LXL04_022309 | RubberDandelionOmics

Gene overview

LXL04_022309

Reference: OH-1004 Chr: Chr04 Coordinates: 147940749-147942564 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

894 bp · LXL04_022309|LXL04_022309|OH1004|cDNA

ATGGCGGTCCAAGCACAGTGCTACTCTGATCTTTATCAGAATAATAGCATGGGGTTCGCTAATTTACCTCAGGATTGGGTTCTCATGACTGGTTCCTCTGTTTTCGGAATTGGGGATGAAAACAGAGCTTTATGTTCTTACGAACAACAACAAGATCAAAGGCTTCTTGAGTCTATGAATTCCGCTTCTGATTACCATAATCTCGTCATGTCTTCTTCAAATTCGAGAAGAAATGGGATGATTGGGTTTCAAAATTTGTC...

CDS

Download CDS FASTA

894 bp · LXL04_022309|LXL04_022309|OH1004|CDS

ATGGCGGTCCAAGCACAGTGCTACTCTGATCTTTATCAGAATAATAGCATGGGGTTCGCTAATTTACCTCAGGATTGGGTTCTCATGACTGGTTCCTCTGTTTTCGGAATTGGGGATGAAAACAGAGCTTTATGTTCTTACGAACAACAACAAGATCAAAGGCTTCTTGAGTCTATGAATTCCGCTTCTGATTACCATAATCTCGTCATGTCTTCTTCAAATTCGAGAAGAAATGGGATGATTGGGTTTCAAAATTTGTC...

Protein

Download Protein FASTA

297 aa · LXL04_022309|LXL04_022309|OH1004|PROTEIN

MAVQAQCYSDLYQNNSMGFANLPQDWVLMTGSSVFGIGDENRALCSYEQQQDQRLLESMNSASDYHNLVMSSSNSRRNGMIGFQNLSSELERQRLEMDCFLHFQNEKLKAVLNEESRRRDLIMMQGYESKMKAIMEAKDDVLNTAANRTRELQNCLLMAEKDAKDWERKAIETEAMVTDLNRKLYEARERNNEDAESVCNGGNNDDEREREREKKKKMACKVCHVRSSCVLLLPCRHLCSCRGCEGLLMFCPVCETVKNG...

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_022309`
TK1151 ID	TkA05G457970
OH-1004 ID	LXL04_022309
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	100.000
Protein coverage (%)	TK1151 98.502 / OH-1004 88.552 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

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_022309

Location Chr04:147940749-147942564 (+)

Description Similar to BRG3: Probable BOI-related E3 ubiquitin-protein ligase 3

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g12920`	Probable E3 ubiquitin-protein ligase.	DELLA proteins and their interacting RING Finger proteins repress gibberellin responses by binding to the promoters of a subset of gibberellin-responsive genes in Arabidopsis.2013 · DOI: 10.1105/tpc.112.108951
`At5g45100`	E3 ubiquitin-protein ligase involved in regulation of abiotic stress responses.	DELLA proteins and their interacting RING Finger proteins repress gibberellin responses by binding to the promoters of a subset of gibberellin-responsive genes in Arabidopsis.2013 · DOI: 10.1105/tpc.112.108951
`At4g19700`	E3 ubiquitin-protein ligase involved in the regulation of pathogen and abiotic stress responses by facilitating degradation of MYB108/BOI.	No verified direct reference in this release
`At1g79110`	Probable E3 ubiquitin-protein ligase.	DELLA proteins and their interacting RING Finger proteins repress gibberellin responses by binding to the promoters of a subset of gibberellin-responsive genes in Arabidopsis.2013 · DOI: 10.1105/tpc.112.108951

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_022309 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006511 ubiquitin-dependent protein catabolic process Biological Process

GO:0006952 defense response Biological Process

GO:0007032 endosome organization Biological Process

GO:0009739 response to gibberellin Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0032479 regulation of type I interferon production Biological Process

GO:0042742 defense response to bacterium Biological Process

GO:0043067 regulation of programmed cell death Biological Process

GO:0043069 negative regulation of programmed cell death Biological Process

GO:0043161 proteasome-mediated ubiquitin-dependent protein catabolic process Biological Process

GO:0050687 negative regulation of defense response to virus Biological Process

GO:0050832 defense response to fungus Biological Process

KEGG gene cross-reference

ath:AT1G79110

ath:AT3G12920

ath:AT4G19700

ath:AT5G45100

hsa:79102

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.

Nucleus0.923

Rank 1 · LXL04_022309 · OH-1004

Cytoplasm0.129

Rank 2 · LXL04_022309 · OH-1004

Cell membrane0.036

Rank 3 · LXL04_022309 · OH-1004

Endoplasmic reticulum0.019

Rank 4 · LXL04_022309 · OH-1004

Plastid0.014

Rank 5 · LXL04_022309 · 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.

PF13920.13zf-C3HC4_3217-257 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_022309	`PF13920.13`	zf-C3HC4_3	217	257	5e-08	33.3

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`Q9LDD1`	Arabidopsis thaliana	Probable BOI-related E3 ubiquitin-protein ligase 3	28.365%	Swiss-Prot	weak database homology
`Q9FHE4`	Arabidopsis thaliana	BOI-related E3 ubiquitin-protein ligase 1	26.042%	Swiss-Prot	weak database homology
`O81851`	Arabidopsis thaliana	E3 ubiquitin-protein ligase BOI	27.861%	Swiss-Prot	weak database homology
`F4IDI6`	Arabidopsis thaliana	Probable BOI-related E3 ubiquitin-protein ligase 2	25.238%	Swiss-Prot	weak database homology

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