Enhancer box gene transcriptions: Difference between revisions

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# A1BG is not transcribed by a downstream enhancer box.
# A1BG is not transcribed by a downstream enhancer box.


==Samplings==
==Enhancer box samplings==
{{main|Sampling models}}
{{main|Sampling models}}
Regarding hypotheses 1:
Regarding hypotheses 1:
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# inverse, positive strand, negative direction, is SuccessablesEi+-.bas, looking for 3'-G-T-(A/C/G/T)-(A/C/G/T)-A-C-5', 10 , 3'-GTGTAC-5', 324 , 3'-GTCTAC-5', 481 , 3'-GTGTAC-5', 797 , 3'-GTTCAC-5', 1179 , 3'-GTCTAC-5', 1224 , 3'-GTCAAC-5', 1513 , 3'-GTGGAC-5', 2116 , 3'-GTCTAC-5', 2988 , 3'-GTAAAC-5', 3482 , 3'-GTCTAC-5', 4212,
# inverse, positive strand, negative direction, is SuccessablesEi+-.bas, looking for 3'-G-T-(A/C/G/T)-(A/C/G/T)-A-C-5', 10 , 3'-GTGTAC-5', 324 , 3'-GTCTAC-5', 481 , 3'-GTGTAC-5', 797 , 3'-GTTCAC-5', 1179 , 3'-GTCTAC-5', 1224 , 3'-GTCAAC-5', 1513 , 3'-GTGGAC-5', 2116 , 3'-GTCTAC-5', 2988 , 3'-GTAAAC-5', 3482 , 3'-GTCTAC-5', 4212,
# inverse, positive strand, positive direction, is SuccessablesEi++.bas, looking for 3'-G-T-(A/C/G/T)-(A/C/G/T)-A-C-5', 26, 3'-GTCCAC-5', 196, 3'-GTGCAC-5', 570, 3'-GTGGAC-5', 858, 3'-GTGGAC-5', 958, 3'-GTCCAC-5', 1968, 3'-GTGTAC-5', 2031, 3'-GTCGAC-5', 2054, 3'-GTCCAC-5', 2127, 3'-GTGGAC-5', 2249, 3'-GTCCAC-5', 2374, 3'-GTCGAC-5', 2404, 3'-GTGGAC-5', 2432, 3'-GTTCAC-5', 2510, 3'-GTGGAC-5', 2568, 3'-GTGGAC-5', 3046, 3'-GTCCAC-5', 3149, 3'-GTCGAC-5', 3241, 3'-GTAGAC-5', 3404, 3'-GTCTAC-5', 3475, 3'-GTGTAC-5', 3707, 3'-GTGTAC-5', 3742, 3'-GTCGAC-5', 3777, 3'-GTACAC-5', 3902, 3'-GTGTAC-5', 3956, 3'-GTACAC-5', 3958, 3'-GTGAAC-5', 4015.
# inverse, positive strand, positive direction, is SuccessablesEi++.bas, looking for 3'-G-T-(A/C/G/T)-(A/C/G/T)-A-C-5', 26, 3'-GTCCAC-5', 196, 3'-GTGCAC-5', 570, 3'-GTGGAC-5', 858, 3'-GTGGAC-5', 958, 3'-GTCCAC-5', 1968, 3'-GTGTAC-5', 2031, 3'-GTCGAC-5', 2054, 3'-GTCCAC-5', 2127, 3'-GTGGAC-5', 2249, 3'-GTCCAC-5', 2374, 3'-GTCGAC-5', 2404, 3'-GTGGAC-5', 2432, 3'-GTTCAC-5', 2510, 3'-GTGGAC-5', 2568, 3'-GTGGAC-5', 3046, 3'-GTCCAC-5', 3149, 3'-GTCGAC-5', 3241, 3'-GTAGAC-5', 3404, 3'-GTCTAC-5', 3475, 3'-GTGTAC-5', 3707, 3'-GTGTAC-5', 3742, 3'-GTCGAC-5', 3777, 3'-GTACAC-5', 3902, 3'-GTGTAC-5', 3956, 3'-GTACAC-5', 3958, 3'-GTGAAC-5', 4015.
===Enhancer box UTRs===
{{main|UTR promoter gene transcriptions}}
Negative strand, negative direction: CAGATG at 4212, CATTTG at 3482, CAGATG at 2988.
Positive strand, negative direction: CACTTG at 4011, CACCTG at 3969, CAGGTG at 3953, CAGATG at 3919, CAACTG at 3850, CAGATG at 3627, CAGATG at 3620, CACTTG at 3241, CACTTG at 3102, CACTTG at 2920.
===Enhancer box proximal promoters===
{{main|Proximal promoter gene transcriptions}}
Positive strand, negative direction: CACATG at 2667.
Positive strand, positive direction: CAAGTG at 4202.
===Enhancer box distal promoters===
{{main|Distal promoter gene transcriptions}}
Negative strand, negative direction: CACCTG at 2116, CAGTTG at 1513, CAGATG at 1224, CAAGTG at 1179, CACATG at 797, CAGATG at 481, CACATG at 324.
Positive strand, negative direction: CACTTG at 2579, CAGGTG at 2570, CACTTG at 2126, CAGGTG at 2079, CAAATG at 1579, CACCTG at 1172, CACCTG at 1130, CACCTG at 393, CATTTG at 364, CATATG at 41.
Negative strand, positive direction: CACTTG at 4015, CATGTG at 3958, CACATG at 3956, CATGTG at 3902, CAGCTG at 3777, CACATG at 3742, CACATG at 3707, CAGATG at 3475, CATCTG at 3404, CAGCTG at 3241, CAGGTG at 3149, CACCTG at 3046, CACCTG at 2568, CAAGTG at 2510, CACCTG at 2432, CAGCTG at 2404, CAGGTG at 2374, CACCTG at 2249, CAGGTG at 2127, CAGCTG at 2054, CACATG at 2031, CAGGTG at 1968, CACCTG at 958, CACCTG at 858, CACGTG at 570, CAGGTG at 196.
Positive strand, positive direction: CACTTG at 3936, CACGTG at 3884, CAGGTG at 3086, CACGTG at 2961, CAGGTG at 2028, CAGGTG at 1843, CACGTG at 1219, CATGTG at 567, CACGTG at 547, CACCTG at 186.


==Transcribed enhancer boxes==
==Transcribed enhancer boxes==

Revision as of 16:54, 20 March 2021

Editor-In-Chief: Henry A. Hoff

File:Klatre08.jpg
This is an image of Dendromus mysticalis, the chestnut climbing mouse. Credit: Kenneth Worm.

"An E-box (Enhancer Box) is a DNA sequence which usually lies upstream of a gene in a promoter region."[1]

Enhancers

Main article: Enhancer gene transcriptions
File:Gene enhancer.svg
The illustration characterizes a DNA enhancer near a gene. Credit: .

"An enhancer is a short region of DNA that can be bound with proteins (namely, the trans-acting factors, much like a set of transcription factors) to enhance transcription levels of genes (hence the name) in a gene cluster. While enhancers are usually cis-acting, an enhancer does not need to be particularly close to the genes it acts on, and sometimes need not be located on the same chromosome.[2]

In eukaryotic cells the structure of the chromatin complex of DNA is folded in a way that although the enhancer DNA is far from the gene in regard to the number of nucleotides, it is geometrically close to the promoter and gene.

