LXL04_037955 | RubberDandelionOmics

Gene overview

LXL04_037955

Reference: OH-1004 Chr: Chr09 Coordinates: 26825664-26826023 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

360 bp · LXL04_037955|LXL04_037955|OH1004|cDNA

ATGAAGGAAACGTTTTGTTCGATTCTTCACACGGTGGGATTCCGTGTCGCATCGCCTAATCAATCCTCACCGGAATCATTTGAGTGCCGGGGAAGTCCGCCGGAGACTTACATCGAGGAGTTCAGAAGCCGGACGCCGTCACTCCGTTACATCTCCCTCCGCCGCGCGATTAAACAGGAATGTTCGGTTTGCTTAACGGAGTTTAAACCAGATGTAGAGATTAATAACCTTTCGTGTGGACATGTTTTTCATAAATCGTG...

CDS

Download CDS FASTA

360 bp · LXL04_037955|LXL04_037955|OH1004|CDS

ATGAAGGAAACGTTTTGTTCGATTCTTCACACGGTGGGATTCCGTGTCGCATCGCCTAATCAATCCTCACCGGAATCATTTGAGTGCCGGGGAAGTCCGCCGGAGACTTACATCGAGGAGTTCAGAAGCCGGACGCCGTCACTCCGTTACATCTCCCTCCGCCGCGCGATTAAACAGGAATGTTCGGTTTGCTTAACGGAGTTTAAACCAGATGTAGAGATTAATAACCTTTCGTGTGGACATGTTTTTCATAAATCGTG...

Protein

Download Protein FASTA

119 aa · LXL04_037955|LXL04_037955|OH1004|PROTEIN

MKETFCSILHTVGFRVASPNQSSPESFECRGSPPETYIEEFRSRTPSLRYISLRRAIKQECSVCLTEFKPDVEINNLSCGHVFHKSCLEKWLKFWNITCPLCRNHMMISTEMEENTCPM

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_037955`
TK1151 ID	TkA02G016770
OH-1004 ID	LXL04_037955
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	70.400
Protein coverage (%)	TK1151 81.579 / 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

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

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Basic Information and Functional Annotation

Gene ID LXL04_037955

Location Chr09:26825664-26826023 (+)

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
`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
`At4g11360`	Possesses E3 ubiquitin-protein ligase activity when associated with the E2 enzyme UBC8 in vitro.	No verified direct reference in this release
`At1g63170`	Mediates E2-dependent protein ubiquitination.	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_037955 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006511 ubiquitin-dependent protein catabolic process Biological Process

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

GO:0016567 protein ubiquitination Biological Process

GO:0047484 regulation of response to osmotic stress Biological Process

GO:0071456 cellular response to hypoxia Biological Process

GO:0005634 nucleus Cellular Component

KEGG gene cross-reference

ath:AT1G15100

ath:AT1G63170

ath:AT2G01150

ath:AT2G04240

ath:AT4G11360

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.

Cytoplasm0.516

Rank 1 · LXL04_037955 · OH-1004

Nucleus0.384

Rank 2 · LXL04_037955 · OH-1004

Cell membrane0.124

Rank 3 · LXL04_037955 · OH-1004

Mitochondrion0.084

Rank 4 · LXL04_037955 · OH-1004

Golgi apparatus0.075

Rank 5 · LXL04_037955 · 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.

PF12678.14zf-rbx154-103 aa

PF13639.13zf-RING_259-103 aa

PF17123.12zf-RING_1160-88 aa

PF13923.13zf-C3HC4_260-102 aa

PF14634.13zf-RING_560-103 aa

PF00097.32zf-C3HC461-102 aa

PF13445.13zf-RING_UBOX61-100 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_037955	`PF12678.14`	zf-rbx1	54	103	6.7e-10	39.8
LXL04_037955	`PF13639.13`	zf-RING_2	59	103	2.6e-13	50.7
LXL04_037955	`PF17123.12`	zf-RING_11	60	88	5.2e-10	39.6
LXL04_037955	`PF13923.13`	zf-C3HC4_2	60	102	2e-08	34.6
LXL04_037955	`PF14634.13`	zf-RING_5	60	103	1e-07	32.5
LXL04_037955	`PF00097.32`	zf-C3HC4	61	102	9.5e-09	35.7
LXL04_037955	`PF13445.13`	zf-RING_UBOX	61	100	1.6e-08	35.1

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q9SI09`	Arabidopsis thaliana	Probable E3 ubiquitin-protein ligase XERICO	59.091%	Swiss-Prot	strong database homology
`Q9ZT50`	Arabidopsis thaliana	E3 ubiquitin-protein ligase RHA2A	52.083%	Swiss-Prot	weak database homology
`Q9ZU51`	Arabidopsis thaliana	E3 ubiquitin-protein ligase RHA2B	50.000%	Swiss-Prot	weak database homology
`Q9SUS5`	Arabidopsis thaliana	E3 ubiquitin-protein ligase RHA1B	43.750%	Swiss-Prot	moderate database homology
`Q8LDB8`	Arabidopsis thaliana	E3 ubiquitin-protein ligase At1g63170	42.857%	Swiss-Prot	weak database homology

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