LXL04_008292 | RubberDandelionOmics

Gene overview

LXL04_008292

Reference: OH-1004 Chr: Chr02 Coordinates: 95924236-95924826 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

528 bp · LXL04_008292|LXL04_008292|OH1004|cDNA

ATGAACAGAATCATATACGACTCGAGGGAAATAGAATTGAGCAAAGTAGCCATGGATGAAATTCCAGCCACCAACATCTCCGGCCTCCGATGTGCCGCCGAATACCTGGAAATGACAGAGGATTTGGAAGAAGGAAATCTCATTTTCAAAACCGAAGCCTTTCTCAGCTACGTTGTGTTATCATCATGGAGAGATTCAATTCTGGTACTCAAAAGCTGCGAAAAGCTATCTCCTTGGGCTGAGAACCTCCAAATCGTTAG...

CDS

Download CDS FASTA

528 bp · LXL04_008292|LXL04_008292|OH1004|CDS

ATGAACAGAATCATATACGACTCGAGGGAAATAGAATTGAGCAAAGTAGCCATGGATGAAATTCCAGCCACCAACATCTCCGGCCTCCGATGTGCCGCCGAATACCTGGAAATGACAGAGGATTTGGAAGAAGGAAATCTCATTTTCAAAACCGAAGCCTTTCTCAGCTACGTTGTGTTATCATCATGGAGAGATTCAATTCTGGTACTCAAAAGCTGCGAAAAGCTATCTCCTTGGGCTGAGAACCTCCAAATCGTTAG...

Protein

Download Protein FASTA

175 aa · LXL04_008292|LXL04_008292|OH1004|PROTEIN

MNRIIYDSREIELSKVAMDEIPATNISGLRCAAEYLEMTEDLEEGNLIFKTEAFLSYVVLSSWRDSILVLKSCEKLSPWAENLQIVRRCSESIAWKACANPKGIRWQYTGKPMKVSSPSWNEMKDSSPSRSPVPPDWWYEDVSILRIDHFVPVSVFLLDASSKWGYVTYHPHFSW

Flanking Sequence Download

Sequence orientation and download details

Upstream/downstream are capped at 10000 bp per side. Negative-strand genes are reverse-complemented so the final FASTA follows transcriptional 5′→3′ orientation.

ID Mapping

Input ID	`LXL04_008292`
Source version	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

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Basic Information and Functional Annotation

Gene ID LXL04_008292

Location Chr02:95924236-95924826 (-)

Description Similar to RPT3: Root phototropism protein 3

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g64330`	May act as a substrate-specific adapter of an E3 ubiquitin-protein ligase complex (CUL3-RBX1-BTB) which mediates the ubiquitination and subsequent proteasomal degradation of target proteins (By similarity).	Arabidopsis NPH3: A NPH1 photoreceptor-interacting protein essential for phototropism.1999 · DOI: 10.1126/science.286.5441.961 RPT2. A signal transducer of the phototropic response in Arabidopsis.2000 · DOI: 10.1105/tpc.12.2.225 RPT2 is a signal transducer involved in phototropic response and stomatal opening by association with phototropin 1 in Arabidopsis thaliana.2004 · DOI: 10.1105/tpc.019901 PHYTOCHROME KINASE SUBSTRATE 1 is a phototropin 1 binding protein required for phototropism.2006 · DOI: 10.1073/pnas.0603799103 The Arabidopsis PHYTOCHROME KINASE SUBSTRATE2 protein is a phototropin signaling element that regulates leaf flattening and leaf positioning.2010 · DOI: 10.1104/pp.109.150441
`At4g31820`	May act as a substrate-specific adapter of an E3 ubiquitin-protein ligase complex (CUL3-RBX1-BTB) which mediates the ubiquitination and subsequent proteasomal degradation of target proteins (By similarity).	NPY1, a BTB-NPH3-like protein, plays a critical role in auxin-regulated organogenesis in Arabidopsis.2007 · DOI: 10.1073/pnas.0708506104 NPY genes and AGC kinases define two key steps in auxin-mediated organogenesis in Arabidopsis.2008 · DOI: 10.1073/pnas.0809761106 NPY genes play an essential role in root gravitropic responses in Arabidopsis.2011 · DOI: 10.1093/mp/ssq052 Polar-localized NPH3-like proteins regulate polarity and endocytosis of PIN-FORMED auxin efflux carriers.2011 · DOI: 10.1242/dev.057745 MAB4-induced auxin sink generates local auxin gradients in Arabidopsis organ formation.2014 · DOI: 10.1073/pnas.1316109111 AGC kinases and MAB4/MEL proteins maintain PIN polarity by limiting lateral diffusion in plant cells.2021 · DOI: 10.1016/j.cub.2021.02.028
`At5g10250`	May act as a substrate-specific adapter of an E3 ubiquitin-protein ligase complex (CUL3-RBX1-BTB) which mediates the ubiquitination and subsequent proteasomal degradation of target proteins (By similarity).	No verified direct reference in this release
`At5g67440`	May act as a substrate-specific adapter of an E3 ubiquitin-protein ligase complex (CUL3-RBX1-BTB) which mediates the ubiquitination and subsequent proteasomal degradation of target proteins (By similarity).	NPY genes and AGC kinases define two key steps in auxin-mediated organogenesis in Arabidopsis.2008 · DOI: 10.1073/pnas.0809761106 NPY genes play an essential role in root gravitropic responses in Arabidopsis.2011 · DOI: 10.1093/mp/ssq052

