LXL04_025838 | RubberDandelionOmics

Gene overview

LXL04_025838

Reference: OH-1004 Chr: Chr05 Coordinates: 117485637-117487660 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1038 bp · LXL04_025838|LXL04_025838|OH1004|cDNA

ATGTACAAATTGGAAACTTGCATTATTGCTCCCATTCTTGGTTTGGTGGATTGTCTTTGTACAAATTATATAAACAATATGTTGGGAGGAAATAACAACAATTCATTACTCCCTGTCTTTGTTGATGGGAGCCTTTTTCAGTATCCTTCAAACACATCAAACCAATTGCAACTATTTGGAAATGGTGGATGTAATGTTGATCAAGTAAATTATTCAGCAAGAGAGCATAACAGCCCTGTTTTTAGACCTAACAAAAGACC...

CDS

Download CDS FASTA

1038 bp · LXL04_025838|LXL04_025838|OH1004|CDS

ATGTACAAATTGGAAACTTGCATTATTGCTCCCATTCTTGGTTTGGTGGATTGTCTTTGTACAAATTATATAAACAATATGTTGGGAGGAAATAACAACAATTCATTACTCCCTGTCTTTGTTGATGGGAGCCTTTTTCAGTATCCTTCAAACACATCAAACCAATTGCAACTATTTGGAAATGGTGGATGTAATGTTGATCAAGTAAATTATTCAGCAAGAGAGCATAACAGCCCTGTTTTTAGACCTAACAAAAGACC...

Protein

Download Protein FASTA

345 aa · LXL04_025838|LXL04_025838|OH1004|PROTEIN

MYKLETCIIAPILGLVDCLCTNYINNMLGGNNNNSLLPVFVDGSLFQYPSNTSNQLQLFGNGGCNVDQVNYSAREHNSPVFRPNKRPREIEANFMQKKLQISLNHNFYNNDDIAPSTIPNPHHVSTGLKLSYDDEERNSSITSASASMTLAPSIMSSFGDSISTELERHKDEFERYLIIQEENMLKGMSDIRQRHMTSFISTMEKNIHNKLREKETEIETINRKNKQLTETIKQVATEAQNWHYRAKYNESMVNILKTNL...

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_025838`
TK1151 ID	TkA06G040180
OH-1004 ID	LXL04_025838
Relationship / confidence	Sequence Supported Annotation Or Model Conflict / Review
Protein identity (%)	100.000
Protein coverage (%)	TK1151 96.907 / OH-1004 54.493 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_025838

Location Chr05:117485637-117487660 (-)

Description Similar to BOI: E3 ubiquitin-protein ligase BOI

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`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
`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
`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_025838 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000209 protein polyubiquitination Biological Process

GO:0001666 response to hypoxia Biological Process

GO:0006351 DNA-templated transcription Biological Process

GO:0006952 defense response Biological Process

GO:0007166 cell surface receptor signaling pathway Biological Process

GO:0007249 canonical NF-kappaB signal transduction Biological Process

GO:0009739 response to gibberellin Biological Process

GO:0031398 positive regulation of protein ubiquitination Biological Process

GO:0033209 tumor necrosis factor-mediated signaling pathway Biological Process

GO:0034121 regulation of toll-like receptor signaling pathway Biological Process

GO:0038061 non-canonical NF-kappaB signal transduction Biological Process

GO:0039535 regulation of RIG-I signaling pathway Biological Process

KEGG gene cross-reference

ath:AT1G79110

ath:AT3G12920

ath:AT4G19700

ath:AT5G45100

hsa:329

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.

Nucleus0.899

Rank 1 · LXL04_025838 · OH-1004

Cytoplasm0.175

Rank 2 · LXL04_025838 · OH-1004

Cell membrane0.028

Rank 3 · LXL04_025838 · OH-1004

Endoplasmic reticulum0.017

Rank 4 · LXL04_025838 · OH-1004

Plastid0.013

Rank 5 · LXL04_025838 · 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_3296-333 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_025838	`PF13920.13`	zf-C3HC4_3	296	333	6.2e-09	36.2

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`O81851`	Arabidopsis thaliana	E3 ubiquitin-protein ligase BOI	31.111%	Swiss-Prot	moderate database homology
`Q9LDD1`	Arabidopsis thaliana	Probable BOI-related E3 ubiquitin-protein ligase 3	30.000%	Swiss-Prot	moderate database homology
`Q9FHE4`	Arabidopsis thaliana	BOI-related E3 ubiquitin-protein ligase 1	31.481%	Swiss-Prot	moderate database homology
`F4IDI6`	Arabidopsis thaliana	Probable BOI-related E3 ubiquitin-protein ligase 2	28.926%	Swiss-Prot	weak database homology

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