GGC triplet gene transcriptions: Difference between revisions

Revision as of 07:42, 21 April 2021

Associate Editor(s)-in-Chief: Henry A. Hoff

"The transcription factors Uga3, Dal81 and Leu3 belong to the class III family (Zn(II)₂Cys₆ proteins), and they recognize highly related sequences rich in GGC triplets [15]."^[1]

Human genes

Gene expressions

Interactions

Consensus sequences

"Known consensus string Type of motifs LEU3 CCGNNNNCGG or GGCNNNNGCC Gapped motif".^[2]

"MEME analysis identified phylogenetically conserved CCGN₄CGG motifs in promoters of several [branched-chain amino acid] BCAA biosynthetic genes"^[3]

"The promoters of the BCAA biosynthetic leuA and the iron-regulatory hapX genes contain an evolutionary conserved CCGN₄CGG motif."^[3]

"LeuB is able to bind to the CCGN₄CGG motifs in the promoters of gdhA, hapX and leuA."^[3]

Binding site for

Enhancer activity

Promoter occurrences

"The regulatory regions of the UGA4 and UGA1 genes contain a UAS_GABA element (5'- AAAAACCGCCGGCGGCAAT-3') target of Uga3 and Dal81 factors. Within this element there is a consensus site for Leu3 [8, 10, 11, 35]. In contrast, UGA2 has a consensus site for Uga3 (5'-SGCGGNWTT-3') but not a defined UAS_GABA element or a Leu3 putative site."^[1]

Hypotheses

A1BG has no regulatory elements in either promoter.
A1BG is not transcribed by a regulatory element.
No regulatory element participates in the transcription of A1BG.

Leu3 samplings

Copying a responsive elements consensus sequence CCGNNNNCGG and putting the sequence in "⌘F" finds none between ZNF497 and A1BG or none between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence CCGNNNNCGG (starting with SuccessablesGGC.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, negative direction, looking for CCGNNNNCGG, 7, CCGAGTACGG at 4118, CCGTGTACGG at 2669, CCGAGTACGG at 2535, CCGAGTGCGG at 2208, CCGCCCACGG at 1255, CCGTGTGCGG at 964, CCGAGTGCGG at 664.
positive strand, negative direction, looking for CCGNNNNCGG, 2, CCGGGTGCGG at 2197, CCGGGTGCGG at 380.
positive strand, positive direction, looking for CCGNNNNCGG, 6, CCGAAGTCGG at 3998, CCGATATCGG at 3702, CCGCCAACGG at 3492, CCGCACTCGG at 2558, CCGCGTGCGG at 1302, CCGGAAGCGG at 595.
negative strand, positive direction, looking for CCGNNNNCGG, 5, CCGAGTGCGG at 1170, CCGAGTGCGG at 1086, CCGACTGCGG at 1002, CCGAGTGCGG at 582, CCGCAGACGG at 399.

Leu3 UTRs

Negative strand, negative direction: CCGAGTACGG at 4118.

Leu3 proximal promoters

Negative strand, negative direction: CCGTGTACGG at 2669.

Leu3 distal promoters

Negative strand, negative direction: CCGAGTACGG at 2535, CCGAGTGCGG at 2208, CCGCCCACGG at 1255, CCGTGTGCGG at 964, CCGAGTGCGG at 664.

Positive strand, negative direction: CCGGGTGCGG at 2197, CCGGGTGCGG at 380.

Negative strand, positive direction: CCGAGTGCGG at 1170, CCGAGTGCGG at 1086, CCGACTGCGG at 1002, CCGAGTGCGG at 582, CCGCAGACGG at 399.

Positive strand, positive direction: CCGAAGTCGG at 3998, CCGATATCGG at 3702, CCGCCAACGG at 3492, CCGCACTCGG at 2558, CCGCGTGCGG at 1302, CCGGAAGCGG at 595.

Acknowledgements

The content on this page was first contributed by: Henry A. Hoff.

References

↑ ^1.0 ^1.1 Marcos Palavecino-Ruiz, Mariana Bermudez-Moretti and Susana Correa-Garcia (12 October 2017). "Unravelling the transcriptional regulation of Saccharomyces cerevisiae UGA genes: the dual role of transcription factor Leu3" (PDF). Microbiology. 163: 1692–1701. doi:10.1099/mic.0.000560. Retrieved 20 April 2021.
↑ Uyyala Srinivasulu Reddy, Michael Arock, A.V. Reddy (20 April 2020). "Discovering of gapped motifs using particle swarm optimisation". International Journal of Computational Intelligence in Bioinformatics and Systems Biology. 2 (1): 1–21. doi:10.1504/IJCIBSB.2020.106858. Retrieved 20 April 2021.
↑ ^3.0 ^3.1 ^3.2 Nanbiao Long, Thomas Orasch, Shizhu Zhang, Lu Gao, Xiaoling Xu, Peter Hortschansky, Jing Ye, Fenli Zhang, Kai Xu, Fabio Gsaller, Maria Straßburger, Ulrike Binder, Thorsten Heinekamp, Axel A. Brakhage, Hubertus Haas, Ling Lu (26 October 2018). "The Zn₂Cys₆-type transcription factor LeuB cross-links regulation of leucine biosynthesis and iron acquisition in Aspergillus fumigatus". PLOS Genetics. 14 (10): e1007762. doi:10.1371/journal.pgen.1007762. Retrieved 20 April 2021.

