Prolamin box gene transcriptions: Difference between revisions

Revision as of 04:10, 15 January 2023

Editor-In-Chief: Henry A. Hoff

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"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.

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.

External links

[Mena1998-1] 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.

[Ruta-2] 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.

[1]

[2]

@@ Line 75: / Line 75: @@
 # 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==

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Transcription resources	A1BG gene transcription core promoters A1BG gene transcriptions A1BG regulatory elements and regions A1BG response element gene transcriptions A1BG response element negative results A1BG response element positive results ABA-response element gene transcriptions Abf1 regulatory factor gene transcriptions A box gene transcriptions ACGT-containing element gene transcriptions Activating protein gene transcriptions Activating transcription factor gene transcriptions Adenylate–uridylate rich element gene transcriptions Adr1p gene transcriptions Aft1p gene transcriptions AGC box gene transcriptions AGCE gene transcriptions Alpha-amylase conserved element gene transcriptions Amino acid response element gene transcriptions AARE-like Androgen response element gene transcriptions Angiotensinogen core promoter element gene transcriptions Antioxidant-electrophile responsive element gene transcriptions ATA box gene transcriptions Auxin response factor gene transcriptions B 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gene transcriptions EIN3 binding site gene transcriptions Enhancer activity copy gene transcriptions E box gene transcriptions Element gene transcriptions Endoplasmic reticulum stress response element gene transcriptions Endosperm expression gene transcriptions Enhancer box gene transcriptions Estrogen response element gene transcriptions Ethylene responsive element gene transcriptions Factor II B recognition element gene transcriptions F box gene transcriptions Focused promoter gene transcriptions Forkhead box gene transcriptions Fur box gene transcriptions GAAC element gene transcriptions Gal4p gene transcriptions Γ-interferon activated sequence gene transcriptions GARE gene transcriptions GA responsive complex gene transcriptions GATA gene transcriptions G box gene transcriptions GC box gene transcriptions GCC box gene transcriptions Gcn4p gene transcriptions Gcr1p gene transcriptions Gene expressions General factor II D gene transcriptions General regulatory factors General transcription factor II A gene transcriptions General transcription factor II B gene transcriptions General transcription factor II D gene transcriptions General transcription factor II F gene transcriptions General transcription factor II H gene transcriptions General transcription factor gene transcriptions Gene transcriptions GGC triplet gene transcriptions Gibberellin responsive element gene transcriptions GLM box gene transcriptions Glucocorticoid response element gene transcriptions Grainy head gene transcriptions Grainy head transcription factor gene transcriptions Growth hormone response element gene transcriptions GT boxes Hac1p gene transcriptions Hair color gene expressions H and ACA box gene transcriptions H box gene transcriptions Heat-responsive element gene transcriptions Hex sequence gene transcriptions HMG box gene transcriptions HNF gene transcriptions Homeobox gene transcriptions Hsf1p gene transcriptions HY box gene transcriptions Hybrid C, A boxes Hybrid C, G boxes Hybrid C, T boxes Hypoxia-inducible factor gene transcriptions Hypoxia response elements I box gene transcriptions Initiator element gene transcriptions Initiator-like element gene transcriptions Inositol/choline-responsive elements Interaction gene transcriptions Interferon regulatory factors Inverse copy gene transcriptions Jasmonic acid-responsive element gene transcriptions K-boxes Kozak sequence gene transcriptions Kruppel-associated box gene transcriptions Krüppel-like factor gene transcriptions L box gene transcriptions Leu3 gene transcriptions M35 box gene transcriptions MADS box gene transcriptions Maf recognition element gene transcriptions M box gene transcriptions Mcm1 regulatory factor gene transcriptions Met31p box gene transcriptions Metal responsive element gene transcriptions Middle sporulation element gene transcriptions Mig1p gene transcriptions Model samplings Motif ten element gene transcriptions Msn2,4p gene transcriptions Musashi binding element gene transcriptions MYB recognition element gene transcriptions Myelocytomatosis transcription factor gene transcriptions Myocyte enhancer factor gene transcriptions N-boxes Ndt80p gene transcriptions Nuclear factor 1 Nuclear factor 𝜿B Nuclear factor gene transcriptions Nuclear factor of activated T cell gene transcriptions (NFAT) Nuclear factor Y gene transcriptions Nutrient-sensing response element gene transcriptions Oaf1p gene transcriptions ORE1 binding site gene transcriptions p53 response element gene transcriptions P63 DNA-binding site gene transcriptions P box gene transcriptions Pdr1,3p gene transcriptions Peroxisome proliferator hormone response element gene transcriptions Phosphate starvation-response transcription factor gene transcriptions Pollen1 element gene transcriptions Polycomb response element gene transcriptions Preinitiation complex Preinitiation complex gene transcriptions Pribnow box gene transcriptions Prolamin box gene transcriptions Promoter gene transcriptions Proximal promoter gene transcriptions Promoter occurrence gene transcriptions Pyrimidine box gene transcriptions Q element gene transcriptions Rap1 regulatory factor gene transcriptions Reb1 general regulatory factor gene transcriptions Retinoblastoma control element gene transcriptions Retinoic acid response element gene transcriptions Rgt1p gene transcriptions Rlm1p gene transcriptions RNA polymerase II gene transcriptions RNA polymerase II holoenzyme complex Root specific element gene transcriptions ROR-response element gene transcriptions Rox1p gene transcriptions Rpn4p gene transcriptions R response element gene transcriptions SARE gene transcriptions Seed-specific element gene transcriptions Serum response element gene transcriptions Servenius sequence gene transcriptions Shoot specific element gene transcriptions Sip4p gene transcriptions Smp1p gene transcriptions Sp1 gene transcriptions Spaceflight gene expressions Specificity protein gene transcriptions STAT gene transcriptions Ste12p gene transcriptions Sterol response element gene transcriptions Sucrose box gene transcriptions Synaptic Activity-Responsive Elements TACTAAC box gene transcriptions TAGteam gene transcriptions Tapetum box gene transcriptions TATA binding protein associated factor gene transcriptions TATA binding protein gene transcriptions TATA box gene transcriptions TAT box gene transcriptions TATC box gene transcriptions Tbf1 regulatory factor gene transcriptions T box gene transcriptions TCCACCATA element gene transcriptions TC element gene transcriptions TCT gene transcriptions TEA consensus sequence gene transcriptions Tec1p gene transcriptions Telomeric repeat DNA-binding factor gene transcriptions Tetradecanoylphorbol-13-acetate response element gene transcriptions TGF-β control elements (TCEs) TGF-β inhibitory elements (TIEs) Thyroid hormone response element gene transcriptions Transcriptional regulation Transcription bubble gene transcriptions Transcription factor gene transcriptions Transcription factor 3 gene transcriptions Transcription factory gene transcriptions Transcription start site gene transcriptions Translational control sequence gene transcriptions U box gene transcriptions Unfolded protein response element gene transcriptions Upstream response element gene transcriptions Upstream stimulatory factor gene transcriptions UTR promoter gene transcriptions V and P box gene transcriptions V box gene transcriptions Vhr1p gene transcriptions Vitamin D response element gene transcriptions W box gene transcriptions X box gene transcriptions Xbp1p gene transcriptions X core promoter element gene transcriptions Xenobiotic response element gene transcriptions Xenobiotic responsive element gene transcriptions Yap1p,2p gene transcriptions Y box gene transcriptions YY1 gene transcriptions Zap1p gene transcriptions Z box gene transcriptions Zinc responsive element gene transcriptions