An enhancer may be located upstream or downstream of the gene it regulates.

Enhancers do not act on the promoter region itself, but are bound by activator proteins. These activator proteins interact with the mediator complex, which recruits polymerase II and the general transcription factors which then begin transcribing the genes. Enhancers can also be found within introns. An enhancer's orientation may even be reversed without affecting its function. Additionally, an enhancer may be excised and inserted elsewhere in the chromosome, and still affect gene transcription.

Def. a "short region of DNA that can increase transcription of genes"[3] is called an enhancer.

Boxes

Main article: Box gene transcriptions

A "repeating sequence of nucleotides that forms a transcription or a regulatory signal"[4] is a box.

Immunoglobulin domains

The immunoglobulin domain is a type of protein domain that consists of a 2-layer sandwich of between 7 and 9 antiparallel β-strands arranged in two β-sheets with a Greek key topology.[5][6]

The E-box is a control element in immunoglobulin heavy-chain promoters.[7]

Consensus sequences

Main article: Consensus sequence gene transcriptions

The consensus sequence for the E-box element is CANNTG, with a palindromic canonical sequence of CACGTG.[8]

Proximal promoters

Main article: Proximal promoter gene transcriptions

"[T]he proximal sequence upstream of the gene that tends to contain primary regulatory elements" is a proximal promoter.[9]

It is "[a]pproximately 250 base pairs [or nucleotides, nts] upstream of the [transcription] start site".[9]

There may be an E box in the proximal promoter of some genes.[8]

Distal promoters

Main article: Distal promoter gene transcriptions
File:Enhancer Nucleotide Sequence.svg
Within this DNA sequence, protein(s) known as transcription factor(s) bind to the enhancer and increases the activity of the promoter. Credit: Jon Cheff.{{free media}}

An E-box usually lies within the distal promoter starting at or near -300 nts, the proximal promoter, or both.[8]

Hypotheses

Main article: Hypotheses
  1. A1BG is not transcribed by an enhancer box.
  2. Existence of an enhancer box on either side of A1BG does not prove that it is actively used to transcribe A1BG.
  3. A1BG is not transcribed by a downstream enhancer box.

Enhancer box samplings

Main article: Sampling models

Regarding hypotheses 1:

A1BG has four possible transcription directions:

  1. on the negative strand from ZSCAN22 to A1BG,
  2. on the positive strand from ZSCAN22 to A1BG,
  3. on the negative strand from ZNF497 to A1BG, and
  4. on the positive strand from ZNF497 to A1BG.

For each transcription promoter that interacts directly with RNA polymerase II holoenzyme, the four possible consensus sequences need to be tested on the four possible transcription directions, even though some genes may only be transcribed from the negative strand in the 3'-direction on the transcribed strand.

For the Basic programs (starting with SuccessablesE.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 looking for, and found:

