LXL04_017334 | RubberDandelionOmics

Gene overview

LXL04_017334

Reference: OH-1004 Chr: Chr03 Coordinates: 146805515-146808819 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1956 bp · LXL04_017334|LXL04_017334|OH1004|cDNA

ATGAAGTTTATGAAACTTGGATCCAAGTCTGATTCGTTTCAGAACGATGGCGACAATGTCTGGTATGTGACTTCGGAGTTGGCAACTGACGTCATCATTAACGTAGGAGATTCGAAGTTCTATCTACACAAGTTAGTGCTGGGAGGGTCAGTTAAGACCGCGATGGCGCCCCCAGCCGTCACCACCACTTTGGTCACTCCGAAGAGCAACCCACCGATCCTTAGgaacccccggacaactgggTTCCCTCTTTTATCGAA...

CDS

Download CDS FASTA

1956 bp · LXL04_017334|LXL04_017334|OH1004|CDS

ATGAAGTTTATGAAACTTGGATCCAAGTCTGATTCGTTTCAGAACGATGGCGACAATGTCTGGTATGTGACTTCGGAGTTGGCAACTGACGTCATCATTAACGTAGGAGATTCGAAGTTCTATCTACACAAGTTAGTGCTGGGAGGGTCAGTTAAGACCGCGATGGCGCCCCCAGCCGTCACCACCACTTTGGTCACTCCGAAGAGCAACCCACCGATCCTTAGGAACCCCCGGACAACTGGGTTCCCTCTTTTATCGAA...

Protein

Download Protein FASTA

651 aa · LXL04_017334|LXL04_017334|OH1004|PROTEIN

MKFMKLGSKSDSFQNDGDNVWYVTSELATDVIINVGDSKFYLHKLVLGGSVKTAMAPPAVTTTLVTPKSNPPILRNPRTTGFPLLSKSGRLQKLIRGSNESEGGEIDIHEIPGGPTAFEICAKFCYGMTVTLNAYNVISTYCAADYLEMHETIDKGNLVYKLNVFLTTSIFRSWKDSIIVLQSTKYMMTSLTEEPKLVNLCINSIASKASVDLSKVDWSYTYNRKKLPEENVTELGVVRARMVPKDWWVEDLAELEIGLY...

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_017334`
TK1151 ID	TkA02G049890
OH-1004 ID	LXL04_017334
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	93.200
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_017334

Location Chr03:146805515-146808819 (+)

Description Similar to NPY2: BTB/POZ domain-containing protein NPY2

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g14820`	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 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
`At4g37590`	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
`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
`At2g23050`	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 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
`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

Rice

No hit for this species in the current source table.

Functional annotation source

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Functional annotation source: OH1004 · LXL04_017334 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009908 flower development Biological Process

GO:0009911 positive regulation of flower development Biological Process

GO:0009958 positive gravitropism Biological Process

GO:0010229 inflorescence development Biological Process

GO:0010540 basipetal auxin transport Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0045176 apical protein localization Biological Process

GO:0048825 cotyledon development Biological Process

GO:0071365 cellular response to auxin stimulus Biological Process

GO:1901703 protein localization involved in auxin polar transport Biological Process

GO:2000012 regulation of auxin polar transport Biological Process

GO:0005634 nucleus Cellular Component

KEGG gene cross-reference

ath:AT2G14820

ath:AT2G23050

ath:AT4G31820

ath:AT4G37590

ath:AT5G67440

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.

Nucleus0.486

Rank 1 · LXL04_017334 · OH-1004

Cytoplasm0.359

Rank 2 · LXL04_017334 · OH-1004

Cell membrane0.197

Rank 3 · LXL04_017334 · OH-1004

Endoplasmic reticulum0.057

Rank 4 · LXL04_017334 · OH-1004

Lysosome / Vacuole0.033

Rank 5 · LXL04_017334 · 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.

PF03000.20NPH3246-496 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_017334	`PF03000.20`	NPH3	246	496	4.7e-83	279.5

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
`O80970`	Arabidopsis thaliana	Phototropic-responsive NPH3 family protein NPY2	55.200%	Swiss-Prot	strong database homology
`Q0WL52`	Arabidopsis thaliana	Phototropic-responsive NPH3 family protein NPY5	47.484%	Swiss-Prot	moderate database homology
`Q9FN09`	Arabidopsis thaliana	Phototropic-responsive NPH3 family protein NPY3	48.137%	Swiss-Prot	moderate database homology
`O64814`	Arabidopsis thaliana	Phototropic-responsive NPH3 family protein NPY4	51.589%	Swiss-Prot	strong database homology
`Q8H1D3`	Arabidopsis thaliana	Phototropic-responsive NPH3 family protein NPY1	40.931%	Swiss-Prot	moderate database homology

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