LXL04_002592 | RubberDandelionOmics

Gene overview

LXL04_002592

Reference: OH-1004 Chr: Chr01 Coordinates: 52555124-52556661 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1308 bp · LXL04_002592|LXL04_002592|OH1004|cDNA

ATGGCCGTAACCCCTGAAGAACAGAACATAGACCATGCAACAGACAGTTTCCCTTTGCTCGTCAATGGTAGAAGAAGCCTTGAAAATGAGCACATAATCGATTTAGAAAGAGGAGGCGATCATGATCATGATGATGATGCTTCATCATCAAATGCATCAAGCAACACTCCTTCTCATTTACTATCAAACAGCCCAAGAACTTCAACTTCCCAACTAATTCGATCATCATCAACTGCATCAAATGGACCTGGGAGAAGAAC...

CDS

Download CDS FASTA

1308 bp · LXL04_002592|LXL04_002592|OH1004|CDS

ATGGCCGTAACCCCTGAAGAACAGAACATAGACCATGCAACAGACAGTTTCCCTTTGCTCGTCAATGGTAGAAGAAGCCTTGAAAATGAGCACATAATCGATTTAGAAAGAGGAGGCGATCATGATCATGATGATGATGCTTCATCATCAAATGCATCAAGCAACACTCCTTCTCATTTACTATCAAACAGCCCAAGAACTTCAACTTCCCAACTAATTCGATCATCATCAACTGCATCAAATGGACCTGGGAGAAGAAC...

Protein

Download Protein FASTA

435 aa · LXL04_002592|LXL04_002592|OH1004|PROTEIN

MAVTPEEQNIDHATDSFPLLVNGRRSLENEHIIDLERGGDHDHDDDASSSNASSNTPSHLLSNSPRTSTSQLIRSSSTASNGPGRRTDGFGRRRWSPFDTLLWISIELVFTLGQIIASIVVLYISRKENPQTPLFAWIVGYAAGCVASLPFLYWRYLHRNQSTEQVASQTRQPPSESNHTPEPNSYITISFARSSEEETRPATPSDTWNGLNVGSNARLTMLVDHFKMALDCFFAVWFVVGNVWIFGGHSSSVDAPNLYR...

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_002592`
TK1151 ID	TkA01G437680
OH-1004 ID	LXL04_002592
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	97.000
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

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_002592

Location Chr01:52555124-52556661 (-)

Description Similar to At4g11680: E3 ubiquitin-protein ligase At4g11680

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g11680`	Mediates E2-dependent protein ubiquitination in vitro.	No verified direct reference in this release
`At1g12760`	Mediates E2-dependent protein ubiquitination in vitro.	No verified direct reference in this release
`At1g63170`	Mediates E2-dependent protein ubiquitination.	No verified direct reference in this release
`At2g01735`	Probable E3 ubiquitin-protein ligase required for embryo development.	A RING-H2 zinc-finger protein gene RIE1 is essential for seed development in Arabidopsis.2003 · DOI: 10.1023/b:plan.0000009256.01620.a6
`At3g55530`	E3 ubiquitin-protein ligase that acts as a positive regulator of abscisic acid-related stress signal transduction.	SDIR1 is a RING finger E3 ligase that positively regulates stress-responsive abscisic acid signaling in Arabidopsis.2007 · DOI: 10.1105/tpc.106.048488 Arabidopsis SDIR1 enhances drought tolerance in crop plants.2008 · DOI: 10.1271/bbb.80286 The RING finger ubiquitin E3 ligase SDIR1 targets SDIR1-INTERACTING PROTEIN1 for degradation to modulate the salt stress response and ABA signaling in Arabidopsis.2015 · DOI: 10.1105/tpc.114.134163

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_002592 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006511 ubiquitin-dependent protein catabolic process Biological Process

GO:0009414 response to water deprivation Biological Process

GO:0009651 response to salt stress Biological Process

GO:0009737 response to abscisic acid Biological Process

GO:0009789 positive regulation of abscisic acid-activated signaling pathway Biological Process

GO:0009793 embryo development ending in seed dormancy Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0000325 plant-type vacuole Cellular Component

GO:0005634 nucleus Cellular Component

GO:0005789 endoplasmic reticulum membrane Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0016020 membrane Cellular Component

KEGG gene cross-reference

ath:AT1G12760

ath:AT1G63170

ath:AT2G01735

ath:AT3G55530

ath:AT4G11680

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.

Lysosome / Vacuole0.423

Rank 1 · LXL04_002592 · OH-1004

Cell membrane0.238

Rank 2 · LXL04_002592 · OH-1004

Cytoplasm0.195

Rank 3 · LXL04_002592 · OH-1004

Endoplasmic reticulum0.190

Rank 4 · LXL04_002592 · OH-1004

Golgi apparatus0.141

Rank 5 · LXL04_002592 · 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.

PF13639.13zf-RING_2373-414 aa

PF17123.12zf-RING_11373-400 aa

PF12678.14zf-rbx1373-414 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_002592	`PF13639.13`	zf-RING_2	373	414	2.9e-12	47.4
LXL04_002592	`PF17123.12`	zf-RING_11	373	400	3.3e-08	33.8
LXL04_002592	`PF12678.14`	zf-rbx1	373	414	6.6e-07	30.2

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
`Q93Z92`	Arabidopsis thaliana	E3 ubiquitin-protein ligase At4g11680	31.595%	Swiss-Prot	moderate database homology
`Q9LN71`	Arabidopsis thaliana	E3 ubiquitin-protein ligase At1g12760	32.317%	Swiss-Prot	moderate database homology
`Q8LDB8`	Arabidopsis thaliana	E3 ubiquitin-protein ligase At1g63170	31.410%	Swiss-Prot	moderate database homology
`Q8GUU2`	Arabidopsis thaliana	E3 ubiquitin protein ligase RIE1	27.829%	Swiss-Prot	weak database homology
`Q9M2S6`	Arabidopsis thaliana	E3 ubiquitin-protein ligase SDIR1	31.193%	Swiss-Prot	weak database homology

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