  1. negative strand in the negative direction is SuccessablesE--.bas, looking for 3'-C-A-(A/C/G/T)-(A/C/G/T)-T-G-5', 10, 3'-CACATG-5', 324, 3'-CAGATG-5', 481, 3'-CACATG-5', 797, 3'-CAAGTG-5', 1179, 3'-CAGATG-5', 1224, 3'-CAGTTG-5', 1513, 3'-CACCTG-5', 2116, 3'-CAGATG-5', 2988, 3'-CATTTG-5', 3482, 3'-CAGATG-5', 4212,
  2. negative strand in the positive direction is SuccessablesE-+.bas, looking for 3'-C-A-(A/C/G/T)-(A/C/G/T)-T-G-5', 26, 3'-CAGGTG-5', 196, 3'-CACGTG-5', 570, 3'-CACCTG-5', 858, 3'-CACCTG-5', 958, 3'-CAGGTG-5', 1968, 3'-CACATG-5', 2031, 3'-CAGCTG-5', 2054, 3'-CAGGTG-5', 2127, 3'-CACCTG-5', 2249, 3'-CAGGTG-5', 2374, 3'-CAGCTG-5', 2404, 3'-CACCTG-5', 2432, 3'-CAAGTG-5', 2510, 3'-CACCTG-5', 2568, 3'-CACCTG-5', 3046, 3'-CAGGTG-5', 3149, 3'-CAGCTG-5', 3241, 3'-CATCTG-5', 3404, 3'-CAGATG-5', 3475, 3'-CACATG-5', 3707, 3'-CACATG-5', 3742, 3'-CAGCTG-5', 3777, 3'-CATGTG-5', 3902, 3'-CACATG-5', 3956, 3'-CATGTG-5', 3958, 3'-CACTTG-5', 4015,
  3. positive strand in the negative direction is SuccessablesE+-.bas, looking for 3'-C-A-(A/C/G/T)-(A/C/G/T)-T-G-5', 21, 3'-CATATG-5', 41, 3'-CATTTG-5', 364, 3'-CACCTG-5', 393, 3'-CACCTG-5', 1130, 3'-CACCTG-5', 1172, 3'-CAAATG-5', 1579, 3'-CAGGTG-5', 2079, 3'-CACTTG-5', 2126, 3'-CAGGTG-5', 2570, 3'-CACTTG-5', 2579, 3'-CACATG-5', 2667, 3'-CACTTG-5', 2920, 3'-CACTTG-5', 3102, 3'-CACTTG-5', 3241, 3'-CAGATG-5', 3620, 3'-CAGATG-5', 3627, 3'-CAACTG-5', 3850, 3'-CAGATG-5', 3919, 3'-CAGGTG-5', 3953, 3'-CACCTG-5', 3969, 3'-CACTTG-5', 4011,
  4. positive strand in the positive direction is SuccessablesE++.bas, looking for 3'-C-A-(A/C/G/T)-(A/C/G/T)-T-G-5', 11, 3'-CACCTG-5', 186, 3'-CACGTG-5', 547, 3'-CATGTG-5', 567, 3'-CACGTG-5', 1219, 3'-CAGGTG-5', 1843, 3'-CAGGTG-5', 2028, 3'-CACGTG-5', 2961, 3'-CAGGTG-5', 3086, 3'-CACGTG-5', 3884, 3'-CACTTG-5', 3936, 3'-CAAGTG-5', 4202,
  5. complement, negative strand, negative direction is SuccessablesEc--.bas, looking for 3'-G-T-(A/C/G/T)-(A/C/G/T)-A-C-5', 21, 3'-GTATAC-5', 41, 3'-GTAAAC-5', 364, 3'-GTGGAC-5', 393, 3'-GTGGAC-5', 1130, 3'-GTGGAC-5', 1172, 3'-GTTTAC-5', 1579, 3'-GTCCAC-5', 2079, 3'-GTGAAC-5', 2126, 3'-GTCCAC-5', 2570, 3'-GTGAAC-5', 2579, 3'-GTGTAC-5', 2667, 3'-GTGAAC-5', 2920, 3'-GTGAAC-5', 3102, 3'-GTGAAC-5', 3241, 3'-GTCTAC-5', 3620, 3'-GTCTAC-5', 3627, 3'-GTTGAC-5', 3850, 3'-GTCTAC-5', 3919, 3'-GTCCAC-5', 3953, 3'-GTGGAC-5', 3969, 3'-GTGAAC-5', 4011,
  6. complement, negative strand, positive direction is SuccessablesEc-+.bas, looking for 3'-G-T-(A/C/G/T)-(A/C/G/T)-A-C-5', 11, 3'-GTGGAC-5', 186, 3'-GTGCAC-5', 547, 3'-GTACAC-5', 567, 3'-GTGCAC-5', 1219, 3'-GTCCAC-5', 1843, 3'-GTCCAC-5', 2028, 3'-GTGCAC-5', 2961, 3'-GTCCAC-5', 3086, 3'-GTGCAC-5', 3884, 3'-GTGAAC-5', 3936, 3'-GTTCAC-5', 4202,
  7. complement, positive strand, negative direction is SuccessablesEc+-.bas, looking for 3'-G-T-(A/C/G/T)-(A/C/G/T)-A-C-5', 10 , 3'-GTGTAC-5', 324 , 3'-GTCTAC-5', 481 , 3'-GTGTAC-5', 797 , 3'-GTTCAC-5', 1179 , 3'-GTCTAC-5', 1224 , 3'-GTCAAC-5', 1513 , 3'-GTGGAC-5', 2116 , 3'-GTCTAC-5', 2988 , 3'-GTAAAC-5', 3482 , 3'-GTCTAC-5', 4212,
  8. complement, positive strand, positive direction is SuccessablesEc++.bas, looking for 3'-G-T-(A/C/G/T)-(A/C/G/T)-A-C-5', 26, 3'-GTCCAC-5', 196, 3'-GTGCAC-5', 570, 3'-GTGGAC-5', 858, 3'-GTGGAC-5', 958, 3'-GTCCAC-5', 1968, 3'-GTGTAC-5', 2031, 3'-GTCGAC-5', 2054, 3'-GTCCAC-5', 2127, 3'-GTGGAC-5', 2249, 3'-GTCCAC-5', 2374, 3'-GTCGAC-5', 2404, 3'-GTGGAC-5', 2432, 3'-GTTCAC-5', 2510, 3'-GTGGAC-5', 2568, 3'-GTGGAC-5', 3046, 3'-GTCCAC-5', 3149, 3'-GTCGAC-5', 3241, 3'-GTAGAC-5', 3404, 3'-GTCTAC-5', 3475, 3'-GTGTAC-5', 3707, 3'-GTGTAC-5', 3742, 3'-GTCGAC-5', 3777, 3'-GTACAC-5', 3902, 3'-GTGTAC-5', 3956, 3'-GTACAC-5', 3958, 3'-GTGAAC-5', 4015,
  9. inverse complement, negative strand, negative direction is SuccessablesEci--.bas, looking for 3'-C-A-(A/C/G/T)-(A/C/G/T)-T-G-5', 10, 3'-CACATG-5', 324, 3'-CAGATG-5', 481, 3'-CACATG-5', 797, 3'-CAAGTG-5', 1179, 3'-CAGATG-5', 1224, 3'-CAGTTG-5', 1513, 3'-CACCTG-5', 2116, 3'-CAGATG-5', 2988, 3'-CATTTG-5', 3482, 3'-CAGATG-5', 4212,
  10. inverse complement, negative strand, positive direction is SuccessablesEci-+.bas, looking for 3'-C-A-(A/C/G/T)-(A/C/G/T)-T-G-5', 26, 3'-CAGGTG-5', 196, 3'-CACGTG-5', 570, 3'-CACCTG-5', 858, 3'-CACCTG-5', 958, 3'-CAGGTG-5', 1968, 3'-CACATG-5', 2031, 3'-CAGCTG-5', 2054, 3'-CAGGTG-5', 2127, 3'-CACCTG-5', 2249, 3'-CAGGTG-5', 2374, 3'-CAGCTG-5', 2404, 3'-CACCTG-5', 2432, 3'-CAAGTG-5', 2510, 3'-CACCTG-5', 2568, 3'-CACCTG-5', 3046, 3'-CAGGTG-5', 3149, 3'-CAGCTG-5', 3241, 3'-CATCTG-5', 3404, 3'-CAGATG-5', 3475, 3'-CACATG-5', 3707, 3'-CACATG-5', 3742, 3'-CAGCTG-5', 3777, 3'-CATGTG-5', 3902, 3'-CACATG-5', 3956, 3'-CATGTG-5', 3958, 3'-CACTTG-5', 4015,
  11. inverse complement, positive strand, negative direction is SuccessablesEci+-.bas, looking for 3'-C-A-(A/C/G/T)-(A/C/G/T)-T-G-5', 21, 3'-CATATG-5', 41, 3'-CATTTG-5', 364, 3'-CACCTG-5', 393, 3'-CACCTG-5', 1130, 3'-CACCTG-5', 1172, 3'-CAAATG-5', 1579, 3'-CAGGTG-5', 2079, 3'-CACTTG-5', 2126, 3'-CAGGTG-5', 2570, 3'-CACTTG-5', 2579, 3'-CACATG-5', 2667, 3'-CACTTG-5', 2920, 3'-CACTTG-5', 3102, 3'-CACTTG-5', 3241, 3'-CAGATG-5', 3620, 3'-CAGATG-5', 3627, 3'-CAACTG-5', 3850, 3'-CAGATG-5', 3919, 3'-CAGGTG-5', 3953, 3'-CACCTG-5', 3969, 3'-CACTTG-5', 4011,
  12. inverse complement, positive strand, positive direction is SuccessablesEci++.bas, looking for 3'-C-A-(A/C/G/T)-(A/C/G/T)-T-G-5', 11, 3'-CACCTG-5', 186, 3'-CACGTG-5', 547, 3'-CATGTG-5', 567, 3'-CACGTG-5', 1219, 3'-CAGGTG-5', 1843, 3'-CAGGTG-5', 2028, 3'-CACGTG-5', 2961, 3'-CAGGTG-5', 3086, 3'-CACGTG-5', 3884, 3'-CACTTG-5', 3936, 3'-CAAGTG-5', 4202,
  13. inverse, negative strand, negative direction, is SuccessablesEi--.bas, looking for 3'-G-T-(A/C/G/T)-(A/C/G/T)-A-C-5', 21, 3'-GTATAC-5', 41, 3'-GTAAAC-5', 364, 3'-GTGGAC-5', 393, 3'-GTGGAC-5', 1130, 3'-GTGGAC-5', 1172, 3'-GTTTAC-5', 1579, 3'-GTCCAC-5', 2079, 3'-GTGAAC-5', 2126, 3'-GTCCAC-5', 2570, 3'-GTGAAC-5', 2579, 3'-GTGTAC-5', 2667, 3'-GTGAAC-5', 2920, 3'-GTGAAC-5', 3102, 3'-GTGAAC-5', 3241, 3'-GTCTAC-5', 3620, 3'-GTCTAC-5', 3627, 3'-GTTGAC-5', 3850, 3'-GTCTAC-5', 3919, 3'-GTCCAC-5', 3953, 3'-GTGGAC-5', 3969, 3'-GTGAAC-5', 4011,
  14. inverse, negative strand, positive direction, is SuccessablesEi-+.bas, looking for 3'-G-T-(A/C/G/T)-(A/C/G/T)-A-C-5', 11, 3'-GTGGAC-5', 186, 3'-GTGCAC-5', 547, 3'-GTACAC-5', 567, 3'-GTGCAC-5', 1219, 3'-GTCCAC-5', 1843, 3'-GTCCAC-5', 2028, 3'-GTGCAC-5', 2961, 3'-GTCCAC-5', 3086, 3'-GTGCAC-5', 3884, 3'-GTGAAC-5', 3936, 3'-GTTCAC-5', 4202,
  15. inverse, positive strand, negative direction, is SuccessablesEi+-.bas, looking for 3'-G-T-(A/C/G/T)-(A/C/G/T)-A-C-5', 10 , 3'-GTGTAC-5', 324 , 3'-GTCTAC-5', 481 , 3'-GTGTAC-5', 797 , 3'-GTTCAC-5', 1179 , 3'-GTCTAC-5', 1224 , 3'-GTCAAC-5', 1513 , 3'-GTGGAC-5', 2116 , 3'-GTCTAC-5', 2988 , 3'-GTAAAC-5', 3482 , 3'-GTCTAC-5', 4212,
  16. inverse, positive strand, positive direction, is SuccessablesEi++.bas, looking for 3'-G-T-(A/C/G/T)-(A/C/G/T)-A-C-5', 26, 3'-GTCCAC-5', 196, 3'-GTGCAC-5', 570, 3'-GTGGAC-5', 858, 3'-GTGGAC-5', 958, 3'-GTCCAC-5', 1968, 3'-GTGTAC-5', 2031, 3'-GTCGAC-5', 2054, 3'-GTCCAC-5', 2127, 3'-GTGGAC-5', 2249, 3'-GTCCAC-5', 2374, 3'-GTCGAC-5', 2404, 3'-GTGGAC-5', 2432, 3'-GTTCAC-5', 2510, 3'-GTGGAC-5', 2568, 3'-GTGGAC-5', 3046, 3'-GTCCAC-5', 3149, 3'-GTCGAC-5', 3241, 3'-GTAGAC-5', 3404, 3'-GTCTAC-5', 3475, 3'-GTGTAC-5', 3707, 3'-GTGTAC-5', 3742, 3'-GTCGAC-5', 3777, 3'-GTACAC-5', 3902, 3'-GTGTAC-5', 3956, 3'-GTACAC-5', 3958, 3'-GTGAAC-5', 4015.

