LXL04_004039 | RubberDandelionOmics

Gene overview

LXL04_004039

Reference: OH-1004 Chr: Chr01 Coordinates: 122847897-122848857 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

822 bp · LXL04_004039|LXL04_004039|OH1004|cDNA

ATGGGACAAAGAGATTGGAGCGAGCTGCCAGTTCACTGTTTGGTTGAAATCTTTGGAAGAGTCGGAATCGAATCACTTGTGGAGGCTATTCCTTTAGTCTGCAGGTCTTGGTATGAGGCTACCTTATATCCCCAATGCTGGCAACAACTCGTCTTTACTAAATCCCCATGTTTAAGAACTTCTAAACGTTCAATCCCAAGACTTAAATTAGACAAAGACTCGCGTTTTGATTTCAATATTGTGGTGTCACTAGACCATAC...

CDS

Download CDS FASTA

822 bp · LXL04_004039|LXL04_004039|OH1004|CDS

ATGGGACAAAGAGATTGGAGCGAGCTGCCAGTTCACTGTTTGGTTGAAATCTTTGGAAGAGTCGGAATCGAATCACTTGTGGAGGCTATTCCTTTAGTCTGCAGGTCTTGGTATGAGGCTACCTTATATCCCCAATGCTGGCAACAACTCGTCTTTACTAAATCCCCATGTTTAAGAACTTCTAAACGTTCAATCCCAAGACTTAAATTAGACAAAGACTCGCGTTTTGATTTCAATATTGTGGTGTCACTAGACCATAC...

Protein

Download Protein FASTA

273 aa · LXL04_004039|LXL04_004039|OH1004|PROTEIN

MGQRDWSELPVHCLVEIFGRVGIESLVEAIPLVCRSWYEATLYPQCWQQLVFTKSPCLRTSKRSIPRLKLDKDSRFDFNIVVSLDHTSNGHDSLEKLVRFAVGRSHGLATEIVFHPKSHLKEGQITWIAQRCPSLKLLALPSYLSYVINFEVSDSICKWKDLEALQVVSLIGLKKTIANISKNCHNFNHLSIYVHRIDGDVALAIASQLPHIKTLDLRFAAIERDDLIVILKGCQELEHLDVSECKGVAGDDEIMKLARR...

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_004039`
TK1151 ID	TkA01G209800
OH-1004 ID	LXL04_004039
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.600
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

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_004039

Location Chr01:122847897-122848857 (+)

Description Similar to At3g48880: F-box/LRR-repeat protein At3g48880

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g48880`	F-box/LRR-repeat protein At3g48880.	No verified direct reference in this release
`At4g05500`	Putative F-box/LRR-repeat protein 23.	No verified direct reference in this release
`At4g08980`	Component of SCF(ASK-cullin-F-box) E3 ubiquitin ligase complexes, which may mediate the ubiquitination and subsequent proteasomal degradation of target proteins.	No verified direct reference in this release
`At4g30640`	Putative F-box/LRR-repeat protein 19.	No verified direct reference in this release
`At4g05460`	Component of SCF(ASK-cullin-F-box) E3 ubiquitin ligase complexes, which may mediate the ubiquitination and subsequent proteasomal degradation of target proteins.	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_004039 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006511 ubiquitin-dependent protein catabolic process Biological Process

GO:0009737 response to abscisic acid Biological Process

GO:0010608 post-transcriptional regulation of gene expression Biological Process

GO:0010629 negative regulation of gene expression Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0031146 SCF-dependent proteasomal ubiquitin-dependent protein catabolic process Biological Process

GO:0050829 defense response to Gram-negative bacterium Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0019005 SCF ubiquitin ligase complex Cellular Component

GO:1905761 SCF ubiquitin ligase complex binding Molecular Function

KEGG gene cross-reference

ath:AT3G48880

ath:AT4G05460

ath:AT4G08980

ath:AT4G30640

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.

Nucleus0.572

Rank 1 · LXL04_004039 · OH-1004

Cytoplasm0.396

Rank 2 · LXL04_004039 · OH-1004

Cell membrane0.084

Rank 3 · LXL04_004039 · OH-1004

Endoplasmic reticulum0.067

Rank 4 · LXL04_004039 · OH-1004

Plastid0.041

Rank 5 · LXL04_004039 · 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.

PF12937.13F-box-like6-52 aa

PF24758.2LRR_At5g56370183-245 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_004039	`PF12937.13`	F-box-like	6	52	2.6e-07	31.0
LXL04_004039	`PF24758.2`	LRR_At5g56370	183	245	2.1e-06	28.3

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
`Q9M2Z5`	Arabidopsis thaliana	F-box/LRR-repeat protein At3g48880	30.738%	Swiss-Prot	moderate database homology
`Q9S9V9`	Arabidopsis thaliana	Putative F-box/LRR-repeat protein 23	27.092%	Swiss-Prot	weak database homology
`Q9ZPE4`	Arabidopsis thaliana	F-box protein FBW2	24.427%	Swiss-Prot	weak database homology
`Q9M096`	Arabidopsis thaliana	Putative F-box/LRR-repeat protein 19	23.985%	Swiss-Prot	weak database homology
`Q9M0U9`	Arabidopsis thaliana	F-box protein SKIP19	26.016%	Swiss-Prot	weak database homology

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