Auxin response factor gene transcriptions: Difference between revisions
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==Human genes== | ==Human genes== | ||
{{main|Human genes}} | {{main|Human genes}} | ||
Gene ID: 206358 is SLC36A1 solute carrier family 36 member 1 on 5q33.1: "This gene encodes a member of the eukaryote-specific amino acid/auxin permease (AAAP) 1 transporter family. The encoded protein functions as a proton-dependent, small amino acid transporter. This gene is clustered with related family members on chromosome 5q33.1. Alternative splicing results in multiple transcript variants."<ref name=RefSeq206358>{{ cite web | |||
|author=RefSeq | |||
|title=SLC36A1 solute carrier family 36 member 1 [ Homo sapiens (human) ] | |||
|publisher=National Center for Biotechnology Information, U.S. National Library of Medicine | |||
|location=8600 Rockville Pike, Bethesda MD, 20894 USA | |||
|date=April 2015 | |||
|url=https://www.ncbi.nlm.nih.gov/gene/206358 | |||
|accessdate=11 November 2020 }}</ref> | |||
==Gene expressions== | ==Gene expressions== |
Revision as of 19:57, 11 November 2020
Associate Editor(s)-in-Chief: Henry A. Hoff
The "genome binding of two [auxin response factors] ARFs (ARF2 and ARF5/Monopteros [MP]) differ largely because these two factors have different preferred ARF binding site (ARFbs) arrangements (orientation and spacing)."[1] "ARFbs were originally defined as TGTCTC (Ulmasov et al., 1995, Guilfoyle et al., 1998), [...]. More recently, protein binding microarray (PBM) experiments suggested that TGTCGG are preferred ARFbs, [...] (Boer et al., 2014, Franco-Zorrilla et al., 2014, Liao et al., 2015)."[1]
Human genes
Gene ID: 206358 is SLC36A1 solute carrier family 36 member 1 on 5q33.1: "This gene encodes a member of the eukaryote-specific amino acid/auxin permease (AAAP) 1 transporter family. The encoded protein functions as a proton-dependent, small amino acid transporter. This gene is clustered with related family members on chromosome 5q33.1. Alternative splicing results in multiple transcript variants."[2]
Gene expressions
Interactions
Consensus sequences
A more general consensus sequence may be 1(C/G/T)-2N-3(G/T)-4G-5(C/T)-6(C/T)-7N-8N-9N-10N, where ARF2[b] is 1(C/G/T)-2(A/C/T)-3(G/T)-4G-5(C/T)-6(C/T)-7(G/T)-8(C/G)-9(A/C/T)-10(A/G/T) and ARF5/MP[b] is 1(C/G/T)-2N-3(G/T)-4G-5T-6C-7(G/T)-8N-9-10N.[1] ARF1[b] has 4G.[1]
Binding site for
Inverse copies
Enhancer activity
Promoter occurrences
Hypotheses
- A1BG has no Auxin response factors in either promoter.
- A1BG is not transcribed by an Auxin response factor.
- Auxin response factor does not participate in the transcription of A1BG.
Samplings
Copying an auxin response factor consensus sequence 5'-TGTCGG-3' and putting the sequence in "⌘F" finds no location between ZNF497 and A1BG or one location between ZSCAN22 and A1BG as can be found by the computer programs.
For the Basic programs testing consensus sequence 5'-(C/G/T)(A/C/T)(G/T)G(C/T)(C/T)(G/T)(C/G)(A/C/T)(A/G/T)-3' (starting with SuccessablesAAA.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 5'-AAAAAAAA-3', 0.
- negative strand, positive direction, looking for 5'-AAAAAAAA-3', 0.
- positive strand, negative direction, looking for 5'-AAAAAAAA-3', 0.
- positive strand, positive direction, looking for 5'-AAAAAAAA-3', 0.
- complement, negative strand, negative direction, looking for 5'-TTTTTTTT-3', 0.
- complement, negative strand, positive direction, looking for 5'-TTTTTTTT-3', 0.
- complement, positive strand, negative direction, looking for 5'-TTTTTTTT-3', 0.
- complement, positive strand, positive direction, looking for 5'-TTTTTTTT-3', 0.
- inverse complement, negative strand, negative direction, looking for 5'-TTTTTTTT-3', 0.
- inverse complement, negative strand, positive direction, looking for 5'-TTTTTTTT-3', 0.
- inverse complement, positive strand, negative direction, looking for 5'-TTTTTTTT-3', 0.
- inverse complement, positive strand, positive direction, looking for 5'-TTTTTTTT-3', 0.
- inverse negative strand, negative direction, looking for 5'-AAAAAAAA-3', 0.
- inverse negative strand, positive direction, looking for 5'-AAAAAAAA-3', 0.
- inverse positive strand, negative direction, looking for 5'-AAAAAAAA-3', 0.
- inverse positive strand, positive direction, looking for 5'-AAAAAAAA-3', 0.
AAA core promoters
AAA proximal promoters
AAA distal promoters
Acknowledgements
The content on this page was first contributed by: Henry A. Hoff.
See also
References
- ↑ 1.0 1.1 1.2 1.3 Arnaud Stigliani, Raquel Martin-Arevalillo, Jérémy Lucas, Adrien Bessy, Thomas Vinos-Poyo, Victoria Mironova, Teva Vernoux, Renaud Dumas and François Parcy (3 June 2019). "Capturing Auxin Response Factors Syntax Using DNA Binding Models". Molecular Plant. 12 (6): 822–832. doi:10.1016/j.molp.2018.09.010. PMID 30336329. Retrieved 29 August 2020.
- ↑ RefSeq (April 2015). "SLC36A1 solute carrier family 36 member 1 [ Homo sapiens (human) ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 11 November 2020.