Enhancer box UTRs

Main article: UTR promoter gene transcriptions

Negative strand, negative direction: CAGATG at 4212, CATTTG at 3482, CAGATG at 2988.

Positive strand, negative direction: CACTTG at 4011, CACCTG at 3969, CAGGTG at 3953, CAGATG at 3919, CAACTG at 3850, CAGATG at 3627, CAGATG at 3620, CACTTG at 3241, CACTTG at 3102, CACTTG at 2920.

Enhancer box proximal promoters

Main article: Proximal promoter gene transcriptions

Positive strand, negative direction: CACATG at 2667.

Positive strand, positive direction: CAAGTG at 4202.

Enhancer box distal promoters

Main article: Distal promoter gene transcriptions

Negative strand, negative direction: CACCTG at 2116, CAGTTG at 1513, CAGATG at 1224, CAAGTG at 1179, CACATG at 797, CAGATG at 481, CACATG at 324.

Positive strand, negative direction: CACTTG at 2579, CAGGTG at 2570, CACTTG at 2126, CAGGTG at 2079, CAAATG at 1579, CACCTG at 1172, CACCTG at 1130, CACCTG at 393, CATTTG at 364, CATATG at 41.

Negative strand, positive direction: CACTTG at 4015, CATGTG at 3958, CACATG at 3956, CATGTG at 3902, CAGCTG at 3777, CACATG at 3742, CACATG at 3707, CAGATG at 3475, CATCTG at 3404, CAGCTG at 3241, CAGGTG at 3149, CACCTG at 3046, CACCTG at 2568, CAAGTG at 2510, CACCTG at 2432, CAGCTG at 2404, CAGGTG at 2374, CACCTG at 2249, CAGGTG at 2127, CAGCTG at 2054, CACATG at 2031, CAGGTG at 1968, CACCTG at 958, CACCTG at 858, CACGTG at 570, CAGGTG at 196.

Positive strand, positive direction: CACTTG at 3936, CACGTG at 3884, CAGGTG at 3086, CACGTG at 2961, CAGGTG at 2028, CAGGTG at 1843, CACGTG at 1219, CATGTG at 567, CACGTG at 547, CACCTG at 186.

Transcribed enhancer boxes

"MYC is a basic helix-loop-helix transcription factor, evolutionarily conserved in all vertebrates with a considerable amount of sequence similarity (Atchley & Fitch, 1995). It binds to thousands of promoters in mammalian cells as MYC-MAX heterodimer (Blackwood & Eisenman, 1991; C. Y. Lin et al., 2012). In particular it binds the motif CACGTG of the enhancer box (E-box) in the core promoter of active genes. Depending on the target gene, MYC can act as transcriptional activator or repressor, and, can affect transcription at both initiation and elongation steps (Rahl et al., 2010)."[10]

"MYC mediates the transcriptional response of growth-factors stimulation. Importantly, MYC does not only regulate the expression of mRNA(s), it also regulates ribosomal and tRNA genes, transcribed by the RNA Pol I and RNA Pol III respectively (Campbell & White, 2014; Dai, Sun, & Lu, 2010; Mitchell et al., 2015). Amongst the major gene ontology categories of protein-coding genes under the control of MYC there are: ribosome biogenesis, apoptosis, cell adhesion, cell size, angiogenesis and metabolic pathways (Nieminen, Partanen, & Klefstrom, 2007; Peterson & Ayer, 2011; A. M. Singh & Dalton, 2009; Uslu et al., 2014; van Riggelen, Yetil, & Felsher, 2010)."[10]

"The ATA box [AAATAT], GC box [GGCGGG], CArG box [CCTATTATGCG], [two E boxes CAGTTG] and M-CAT [CATTCCT] consensus sequences are [described from the mouse dystrophin promoter]."[11]

"The E box [ enhancer box ] sites that are most important are those of the E2 box class (GCAGXTGG/T). Two E2 box sites are present in the immunoglobulin heavy chain gene enhancer [...] and one is present in the kappa enhancer, designated KE2 [29-31]."[12]

"The developmental regulation of Ig gene expression is dependent on various sequences in the Ig enhancer. One class of such sequence elements is the E boxes. They share as a consensus sequence NNCANNTGNN. The E-box sites were first identified by dimethylsulfate protection experiments (6, 12). Factors were found to protect certain sequences from methylation in the Ig heavy- and light-chain enhancer in B cells but not in non-B cells (6,12). That the E-box elements are critical for B-cell-specific gene expression became evident from mutational analysis. Mutation of E-box sites caused a significant decrease in Ig transcription (18, 21). The most dramatic impact on Ig expression was found in mutations of elements that contain an E2 box (G/ACAGNTGT/G) (21). The E2 boxes are particularly interesting because they are also present in muscle-and pancreas-specific enhancers (3,4,32). Mutation of the E2-box elements present in these enhancers revealed the crucial role of these elements in regulating muscle- and pancreas-specific genes (16, 22, 26, 27, 32)."[13]

