Prolamin box gene transcriptions: Difference between revisions
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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: | 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 | # 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 | # 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 | # 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 | # 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 | # complement, negative strand, negative direction is SuccessablesProlc--.bas, looking for AC(A/T)TTTC, 1, ACTTTTC at 1627, | ||
# complement, negative strand, positive direction is | # complement, negative strand, positive direction is SuccessablesProlc-+.bas, looking for AC(A/T)TTTC, ACTTTC at 3928, | ||
# complement, positive strand, negative direction is | # complement, positive strand, negative direction is SuccessablesProlc+-.bas, looking for AC(A/T)TTTC, 1, ACATTTC at 2884, | ||
# complement, positive strand, positive direction is | # 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 | # inverse complement, negative strand, negative direction is SuccessablesProlci--.bas, looking for CTTT(A/T)CA, 0, | ||
# inverse complement, negative strand, positive direction is | # inverse complement, negative strand, positive direction is SuccessablesProlci-+.bas, looking for CTTT(A/T)CA, 0, | ||
# inverse complement, positive strand, negative direction is | # inverse complement, positive strand, negative direction is SuccessablesProlci+-.bas, looking for CTTT(A/T)CA, 0, | ||
# inverse complement, positive strand, positive direction is | # inverse complement, positive strand, positive direction is SuccessablesProlci++.bas, looking for CTTT(A/T)CA, 0, | ||
# inverse, negative strand, negative direction, is | # inverse, negative strand, negative direction, is SuccessablesProli--.bas, looking for GAAA(A/T)GT, 0, | ||
# inverse, negative strand, positive direction, is | # inverse, negative strand, positive direction, is SuccessablesProli-+.bas, looking for GAAA(A/T)GT, 0, | ||
# inverse, positive strand, negative direction, is | # inverse, positive strand, negative direction, is SuccessablesProli+-.bas, looking for GAAA(A/T)GT, 0, | ||
# inverse, positive strand, positive direction, is | # inverse, positive strand, positive direction, is SuccessablesProli++.bas, looking for GAAA(A/T)GT, 0. | ||
===Prol distal promoters=== | |||
{{main|Distal promoter gene transcriptions}} | |||
Negative strand, negative direction: TGTAAAG at 2884, and complement. | |||
Positive strand, negative direction: TGAAAAG at 1627, and complement. | |||
Negative strand, positive direction: TGAAAAG at 3928, and complement. | |||
Positive strand, positive direction: TGAAAAG at 2275, and complement. | |||
==Acknowledgements== | ==Acknowledgements== | ||
Revision as of 03:05, 8 January 2021
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]
A1BG 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 distal promoters
Negative strand, negative direction: TGTAAAG at 2884, and complement.
Positive strand, negative direction: TGAAAAG at 1627, and complement.
Negative strand, positive direction: TGAAAAG at 3928, and complement.
Positive strand, positive direction: TGAAAAG at 2275, and complement.
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 (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. Unknown parameter
|month=ignored (help) - ↑ 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.