LXL04_000067 | RubberDandelionOmics

Gene overview

LXL04_000067

Reference: OH-1004 Chr: Chr01 Coordinates: 1531864-1533867 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2004 bp · LXL04_000067|LXL04_000067|OH1004|cDNA

ATGGCCATTTCACCGGAACCTTTGCCGCCAAAAAAGAAGCGATCGTCGGATTCAGATGAAAGGCTTCTCCGATCATTGTTGCTCCGATCGAAAGAAACTTCGTCTCTGAATCCGATTCCGTTTGTTCTTCATCGGAATTCGAATTCGATTATTCGGAAAACTAAGCTGTTGACTTTGCTTCTTGAGGAATTGGTTGTTGATCATGTTTTATCGAGTTTTCCGGCATCGGCGGTGTTGTGTTTTGAGGAGTTATACATCGT...

CDS

Download CDS FASTA

2004 bp · LXL04_000067|LXL04_000067|OH1004|CDS

ATGGCCATTTCACCGGAACCTTTGCCGCCAAAAAAGAAGCGATCGTCGGATTCAGATGAAAGGCTTCTCCGATCATTGTTGCTCCGATCGAAAGAAACTTCGTCTCTGAATCCGATTCCGTTTGTTCTTCATCGGAATTCGAATTCGATTATTCGGAAAACTAAGCTGTTGACTTTGCTTCTTGAGGAATTGGTTGTTGATCATGTTTTATCGAGTTTTCCGGCATCGGCGGTGTTGTGTTTTGAGGAGTTATACATCGT...

Protein

Download Protein FASTA

667 aa · LXL04_000067|LXL04_000067|OH1004|PROTEIN

MAISPEPLPPKKKRSSDSDERLLRSLLLRSKETSSLNPIPFVLHRNSNSIIRKTKLLTLLLEELVVDHVLSSFPASAVLCFEELYIVLQSIKTLIEDCCNGSKLWLLIEQQSVANKFHEFTLELSTLIDIFPVKAMNLGQDVEELVNLIRKQCSNTPALLDDKDINLRNDVLEKLARIKSEIIPQETKLKEVFTRLQLNDSTSCTEEIEILEEEVRNQSDEKSKAEIVSLIGLVRYAKCVLYGESSPRRIIDRKKSNSTD...

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_000067`
TK1151 ID	TkA01G637580
OH-1004 ID	LXL04_000067
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	100.000
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_000067

Location Chr01:1531864-1533867 (+)

Description Similar to PUB16: U-box domain-containing protein 16

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g01830`	Functions as an E3 ubiquitin ligase.	No verified direct reference in this release
`At1g29340`	Functions as an E3 ubiquitin ligase.	The E3 ubiquitin ligase activity of arabidopsis PLANT U-BOX17 and its functional tobacco homolog ACRE276 are required for cell death and defense.2006 · DOI: 10.1105/tpc.105.039198
`At1g60190`	Functions as an E3 ubiquitin ligase.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os02g0234300`	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_000067 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0002237 response to molecule of bacterial origin Biological Process

GO:0009609 response to symbiotic bacterium Biological Process

GO:0009610 response to symbiotic fungus Biological Process

GO:0009877 nodulation Biological Process

GO:0010029 regulation of seed germination Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0036377 arbuscular mycorrhizal association Biological Process

GO:0098542 defense response to other organism Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005886 plasma membrane Cellular Component

GO:0009507 chloroplast Cellular Component

KEGG gene cross-reference

ath:AT1G29340

ath:AT1G60190

ath:AT5G01830

dosa:Os02g0234300

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.

Cytoplasm0.598

Rank 1 · LXL04_000067 · OH-1004

Nucleus0.371

Rank 2 · LXL04_000067 · OH-1004

Cell membrane0.148

Rank 3 · LXL04_000067 · OH-1004

Endoplasmic reticulum0.054

Rank 4 · LXL04_000067 · OH-1004

Lysosome / Vacuole0.035

Rank 5 · LXL04_000067 · 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_N47-152 aa

PF04564.22U-box263-334 aa

PF25598.2ARM_PUB368-640 aa

PF00514.30Arm396-432 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_000067	`PF25368.2`	PUB10_N	47	152	9e-11	43.2
LXL04_000067	`PF04564.22`	U-box	263	334	1.7e-17	64.0
LXL04_000067	`PF25598.2`	ARM_PUB	368	640	5.7e-14	52.9
LXL04_000067	`PF00514.30`	Arm	396	432	3e-12	46.8

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
`Q9LZW3`	Arabidopsis thaliana	U-box domain-containing protein 16	53.720%	Swiss-Prot	strong database homology
`Q9C7R6`	Arabidopsis thaliana	U-box domain-containing protein 17	35.982%	Swiss-Prot	moderate database homology
`O80742`	Arabidopsis thaliana	U-box domain-containing protein 19	30.091%	Swiss-Prot	moderate database homology
`Q6EUK7`	Oryza sativa subsp. japonica	U-box domain-containing protein 4	34.240%	Swiss-Prot	moderate database homology

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