"The two E2 boxes in the mouse and human E-cadherin promoter sequences were demonstrated to play a crucial role in the epithelial-specific expression of E-cadherin Behrens et al. 1991, Giroldi et al. 1997. Mutation of these sequence elements results in upregulation of the E-cadherin promoter in dedifferentiated cancer cells, whereas the wild-type promoter shows low activity in such cells. Recently, it was shown that the zinc finger transcriptional repressor Snail can downregulate E-cadherin by binding to the E boxes in the E-cadherin promoter Batlle et al. 2000, Cano et al. 2000. Human Snail belongs to a family of zinc finger proteins, which contain four or five zinc finger domains of the C2H2 type at their C-terminal end. These zinc fingers bind to the CANNTG sequence in E box motifs."[14]

The CArG boxes occur between -400 and -200 nts, between the E boxes and the TCE element.[15]

The "isolated mouse chromogranin B promoter [specifically] the proximal chromogranin B promoter (from −216 to −91 bp); [...] contains an E box (at [−206 bp]CACCTG[−201 bp]), four G/C-rich regions (at[− 196 bp]CCCCGC[−191 bp], [−134 bp]CCGCCCGC[−127 bp],[− 125 bp]GGCGCCGCC[−117 bp], and [−115 bp]CGGGGC[−110 bp]), and a cAMP response element (CRE; at [−102 bp]TGACGTCA[−95 bp]). A 60-bp core promoter region, defined by an internal deletion from −134 to −74 bp upstream of the cap site and spanning the CRE and three G/C-rich regions, directed tissue-specific expression of the gene. The CRE motif directed cell type-specific expression of the chromogranin B gene in neurons, whereas three of the G/C-rich regions played a crucial role in neuroendocrine cells. Both the endogenous chromogranin B gene and the transfected chromogranin B promoter were induced by preganglionic secretory stimuli (pituitary adenylyl cyclase-activating polypeptide, vasoactive intestinal peptide, or a nicotinic cholinergic agonist), establishing stimulus-transcription coupling for this promoter. The adenylyl cyclase activator forskolin, nerve growth factor, and retinoic acid also activated the chromogranin B gene. Secretagogue-inducible expression of chromogranin B also mapped onto the proximal promoter; inducible expression was entirely lost upon internal deletion of the 60-bp core (from −134 to −74 bp). [...] CRE and G/C-rich domains are crucial determinants of both cell type-specific and secretagogue-inducible expression of the chromogranin B gene."[16]

"TCF4 is a member of the family of basic helix-loop-helix (bHLH) TFs. These proteins have a DNA-binding domain and form homo- or heterodimers to regulate gene expression. The dimers of TFs can exert different functions depending on their dimerization partners (Jones, 2004). Within the family of bHLH TFs, TCF4 belongs to the subgroup of E-proteins, which share the recognition of the pseudo-palindromic Ephrussi box (E-box) DNA element (Massari & Murre, 2000). TCF4 can dimerize with numerous other TFs, and interactions of TCF4 with ATHO1 (MATH1), HASH1 and NEUROD1 have been described in the brain (Flora, Garcia, Thaller, & Zoghbi, 2007; Navarrete et al., 2013)."[17]

Gene ID: 4609 is MYC MYC proto-oncogene, bHLH transcription factor on 8q24.21: "This gene is a proto-oncogene and encodes a nuclear phosphoprotein that plays a role in cell cycle progression, apoptosis and cellular transformation. The encoded protein forms a heterodimer with the related transcription factor MAX. This complex binds to the E box DNA consensus sequence and regulates the transcription of specific target genes. Amplification of this gene is frequently observed in numerous human cancers. Translocations involving this gene are associated with Burkitt lymphoma and multiple myeloma in human patients. There is evidence to show that translation initiates both from an upstream, in-frame non-AUG (CUG) and a downstream AUG start site, resulting in the production of two isoforms with distinct N-termini."[18]

  1. NP_001341799.1 myc proto-oncogene protein isoform 2.[18]
  2. NP_002458.2 myc proto-oncogene protein isoform 1.[18]

Gene ID: 6925 is TCF4 transcription factor 4 on 18q21.2: "This gene encodes transcription factor 4, a basic helix-loop-helix transcription factor. The encoded protein recognizes an Ephrussi-box ('E-box') binding site ('CANNTG') - a motif first identified in immunoglobulin enhancers. This gene is broadly expressed, and may play an important role in nervous system development. Defects in this gene are a cause of Pitt-Hopkins syndrome. In addition, an intronic CTG repeat normally numbering 10-37 repeat units can expand to >50 repeat units and cause Fuchs endothelial corneal dystrophy. Multiple alternatively spliced transcript variants that encode different proteins have been described."[19]