External links

[Ruiz-1] 1.0 ^1.1 Marcos Palavecino-Ruiz, Mariana Bermudez-Moretti and Susana Correa-Garcia (12 October 2017). "Unravelling the transcriptional regulation of Saccharomyces cerevisiae UGA genes: the dual role of transcription factor Leu3" (PDF). Microbiology. 163: 1692–1701. doi:10.1099/mic.0.000560. Retrieved 20 April 2021.

[Reddy-2] Uyyala Srinivasulu Reddy, Michael Arock, A.V. Reddy (20 April 2020). "Discovering of gapped motifs using particle swarm optimisation". International Journal of Computational Intelligence in Bioinformatics and Systems Biology. 2 (1): 1–21. doi:10.1504/IJCIBSB.2020.106858. Retrieved 20 April 2021.

[Long-3] 3.0 ^3.1 ^3.2 Nanbiao Long, Thomas Orasch, Shizhu Zhang, Lu Gao, Xiaoling Xu, Peter Hortschansky, Jing Ye, Fenli Zhang, Kai Xu, Fabio Gsaller, Maria Straßburger, Ulrike Binder, Thorsten Heinekamp, Axel A. Brakhage, Hubertus Haas, Ling Lu (26 October 2018). "The Zn₂Cys₆-type transcription factor LeuB cross-links regulation of leucine biosynthesis and iron acquisition in Aspergillus fumigatus". PLOS Genetics. 14 (10): e1007762. doi:10.1371/journal.pgen.1007762. Retrieved 20 April 2021.

[1]

[2]

[3]

@@ Line 81: / Line 81: @@
 For the Basic programs testing consensus sequence CCGNNNNCGG (starting with SuccessablesGGC.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, negative direction, looking for CCGNNNNCGG, 0.
+# negative strand, negative direction, looking for CCGNNNNCGG, 7, CCGAGTACGG at 4118, CCGTGTACGG at 2669, CCGAGTACGG at 2535, CCGAGTGCGG at 2208, CCGCCCACGG at 1255, CCGTGTGCGG at 964, CCGAGTGCGG at 664.
-# positive strand, negative direction, looking for AAAAAAAA, 0.
+# positive strand, negative direction, looking for CCGNNNNCGG, 2, CCGGGTGCGG at 2197, CCGGGTGCGG at 380.
-# positive strand, positive direction, looking for AAAAAAAA, 0.
+# positive strand, positive direction, looking for CCGNNNNCGG, 6, CCGAAGTCGG at 3998, CCGATATCGG at 3702, CCGCCAACGG at 3492, CCGCACTCGG at 2558, CCGCGTGCGG at 1302, CCGGAAGCGG at 595.
-# negative strand, positive direction, looking for AAAAAAAA, 0.
+# negative strand, positive direction, looking for CCGNNNNCGG, 5, CCGAGTGCGG at 1170, CCGAGTGCGG at 1086, CCGACTGCGG at 1002, CCGAGTGCGG at 582, CCGCAGACGG at 399.
-# complement, negative strand, negative direction, looking for TTTTTTTT, 0.
-# complement, positive strand, negative direction, looking for GGCNNNNGCC, 0.
-# complement, positive strand, positive direction, looking for TTTTTTTT, 0.
-# complement, negative strand, positive direction, looking for TTTTTTTT, 0.
-# inverse complement, negative strand, negative direction, looking for CCGNNNNCGG, 0.
-# inverse complement, positive strand, negative direction, looking for TTTTTTTT, 0.
-# inverse complement, positive strand, positive direction, looking for TTTTTTTT, 0.
-# inverse complement, negative strand, positive direction, looking for TTTTTTTT, 0.
-# inverse negative strand, negative direction, looking for AAAAAAAA, 0.
-# inverse positive strand, negative direction, looking for GGCNNNNGCC, 0.
-# inverse positive strand, positive direction, looking for AAAAAAAA, 0.
-# inverse negative strand, positive direction, looking for AAAAAAAA, 0.
 ===Leu3 UTRs===
 {{main|UTR promoter gene transcriptions}}
+Negative strand, negative direction: CCGAGTACGG at 4118.
-===Leu3 core promoters===
-{{main|Core promoter gene transcriptions}}
 ===Leu3 proximal promoters===
 {{main|Proximal promoter gene transcriptions}}
+Negative strand, negative direction: CCGTGTACGG at 2669.
 ===Leu3 distal promoters===
 {{main|Distal promoter gene transcriptions}}
+Negative strand, negative direction: CCGAGTACGG at 2535, CCGAGTGCGG at 2208, CCGCCCACGG at 1255, CCGTGTGCGG at 964, CCGAGTGCGG at 664.
+Positive strand, negative direction: CCGGGTGCGG at 2197, CCGGGTGCGG at 380.
+Negative strand, positive direction: CCGAGTGCGG at 1170, CCGAGTGCGG at 1086, CCGACTGCGG at 1002, CCGAGTGCGG at 582, CCGCAGACGG at 399.
+Positive strand, positive direction: CCGAAGTCGG at 3998, CCGATATCGG at 3702, CCGCCAACGG at 3492, CCGCACTCGG at 2558, CCGCGTGCGG at 1302, CCGGAAGCGG at 595.
 ==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