistry
* Gene project
* History of biology
* Molecular Biology
* Molecular evolution
* Topobiology

Proposals|

* Gene expressions/Cost sharing and research products
* Gene expressions in human exploration beyond low earth orbits
* Gene expressions/Project narrative

Resources|

* 5' cap
* Acid-base homeostasis
* Actins
* Adenines
* Allergies
* Alpha-1-B glycoprotein
* Ammonoids
* Original research/Amino acids
* Amphiphiles
* Anabolism
* Animal physiology
* Anomeric carbons
* Autocatalytic reactions
* Autonomously replicating sequences
* Base pairs
* Biology
* Biodegradation
* Biosynthesis
* Biosynthesis of a human protein
* Biosynthesis of amino acids
* Blood
* Bodily fluids
* Botany
* Brain box
* Calcium signaling
* Capping enzymes
* Carbohydrates
* Carcinoembryonic antigen gene family
* Catabolism
* Catalysis
* Cells
* Cell signaling
* Centrosomes
* Chromatins
* Chromoboxes
* Coactivators
* Corepressors
* Cofactors
* Consensus sequences
* Cytogenetics
* Cytokinesis
* Cytosines
* Deoxyribonucleic acids
* Digestion
* Disaccharides
* Dispersed promoters
* Dominant group metagenomes
* Downregulations
* Endochondral ossification
* Enzyme inhibitors
* Enzymology
* Epigenetics
* Epigenomes
* Esters
* Esterification
* Eukaryotes
* Eukaryotic initiation factors
* Evolution
* Exaptation
* Excision repair cross-complementing
* Factors
* Fatty acids
* Ferredoxin
* Foldings
* Foods
* Forkhead boxes
* Functional groups
* Genome surveillance complexes
* Genealogy
* Genes
* Genetics
* Gene transcriptions
* Genomes
* Genomics
* Glycoproteins
* Glycosides
* Glycosidic bond
* Guanines
* Hair color gene expressions
* Helicases
* Heredity
* History of agriculture
* Greek and Roman histories of biology
* Homeostasis
* Human amino acid synthesis
* Human DNAs
* Human genes
* Human RNA
* Human teeth
* Human temperatures
* Immunoglobulin domain cl11960
* Immunoglobulin domain genes
* Immunoglobulin like domain cd05751
* Immunoglobulin like domain pfam13895
* Immunoglobulin like domain smart00410
* Immunoglobulin receptor superfamily genes
* Immunoglobulin supergene family
* Inhibitory peptides
* Insulators
* Intranuclear localizations
* Introduction to Cell Biology
* Introduction to polymer chemistry
* Lamarckism
* Leucine zipper
* Localization
* Major histocompatibility complex class I gene family
* Major histocompatibility complex class II gene family
* Major histocompatibility complex class III gene family
* Mammalogy
* Mathematical molecular biology
* Mediator complexes
* Medicine
* Melanocytes
* Membranes
* Metagenomes
* Molecular biology
* Molecular genetics
* Nitrogen metabolism
* Nucleotide Synthesis
* Origin of life
* Orthomolecular medicine
* Osteoarthritis
* Paleanthropology
* Paleontology
* Phosphate biochemistry
* Phosphate budgets
* Phosphate reactions
* Post translational modifications
* Principles of biosynthesis
* Protein isoform
* Proteins
* Proteomics
* Regulations
* Ribonucleotides
* Ribosomes
* RNA polymerases
* RNA polymerase II holoenzymes
* RNA polymerase II holoenzyme complexes
* RNA translations
* Salinity
* Stroke management
* Teeth
* TFIIA
* Transports
* Vascular endothelial growth factor A
* What is a human?
* Upregulations
* Upstream and downstream
* ZSCAN22
* Zoology