  1. NP_001077431.1 transcription factor 4 isoform a: "Transcript Variant: This variant (1) differs in the 5' UTR and coding sequence compared to variant 3. The resulting isoform (a, also known as TCF4-B+) is shorter at the N-terminus compared to isoform c."[19]
  2. NP_001230155.2 transcription factor 4 isoform c: "Transcript Variant: This variant (3) encodes the longest isoform (c)."[19]
  3. NP_001230156.1 transcription factor 4 isoform d: "Transcript Variant: This variant (4) differs in the 5' UTR and coding sequence compared to variant 3. The resulting isoform (d) is shorter at the N-terminus compared to isoform c."[19]
  4. NP_001230157.1 transcription factor 4 isoform e: "Transcript Variant: This variant (5) differs in the 5' UTR and coding sequence and uses an alternate in-frame splice site at the 5' end of an exon compared to variant 3. The resulting isoform (e) is shorter at the N-terminus and contains an alternate internal segment compared to isoform c."[19]
  5. NP_001230159.1 transcription factor 4 isoform f: "Transcript Variant: This variant (6) differs in the 5' UTR and coding sequence and uses an alternate in-frame splice site at the 3' end of an exon compared to variant 3. The resulting isoform (f, also known as TCF4-E-) has a shorter and distinct N-terminus and lacks an alternate internal segment compared to isoform c."[19]
  6. NP_001230160.1 transcription factor 4 isoform g: "Transcript Variant: This variant (7) differs in the 5' UTR and coding sequence and uses an alternate in-frame splice site at the 3' end of an exon compared to variant 3. The resulting isoform (g) has a shorter and distinct N-terminus and lacks an alternate internal segment compared to isoform c."[19]
  7. NP_001230161.1 transcription factor 4 isoform h: "Transcript Variant: This variant (8) differs in the 5' UTR and coding sequence and uses an alternate in-frame splice site at the 5' end of an exon compared to variant 3. The resulting isoform (h) has a shorter and distinct N-terminus and contains an alternate internal segment compared to isoform c."[19]
  8. NP_001230162.1 transcription factor 4 isoform i: "Transcript Variant: This variant (9) differs in the 5' UTR and coding sequence and uses an alternate in-frame splice site at the 3' end of an exon compared to variant 3. The resulting isoform (i) is shorter at the N-terminus and lacks an alternate internal segment compared to isoform c."[19]
  9. NP_001230163.1 transcription factor 4 isoform j: "Transcript Variant: This variant (10) differs in the 5' UTR and coding sequence compared to variant 3. The resulting isoform (j, also known as TCF4-A+) has a shorter and distinct N-terminus compared to isoform c."[19]
  10. NP_001230164.1 transcription factor 4 isoform k: "Transcript Variant: This variant (11) differs in the 5' UTR and coding sequence and uses an alternate in-frame splice site at the 3' end of an exon compared to variant 3. The resulting isoform (k, also known as TCF4-A-) has a shorter and distinct N-terminus and lacks an alternate internal segment compared to isoform c."[19]
  11. NP_001230165.1 transcription factor 4 isoform l: "Transcript Variant: This variant (12) differs in the 5' UTR and coding sequence and uses an alternate in-frame splice site at the 3' end of an exon compared to variant 3. The resulting isoform (l) has a shorter and distinct N-terminus and lacks an alternate internal segment compared to isoform c."[19]
  12. NP_001293136.1 transcription factor 4 isoform m: "Transcript Variant: This variant (13) differs in the 5' UTR and coding sequence, and uses an alternate in-frame splice site in the 3' coding region, compared to variant 3. The encoded isoform (m) has a shorter N-terminus compared to isoform c."[19]
  13. NP_001293137.1 transcription factor 4 isoform n: "Transcript Variant: This variant (14) differs in the 5' UTR and coding sequence, and uses two alternate in-frame splice sites in the coding region, compared to variant 3. The encoded isoform (n) has a shorter and distinct N-terminus compared to isoform c."[19]
  14. NP_001317533.1 transcription factor 4 isoform o: "Transcript Variant: This variant (15) differs in the 5' UTR, lacks a portion of the 5' coding region, initiates translation at a downstream start codon, and uses an alternate in-frame splice site in the central coding region, compared to variant 3. The resulting isoform (o) is shorter at the N-terminus and lacks an internal aa compared to isoform c."[19]
  15. NP_001317534.1 transcription factor 4 isoform p: "Transcript Variant: This variant (16) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 3. The resulting isoform (p) is shorter at the N-terminus compared to isoform c. Variants 16 and 19 encode the same isoform (p)."[19]
  16. NP_001335140.1 transcription factor 4 isoform q: "Transcript Variant: This variant (17) contains an alternate exon in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 3. The resulting isoform (q) is shorter at the N-terminus compared to isoform c."[19]
  17. NP_001335141.1 transcription factor 4 isoform i: "Transcript Variant: This variant (18) differs in the 5' UTR, lacks a portion of the 5' coding region, initiates translation at a downstream start codon, and uses an alternate in-frame splice site in the 3' coding region, compared to variant 3. The resulting isoform (i) is shorter at the N-terminus and lacks a small internal segment compared to isoform c. Variants 9 and 18 encode the same isoform (i)."[19]
  18. NP_001335142.1 transcription factor 4 isoform p: "Transcript Variant: This variant (19) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 3. The resulting isoform (p) is shorter at the N-terminus compared to isoform c. Variants 16 and 19 encode the same isoform (p)."[19]
  19. NP_001335143.1 transcription factor 4 isoform r: "Transcript Variant: This variant (20) contains an alternate exon in the 5' UTR, lacks a portion of the 5' coding region, initiates translation at an alternate start codon, and uses two alternate in-frame splice sites, compared to variant 3. The resulting isoform (r) is shorter at the N-terminus and lacks several internal amino acids compared to isoform c."[19]
  20. NP_001335144.1 transcription factor 4 isoform s: "Transcript Variant: This variant (21) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 3. The resulting isoform (s) is shorter at the N-terminus compared to isoform c."[19]
  21. NP_001335145.1 transcription factor 4 isoform t: "Transcript Variant: This variant (22) contains an alternate exon in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 3. The resulting isoform (t) is shorter at the N-terminus compared to isoform c."[19]
  22. NP_001335146.1 transcription factor 4 isoform d: "Transcript Variant: This variant (23) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 3. The resulting isoform (d) is shorter at the N-terminus compared to isoform c. Variants 4, 23 and 24 all encode the same isoform (d)."[19]
  23. NP_001335147.1 transcription factor 4 isoform d: "Transcript Variant: This variant (24) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 3. The resulting isoform (d) is shorter at the N-terminus compared to isoform c. Variants 4, 23 and 24 all encode the same isoform (d)."[19]
  24. NP_001335148.1 transcription factor 4 isoform m: "Transcript Variant: This variant (25) differs in the 5' UTR, lacks a portion of the 5' coding region, initiates translation at a downstream start codon, and uses an alternate in-frame splice site in the 3' coding region compared to variant 3. The resulting isoform (m) is shorter at the N-terminus and lacks an alternate internal segment compared to isoform c. Variants 13 and 25 encode the same isoform (m)."[19]
  25. NP_001335149.1 transcription factor 4 isoform u: "Transcript Variant: This variant (26) differs in the 5' UTR, lacks a portion of the 5' coding region, initiates translation at a downstream start codon, and uses two alternate in-frame splice sites compared to variant 3. The resulting isoform (u) is shorter at the N-terminus and lacks several internal amino acids compared to isoform c."[19]
  26. NP_001356496.1 transcription factor 4 isoform a [variant 27].[19]
  27. NP_001356497.1 transcription factor 4 isoform a [variant 28].[19]
  28. NP_001356498.1 transcription factor 4 isoform v [variant 29].[19]
  29. NP_001356499.1 transcription factor 4 isoform v [variant 30].[19]
  30. NP_001356500.1 transcription factor 4 isoform w [variant 31].[19]
  31. NP_001356501.1 transcription factor 4 isoform w [variant 32].[19]
  32. NP_001356502.1 transcription factor 4 isoform x [variant 33].[19]
  33. NP_001356503.1 transcription factor 4 isoform 27 [variant 34].[19]
  34. NP_001356504.1 transcription factor 4 isoform d [variant 35].[19]
  35. NP_001356505.1 transcription factor 4 isoform y [variant 36].[19]
  36. NP_001356506.1 transcription factor 4 isoform 28 [variant 37].[19]
  37. NP_001356507.1 transcription factor 4 isoform y [variant 38].[19]
  38. NP_001356508.1 transcription factor 4 isoform 28 [variant 39].[19]
  39. NP_001356509.1 transcription factor 4 isoform 28 [variant 40].[19]
  40. NP_001356510.1 transcription factor 4 isoform y [variant 41].[19]
  41. NP_001356511.1 transcription factor 4 isoform m [variant 42].[19]
  42. NP_001356512.1 transcription factor 4 isoform m [variant 43].[19]
  43. NP_001356513.1 transcription factor 4 isoform u [variant 44].[19]
  44. NP_001356514.1 transcription factor 4 isoform u [variant 45].[19]
  45. NP_001356515.1 transcription factor 4 isoform z [variant 46].[19]
  46. NP_003190.1 transcription factor 4 isoform b: "Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence and uses an alternate in-frame splice site at the 3' end of an exon compared to variant 3. The resulting isoform (b, also known as TCF4-B-) is shorter at the N-terminus and lacks an alternate internal segment compared to isoform c."[19]

Gene ID: 6927 is HNF1A HNF1 homeobox A aka TCF1 on 12q24.31: "The protein encoded by this gene is a transcription factor required for the expression of several liver-specific genes. The encoded protein functions as a homodimer and binds to the inverted palindrome 5'-GTTAATNATTAAC-3'. Defects in this gene are a cause of maturity onset diabetes of the young type 3 (MODY3) and also can result in the appearance of hepatic adenomas. Alternative splicing results in multiple transcript variants encoding different isoforms."[20]

