Auxin response factor gene transcriptions: Difference between revisions

Revision as of 20:16, 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: 84514 is GHDC GH3 domain containing on 17q21.2.

NP_001136095.1 GH3 domain-containing protein isoform 3 precursor: "Transcript Variant: This variant (3) uses an alternate splice site, resulting in a frameshifted and alternate 3' coding region, compared to variant 1. The encoded isoform (3) has a shorter and distinct C-terminus, compared to isoform 1."^[2] Conserved Domains (2) summary

cl21606, Location:249 → 410, PLN02247; indole-3-acetic acid-amido synthetase, pfam03321, Location:54 → 420, GH3; GH3 auxin-responsive promoter.^[2]

NP_115873.1 GH3 domain-containing protein isoform 1 precursor: "Transcript Variant: This variant (1) encodes the longer isoform (1)."^[2] Conserved Domains (2) summary, cl21606, Location:89 → 530, PLN02247; indole-3-acetic acid-amido synthetase, pfam03321, Location:54 → 490, GH3; GH3 auxin-responsive promoter.^[2]

Gene ID: 153201 is SLC36A2 solute carrier family 36 member 2 on 5q33.1: "This gene encodes a pH-dependent proton-coupled amino acid transporter that belongs to the amino acid auxin permease 1 protein family. The encoded protein primarily transports small amino acids such as glycine, alanine and proline. Mutations in this gene are associated with iminoglycinuria and hyperglycinuria."^[3]

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."^[4]

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.

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.
↑ ^2.0 ^2.1 ^2.2 ^2.3 HGNC (8 November 2020). "GHDC GH3 domain containing [ 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.
↑ RefSeq (September 2010). "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.
↑ 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.

External links

[Stigliani-1] 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.

[HGNC84514-2] 2.0 ^2.1 ^2.2 ^2.3 HGNC (8 November 2020). "GHDC GH3 domain containing [ 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.

[RefSeq153201-3] RefSeq (September 2010). "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.

[RefSeq206358-4] 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.

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[2]

[3]

[4]

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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 Immunoglobulin like domain containing family 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 M-CAT boxes Mcm1 regulatory factor gene transcriptions Met3 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 Nanos/Pumilio response element 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 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Auxin response factor gene transcriptions: Difference between revisions

Revision as of 20:16, 11 November 2020

Contents

Human genes

Gene expressions

Interactions

Consensus sequences

Binding site for

Inverse copies

Enhancer activity

Promoter occurrences

Hypotheses

Samplings

AAA core promoters

AAA proximal promoters

AAA distal promoters

Acknowledgements

See also

References

External links

Navigation menu

@@ Line 27: / Line 27: @@
 |url=https://www.ncbi.nlm.nih.gov/gene/84514
 |accessdate=11 November 2020 }}</ref> Conserved Domains (2) summary
-cl21606
+cl21606, Location:249 → 410, PLN02247; indole-3-acetic acid-amido synthetase, pfam03321, Location:54 → 420, GH3; GH3 auxin-responsive promoter.<ref name=HGNC84514/>
-Location:249 → 410
+# NP_115873.1 GH3 domain-containing protein isoform 1 precursor: "Transcript Variant: This variant (1) encodes the longer isoform (1)."<ref name=HGNC84514/> Conserved Domains (2) summary, cl21606, Location:89 → 530, PLN02247; indole-3-acetic acid-amido synthetase, pfam03321, Location:54 → 490, GH3; GH3 auxin-responsive promoter.<ref name=HGNC84514/>
-PLN02247; indole-3-acetic acid-amido synthetase
-pfam03321
-Location:54 → 420
-GH3; GH3 auxin-responsive promoter.<ref name=HGNC84514/>
-# NP_115873.1 GH3 domain-containing protein isoform 1 precursor: "Transcript Variant: This variant (1) encodes the longer isoform (1)."<ref name=HGNC84514/>
-Conserved Domains (2) summary
-cl21606
-Location:89 → 530
-PLN02247; indole-3-acetic acid-amido synthetase
-pfam03321
-Location:54 → 490
-GH3; GH3 auxin-responsive promoter.<ref name=HGNC84514/>
 Gene ID: 153201 is SLC36A2 solute carrier family 36 member 2 on 5q33.1: "This gene encodes a pH-dependent proton-coupled amino acid transporter that belongs to the amino acid auxin permease 1 protein family. The encoded protein primarily transports small amino acids such as glycine, alanine and proline. Mutations in this gene are associated with iminoglycinuria and hyperglycinuria."<ref name=RefSeq153201>{{ cite web

Auxin response factor gene transcriptions: Difference between revisions

Revision as of 20:16, 11 November 2020

Human genes

Gene expressions

Interactions

Consensus sequences

Binding site for

Inverse copies

Enhancer activity

Promoter occurrences

Hypotheses

Samplings

AAA core promoters

AAA proximal promoters

AAA distal promoters

Acknowledgements

See also

References

External links

Navigation menu

Search