Transcription resources|

* A1BG gene transcription core promoters
* A1BG gene transcriptions
* A1BG regulatory elements and regions
* A1BG response element gene transcriptions
* A1BG response element negative results
* A1BG response element positive results
* ABA-response element gene transcriptions
* Abf1 regulatory factor gene transcriptions
* A box gene transcriptions
* Abscisic acid-responsive elements
* ACGT-containing element gene transcriptions
* Activating protein gene transcriptions
* Activating transcription factor gene transcriptions
* Adenylate–uridylate rich element gene transcriptions
* Adr1p gene transcriptions
* Aft1p gene transcriptions
* AGC box gene transcriptions
* AGCE gene transcriptions
* Alpha-amylase conserved element gene transcriptions
* Amino acid response element gene transcriptions
* AARE-like
* Androgen response element gene transcriptions
* Angiotensinogen core promoter element gene transcriptions
* Antioxidant-electrophile responsive element gene transcriptions
* AP-2 (Roesler) elements
* ATA box gene transcriptions
* Auxin response factor gene transcriptions
* B box gene transcriptions
* Bioinformatics tool gene transcriptions
* Box gene transcriptions
* B recognition element upstream
* Bridge gene transcriptions
* CAAT box gene transcriptions
* CACA elements
* CadC binding domain gene transcriptions
* Calcineurin-responsive transcription factor gene transcriptions
* Calcium-response element gene transcriptions
* cAMP response element gene transcriptions
* C and D boxes gene transcriptions
* Carbohydrate response element gene transcriptions
* Carbon source-responsive element gene transcriptions
* Carcinoembryonic antigen gene family
* CARE gene transcriptions
* CArG box gene transcriptions
* CAT box gene transcriptions
* CAT-box-like elements
* Cat8p gene transcriptions
* Cbf1 regulatory factor gene transcriptions
* C box gene transcriptions
* CCCTC-binding factor gene transcriptions
* C-EBP box gene transcriptions
* Cell-cycle box gene transcriptions
* Cell cycle regulation gene transcriptions
* CENP-B box gene transcriptions
* CGCG box gene transcriptions
* Circadian control element gene transcriptions
* "Class C" (Leal) samplings
* Cold-responsive element gene transcriptions
* Complement copy gene transcriptions
* Complement-inverse copy gene transcriptions
* Consensus sequence gene transcriptions
* Constitutive decay elements
* Copper response element gene transcriptions
* Core promoter gene transcriptions
* Coupling element gene transcriptions
* CRE box gene transcriptions
* Cytokinin response regulator gene transcriptions
* Cytoplasmic polyadenylation element gene transcriptions
* DAF-16-associated element gene transcriptions
* DAF-16 binding element gene transcriptions
* D box gene transcriptions
* Defense and stress-responsive element gene transcriptions
* Degenerate nucleotide gene transcriptions
* Dispersed promoter gene transcriptions
* Distal promoter gene transcriptions
* DNA melting gene transcriptions
* DNA damage response element gene transcriptions
* DNA replication-related element gene transcriptions
* Downstream core element gene transcriptions
* Downstream promoter element gene transcriptions
* Downstream TFIIB recognition element gene transcriptions
* DREB box gene transcriptions
* E2 box gene transcriptions
* EIF4E basal element gene transcriptions
* EIN3 binding site gene transcriptions
* Enhancer activity copy gene transcriptions
* E box gene transcriptions
* Element gene transcriptions
* Endoplasmic reticulum stress response element gene transcriptions
* Endosperm expression gene transcriptions
* Enhancer box gene transcriptions
* Estrogen response element gene transcriptions
* Ethylene responsive element gene transcriptions
* Families of TATA box genes
* F box gene transcriptions
* Focused promoter gene transcriptions
* Forkhead box gene transcriptions
* Fur box gene transcriptions
* GAAC element gene transcriptions
* Gal4p gene transcriptions
* Γ-interferon activated sequence gene transcriptions
* GARE gene transcriptions
* GA responsive complex gene transcriptions
* GATA gene transcriptions
* G box gene transcriptions
* GC box gene transcriptions
* GCC box gene transcriptions
* Gcn4p gene transcriptions
* Gcr1p gene transcriptions
* Gene expressions
* General factor II D gene transcriptions
* General regulatory factors
* General transcription factor II A gene transcriptions
* General transcription factor II B gene transcriptions
* General transcription factor II D gene transcriptions
* General transcription factor II F gene transcriptions
* General transcription factor II H gene transcriptions
* General transcription factor gene transcriptions
* Gene transcriptions
* GGC triplet gene transcriptions
* Gibberellin responsive element gene transcriptions
* GLM box gene transcriptions
* Glucocorticoid response element gene transcriptions
* Grainy head gene transcriptions
* Grainy head transcription factor gene transcriptions
* Growth hormone response element gene transcriptions
* GT boxes
* Hac1p gene transcriptions
* Hair color gene expressions
* H and ACA box gene transcriptions
* H box gene transcriptions
* Heat-responsive element gene transcriptions
* Heat shock elements
* Hex sequence gene transcriptions
* HMG box gene transcriptions
* HNF gene transcriptions
* Homeobox gene transcriptions
* Hsf1p gene transcriptions
* HY box gene transcriptions
* Hybrid C, A boxes
* Hybrid C, G boxes
* Hybrid C, T boxes
* Hypoxia-inducible factor gene transcriptions
* Hypoxia response elements
* I box gene transcriptions
* Immunoglobulin like domain containing family
* Initiator element gene transcriptions
* Initiator-like element gene transcriptions
* Inositol/choline-responsive elements
* Interaction gene transcriptions
