LXL04_021313 | RubberDandelionOmics

Gene overview

LXL04_021313

Reference: OH-1004 Chr: Chr04 Coordinates: 127061945-127062448 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

504 bp · LXL04_021313|LXL04_021313|OH1004|cDNA

ATGGGTTTACAGAACCAACTCACCGACGTTTCCTCCGATTCCCTTCCGGTTTTCTTTCTCGCTGTAATCGCAAACGGCGTTTGCTATATCCGCTCACTCGTTTTCACCTTCCTCCACTCATTAGGCATCTCTGGCTGCCGATCCGATGAGGTCGACGACGCCATGCTGTTTGACGCCGTTGGCTCCGGTTTAGCCGGACTTATCCTACTCGCCGACCAGCTCAACTTGAACCGTGTGTTCTCTTATACATACAGCTCGTG...

CDS

Download CDS FASTA

504 bp · LXL04_021313|LXL04_021313|OH1004|CDS

ATGGGTTTACAGAACCAACTCACCGACGTTTCCTCCGATTCCCTTCCGGTTTTCTTTCTCGCTGTAATCGCAAACGGCGTTTGCTATATCCGCTCACTCGTTTTCACCTTCCTCCACTCATTAGGCATCTCTGGCTGCCGATCCGATGAGGTCGACGACGCCATGCTGTTTGACGCCGTTGGCTCCGGTTTAGCCGGACTTATCCTACTCGCCGACCAGCTCAACTTGAACCGTGTGTTCTCTTATACATACAGCTCGTG...

Protein

Download Protein FASTA

167 aa · LXL04_021313|LXL04_021313|OH1004|PROTEIN

MGLQNQLTDVSSDSLPVFFLAVIANGVCYIRSLVFTFLHSLGISGCRSDEVDDAMLFDAVGSGLAGLILLADQLNLNRVFSYTYSSCSDGPDPAGSECVVCLNRLSDGEQVRKLDCHHVFHKECFDGWLDHLNFNCPLCRSPLVSDQRVAVTRRRVTDDVVDWFSFR

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_021313`
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_021313

Location Chr04:127061945-127062448 (-)

Description Similar to RHA2A: E3 ubiquitin-protein ligase RHA2A

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`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
`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
`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

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_021313 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000209 protein polyubiquitination 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: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

KEGG gene cross-reference

ath:AT1G15100

ath:AT2G01150

ath:AT2G04240

ath:AT3G61460

mmu:225743

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.

Endoplasmic reticulum0.295

Rank 1 · LXL04_021313 · OH-1004

Nucleus0.246

Rank 2 · LXL04_021313 · OH-1004

Cytoplasm0.241

Rank 3 · LXL04_021313 · OH-1004

Golgi apparatus0.177

Rank 4 · LXL04_021313 · OH-1004

Cell membrane0.163

Rank 5 · LXL04_021313 · 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-rbx196-140 aa

PF13639.13zf-RING_297-140 aa

PF13923.13zf-C3HC4_297-139 aa

PF17123.12zf-RING_1197-124 aa

PF00097.32zf-C3HC498-139 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_021313	`PF12678.14`	zf-rbx1	96	140	5e-07	30.6
LXL04_021313	`PF13639.13`	zf-RING_2	97	140	2e-13	51.1
LXL04_021313	`PF13923.13`	zf-C3HC4_2	97	139	1.2e-09	38.5
LXL04_021313	`PF17123.12`	zf-RING_11	97	124	8.3e-09	35.7
LXL04_021313	`PF00097.32`	zf-C3HC4	98	139	1.2e-06	29.0

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
`Q9ZT50`	Arabidopsis thaliana	E3 ubiquitin-protein ligase RHA2A	49.398%	Swiss-Prot	moderate database homology
`Q9ZU51`	Arabidopsis thaliana	E3 ubiquitin-protein ligase RHA2B	52.083%	Swiss-Prot	strong database homology
`Q9SI09`	Arabidopsis thaliana	Probable E3 ubiquitin-protein ligase XERICO	41.176%	Swiss-Prot	weak database homology
`Q9XF92`	Arabidopsis thaliana	Brassinosteroid-responsive RING protein 1	29.870%	Swiss-Prot	weak database homology

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