LXL04_027164 | RubberDandelionOmics

Gene overview

LXL04_027164

Reference: OH-1004 Chr: Chr06 Coordinates: 9923108-9924246 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1068 bp · LXL04_027164|LXL04_027164|OH1004|cDNA

ATGGCAACAACAACAAACGCCACCACCACCCACTATCCAGACGACTTCAAATGCCCGATTTCTCTCGAGATAATGTCGGAGCCAGTCATCCTTTCTTCCGGCCACACCTTTGACCGCTCTTCAATCCAACGTTGGCTTGACGCAGGCCACCGTACTTGCCCCATCAGCAAATTGCCCCTCTCCGACCCTCCTTCTCTTATCCCTAACCACGCCCTTCGCAGCCTTATCACCAGCTACACCGCCCTCAATTTATCAAAGCC...

CDS

Download CDS FASTA

1068 bp · LXL04_027164|LXL04_027164|OH1004|CDS

ATGGCAACAACAACAAACGCCACCACCACCCACTATCCAGACGACTTCAAATGCCCGATTTCTCTCGAGATAATGTCGGAGCCAGTCATCCTTTCTTCCGGCCACACCTTTGACCGCTCTTCAATCCAACGTTGGCTTGACGCAGGCCACCGTACTTGCCCCATCAGCAAATTGCCCCTCTCCGACCCTCCTTCTCTTATCCCTAACCACGCCCTTCGCAGCCTTATCACCAGCTACACCGCCCTCAATTTATCAAAGCC...

Protein

Download Protein FASTA

355 aa · LXL04_027164|LXL04_027164|OH1004|PROTEIN

MATTTNATTTHYPDDFKCPISLEIMSEPVILSSGHTFDRSSIQRWLDAGHRTCPISKLPLSDPPSLIPNHALRSLITSYTALNLSKPHQNRGNSETLISNLTSKSSSPEAKLFSIEQLCQLSKHDFELRKRLTESGAVAAVLGCISRKNYITLQEKALKLLLNLSLDDDNKVGLVAEGAICSIIAALSDGESADCRATAATVLTSLAVVEVNKATIGAYPFAIRGLVTLLKEGGGRERKEAATALYALCSFPDNRRRAVE...

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_027164`
TK1151 ID	TkA07G036270
OH-1004 ID	LXL04_027164
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	100.000
Protein coverage (%)	TK1151 93.067 / OH-1004 98.310 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

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Basic Information and Functional Annotation

Gene ID LXL04_027164

Location Chr06:9923108-9924246 (-)

Description Similar to PUB8: U-box domain-containing protein 8

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g21350`	Functions as an E3 ubiquitin ligase (By similarity).	A cryptic modifier causing transient self-incompatibility in Arabidopsis thaliana.2007 · DOI: 10.1016/j.cub.2007.03.022
`At3g46510`	Functions as an E3 ubiquitin ligase.	No verified direct reference in this release
`At2g28830`	Functions as an E3 ubiquitin ligase.	No verified direct reference in this release

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_027164 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0002237 response to molecule of bacterial origin Biological Process

GO:0006511 ubiquitin-dependent protein catabolic process Biological Process

GO:0007166 cell surface receptor signaling pathway Biological Process

GO:0009609 response to symbiotic bacterium Biological Process

GO:0009610 response to symbiotic fungus Biological Process

GO:0009738 abscisic acid-activated signaling pathway Biological Process

GO:0009877 nodulation Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0036377 arbuscular mycorrhizal association Biological Process

GO:0042742 defense response to bacterium Biological Process

GO:0050777 negative regulation of immune response Biological Process

GO:2000028 regulation of photoperiodism, flowering Biological Process

KEGG gene cross-reference

ath:AT2G28830

ath:AT3G46510

ath:AT4G21350

dosa:Os06g0102700

mtr:11430446

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.

Nucleus0.662

Rank 1 · LXL04_027164 · OH-1004

Cytoplasm0.422

Rank 2 · LXL04_027164 · OH-1004

Cell membrane0.041

Rank 3 · LXL04_027164 · OH-1004

Endoplasmic reticulum0.027

Rank 4 · LXL04_027164 · OH-1004

Mitochondrion0.020

Rank 5 · LXL04_027164 · 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-box13-81 aa

PF11789.15zf-Nse15-55 aa

PF13445.13zf-RING_UBOX18-54 aa

PF24768.2ARM_ARMC590-272 aa

PF25598.2ARM_PUB98-348 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_027164	`PF04564.22`	U-box	13	81	6.5e-19	68.6
LXL04_027164	`PF11789.15`	zf-Nse	15	55	3.9e-07	30.5
LXL04_027164	`PF13445.13`	zf-RING_UBOX	18	54	6.6e-08	33.1
LXL04_027164	`PF24768.2`	ARM_ARMC5	90	272	1.5e-07	31.8
LXL04_027164	`PF25598.2`	ARM_PUB	98	348	2.3e-16	60.8

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`O81902`	Arabidopsis thaliana	U-box domain-containing protein 8	60.350%	Swiss-Prot	strong database homology
`Q9SNC6`	Arabidopsis thaliana	U-box domain-containing protein 13	34.188%	Swiss-Prot	moderate database homology
`Q9ZV31`	Arabidopsis thaliana	U-box domain-containing protein 12	33.884%	Swiss-Prot	moderate database homology
`Q5VRH9`	Oryza sativa subsp. japonica	U-box domain-containing protein 12	35.440%	Swiss-Prot	moderate database homology

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