LXL04_009590 | RubberDandelionOmics

Gene overview

LXL04_009590

Reference: OH-1004 Chr: Chr02 Coordinates: 129289236-129290843 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1608 bp · LXL04_009590|LXL04_009590|OH1004|cDNA

ATGCTCGTTGAATTCGTAAACTGTGAAGACATGGTGGGAAATGGTAAGCTACGCCGGTGGAGATTTTCTATAAGGTCAGCGTCGGCCGCGACGAAATCGGAGAAAACGAAGCCTCCGGATGAATTTCTTTGTCCGATTTCTGGTGTATTGATGTTTGAACCAGTTGTGGTTTCCTCTGGACACACGTTTGAGAAGACATCAGTTGACGTTTGTAAAGACCTGAAATTTGTTCCGATTCTCGCCGATGGATCAAGGCCTGA...

CDS

Download CDS FASTA

1608 bp · LXL04_009590|LXL04_009590|OH1004|CDS

ATGCTCGTTGAATTCGTAAACTGTGAAGACATGGTGGGAAATGGTAAGCTACGCCGGTGGAGATTTTCTATAAGGTCAGCGTCGGCCGCGACGAAATCGGAGAAAACGAAGCCTCCGGATGAATTTCTTTGTCCGATTTCTGGTGTATTGATGTTTGAACCAGTTGTGGTTTCCTCTGGACACACGTTTGAGAAGACATCAGTTGACGTTTGTAAAGACCTGAAATTTGTTCCGATTCTCGCCGATGGATCAAGGCCTGA...

Protein

Download Protein FASTA

535 aa · LXL04_009590|LXL04_009590|OH1004|PROTEIN

MLVEFVNCEDMVGNGKLRRWRFSIRSASAATKSEKTKPPDEFLCPISGVLMFEPVVVSSGHTFEKTSVDVCKDLKFVPILADGSRPDFSTVIFNLALKKAIGSWSVSTGADLPCRPDYSSIEDLVRKMMASSSQNEGDLRFRDSERDLLKGMAEKPPVILTHAVTQLNPRSIIPHRHFYSSSSEESVLANVPDTPPLPFVTRPSCYSSSASSEIVVDESPDPNSSTSDDQHFSTKLLSLDVFEQEQCVISLRKVTRADEE...

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_009590`
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_009590

Location Chr02:129289236-129290843 (-)

Description Similar to PUB38: U-box domain-containing protein 38

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g65200`	Functions as an E3 ubiquitin ligase.	No verified direct reference in this release
`At5g40140`	Functions as an E3 ubiquitin ligase.	No verified direct reference in this release
`At5g62560`	Functions as an E3 ubiquitin ligase.	No verified direct reference in this release
`At3g47820`	Functions as an E3 ubiquitin ligase.	No verified direct reference in this release
`At2g23140`	Functions as an E3 ubiquitin ligase.	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_009590 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0016567 protein ubiquitination Biological Process

GO:0034614 cellular response to reactive oxygen species Biological Process

GO:0048364 root development Biological Process

GO:0048658 anther wall tapetum development Biological Process

GO:1904821 chloroplast disassembly Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0004842 ubiquitin-protein transferase activity Molecular Function

GO:0061630 ubiquitin protein ligase activity Molecular Function

GO:0070696 transmembrane receptor protein serine/threonine kinase binding Molecular Function

KEGG gene cross-reference

ath:AT2G23140

ath:AT3G47820

ath:AT5G40140

ath:AT5G62560

ath:AT5G65200

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.

Cytoplasm0.568

Rank 1 · LXL04_009590 · OH-1004

Nucleus0.363

Rank 2 · LXL04_009590 · OH-1004

Cell membrane0.138

Rank 3 · LXL04_009590 · OH-1004

Lysosome / Vacuole0.047

Rank 4 · LXL04_009590 · OH-1004

Endoplasmic reticulum0.046

Rank 5 · LXL04_009590 · 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.

PF04564.22U-box39-105 aa

PF25598.2ARM_PUB243-505 aa

PF24768.2ARM_ARMC5284-465 aa

PF00514.30Arm300-338 aa

PF00514.30Arm342-379 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_009590	`PF04564.22`	U-box	39	105	8.1e-09	36.2
LXL04_009590	`PF25598.2`	ARM_PUB	243	505	9.9e-13	48.9
LXL04_009590	`PF24768.2`	ARM_ARMC5	284	465	1.4e-08	35.3
LXL04_009590	`PF00514.30`	Arm	300	338	4.6e-21	74.8
LXL04_009590	`PF00514.30`	Arm	342	379	4.6e-21	74.8

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
`Q9FJP6`	Arabidopsis thaliana	U-box domain-containing protein 38	51.830%	Swiss-Prot	strong database homology
`Q9FL17`	Arabidopsis thaliana	U-box domain-containing protein 40	49.702%	Swiss-Prot	moderate database homology
`Q0WUF6`	Arabidopsis thaliana	U-box domain-containing protein 41	47.197%	Swiss-Prot	moderate database homology
`Q9STT1`	Arabidopsis thaliana	U-box domain-containing protein 39	46.629%	Swiss-Prot	moderate database homology
`O22193`	Arabidopsis thaliana	U-box domain-containing protein 4	33.212%	Swiss-Prot	moderate database homology

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