* Interferon regulatory factors
* Inverse copy gene transcriptions
* Jasmonic acid-responsive element gene transcriptions
* K-boxes
* Kozak sequence gene transcriptions
* Kruppel-associated box gene transcriptions
* Krüppel-like factor gene transcriptions
* L box gene transcriptions
* Leu3 gene transcriptions
* M35 box gene transcriptions
* MADS box gene transcriptions
* Maf recognition element gene transcriptions
* M box gene transcriptions
* M-CAT boxes
* Mcm1 regulatory factor gene transcriptions
* Met3 gene transcriptions
* Met31p box gene transcriptions
* Metal responsive element gene transcriptions
* Middle sporulation element gene transcriptions
* Mig1p gene transcriptions
* Model samplings
* Motif ten element gene transcriptions
* Msn2,4p gene transcriptions
* Musashi binding element gene transcriptions
* MYB recognition element gene transcriptions
* Myelocytomatosis transcription factor gene transcriptions
* Myocyte enhancer factor gene transcriptions
* N-boxes
* Nanos/Pumilio response element
* Ndt80p gene transcriptions
* Nuclear factor 1
* Nuclear factor 𝜿B
* Nuclear factor gene transcriptions
* Nuclear factor of activated T cell gene transcriptions (NFAT)
* Nuclear factor Y gene transcriptions
* Nutrient-sensing response element gene transcriptions
* Oaf1p gene transcriptions
* ORE1 binding site gene transcriptions
* p53 response element gene transcriptions
* P63 DNA-binding site gene transcriptions
* P box gene transcriptions
* Pdr1,3p gene transcriptions
* Peroxisome proliferator hormone response element gene transcriptions
* Phosphate starvation-response transcription factor gene transcriptions
* Pollen1 element gene transcriptions
* Polycomb response element gene transcriptions
* Preinitiation complex
* Preinitiation complex gene transcriptions
* Pribnow box gene transcriptions
* Prolamin box gene transcriptions
* Promoter gene transcriptions
* Proximal promoter gene transcriptions
* Promoter occurrence gene transcriptions
* Pyrimidine box gene transcriptions
* Q element gene transcriptions
* Rap1 regulatory factor gene transcriptions
* Reb1 general regulatory factor gene transcriptions
* Retinoblastoma control element gene transcriptions
* Retinoic acid response element gene transcriptions
* Rgt1p gene transcriptions
* Rlm1p gene transcriptions
* RNA polymerase II gene transcriptions
* RNA polymerase II holoenzyme complex
* Root specific element gene transcriptions
* ROR-response element gene transcriptions
* Rox1p gene transcriptions
* Rpn4p gene transcriptions
* R response element gene transcriptions
* SARE gene transcriptions
* Seed-specific element gene transcriptions
* Serum response element gene transcriptions
* Servenius sequence gene transcriptions
* Shoot specific element gene transcriptions
* Shue boxes
* Sip4p gene transcriptions
* Smp1p gene transcriptions
* Sp1 (Berberich) elements
* Sp1 gene transcriptions
* Spaceflight gene expressions
* Specificity protein gene transcriptions
* STAT gene transcriptions
* Ste12p gene transcriptions
* Sterol response element gene transcriptions
* Sucrose box gene transcriptions
* Synaptic Activity-Responsive Elements
* TACTAAC box gene transcriptions
* TAGteam gene transcriptions
* Tapetum box gene transcriptions
* TATA binding protein associated factor gene transcriptions
* TATA binding protein gene transcriptions
* TATA box actin/cytoskeleton/contractile family
* TATA box albumin family
* TATA box aldolase family
* TATA box alkaline phosphatase family
* TATA box annexin family
* TATA box cytochrome superfamily
* TATA box gene transcriptions
* TATA box heat shock family
* TATA box histone family
* TATA box human genes
* TATA box keratin family
* TATA box lipase family
* TATA box peptidase family
* TATA box platelet-derived growth factor family
* TATA box selenium-binding family
* TATA box serine protease family
* TATA box serpin superfamily
* TATA box transforming growth factor superfamily
* TATA box trefoil family
* TATA box tumor necrosis factor superfamily
* TATA box zinc metalloenzyme family
* TAT box gene transcriptions
* TATC box gene transcriptions
* Tbf1 regulatory factor gene transcriptions
* T box gene transcriptions
* TCCACCATA element gene transcriptions
* TC element gene transcriptions
* TCT gene transcriptions
* TEA consensus sequence gene transcriptions
* Tec1p gene transcriptions
* Telomeric repeat DNA-binding factor gene transcriptions
* Tetradecanoylphorbol-13-acetate response element gene transcriptions
* TGF-β control elements (TCEs)
* TGF-β inhibitory elements (TIEs)
* Thyroid hormone response element gene transcriptions
* Transcriptional regulation
* Transcription bubble gene transcriptions
* Transcription factor gene transcriptions
* Transcription factor 3 gene transcriptions
* Transcription factory gene transcriptions
* Transcription start site gene transcriptions
* Translational control sequence gene transcriptions
* Tryptophan residue
* U box gene transcriptions
* Unfolded protein response element gene transcriptions
* Upstream repressor site 1
* Upstream response element gene transcriptions
* Upstream stimulatory factor gene transcriptions
* UTR promoter gene transcriptions
* V and P box gene transcriptions
* V box gene transcriptions
* Vhr1p gene transcriptions
* Vitamin D response element gene transcriptions
* W box gene transcriptions
* X box gene transcriptions
* Xbp1p gene transcriptions
* X core promoter element gene transcriptions
* Xenobiotic response element gene transcriptions
* Xenobiotic responsive element gene transcriptions
* Yap1p,2p gene transcriptions
* Y box gene transcriptions
* YY1 gene transcriptions
* Zap1p gene transcriptions
* Z box gene transcriptions
* Zinc responsive element gene transcriptions

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