# Gene transcriptions/Boxes/Xs

"The so-called X (or X1) box in the promoter of the human MHC class II DRA gene is the binding site for a ubiquitous mammalian sequence-specific DNA-binding protein called RFX, NF-X, NF-Xc, or RFX1 (4,19,23,24,27)."
"RFX is MDBP [...] the MDBP (RFX) recognition site region in the DRA promoter can be considered to extend from positions -100 to -112 [...] a possible binding site for MDBP which begins 88 bp after the first residue of the presumably full-length RFX1 (MDBP) cDNA (26). This site (RFX+88) is as follows: 5'-GTTGGCATGGCAAC-3'."

## X-box motifs

"Based on sequence variability in the X box region (position -188 to -152), three different sequence motifs can be distinguished (X-A, X-B and X-C). Identical bases are marked by a dash; the region of the X1 box is underlined; the region corresponding to the X2 box is given in italics."
X2 box is 5'-AGGTCCA-3'.
X-A box is 5'-AAAAAAAA//TCTGCCCAGAGACAGATGAGGTCCA-3', where TG is missing at //, which contains X1 = 5'-CCCAGAGACAGATGA-3' and disrupts the palindrome 5'- TGTCNNNNNNNNGACA-3' .
X-B box is 5'-AAAAAAAATGTCTGCCTAGAGACAGATTAGGTCCA-3' which contains X1 = 5'-CCTAGAGACAGATTA-3' and the palindrome 5'-CCTANNNNNNNNNTAGG-3'.
X-C box is 5'-AAAAAAAATGTCTGCCTAGAGACAGATGAGGTCCA-3' which contains X1 = 5'-TGCCTAGAGAC-3' and the palindrome 5'-CCTANNNNNNNNNTAGG-3'.

## Sampling of A1BG promoters

For the Basic programs (starting with SuccessablesXbox.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 (+), including extending the number of nts from 958 to 4445, the programs are, are looking for, and found:
* negative strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesXbox--.bas, looking for 3'-GTTGGCATGGCAAC-5', 0,
* negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesXbox-+.bas, looking for 3'-GTTGGCATGGCAAC-5', 0,
* positive strand in the negative direction is SuccessablesXbox+-.bas, looking for 3'-GTTGGCATGGCAAC-5', 0,
* positive strand in the positive direction is SuccessablesXbox++.bas, looking for 3'-GTTGGCATGGCAAC-5', 0,
* complement, negative strand, negative direction is SuccessablesXboxc--.bas, looking for 3'-CAACCGTACCGTTG-5', 0,
* complement, negative strand, positive direction is SuccessablesXboxc-+.bas, looking for 3'-CAACCGTACCGTTG-5', 0,
* complement, positive strand, negative direction is SuccessablesXboxc+-.bas, looking for 3'-CAACCGTACCGTTG-5', 0,
* complement, positive strand, positive direction is SuccessablesXboxc++.bas, looking for 3'-CAACCGTACCGTTG-5', 0,
* inverse complement, negative strand, negative direction is SuccessablesXboxci--.bas, looking for 3'-GTTGCCATGCCAAC-5', 0,
* inverse complement, negative strand, positive direction is SuccessablesXboxci-+.bas, looking for 3'-GTTGCCATGCCAAC-5', 0,
* inverse complement, positive strand, negative direction is SuccessablesXboxci+-.bas, looking for 3'-GTTGCCATGCCAAC-5', 0,
* inverse complement, positive strand, positive direction is SuccessablesXboxci++.bas, looking for 3'-GTTGCCATGCCAAC-5', 0,
* inverse, negative strand, negative direction, is SuccessablesXboxi--.bas, looking for 3'-CAACGGTACGGTTG-5', 0,
* inverse, negative strand, positive direction, is SuccessablesXboxi-+.bas, looking for 3'-CAACGGTACGGTTG-5', 0,
* inverse, positive strand, negative direction, is SuccessablesXboxi+-.bas, looking for 3'-CAACGGTACGGTTG-5', 0,
* inverse, positive strand, positive direction, is SuccessablesXboxi++.bas, looking for 3'-CAACGGTACGGTTG-5', 0.