  1. NP_000536.6 hepatocyte nuclear factor 1-alpha isoform 2 [variant 2].[20]
  2. NP_001293108.2 hepatocyte nuclear factor 1-alpha isoform 1: "Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1)."[20]

Gene ID: 6929 is TCF3 transcription factor 3 aka immunoglobulin transcription factor 1 on 19p13.3: "This gene encodes a member of the E protein (class I) family of helix-loop-helix transcription factors. E proteins activate transcription by binding to regulatory E-box sequences on target genes as heterodimers or homodimers, and are inhibited by heterodimerization with inhibitor of DNA-binding (class IV) helix-loop-helix proteins. E proteins play a critical role in lymphopoiesis, and the encoded protein is required for B and T lymphocyte development. Deletion of this gene or diminished activity of the encoded protein may play a role in lymphoid malignancies. This gene is also involved in several chromosomal translocations that are associated with lymphoid malignancies including pre-B-cell acute lymphoblastic leukemia (t(1;19), with PBX1), childhood leukemia (t(19;19), with TFPT) and acute leukemia (t(12;19), with ZNF384). Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene, and a pseudogene of this gene is located on the short arm of chromosome 9."[21]

  1. NP_001129611.1 transcription factor E2-alpha isoform E47: "Transcript Variant: This variant (2) differs in the 3' UTR, lacks an exon and includes an alternate exon in the 3' coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (E47, also known as Pan-1) is shorter than isoform E12. Variants 2 and 4 encode the same isoform (E47)."[21]
  2. NP_001338707.1 transcription factor E2-alpha isoform 3: "Transcript Variant: This variant (3) uses an alternate in-frame splice site in the central coding region, and contains an alternate splice structure in the 3' region, resulting in differences in the 3' UTR. The encoded isoform (3) has the same N- and C-termini, but is one aa shorter than isoform 1."[21]
  3. NP_001338708.1 transcription factor E2-alpha isoform E47: "Transcript Variant: This variant (4) contains an alternate penultimate exon compared to variant 1. The encoded isoform (E47, also known as Pan-1) is shorter than isoform E12. Variants 2 and 4 encode the same isoform (E47)."[21]
  4. NP_003191.1 transcription factor E2-alpha isoform E12: "Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (E12). This isoform is also known as Pan-2."[21]

Gene ID: 6935 is ZEB1 zinc finger E-box binding homeobox 1 on 10p11.22: "This gene encodes a zinc finger transcription factor. The encoded protein likely plays a role in transcriptional repression of interleukin 2. Mutations in this gene have been associated with posterior polymorphous corneal dystrophy-3 and late-onset Fuchs endothelial corneal dystrophy. Alternatively spliced transcript variants encoding different isoforms have been described."[22]

  1. NP_001121600.1 zinc finger E-box-binding homeobox 1 isoform a [variant 1].[22]
  2. NP_001167564.1 zinc finger E-box-binding homeobox 1 isoform c [variant 6].[22]
  3. NP_001167565.1 zinc finger E-box-binding homeobox 1 isoform d [variant 7].[22]
  4. NP_001167566.1 zinc finger E-box-binding homeobox 1 isoform e [variant 8].[22]
  5. NP_001167567.1 zinc finger E-box-binding homeobox 1 isoform f [variant 9].[22]
  6. NP_001310567.1 zinc finger E-box-binding homeobox 1 isoform g [variant 3].[22]
  7. NP_001310570.1 zinc finger E-box-binding homeobox 1 isoform g [variant 4].[22]
  8. NP_001310571.1 zinc finger E-box-binding homeobox 1 isoform g [variant 5].[22]
  9. NP_001310572.1 zinc finger E-box-binding homeobox 1 isoform g [variant 10].[22]
  10. NP_001310573.1 zinc finger E-box-binding homeobox 1 isoform g [variant 11].[22]
  11. NP_001310574.1 zinc finger E-box-binding homeobox 1 isoform g [variant 12].[22]
  12. NP_001310575.1 zinc finger E-box-binding homeobox 1 isoform g [variant 13].[22]
  13. NP_001310576.1 zinc finger E-box-binding homeobox 1 isoform g [variant 14].[22]
  14. NP_001310577.1 zinc finger E-box-binding homeobox 1 isoform g [variant 15].[22]
  15. NP_001310578.1 zinc finger E-box-binding homeobox 1 isoform g [variant 16].[22]
  16. NP_001310579.1 zinc finger E-box-binding homeobox 1 isoform g [variant 17].[22]
  17. NP_001310580.1 zinc finger E-box-binding homeobox 1 isoform g [variant 18].[22]
  18. NP_001310581.1 zinc finger E-box-binding homeobox 1 isoform g [variant 19].[22]
  19. NP_001310582.1 zinc finger E-box-binding homeobox 1 isoform g [variant 20].[22]
  20. NP_001310583.1 zinc finger E-box-binding homeobox 1 isoform g [variant 21].[22]
  21. NP_001310584.1 zinc finger E-box-binding homeobox 1 isoform g [variant 22].[22]
  22. NP_001310585.1 zinc finger E-box-binding homeobox 1 isoform g [variant 23].[22]
  23. NP_001310586.1 zinc finger E-box-binding homeobox 1 isoform g [variant 24].[22]
  24. NP_001310587.1 zinc finger E-box-binding homeobox 1 isoform g [variant 25].[22]
  25. NP_001310588.1 zinc finger E-box-binding homeobox 1 isoform g [variant 26].[22]
  26. NP_001310589.1 zinc finger E-box-binding homeobox 1 isoform g [variant 27].[22]
  27. NP_001310590.1 zinc finger E-box-binding homeobox 1 isoform g [variant 28].[22]
  28. NP_001310591.1 zinc finger E-box-binding homeobox 1 isoform g [variant 29].[22]
  29. NP_001310592.1 zinc finger E-box-binding homeobox 1 isoform g [variant 30].[22]
  30. NP_001310593.1 zinc finger E-box-binding homeobox 1 isoform g [variant 31].[22]
  31. NP_001310594.1 zinc finger E-box-binding homeobox 1 isoform g [variant 32].[22]
  32. NP_001310595.1 zinc finger E-box-binding homeobox 1 isoform g [variant 33].[22]
  33. NP_001310600.1 zinc finger E-box-binding homeobox 1 isoform g [variant 34].[22]
  34. NP_001310601.1 zinc finger E-box-binding homeobox 1 isoform g [variant 35].[22]
  35. NP_001310602.1 zinc finger E-box-binding homeobox 1 isoform g [variant 36].[22]
  36. NP_001310603.1 zinc finger E-box-binding homeobox 1 isoform h [variant 37].[22]
  37. NP_001310604.1 zinc finger E-box-binding homeobox 1 isoform i [variant 38].[22]
  38. NP_001310605.1 zinc finger E-box-binding homeobox 1 isoform j [variant 39].[22]
  39. NP_001310606.1 zinc finger E-box-binding homeobox 1 isoform k [variant 40].[22]
  40. NP_001310607.1 zinc finger E-box-binding homeobox 1 isoform l [variant 41].[22]
  41. NP_110378.3 zinc finger E-box-binding homeobox 1 isoform b [variant 2].[22]

