LXL04_015213 | RubberDandelionOmics

Gene overview

LXL04_015213

Reference: OH-1004 Chr: Chr03 Coordinates: 66063253-66066202 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1905 bp · LXL04_015213|LXL04_015213|OH1004|cDNA

atggaagaagaaaaggagCTATCCAAGTGTAATAATTGCAGAATCGCTAGGGATGTTGTCGAAGAATTAATTGGGATTACCGAAGCTGCTAAATCAATGGGAGAGTTTCGAGGAACGCAGAAGAAAGAGAGCCAAATGCTCCTAAGGCGATTGAGGCAGTGTCTGCCCTTATTGGAAGAGCTTCGAGATCTTGATGCACAGATTCCAGAAAATTGCTTATCATGTTTGCATAGATTGAAAAGAGCGTTTATCCTGGCCAA...

CDS

Download CDS FASTA

1905 bp · LXL04_015213|LXL04_015213|OH1004|CDS

ATGGAAGAAGAAAAGGAGCTATCCAAGTGTAATAATTGCAGAATCGCTAGGGATGTTGTCGAAGAATTAATTGGGATTACCGAAGCTGCTAAATCAATGGGAGAGTTTCGAGGAACGCAGAAGAAAGAGAGCCAAATGCTCCTAAGGCGATTGAGGCAGTGTCTGCCCTTATTGGAAGAGCTTCGAGATCTTGATGCACAGATTCCAGAAAATTGCTTATCATGTTTGCATAGATTGAAAAGAGCGTTTATCCTGGCCAA...

Protein

Download Protein FASTA

634 aa · LXL04_015213|LXL04_015213|OH1004|PROTEIN

MEEEKELSKCNNCRIARDVVEELIGITEAAKSMGEFRGTQKKESQMLLRRLRQCLPLLEELRDLDAQIPENCLSCLHRLKRAFILAKKLLKTCHAGSKIYLVLETNAMLSRFQSVYDKLNHAMDGFPYKEIGISEEVKEQVELMCTQLKRAKPQVDSQEMELTSDMMTILSADTDRISECEAIRRLANKLSLNTLEELRTETVVVRKLVKERRGQNAQGTEKIINLLDKFKRFAGIEQANVLDDPAPCNRTLQKCASITI...

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_015213`
TK1151 ID	TkA02G355660
OH-1004 ID	LXL04_015213
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.500
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

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_015213

Location Chr03:66063253-66066202 (+)

Description Similar to PUB15: U-box domain-containing protein 15

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g42340`	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
`At2g28830`	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_015213 · 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:0042742 defense response to bacterium Biological Process

GO:0050777 negative regulation of immune response 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

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:AT2G28830

ath:AT3G46510

ath:AT3G54850

ath:AT5G42340

dosa:Os06g0102700

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.

Cytoplasm0.587

Rank 1 · LXL04_015213 · OH-1004

Nucleus0.333

Rank 2 · LXL04_015213 · OH-1004

Cell membrane0.185

Rank 3 · LXL04_015213 · OH-1004

Mitochondrion0.062

Rank 4 · LXL04_015213 · OH-1004

Endoplasmic reticulum0.060

Rank 5 · LXL04_015213 · 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_N41-152 aa

PF04564.22U-box260-330 aa

PF25598.2ARM_PUB351-625 aa

PF00514.30Arm380-419 aa

PF24768.2ARM_ARMC5382-584 aa

PF00514.30Arm463-501 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_015213	`PF25368.2`	PUB10_N	41	152	1.9e-31	110.0
LXL04_015213	`PF04564.22`	U-box	260	330	8e-21	74.7
LXL04_015213	`PF25598.2`	ARM_PUB	351	625	1.8e-24	87.4
LXL04_015213	`PF00514.30`	Arm	380	419	7.1e-28	96.4
LXL04_015213	`PF24768.2`	ARM_ARMC5	382	584	3.6e-16	60.1
LXL04_015213	`PF00514.30`	Arm	463	501	7.1e-28	96.4

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
`Q681N2`	Arabidopsis thaliana	U-box domain-containing protein 15	52.941%	Swiss-Prot	strong database homology
`Q9SNC6`	Arabidopsis thaliana	U-box domain-containing protein 13	40.498%	Swiss-Prot	moderate database homology
`Q9ZV31`	Arabidopsis thaliana	U-box domain-containing protein 12	40.266%	Swiss-Prot	moderate database homology
`Q8VZ40`	Arabidopsis thaliana	U-box domain-containing protein 14	37.379%	Swiss-Prot	moderate database homology
`Q5VRH9`	Oryza sativa subsp. japonica	U-box domain-containing protein 12	38.752%	Swiss-Prot	moderate database homology

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