LXL04_021255 | RubberDandelionOmics

Gene overview

LXL04_021255

Reference: OH-1004 Chr: Chr04 Coordinates: 125845630-125848079 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1902 bp · LXL04_021255|LXL04_021255|OH1004|cDNA

ATGGCCGGCGTTGATTCCACCGCCATCCTTGCTGCTATCCAGTCCCTCCTTCGTCTTGTCAGGGATATCGCTCGTTCCTCTGGCGCCGGATTCTCTGGAGACTTCAAGAAAGATTGCACGGACTTATCTAGAAGGGTGGCCTTGCTATCGCATTTGTTGGAGGAGATTAGGGACTTTAAAGGCGATTTGAGGTTATTGTATGAATCGGCTTCATCGTCGTCTTCTTTATCTTGCTTGTCTGACCTAACCGTTGCTCTTCA...

CDS

Download CDS FASTA

1902 bp · LXL04_021255|LXL04_021255|OH1004|CDS

ATGGCCGGCGTTGATTCCACCGCCATCCTTGCTGCTATCCAGTCCCTCCTTCGTCTTGTCAGGGATATCGCTCGTTCCTCTGGCGCCGGATTCTCTGGAGACTTCAAGAAAGATTGCACGGACTTATCTAGAAGGGTGGCCTTGCTATCGCATTTGTTGGAGGAGATTAGGGACTTTAAAGGCGATTTGAGGTTATTGTATGAATCGGCTTCATCGTCGTCTTCTTTATCTTGCTTGTCTGACCTAACCGTTGCTCTTCA...

Protein

Download Protein FASTA

633 aa · LXL04_021255|LXL04_021255|OH1004|PROTEIN

MAGVDSTAILAAIQSLLRLVRDIARSSGAGFSGDFKKDCTDLSRRVALLSHLLEEIRDFKGDLRLLYESASSSSSLSCLSDLTVALQAAKKLLVIAGNFDHKISREGSAKKIAFQFQCVTWKLEKALANIPYDDFEISEEVQEQVELVRGQLRRARERYGKPLNSAILSHGLPQPSDKEHVENTGDINHQQQLETTKDEIRSKENHSKVKNNNQNDTIYQSDISKISSASSQIEICKNIDENKKVDTPSIPDDFLCPISL...

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_021255`
TK1151 ID	TkA05G372460
OH-1004 ID	LXL04_021255
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.800
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_021255

Location Chr04:125845630-125848079 (-)

Description Similar to PUB11: U-box domain-containing protein 11

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g23030`	Functions as an E3 ubiquitin ligase.	No verified direct reference in this release
`At1g71020`	Functions as an E3 ubiquitin ligase.	No verified direct reference in this release
`At3g46510`	Functions as an E3 ubiquitin ligase.	No verified direct reference in this release
`At3g54850`	Functions as an E3 ubiquitin ligase with specific E2 ubiquitin-conjugating enzymes.	Structure and biochemical function of a prototypical Arabidopsis U-box domain.2004 · DOI: 10.1074/jbc.m405057200

Rice

Reference gene ID	Possible function	Papers / DOI
`Os06g0102700`	Possesses E3 ubiquitin-protein ligase in vitro.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_021255 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0007166 cell surface receptor signaling pathway Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0031648 protein destabilization Biological Process

GO:0042742 defense response to bacterium Biological Process

GO:0050777 negative regulation of immune response Biological Process

GO:0051865 protein autoubiquitination Biological Process

GO:0090333 regulation of stomatal closure Biological Process

GO:2000022 regulation of jasmonic acid mediated signaling pathway Biological Process

GO:2000028 regulation of photoperiodism, flowering Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005829 cytosol Cellular Component

KEGG gene cross-reference

ath:AT1G23030

ath:AT1G71020

ath:AT3G46510

dosa:Os06g0102700

These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.

Open Annotation Module

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.

Cytoplasm0.580

Rank 1 · LXL04_021255 · OH-1004

Nucleus0.419

Rank 2 · LXL04_021255 · OH-1004

Cell membrane0.120

Rank 3 · LXL04_021255 · OH-1004

Endoplasmic reticulum0.045

Rank 4 · LXL04_021255 · OH-1004

Lysosome / Vacuole0.039

Rank 5 · LXL04_021255 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

Open Subcellular Module

Predicted Functional Domains

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

PF25368.2PUB10_N36-155 aa

PF04564.22U-box250-320 aa

PF24768.2ARM_ARMC5341-518 aa

PF25598.2ARM_PUB343-629 aa

PF00514.30Arm370-409 aa

PF00514.30Arm453-491 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_021255	`PF25368.2`	PUB10_N	36	155	1.3e-47	162.2
LXL04_021255	`PF04564.22`	U-box	250	320	1.4e-20	73.9
LXL04_021255	`PF24768.2`	ARM_ARMC5	341	518	1.2e-11	45.2
LXL04_021255	`PF25598.2`	ARM_PUB	343	629	1.5e-25	90.9
LXL04_021255	`PF00514.30`	Arm	370	409	9.3e-31	105.6
LXL04_021255	`PF00514.30`	Arm	453	491	9.3e-31	105.6

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
`Q8GUG9`	Arabidopsis thaliana	U-box domain-containing protein 11	58.509%	Swiss-Prot	strong database homology
`Q9C9A6`	Arabidopsis thaliana	U-box domain-containing protein 10	57.395%	Swiss-Prot	strong database homology
`Q9SNC6`	Arabidopsis thaliana	U-box domain-containing protein 13	41.642%	Swiss-Prot	moderate database homology
`Q8VZ40`	Arabidopsis thaliana	U-box domain-containing protein 14	41.614%	Swiss-Prot	moderate database homology
`Q5VRH9`	Oryza sativa subsp. japonica	U-box domain-containing protein 12	44.013%	Swiss-Prot	moderate database homology

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