LXL04_007527 | RubberDandelionOmics

Gene overview

LXL04_007527

Reference: OH-1004 Chr: Chr02 Coordinates: 51310588-51312440 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

996 bp · LXL04_007527|LXL04_007527|OH1004|cDNA

ATGTGTATGAAATCGATATTTGTTCAGTTCTCGAATGTGTGCTTTTCTGAAATTGGTGAGAAAGAAGGGCATAAGAAGAAAGAAGGGCATAAGAAGATGACTAGCAGTTCAAAGTGTGTTAATATAATAGATGTGGATAAATATGAAGATGCAAAGTATGATATTATAGATTTAGATAAAGATGAAGTTGTAGATGATTTCTACATGTATGACGAGGATGAGCTGTTACTGATTTCCGCTGAGAAGTATACCCACAACTC...

CDS

Download CDS FASTA

996 bp · LXL04_007527|LXL04_007527|OH1004|CDS

ATGTGTATGAAATCGATATTTGTTCAGTTCTCGAATGTGTGCTTTTCTGAAATTGGTGAGAAAGAAGGGCATAAGAAGAAAGAAGGGCATAAGAAGATGACTAGCAGTTCAAAGTGTGTTAATATAATAGATGTGGATAAATATGAAGATGCAAAGTATGATATTATAGATTTAGATAAAGATGAAGTTGTAGATGATTTCTACATGTATGACGAGGATGAGCTGTTACTGATTTCCGCTGAGAAGTATACCCACAACTC...

Protein

Download Protein FASTA

331 aa · LXL04_007527|LXL04_007527|OH1004|PROTEIN

MCMKSIFVQFSNVCFSEIGEKEGHKKKEGHKKMTSSSKCVNIIDVDKYEDAKYDIIDLDKDEVVDDFYMYDEDELLLISAEKYTHNSQKDNKLKRKQAMVRWSFCGICMDTKSGSEMFSNPKVCGHLFCLDCIRQHVSVKIQENVAMVKCPDPTCKSLIGPELCGSIVPKQVLERWEDALCESWIVKKFYCPFKDCSAMLVDDSGKVVTSSECPNCNRLEYKKRNPEDDIMLMELAKNQKWQRCPSCNYLVEKRGGCSII...

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_007527`
TK1151 ID	TkA03G186940
OH-1004 ID	LXL04_007527
Relationship / confidence	Sequence Supported Annotation Or Model Conflict / Review
Protein identity (%)	99.500
Protein coverage (%)	TK1151 98.421 / OH-1004 56.495 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

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_007527

Location Chr02:51310588-51312440 (-)

Description Similar to ARI10: Probable E3 ubiquitin-protein ligase ARI10

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g26130`	Acts as an E3 ubiquitin-protein ligase, or as part of E3 complex, which accepts ubiquitin from specific E2 ubiquitin-conjugating enzymes and then transfers it to substrates.	A forward genetic approach in Arabidopsis thaliana identifies a RING-type ubiquitin ligase as a novel determinant of seed longevity.2014 · DOI: 10.1016/j.plantsci.2013.11.004
`At2g31760`	Might act as an E3 ubiquitin-protein ligase, or as part of E3 complex, which accepts ubiquitin from specific E2 ubiquitin-conjugating enzymes and then transfers it to substrates.	No verified direct reference in this release
`At2g31770`	Might act as an E3 ubiquitin-protein ligase, or as part of E3 complex, which accepts ubiquitin from specific E2 ubiquitin-conjugating enzymes and then transfers it to substrates.	No verified direct reference in this release
`At3g27710`	Might act as an E3 ubiquitin-protein ligase, or as part of E3 complex, which accepts ubiquitin from specific E2 ubiquitin-conjugating enzymes and then transfers it to substrates.	No verified direct reference in this release
`At1g05890`	Might act as an E3 ubiquitin-protein ligase, or as part of E3 complex, which accepts ubiquitin from specific E2 ubiquitin-conjugating enzymes and then transfers it to substrates.	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_007527 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000209 protein polyubiquitination Biological Process

GO:0006511 ubiquitin-dependent protein catabolic process Biological Process

GO:0009738 abscisic acid-activated signaling pathway Biological Process

GO:0009740 gibberellic acid mediated signaling pathway Biological Process

GO:0009788 negative regulation of abscisic acid-activated signaling pathway Biological Process

GO:0010431 seed maturation Biological Process

GO:0010476 gibberellin mediated signaling pathway Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0140547 acquisition of seed longevity Biological Process

GO:0000151 ubiquitin ligase complex Cellular Component

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

KEGG gene cross-reference

ath:AT1G05890

ath:AT2G26130

ath:AT2G31760

ath:AT2G31770

ath:AT3G27710

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.

Nucleus0.928

Rank 1 · LXL04_007527 · OH-1004

Cytoplasm0.143

Rank 2 · LXL04_007527 · OH-1004

Cell membrane0.031

Rank 3 · LXL04_007527 · OH-1004

Endoplasmic reticulum0.020

Rank 4 · LXL04_007527 · OH-1004

Mitochondrion0.013

Rank 5 · LXL04_007527 · 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.

PF13445.13zf-RING_UBOX105-151 aa

PF01485.28IBR235-282 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_007527	`PF13445.13`	zf-RING_UBOX	105	151	5.1e-06	27.1
LXL04_007527	`PF01485.28`	IBR	235	282	1.2e-09	38.8

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
`F4ITM1`	Arabidopsis thaliana	E3 ubiquitin-protein ligase RSL1	31.959%	Swiss-Prot	moderate database homology
`Q9SKC4`	Arabidopsis thaliana	Probable E3 ubiquitin-protein ligase ARI10	24.561%	Swiss-Prot	weak database homology
`Q9SKC3`	Arabidopsis thaliana	Probable E3 ubiquitin-protein ligase ARI9	25.957%	Swiss-Prot	weak database homology
`Q9LVX0`	Arabidopsis thaliana	Probable E3 ubiquitin-protein ligase ARI3	27.885%	Swiss-Prot	weak database homology
`Q8L829`	Arabidopsis thaliana	Probable E3 ubiquitin-protein ligase ARI5	25.957%	Swiss-Prot	weak database homology

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