LXL04_007517 | RubberDandelionOmics

Gene overview

LXL04_007517

Reference: OH-1004 Chr: Chr02 Coordinates: 51201371-51202572 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1140 bp · LXL04_007517|LXL04_007517|OH1004|cDNA

ATGTTAAATTGTTGCTTGATAAATGTGATAGTGTTGTTGATATACAAATCTTTGTTGGCATTCATATCTGCCATCTTGGTATCACTTGTTTGGGTTTTTATTACACATAAATTAAATAATGTGTTTGATACAAATTTTACAGGTGAGAAAGAAGGTCATAAGAAGATGACTAGCAGTTCAAAGTGTGTTAATATAATAGATGTGGATAAATATGAAGATGCAAAGTCTGATATTATAGATTTAGATAAAGATGAAGCTGT...

CDS

Download CDS FASTA

1140 bp · LXL04_007517|LXL04_007517|OH1004|CDS

ATGTTAAATTGTTGCTTGATAAATGTGATAGTGTTGTTGATATACAAATCTTTGTTGGCATTCATATCTGCCATCTTGGTATCACTTGTTTGGGTTTTTATTACACATAAATTAAATAATGTGTTTGATACAAATTTTACAGGTGAGAAAGAAGGTCATAAGAAGATGACTAGCAGTTCAAAGTGTGTTAATATAATAGATGTGGATAAATATGAAGATGCAAAGTCTGATATTATAGATTTAGATAAAGATGAAGCTGT...

Protein

Download Protein FASTA

379 aa · LXL04_007517|LXL04_007517|OH1004|PROTEIN

MLNCCLINVIVLLIYKSLLAFISAILVSLVWVFITHKLNNVFDTNFTGEKEGHKKMTSSSKCVNIIDVDKYEDAKSDIIDLDKDEAVDDFYMYDEDELLLISAEKYTQISERKASSTPHNSQKDNKLMVRSEGESFCGICMDTKSGSEMFSNPKVCGHLFCLDCIRQHVSVKIQENVAMVKCPDPTCKSLIGPEVCGSIVPKQVLERWEDALCESWILKKFYCPFKDCSAMLVDDSGKVVTSSECPNCNRLFCAQCKVAW...

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_007517`
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_007517

Location Chr02:51201371-51202572 (-)

Description Similar to ARI3: Probable E3 ubiquitin-protein ligase ARI3

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
`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
`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
`At2g31780`	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_007517 · 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:AT2G26130

ath:AT2G31760

ath:AT2G31770

ath:AT2G31780

ath:AT3G27710

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.

Nucleus0.587

Rank 1 · LXL04_007517 · OH-1004

Cytoplasm0.354

Rank 2 · LXL04_007517 · OH-1004

Cell membrane0.106

Rank 3 · LXL04_007517 · OH-1004

Endoplasmic reticulum0.070

Rank 4 · LXL04_007517 · OH-1004

Lysosome / Vacuole0.032

Rank 5 · LXL04_007517 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

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Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF13445.13zf-RING_UBOX137-183 aa

PF01485.28IBR207-266 aa

PF01485.28IBR283-327 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_007517	`PF13445.13`	zf-RING_UBOX	137	183	6.1e-06	26.8
LXL04_007517	`PF01485.28`	IBR	207	266	3.2e-17	63.1
LXL04_007517	`PF01485.28`	IBR	283	327	3.2e-17	63.1

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
`F4ITM1`	Arabidopsis thaliana	E3 ubiquitin-protein ligase RSL1	35.052%	Swiss-Prot	weak database homology
`Q9LVX0`	Arabidopsis thaliana	Probable E3 ubiquitin-protein ligase ARI3	29.493%	Swiss-Prot	weak database homology
`Q9SKC4`	Arabidopsis thaliana	Probable E3 ubiquitin-protein ligase ARI10	25.941%	Swiss-Prot	weak database homology
`Q9SKC3`	Arabidopsis thaliana	Probable E3 ubiquitin-protein ligase ARI9	26.778%	Swiss-Prot	weak database homology
`Q9SKC2`	Arabidopsis thaliana	Probable E3 ubiquitin-protein ligase ARI11	27.193%	Swiss-Prot	weak database homology

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