LXL04_011171 | RubberDandelionOmics

Gene overview

LXL04_011171

Reference: OH-1004 Chr: Chr02 Coordinates: 159325501-159325935 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

435 bp · LXL04_011171|LXL04_011171|OH1004|cDNA

ATGTTCCCTGAATCAAGAATGTCATCTTATCTTGTATCGATAGCTACTTACTTGATTTGGGCATTGGATTTCATGACTCATCTTGCTTTCTTTCAGCAAAGGGTACAACTTGAGGTTGCCGGAAAGAATCATGATCAGCTCGGCGTCACACATTTTCATCAGAAGATGAGCTCCGATGAGTCTGTGGAATGTGCTGTGTGCTTGTCCAAGATAGACGAAGATGACGAGATAAGATTGTTGAGATGCGATCATCTTTTTCA...

CDS

Download CDS FASTA

435 bp · LXL04_011171|LXL04_011171|OH1004|CDS

ATGTTCCCTGAATCAAGAATGTCATCTTATCTTGTATCGATAGCTACTTACTTGATTTGGGCATTGGATTTCATGACTCATCTTGCTTTCTTTCAGCAAAGGGTACAACTTGAGGTTGCCGGAAAGAATCATGATCAGCTCGGCGTCACACATTTTCATCAGAAGATGAGCTCCGATGAGTCTGTGGAATGTGCTGTGTGCTTGTCCAAGATAGACGAAGATGACGAGATAAGATTGTTGAGATGCGATCATCTTTTTCA...

Protein

Download Protein FASTA

144 aa · LXL04_011171|LXL04_011171|OH1004|PROTEIN

MFPESRMSSYLVSIATYLIWALDFMTHLAFFQQRVQLEVAGKNHDQLGVTHFHQKMSSDESVECAVCLSKIDEDDEIRLLRCDHLFHKGCLDRCVEYKHTTCPLCRDILAGPRMVCELGRELLFFTFCSNDKSSDDDFDRWWIR

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_011171`
TK1151 ID	TkA03G570170
OH-1004 ID	LXL04_011171
Relationship / confidence	Non Reciprocal Best Hit / Complex relationship
Protein identity (%)	96.200
Protein coverage (%)	TK1151 84.874 / OH-1004 72.917 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

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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_011171

Location Chr02:159325501-159325935 (+)

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

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g04240`	Function on abscisic acid homeostasis at post-translational level, probably through ubiquitin/proteasome-dependent substrate- specific degradation.	Upregulation of an Arabidopsis RING-H2 gene, XERICO, confers drought tolerance through increased abscisic acid biosynthesis.2006 · DOI: 10.1111/j.1365-313x.2006.02782.x Global analysis of della direct targets in early gibberellin signaling in Arabidopsis.2007 · DOI: 10.1105/tpc.107.054999
`At3g05200`	E3 ubiquitin-protein ligase able to catalyze polyubiquitination with ubiquitin-conjugating enzyme E2 UBC8 in vitro.	No verified direct reference in this release
`At3g61460`	May be involved in the brassinosteroids (BRs) signaling pathway and regulate the growth and development of rosette leaves.	Characterisation of BRH1, a brassinosteroid-responsive RING-H2 gene from Arabidopsis thaliana.2002 · DOI: 10.1007/s00425-001-0723-z Overexpressed BRH1, a RING finger gene, alters rosette leaf shape in Arabidopsis thaliana.2018 · DOI: 10.1007/s11427-017-9133-8
`At4g28890`	E3 ubiquitin-protein ligase able to catalyze polyubiquitination with ubiquitin-conjugating enzyme E2 UBC8 in vitro.	No verified direct reference in this release
`At2g01150`	E3 ubiquitin-protein ligase involved in the positive regulation of abscisic acid (ABA) signaling and responses to salt and osmotic stresses during seed germination and early seedling development.	The Arabidopsis RING finger E3 ligase RHA2b acts additively with RHA2a in regulating abscisic acid signaling and drought response.2011 · DOI: 10.1104/pp.111.176214

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_011171 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006970 response to osmotic stress Biological Process

GO:0009651 response to salt stress Biological Process

GO:0009687 abscisic acid metabolic process Biological Process

GO:0009688 abscisic acid biosynthetic process Biological Process

GO:0009738 abscisic acid-activated signaling pathway Biological Process

GO:0009739 response to gibberellin Biological Process

GO:0009741 response to brassinosteroid Biological Process

GO:0009742 brassinosteroid mediated signaling pathway Biological Process

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

GO:0010200 response to chitin Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0042742 defense response to bacterium Biological Process

KEGG gene cross-reference

ath:AT2G01150

ath:AT2G04240

ath:AT3G05200

ath:AT3G61460

ath:AT4G28890

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.

Cytoplasm0.314

Rank 1 · LXL04_011171 · OH-1004

Nucleus0.311

Rank 2 · LXL04_011171 · OH-1004

Endoplasmic reticulum0.238

Rank 3 · LXL04_011171 · OH-1004

Cell membrane0.158

Rank 4 · LXL04_011171 · OH-1004

Golgi apparatus0.130

Rank 5 · LXL04_011171 · 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.

PF13639.13zf-RING_263-106 aa

PF17123.12zf-RING_1163-91 aa

PF14634.13zf-RING_563-106 aa

PF00097.32zf-C3HC464-105 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_011171	`PF13639.13`	zf-RING_2	63	106	1.1e-11	45.6
LXL04_011171	`PF17123.12`	zf-RING_11	63	91	3.4e-10	40.2
LXL04_011171	`PF14634.13`	zf-RING_5	63	106	3.1e-07	31.0
LXL04_011171	`PF00097.32`	zf-C3HC4	64	105	4.1e-07	30.5

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
`Q9SI09`	Arabidopsis thaliana	Probable E3 ubiquitin-protein ligase XERICO	56.250%	Swiss-Prot	weak database homology
`Q8RXX9`	Arabidopsis thaliana	E3 ubiquitin-protein ligase ATL6	31.343%	Swiss-Prot	moderate database homology
`Q9XF92`	Arabidopsis thaliana	Brassinosteroid-responsive RING protein 1	40.506%	Swiss-Prot	moderate database homology
`Q5XF85`	Arabidopsis thaliana	E3 ubiquitin-protein ligase ATL42	43.750%	Swiss-Prot	weak database homology
`Q9ZU51`	Arabidopsis thaliana	E3 ubiquitin-protein ligase RHA2B	40.909%	Swiss-Prot	weak database homology

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