# Gene transcriptions/Boxes/Vs

"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."
* NP_002114.3 HLA class II histocompatibility antigen, DQ beta 1 chain isoform 1 precursor (variant 1).
* NP_001230890.1 HLA class II histocompatibility antigen, DQ beta 1 chain isoform 2 precursor (variant 2).
* 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."
* NP_001287719.1 HLA class II histocompatibility antigen, DQ beta 2 chain isoform 1 precursor (variant 1).
* NP_001185787.1 HLA class II histocompatibility antigen, DQ beta 2 chain isoform 2 precursor (variant 2).
* XP_005249108.1 HLA class II histocompatibility antigen, DQ beta 2 chain isoform X1.
* XP_011512862.1 HLA class II histocompatibility antigen, DQ beta 2 chain isoform X2.
* 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."
* NP_001276928.1 nuclear factor interleukin-3-regulated protein (variant 1).
* NP_001276929.1 nuclear factor interleukin-3-regulated protein (variant 2).
* NP_005375.2 nuclear factor interleukin-3-regulated protein (variant 3).
* XP_016870232.1 nuclear factor interleukin-3-regulated protein isoform X1.
* XP_016870233.1 nuclear factor interleukin-3-regulated protein isoform X1.