LXL04_019584 | RubberDandelionOmics

Gene overview

LXL04_019584

Reference: OH-1004 Chr: Chr04 Coordinates: 34551543-34554355 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1920 bp · LXL04_019584|LXL04_019584|OH1004|cDNA

ATGGCCGTGGAGAACGCAACAATGGAGATTTCGAATAGCAATGAAGGCGACGAGGGCAATGATTTGGTCGCAGGAATGATGGAAATTATTGAAACAGTGGGATCGTACATGGGGTTTCGAAGAACACAGAGAAAAGAGTGTTTAAAGCTCGTAAGAAGATTGAAGCTTCTAGTCCCACTTTTTGAAGAAATCAAAGAGATGAATCTATCAATACCCACAAGGGCATTTCAGTCTTTCGTTAATCTACAGAAGGCACTTCT...

CDS

Download CDS FASTA

1920 bp · LXL04_019584|LXL04_019584|OH1004|CDS

ATGGCCGTGGAGAACGCAACAATGGAGATTTCGAATAGCAATGAAGGCGACGAGGGCAATGATTTGGTCGCAGGAATGATGGAAATTATTGAAACAGTGGGATCGTACATGGGGTTTCGAAGAACACAGAGAAAAGAGTGTTTAAAGCTCGTAAGAAGATTGAAGCTTCTAGTCCCACTTTTTGAAGAAATCAAAGAGATGAATCTATCAATACCCACAAGGGCATTTCAGTCTTTCGTTAATCTACAGAAGGCACTTCT...

Protein

Download Protein FASTA

639 aa · LXL04_019584|LXL04_019584|OH1004|PROTEIN

MAVENATMEISNSNEGDEGNDLVAGMMEIIETVGSYMGFRRTQRKECLKLVRRLKLLVPLFEEIKEMNLSIPTRAFQSFVNLQKALLSAKKLLKHCNFGSKIFLAMESDAMMSRFLSVYDKLNDALDGLMYQELGISEEVQEQIELLRKQLQGANRRTDTLDIELAMDMMVIFSKNDERNADIAILERLAKRLDLYSIGDLEIETEAVKRLVKERGGTKHVESTEQIKDLLRKFKQIAGFEENNGDNKAFDDSSSLRCFD...

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_019584`
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_019584

Location Chr04:34551543-34554355 (-)

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_019584 · 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.

Cytoplasm0.556

Rank 1 · LXL04_019584 · OH-1004

Nucleus0.377

Rank 2 · LXL04_019584 · OH-1004

Cell membrane0.178

Rank 3 · LXL04_019584 · OH-1004

Endoplasmic reticulum0.058

Rank 4 · LXL04_019584 · OH-1004

Golgi apparatus0.048

Rank 5 · LXL04_019584 · 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_N44-154 aa

PF04564.22U-box267-336 aa

PF24768.2ARM_ARMC5358-494 aa

PF25598.2ARM_PUB358-629 aa

PF00514.30Arm388-427 aa

PF24768.2ARM_ARMC5423-581 aa

PF24768.2ARM_ARMC5468-634 aa

PF00514.30Arm471-509 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_019584	`PF25368.2`	PUB10_N	44	154	3.2e-34	119.0
LXL04_019584	`PF04564.22`	U-box	267	336	1.6e-21	76.9
LXL04_019584	`PF24768.2`	ARM_ARMC5	358	494	6.7e-23	82.2
LXL04_019584	`PF25598.2`	ARM_PUB	358	629	4.6e-19	69.7
LXL04_019584	`PF00514.30`	Arm	388	427	2e-33	114.1
LXL04_019584	`PF24768.2`	ARM_ARMC5	423	581	6.7e-23	82.2
LXL04_019584	`PF24768.2`	ARM_ARMC5	468	634	6.7e-23	82.2
LXL04_019584	`PF00514.30`	Arm	471	509	2e-33	114.1

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	58.013%	Swiss-Prot	strong database homology
`Q9SNC6`	Arabidopsis thaliana	U-box domain-containing protein 13	43.156%	Swiss-Prot	moderate database homology
`Q9ZV31`	Arabidopsis thaliana	U-box domain-containing protein 12	41.232%	Swiss-Prot	moderate database homology
`Q8VZ40`	Arabidopsis thaliana	U-box domain-containing protein 14	40.128%	Swiss-Prot	moderate database homology
`Q5VRH9`	Oryza sativa subsp. japonica	U-box domain-containing protein 12	43.456%	Swiss-Prot	moderate database homology

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