LXL04_038590 | RubberDandelionOmics

Gene overview

LXL04_038590

Reference: OH-1004 Chr: Chr09 Coordinates: 44614127-44616322 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2106 bp · LXL04_038590|LXL04_038590|OH1004|cDNA

ATGTGGGATTCAGAGTCTGAATCAGGTGCCGGAAGAGACTACGATAATGGAGTTCTTTCTTCAACCAAACATGGCGTCCAGACTGATCGATTTGAACAAAGAGGCAAATCTTGGTATATACTATATGCCCAGTTACCTTATCCGTTTTCATATAAGTTTATAGAGTATGATGAAGTTAACAAGTTTTTTGGTAACGATAGGTTTGTTGCAACTGATGTTCCAAGTGATTTGTTGGTTCAGATCGGTGATTTTAGTTTCCA...

CDS

Download CDS FASTA

2106 bp · LXL04_038590|LXL04_038590|OH1004|CDS

ATGTGGGATTCAGAGTCTGAATCAGGTGCCGGAAGAGACTACGATAATGGAGTTCTTTCTTCAACCAAACATGGCGTCCAGACTGATCGATTTGAACAAAGAGGCAAATCTTGGTATATACTATATGCCCAGTTACCTTATCCGTTTTCATATAAGTTTATAGAGTATGATGAAGTTAACAAGTTTTTTGGTAACGATAGGTTTGTTGCAACTGATGTTCCAAGTGATTTGTTGGTTCAGATCGGTGATTTTAGTTTCCA...

Protein

Download Protein FASTA

701 aa · LXL04_038590|LXL04_038590|OH1004|PROTEIN

MWDSESESGAGRDYDNGVLSSTKHGVQTDRFEQRGKSWYILYAQLPYPFSYKFIEYDEVNKFFGNDRFVATDVPSDLLVQIGDFSFHLHKYPLLSRSGKMNRIIYDSREIELSKVAMDEIPGGAEAFELAAKFCYGIAVDLTATNISGLRCAAEYLEMTEDLEEGNLIFKTEAFLSYVVLSSWRDSILVLKSCEKLSPWAENLQIVRRCSESIAWKACANPKGIRWQYTGKPMKVSSPSWNEMKDSSPSRSPVPPDWWYE...

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_038590`
TK1151 ID	TkA04G444670
OH-1004 ID	LXL04_038590
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	95.900
Protein coverage (%)	TK1151 100.000 / OH-1004 100.000 Coverage and evidence Coverage is the aligned span of the best-scoring HSP divided by representative protein length. A homolog match does not establish functional validation.
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_038590

Location Chr09:44614127-44616322 (-)

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
`At1g30440`	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.	No verified direct reference in this release
`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
`At5g03250`	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.	No verified direct reference in this release

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

View annotation sources

Functional annotation source: OH1004 · LXL04_038590 · 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:0010087 phloem or xylem histogenesis Biological Process

GO:0010305 leaf vascular tissue pattern formation Biological Process

GO:0010588 cotyledon vascular tissue pattern formation Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0048367 shoot system development Biological Process

GO:0080022 primary root development Biological Process

GO:0005634 nucleus Cellular Component

GO:0005886 plasma membrane Cellular Component

KEGG gene cross-reference

ath:AT1G30440

ath:AT5G03250

ath:AT5G10250

ath:AT5G64330

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.

View expression for this gene

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.

Nucleus0.578

Rank 1 · LXL04_038590 · OH-1004

Cytoplasm0.307

Rank 2 · LXL04_038590 · OH-1004

Cell membrane0.155

Rank 3 · LXL04_038590 · OH-1004

Endoplasmic reticulum0.047

Rank 4 · LXL04_038590 · OH-1004

Lysosome / Vacuole0.035

Rank 5 · LXL04_038590 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

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Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF03000.20NPH3256-548 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_038590	`PF03000.20`	NPH3	256	548	7.8e-99	331.2

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	66.887%	Swiss-Prot	strong database homology
`Q9S9Q9`	Arabidopsis thaliana	BTB/POZ domain-containing protein At1g30440	37.781%	Swiss-Prot	moderate database homology
`Q9LFU0`	Arabidopsis thaliana	BTB/POZ domain-containing protein DOT3	39.297%	Swiss-Prot	moderate database homology
`Q9LYW0`	Arabidopsis thaliana	BTB/POZ domain-containing protein At5g03250	39.695%	Swiss-Prot	moderate database homology
`Q5KS50`	Oryza sativa subsp. japonica	Coleoptile phototropism protein 1	57.215%	Swiss-Prot	strong database homology

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