Gene transcriptions/Boxes/GLMs

"The primary structure of hordein [barley prolamins] polypeptides is closely related to that of prolamins from other grass species from the Pooideae subfamily, such as wheat and rye (Shewry & Tatham 1990;Shewry et al. 1995). The close evolutionary relationship is also manifested by the conservation of a putative regulatory element in their gene promoters, the endosperm box (Forde et al. 1985;Kreis et al. 1985). This conserved region consists of two motifs, a 7 bp element (5′TGTAAAG3′) termed the Prolamin Box (P-box) or endosperm motif (EM) followed at a distance of up to 8 nucleotides by the GCN4-like motif (GLM) which has the 5′(G/A)TGA(G/C)TCA(T/C)3′ consensus sequence (reviewed by Müller et al. 1995)."

Gerstenfeld (Hordeum vulgare) mid June 2009 in Heidelberg-Wieblingen. Credit: 3268zauber.{{free media}}

Consensus sequences

The GCN4-like motif (GLM) [...] has the 5′(G/A)TGA(G/C)TCA(T/C)3′ consensus sequence (reviewed by Müller et al. 1995)."

Hypotheses

1. A1BG is not transcribed by a GLM box.

GLM box sampling of A1BG promoters

For the Basic programs (starting with SuccessablesGLM.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:

1. negative strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesGLM--.bas, looking for 3'-(G/A)TGA(G/C)TCA(T/C)-5', 0,
2. negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesGLM-+.bas, looking for 3'-(G/A)TGA(G/C)TCA(T/C)-5', 0,
3. positive strand in the negative direction is SuccessablesGLM+-.bas, looking for 3'-(G/A)TGA(G/C)TCA(T/C)-5', 0,
4. positive strand in the positive direction is SuccessablesGLM++.bas, looking for 3'-(G/A)TGA(G/C)TCA(T/C)-5', 0,
5. complement, negative strand, negative direction is SuccessablesGLMc--.bas, looking for 3'-(C/T)ACT(G/C)AGT(A/G)-5', 0,
6. complement, negative strand, positive direction is SuccessablesGLMc-+.bas, looking for 3'-(C/T)ACT(G/C)AGT(A/G)-5', 0,
7. complement, positive strand, negative direction is SuccessablesGLMc+-.bas, looking for 3'-(C/T)ACT(G/C)AGT(A/G)-5', 0,
8. complement, positive strand, positive direction is SuccessablesGLMc++.bas, looking for 3'-(C/T)ACT(G/C)AGT(A/G)-5', 0,
9. inverse complement, negative strand, negative direction is SuccessablesGLMci--.bas, looking for 3'-(A/G)TGA(G/C)TCA(C/T)-5', 0,
10. inverse complement, negative strand, positive direction is SuccessablesGLMci-+.bas, looking for 3'-(A/G)TGA(G/C)TCA(C/T)-5', 0,
11. inverse complement, positive strand, negative direction is SuccessablesGLMci+-.bas, looking for 3'-(A/G)TGA(G/C)TCA(C/T)-5', 0,
12. inverse complement, positive strand, positive direction is SuccessablesGLMci++.bas, looking for 3'-(A/G)TGA(G/C)TCA(C/T)-5', 0,
13. inverse, negative strand, negative direction, is SuccessablesGLMi--.bas, looking for 3'-(T/C)ACT(G/C)AGT(G/A)-5', 0,
14. inverse, negative strand, positive direction, is SuccessablesGLMi-+.bas, looking for 3'-(T/C)ACT(G/C)AGT(G/A)-5', 0,
15. inverse, positive strand, negative direction, is SuccessablesGLMi+-.bas, looking for 3'-(T/C)ACT(G/C)AGT(G/A)-5', 0,
16. inverse, positive strand, positive direction, is SuccessablesGLMi++.bas, looking for 3'-(T/C)ACT(G/C)AGT(G/A)-5', 0.

Results

As the sampling demonstrates A1BG is not transcribed by any GLM box in the promoters on either side.

See also

• Gene transcriptions/GA responsive complex/Laboratory