Rice

Reference gene ID	Possible function	Papers / DOI
`Os02g0568200`	May act as a substrate-specific adapter of an E3 ubiquitin-protein ligase complex (CUL3-RBX1-BTB) which mediates the ubiquitination and subsequent proteasomal degradation of target proteins (By similarity).	The Rice COLEOPTILE PHOTOTROPISM1 gene encoding an ortholog of Arabidopsis NPH3 is required for phototropism of coleoptiles and lateral translocation of auxin.2005 · DOI: 10.1105/tpc.104.028357

Functional annotation source

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Functional annotation source: OH1004 · LXL04_008292 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009638 phototropism Biological Process

GO:0009785 blue light signaling pathway Biological Process

GO:0009908 flower development Biological Process

GO:0009911 positive regulation of flower development Biological Process

GO:0009958 positive gravitropism Biological Process

GO:0010087 phloem or xylem histogenesis Biological Process

GO:0010229 inflorescence development Biological Process

GO:0010305 leaf vascular tissue pattern formation Biological Process

GO:0010540 basipetal auxin transport Biological Process

GO:0010588 cotyledon vascular tissue pattern formation Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0045176 apical protein localization Biological Process

KEGG gene cross-reference

ath:AT4G31820

ath:AT5G10250

ath:AT5G64330

ath:AT5G67440

dosa:Os02g0568200

These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.

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Gene expression

View expression in different studies, tissues and treatments. Results are presented separately by study and measurement unit.

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Data sources and gene correspondence

Expression data come from public transcriptome studies. Reference genomes, sample metadata and measurement units are shown with the results. Ambiguous cross-reference correspondences do not select an expression record automatically; missing values do not mean zero expression.

Subcellular Localization Top 5

Computational predictions or homology annotations below do not replace localization experiments.

Nucleus0.558

Rank 1 · LXL04_008292 · OH-1004

Cytoplasm0.357

Rank 2 · LXL04_008292 · OH-1004

Cell membrane0.111

Rank 3 · LXL04_008292 · OH-1004

Endoplasmic reticulum0.070

Rank 4 · LXL04_008292 · OH-1004

Golgi apparatus0.047

Rank 5 · LXL04_008292 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

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Predicted Functional Domains

No result was found for this query.

Arabidopsis / Rice Protein Homology

Only Arabidopsis and rice are shown. Swiss-Prot entries are reviewed; TrEMBL entries are supplementary sequence candidates. Similarity is not experimental validation.

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Protein	Organism	Description	Identity	Database	Confidence
`Q9FMF5`	Arabidopsis thaliana	Root phototropism protein 3	68.254%	Swiss-Prot	strong database homology
`Q8H1D3`	Arabidopsis thaliana	Phototropic-responsive NPH3 family protein NPY1	46.269%	Swiss-Prot	moderate database homology
`Q9LFU0`	Arabidopsis thaliana	BTB/POZ domain-containing protein DOT3	47.287%	Swiss-Prot	moderate database homology
`Q9FN09`	Arabidopsis thaliana	Phototropic-responsive NPH3 family protein NPY3	45.312%	Swiss-Prot	moderate database homology
`Q5KS50`	Oryza sativa subsp. japonica	Coleoptile phototropism protein 1	67.702%	Swiss-Prot	strong database homology

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