LXL04_006739 | RubberDandelionOmics

Gene overview

LXL04_006739

Reference: OH-1004 Chr: Chr02 Coordinates: 23794122-23799236 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2616 bp · LXL04_006739|LXL04_006739|OH1004|cDNA

ATGGTCTCTACATTCATCTGTCTCATGTCGATCATTTGGTTTCGTATTTTGATGCTGACTGAGTTGGTTGTCCTTAGACACGCCAAACCACATCTGTGCGTAAGTCGAGTACATGGGGTAGCTAATGTTGTTGCTGAGGCTGCTTGGCTTCGTAACCACTTACTCGGGTTGTCATGTCCTTTCACTTGTATCACAGTGTTTTGTGACAACATTAGTGCCATATACTTGACTTCTAACCCAGTGCAACACCAAATAACCAA...

CDS

Download CDS FASTA

2616 bp · LXL04_006739|LXL04_006739|OH1004|CDS

ATGGTCTCTACATTCATCTGTCTCATGTCGATCATTTGGTTTCGTATTTTGATGCTGACTGAGTTGGTTGTCCTTAGACACGCCAAACCACATCTGTGCGTAAGTCGAGTACATGGGGTAGCTAATGTTGTTGCTGAGGCTGCTTGGCTTCGTAACCACTTACTCGGGTTGTCATGTCCTTTCACTTGTATCACAGTGTTTTGTGACAACATTAGTGCCATATACTTGACTTCTAACCCAGTGCAACACCAAATAACCAA...

Protein

Download Protein FASTA

871 aa · LXL04_006739|LXL04_006739|OH1004|PROTEIN

MVSTFICLMSIIWFRILMLTELVVLRHAKPHLCVSRVHGVANVVAEAAWLRNHLLGLSCPFTCITVFCDNISAIYLTSNPVQHQITKHMIELHFVREHIASDHKVRYKEGPSSHFNQLGPLSKRSNKNSQLIRSKIMIGQLFAGVMEISLLKVLLKNISSFFHRENTNQEIVSKYYQKIEEILKLIKPVLESITDSQISSNESLQKEFTSMSQSIDELKDLLEDSHPLMSKVYFVMQVESLFAKVKSQTLQLFELLQSFP...

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_006739`
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_006739

Location Chr02:23794122-23799236 (-)

Description Similar to PUB2: U-box domain-containing protein 2

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g67340`	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
`At3g54790`	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

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_006739 · 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:0034614 cellular response to reactive oxygen species Biological Process

GO:0042742 defense response to bacterium Biological Process

GO:0048364 root development Biological Process

GO:0048658 anther wall tapetum development Biological Process

GO:0050777 negative regulation of immune response Biological Process

GO:1904821 chloroplast disassembly 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

KEGG gene cross-reference

ath:AT2G23140

ath:AT3G46510

ath:AT3G54790

ath:AT5G67340

These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.

Open Annotation Module

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.

Cytoplasm0.485

Rank 1 · LXL04_006739 · OH-1004

Nucleus0.328

Rank 2 · LXL04_006739 · OH-1004

Cell membrane0.198

Rank 3 · LXL04_006739 · OH-1004

Endoplasmic reticulum0.087

Rank 4 · LXL04_006739 · OH-1004

Golgi apparatus0.071

Rank 5 · LXL04_006739 · 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.

PF25240.2PUB2_N147-279 aa

PF04564.22U-box375-445 aa

PF25598.2ARM_PUB588-862 aa

PF24768.2ARM_ARMC5588-760 aa

PF00514.30Arm619-656 aa

PF00514.30Arm658-697 aa

PF00514.30Arm701-738 aa

PF24768.2ARM_ARMC5732-860 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_006739	`PF25240.2`	PUB2_N	147	279	5e-43	147.2
LXL04_006739	`PF04564.22`	U-box	375	445	7e-22	78.1
LXL04_006739	`PF25598.2`	ARM_PUB	588	862	2.4e-25	90.3
LXL04_006739	`PF24768.2`	ARM_ARMC5	588	760	3.1e-16	60.3
LXL04_006739	`PF00514.30`	Arm	619	656	7.7e-40	134.4
LXL04_006739	`PF00514.30`	Arm	658	697	7.7e-40	134.4
LXL04_006739	`PF00514.30`	Arm	701	738	7.7e-40	134.4
LXL04_006739	`PF24768.2`	ARM_ARMC5	732	860	3.1e-16	60.3

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
`Q5XEZ8`	Arabidopsis thaliana	U-box domain-containing protein 2	48.575%	Swiss-Prot	moderate database homology
`O22193`	Arabidopsis thaliana	U-box domain-containing protein 4	74.142%	Swiss-Prot	weak database homology
`Q8GWV5`	Arabidopsis thaliana	U-box domain-containing protein 3	60.825%	Swiss-Prot	weak database homology
`Q9SNC6`	Arabidopsis thaliana	U-box domain-containing protein 13	49.498%	Swiss-Prot	weak database homology
`Q5VRH9`	Oryza sativa subsp. japonica	U-box domain-containing protein 12	50.530%	Swiss-Prot	weak database homology

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