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. ↑ "E-box". San Francisco, California: Wikimedia Foundation, Inc. April 13, 2013. Retrieved 2013-04-17.
  2. ↑ Charalampos G. Spilianakis, Maria D. Lalioti, Terrence Town, Gap Ryol Lee, Richard A. Flavell (2005). "Interchromosomal associations between alternatively expressed loci". Nature. 435 (7042): 637–45. doi:10.1038/nature03574. PMID 15880101.
  3. ↑ SemperBlotto (16 January 2011). "enhancer". San Francisco, California: Wikimedia Foundation, Inc. Retrieved 2017-08-25.
  4. ↑ "Box (disambiguation)". San Francisco, California: Wikimedia Foundation, Inc. May 23, 2013. Retrieved 2013-06-15.
  5. ↑ Bork P, Holm L, Sander C (September 1994). "The immunoglobulin fold. Structural classification, sequence patterns and common core". Journal of Molecular Biology. 242 (4): 309–20. doi:10.1006/jmbi.1994.1582. PMID 7932691.
  6. ↑ Brümmendorf T, Rathjen FG (1995). "Cell adhesion molecules 1: immunoglobulin superfamily". Protein Profile. 2 (9): 963–1108. PMID 8574878.
  7. ↑ George M. Church, Anne Ephrussi, Walter Gilbert, Susumu Tonegawa (1985). Nature. 313 (6005): 798–801. Missing or empty |title= (help)
  8. ↑ 8.0 8.1 8.2 Jaideep Chaudhary and Michael K. Skinner (May 1999). "Basic Helix-Loop-Helix Proteins Can Act at the E-Box within the Serum Response Element of the c-fos Promoter to Influence Hormone-Induced Promoter Activation in Sertoli Cells". Molecular Endocrinology. 13 (5): 774–86. doi:10.1210/me.13.5.774. PMID 10319327. Retrieved 2013-06-14.
  9. ↑ 9.0 9.1 "Promoter (genetics)". San Francisco, California: Wikimedia Foundation, Inc. June 14, 2013. Retrieved 2013-06-15.
  10. ↑ 10.0 10.1 Massimo Petretich (20 September 2016). Importance of Chromosomal Architecture to Organize Promoter-Enhancer Long-Range Interactions in c-Myc locus (PDF). Heidelberg, Germany: Ruperto-Carola University of Heidelberg. p. 195. Retrieved 2017-09-05.
  11. ↑ Shigemi Kimura, Kuniya Abe, Misao Suzuki, Masakatsu Ogawa, Kowashi Yoshioka, Tadasi Kaname, Teruhisa Miike, Ken‐ichi Yamamura (June 1997). "A 900 bp genomic region from the mouse dystrophin promoter directs lacZ reporter expression only to the right heart of transgenic mice". Development, Growth & Differentiation. 39 (1): 257–265. doi:10.1046/j.1440-169X.1997.t01-2-00001.x. Retrieved 25 March 2019.
  12. ↑ Cornelis Murre, Gretchen Bain, Marc A. van Dijk, Isaac Engel, Beth A. Furnari, Mark E. Massari, James R. Matthews, Melanie W. Quong, Richard R. Rivera, Maarten H. Stuiver (June 1994). "Structure and function of helix-loop-helix proteins". Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression. 1218 (2): 129–35. Retrieved 2017-02-08.
  13. ↑ Gretchen Bain, Stefan Gruenwald, and Cornelis Murre (June 1993). "E2A and E2-2 are subunits of B-cell-specific E2-box DNA-binding proteins" (PDF). Molecular and Cellular Biology. 13 (6): 3522–3529. doi:10.1128/MCB.13.6.3522. Retrieved 2 February 2019.
  14. ↑ Joke Comijn, Geert Berx, Petra Vermassen, Kristin Verschueren, Leo van Grunsven, Erik Bruyneel, Marc Mareel, Danny Huylebroeck, Frans van Roy (June 2001). "The Two-Handed E Box Binding Zinc Finger Protein SIP1 Downregulates E-Cadherin and Induces Invasion". Molecular Cell. 7 (6): 1267–78. doi:10.1016/S1097-2765(01)00260-X. Retrieved 11 January 2019.
  15. ↑ Oliver G. McDonald, Brian R. Wamhoff, Mark H. Hoofnagle, and Gary K. Owens (January 4, 2006). "Control of SRF binding to CArG box chromatin regulates smooth muscle gene expression in vivo". The Journal of Clinical Investigation. 116 (1): 36–48. Retrieved 2014-06-05.
  16. ↑ Nitish R. Mahapatra, Manjula Mahata, Arun K. Datta, Hans-Hermann Gerdes, Wieland B. Huttner, Daniel T. O’Connor, Sushil K. Mahata (1 October 2000). "Neuroendocrine Cell Type-Specific and Inducible Expression of the Chromogranin B Gene: Crucial Role of the Proximal Promoter". Endocrinology. 141 (10): 3668–3678. doi:10.1210/endo.141.10.7725. Retrieved 15 September 2018.
  17. ↑ Melanie Schoof, Malte Hellwig, Luke Harrison, Dörthe Holdhof, Marlen C. Lauffer, Judith Niesen, Sanamjeet Virdi, Daniela Indenbirken and Ulrich Schüller (9 January 2020). "The basic helix-loop-helix transcription factor TCF4 impacts brain architecture as well as neuronal morphology and differentiation" (PDF). European Journal of Neuroscience. 00 (14674): 1–17. doi:10.1111/ejn.14674. Retrieved 29 April 2020.
  18. ↑ 18.0 18.1 18.2 RefSeq (August 2017). "MYC MYC proto-oncogene, bHLH transcription factor [ Homo sapiens (human) ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 1 May 2020.
  19. ↑ 19.00 19.01 19.02 19.03 19.04 19.05 19.06 19.07 19.08 19.09 19.10 19.11 19.12 19.13 19.14 19.15 19.16 19.17 19.18 19.19 19.20 19.21 19.22 19.23 19.24 19.25 19.26 19.27 19.28 19.29 19.30 19.31 19.32 19.33 19.34 19.35 19.36 19.37 19.38 19.39 19.40 19.41 19.42 19.43 19.44 19.45 19.46 RefSeq (July 2016). "TCF4 transcription factor 4 [ Homo sapiens (human) ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 5 April 2020.
  20. ↑ 20.0 20.1 20.2 RefSeq (April 2015). HNF1A HNF1 homeobox A [ Homo sapiens (human) ]. 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 7 November 2018.
  21. ↑ 21.0 21.1 21.2 21.3 21.4 RefSeq (September 2011). "TCF3 transcription factor 3 [ Homo sapiens (human) ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 29 April 2020.
  22. ↑ 22.00 22.01 22.02 22.03 22.04 22.05 22.06 22.07 22.08 22.09 22.10 22.11 22.12 22.13 22.14 22.15 22.16 22.17 22.18 22.19 22.20 22.21 22.22 22.23 22.24 22.25 22.26 22.27 22.28 22.29 22.30 22.31 22.32 22.33 22.34 22.35 22.36 22.37 22.38 22.39 22.40 22.41 RefSeq (March 2010). "ZEB1 zinc finger E-box binding homeobox 1 [ Homo sapiens (human) ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 1 May 2020.

Further reading

External links

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