LXL04_021424 | RubberDandelionOmics

Gene overview

LXL04_021424

Reference: OH-1004 Chr: Chr04 Coordinates: 129613011-129613469 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

459 bp · LXL04_021424|LXL04_021424|OH1004|cDNA

ATGATGATCGCACAAAGCTTCTCACCTTCTTCATCAATAGACCTTCTCTATATATCCATTTGCATCCTTACCGATGTGATCCAATCCAACATAAAACTCCTAACTTCAAACCTAAAGTGGGCAAAGTGGGCATGGAGTTTTCTTCTACACCAATGCTTTTTCCACCACCAATTACTAAATCTTCAAGGACTCATATCTAGCCAAGCAAGATTTGAAGAGCCGTCTATGGAACAAGTGGAATGCGTTGTTTGCCTGAGTAT...

CDS

Download CDS FASTA

459 bp · LXL04_021424|LXL04_021424|OH1004|CDS

ATGATGATCGCACAAAGCTTCTCACCTTCTTCATCAATAGACCTTCTCTATATATCCATTTGCATCCTTACCGATGTGATCCAATCCAACATAAAACTCCTAACTTCAAACCTAAAGTGGGCAAAGTGGGCATGGAGTTTTCTTCTACACCAATGCTTTTTCCACCACCAATTACTAAATCTTCAAGGACTCATATCTAGCCAAGCAAGATTTGAAGAGCCGTCTATGGAACAAGTGGAATGCGTTGTTTGCCTGAGTAT...

Protein

Download Protein FASTA

152 aa · LXL04_021424|LXL04_021424|OH1004|PROTEIN

MMIAQSFSPSSSIDLLYISICILTDVIQSNIKLLTSNLKWAKWAWSFLLHQCFFHHQLLNLQGLISSQARFEEPSMEQVECVVCLSMIGEDEEIRELRCGHLFHEACLDRWIRFRNRTCPLCRDSLVLPGHEVLVFDFCSNNTRHQGSWWLR

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_021424`
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_021424

Location Chr04:129613011-129613469 (-)

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

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

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
`At1g15100`	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 RHA2a is a novel positive regulator of abscisic acid signaling during seed germination and early seedling development.2009 · DOI: 10.1104/pp.109.135269 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
`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_021424 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000209 protein polyubiquitination Biological Process

GO:0006281 DNA repair Biological Process

GO:0006511 ubiquitin-dependent protein catabolic process Biological Process

GO:0006970 response to osmotic stress Biological Process

GO:0007389 pattern specification process 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:0009789 positive regulation of abscisic acid-activated signaling pathway Biological Process

GO:0016567 protein ubiquitination Biological Process

KEGG gene cross-reference

ath:AT1G15100

ath:AT2G01150

ath:AT2G04240

mmu:93836

xla:447448

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.

Nucleus0.366

Rank 1 · LXL04_021424 · OH-1004

Cytoplasm0.353

Rank 2 · LXL04_021424 · OH-1004

Endoplasmic reticulum0.189

Rank 3 · LXL04_021424 · OH-1004

Cell membrane0.118

Rank 4 · LXL04_021424 · OH-1004

Golgi apparatus0.103

Rank 5 · LXL04_021424 · 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.

PF13920.13zf-C3HC4_378-124 aa

PF13639.13zf-RING_280-123 aa

PF17123.12zf-RING_1180-108 aa

PF13923.13zf-C3HC4_280-122 aa

PF14634.13zf-RING_580-123 aa

PF00097.32zf-C3HC481-122 aa

PF12678.14zf-rbx192-123 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_021424	`PF13920.13`	zf-C3HC4_3	78	124	6.3e-06	26.6
LXL04_021424	`PF13639.13`	zf-RING_2	80	123	1.6e-14	54.6
LXL04_021424	`PF17123.12`	zf-RING_11	80	108	6.1e-09	36.1
LXL04_021424	`PF13923.13`	zf-C3HC4_2	80	122	1.3e-07	32.0
LXL04_021424	`PF14634.13`	zf-RING_5	80	123	1.5e-07	32.0
LXL04_021424	`PF00097.32`	zf-C3HC4	81	122	1.2e-08	35.3
LXL04_021424	`PF12678.14`	zf-rbx1	92	123	8.9e-09	36.2

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
`Q9SI09`	Arabidopsis thaliana	Probable E3 ubiquitin-protein ligase XERICO	59.184%	Swiss-Prot	weak database homology
`Q9ZT50`	Arabidopsis thaliana	E3 ubiquitin-protein ligase RHA2A	56.250%	Swiss-Prot	weak database homology
`Q9ZU51`	Arabidopsis thaliana	E3 ubiquitin-protein ligase RHA2B	43.243%	Swiss-Prot	weak database homology

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