GGC triplet gene transcriptions

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.

GGCGGC triplet samplings

Negative strand, negative direction, looking for GGCGGC, 0.
Positive strand, negative direction, looking for GGCGGC, 1, GGCGGC at 1753.
Positive strand, positive direction, looking for GGCGGC, 0.
Negative strand, positive direction, looking for GGCGGC, 3, GGCGGC at 1902, GGCGGC at 1794, GGCGGC at 354.

inverse complement, negative strand, negative direction, looking for GCCGCC, 1, GCCGCC at 2727.
inverse complement, positive strand, negative direction, looking for GCCGCC, 0.
inverse complement, positive strand, positive direction, looking for GCCGCC, 1, GCCGCC at 356.
inverse complement, negative strand, positive direction, looking for GCCGCC, 2, GCCGCC at 1757, GCCGCC at 904.

GGCGGC proximal promoters

Negative strand, negative direction: GCCGCC at 2727.

GGCGGC distal promoters

Positive strand, negative direction: GGCGGC at 1753.

Negative strand, positive direction: GGCGGC at 1902, GGCGGC at 1794, GCCGCC at 1757, GCCGCC at 904, GGCGGC at 354.

Positive strand, positive direction, looking for GCCGCC, 1, GCCGCC at 356.

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]

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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 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