Prolamin box gene transcriptions
Editor-In-Chief: Henry A. Hoff
{{free media}}"The BPBF [barley prolamin-box (P-box) binding factor] expressed in bacteria as a GST-fusion binds a P-box 5′-TGTAAAG-3′ containing oligonucleotide derived from the promoter region of anHor2gene."[1]
"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)."[1]
Consensus sequences
"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)."[1]
"The main cis-element present in their promoters is an endosperm-specific box [19,20], which consists of two motifs: a GLM (GCN4-like motif) (5′ G(A)TGA(G) GTCAT 3′) that shares homology with yeast GCN4 [21], and a 7 bp P-box (Prolamin box) (5′TGTAAAG3′) [22–24]."[2]
Prolamin box sampling
For the Basic programs (starting with SuccessablesProl.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:
- negative strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesProl--.bas, looking for TG(A/T)AAAG, 1, TGTAAAG-5 at 2884,
- negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesProl-+.bas, looking for TG(A/T)AAAG, 1, TGAAAAG at 3928,
- positive strand in the negative direction is SuccessablesProl+-.bas, looking for TG(A/T)AAAG, 1, TGAAAAG at 1627,
- positive strand in the positive direction is SuccessablesProl++.bas, looking for TG(A/T)AAAG, 1, TGAAAAG at 2275, and complement.
- complement, negative strand, negative direction is SuccessablesProlc--.bas, looking for AC(A/T)TTTC, 1, ACTTTTC at 1627,
- complement, negative strand, positive direction is SuccessablesProlc-+.bas, looking for AC(A/T)TTTC, ACTTTC at 3928,
- complement, positive strand, negative direction is SuccessablesProlc+-.bas, looking for AC(A/T)TTTC, 1, ACATTTC at 2884,
- complement, positive strand, positive direction is SuccessablesProlc++.bas, looking for AC(A/T)TTTC, 1, ACTTTTC at 3928,
- inverse complement, negative strand, negative direction is SuccessablesProlci--.bas, looking for CTTT(A/T)CA, 0,
- inverse complement, negative strand, positive direction is SuccessablesProlci-+.bas, looking for CTTT(A/T)CA, 0,
- inverse complement, positive strand, negative direction is SuccessablesProlci+-.bas, looking for CTTT(A/T)CA, 0,
- inverse complement, positive strand, positive direction is SuccessablesProlci++.bas, looking for CTTT(A/T)CA, 0,
- inverse, negative strand, negative direction, is SuccessablesProli--.bas, looking for GAAA(A/T)GT, 0,
- inverse, negative strand, positive direction, is SuccessablesProli-+.bas, looking for GAAA(A/T)GT, 0,
- inverse, positive strand, negative direction, is SuccessablesProli+-.bas, looking for GAAA(A/T)GT, 0,
- inverse, positive strand, positive direction, is SuccessablesProli++.bas, looking for GAAA(A/T)GT, 0.
Prol (4560-2846) UTRs
- Negative strand, negative direction: TGTAAAG at 2884.
Prol positive direction (4445-4265) core promoters
- Negative strand, positive direction: TGAAAAG at 3928.
Prol negative direction (2596-1) distal promoters
- Positive strand, negative direction: TGAAAAG at 1627.
Prol positive direction (4050-1) distal promoters
- Negative strand, positive direction: TGAAAAG at 3928.
- Positive strand, positive direction: TGAAAAG at 2275.
Prolamin box random dataset samplings
- RDr0: 0.
- RDr1: 0.
- RDr2: 0.
- RDr3: 0.
- RDr4: 0.
- RDr5: 0.
- RDr6: 0.
- RDr7: 0.
- RDr8: 0.
- RDr9: 0.
- RDr0ci: 0.
- RDr1ci: 0.
- RDr2ci: 0.
- RDr3ci: 0.
- RDr4ci: 0.
- RDr5ci: 0.
- RDr6ci: 0.
- RDr7ci: 0.
- RDr8ci: 0.
- RDr9ci: 0.
RDr arbitrary (evens) (4560-2846) UTRs
RDr alternate (odds) (4560-2846) UTRs
RDr arbitrary negative direction (evens) (2846-2811) core promoters
RDr alternate negative direction (odds) (2846-2811) core promoters
RDr arbitrary positive direction (odds) (4445-4265) core promoters
RDr alternate positive direction (evens) (4445-4265) core promoters
RDr arbitrary negative direction (evens) (2811-2596) proximal promoters
RDr alternate negative direction (odds) (2811-2596) proximal promoters
RDr arbitrary positive direction (odds) (4265-4050) proximal promoters
RDr alternate positive direction (evens) (4265-4050) proximal promoters
RDr arbitrary negative direction (evens) (2596-1) distal promoters
RDr alternate negative direction (odds) (2596-1) distal promoters
RDr arbitrary positive direction (odds) (4050-1) distal promoters
RDr alternate positive direction (evens) (4050-1) distal promoters
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
- ↑ 1.0 1.1 1.2 Montaña Mena, Jesus Vicente-Carbajosa, Robert J. Schmidt and Pilar Carbonero (October 1998). "An endosperm-specific DOF protein from barley, highly conserved in wheat, binds to and activates transcription from the prolamin-box of a native B-hordein promoter in barley endosperm". The Plant Journal. 16 (1): 53–62. doi:10.1046/j.1365-313x.1998.00275.x. Retrieved 2017-02-19.
- ↑ Veronica Ruta, Chiara Longo, Andrea Lepri, Veronica De Angelis, Sara Occhigrossi, Paolo Costantino and Paola Vittorioso (8 February 2020). "The DOF Transcription Factors in Seed and Seedling Development". Plants. 9 (2): 218. doi:10.3390/plants9020218. Retrieved 7 January 2021.