LXL04_030237 | RubberDandelionOmics

Gene overview

LXL04_030237

Reference: OH-1004 Chr: Chr06 Coordinates: 112108560-112110923 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2283 bp · LXL04_030237|LXL04_030237|OH1004|cDNA

ATGGGTACTGGTTGGCGAAGAGCTTTTTGCACAACAATTCCTAGAAATTCATCTGATTCGCCGGTGCTCGGAGGTGTCCAACAGAATCCGGCTCCAAGTCCCAGAGCCTCTGGAAAACTTGGATTCTTCAAGAGCTCTGGTTCGAATCCATCAACACCTCGATTGCAGTCGAATTGGGGGTTGCGTTCCAGAAGCGGTAACAGCAACAATGGCGTTGATGCCACTGCTAATTCCAATGCATCAACTCCTCGATTGCGTTT...

CDS

Download CDS FASTA

2283 bp · LXL04_030237|LXL04_030237|OH1004|CDS

ATGGGTACTGGTTGGCGAAGAGCTTTTTGCACAACAATTCCTAGAAATTCATCTGATTCGCCGGTGCTCGGAGGTGTCCAACAGAATCCGGCTCCAAGTCCCAGAGCCTCTGGAAAACTTGGATTCTTCAAGAGCTCTGGTTCGAATCCATCAACACCTCGATTGCAGTCGAATTGGGGGTTGCGTTCCAGAAGCGGTAACAGCAACAATGGCGTTGATGCCACTGCTAATTCCAATGCATCAACTCCTCGATTGCGTTT...

Protein

Download Protein FASTA

760 aa · LXL04_030237|LXL04_030237|OH1004|PROTEIN

MGTGWRRAFCTTIPRNSSDSPVLGGVQQNPAPSPRASGKLGFFKSSGSNPSTPRLQSNWGLRSRSGNSNNGVDATANSNASTPRLRLRPKSNNNVDCGDEGGAKFHSSVIDNLNITPRLRCKTNTKNPKSSLLGSNPSSPRSPFSIFKNSLGFSRSNCGLCLQSVKTGHKTAIFTAECSHTFHFPCISNHVKKENILACPICKSTWRDGSFLAIHKLQSNEIQKLNDDKNENSITTPRAKPDFTRSHENFVKAKPYDDDE...

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_030237`
TK1151 ID	TkA07G388230
OH-1004 ID	LXL04_030237
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.200
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_030237

Location Chr06:112108560-112110923 (+)

Description Similar to WAV3: E3 ubiquitin-protein ligase WAV3

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g49665`	E3 ubiquitin-protein ligase involved in the regulation of root growth.	The wavy growth 3 E3 ligase family controls the gravitropic response in Arabidopsis roots.2012 · DOI: 10.1111/j.1365-313x.2011.04870.x
`At2g22680`	E3 ubiquitin-protein ligase involved in the regulation of root growth.	The wavy growth 3 E3 ligase family controls the gravitropic response in Arabidopsis roots.2012 · DOI: 10.1111/j.1365-313x.2011.04870.x
`At4g37890`	Probable E3 ubiquitin-protein ligase involved in female gametophyte development.	No verified direct reference in this release
`At5g65683`	Probable E3 ubiquitin-protein ligase involved in the regulation of root growth.	The wavy growth 3 E3 ligase family controls the gravitropic response in Arabidopsis roots.2012 · DOI: 10.1111/j.1365-313x.2011.04870.x

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_030237 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009630 gravitropism Biological Process

GO:0010197 polar nucleus fusion Biological Process

GO:0010274 hydrotropism Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0048364 root development Biological Process

GO:0005576 extracellular region Cellular Component

GO:0005634 nucleus Cellular Component

GO:0009506 plasmodesma Cellular Component

GO:0008270 zinc ion binding Molecular Function

GO:0061630 ubiquitin protein ligase activity Molecular Function

KEGG gene cross-reference

ath:AT2G22680

ath:AT4G37890

ath:AT5G49665

ath:AT5G65683

syn:sll0103

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.

Nucleus0.416

Rank 1 · LXL04_030237 · OH-1004

Cytoplasm0.381

Rank 2 · LXL04_030237 · OH-1004

Cell membrane0.286

Rank 3 · LXL04_030237 · OH-1004

Endoplasmic reticulum0.063

Rank 4 · LXL04_030237 · OH-1004

Plastid0.044

Rank 5 · LXL04_030237 · 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_2157-203 aa

PF17123.12zf-RING_11157-187 aa

PF00092.35VWA365-475 aa

PF13768.13VWA_3365-490 aa

PF13519.13VWA_2366-472 aa

PF25243.2WAV3_C639-710 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_030237	`PF13639.13`	zf-RING_2	157	203	7.2e-08	33.3
LXL04_030237	`PF17123.12`	zf-RING_11	157	187	4.9e-07	30.1
LXL04_030237	`PF00092.35`	VWA	365	475	2.6e-13	51.3
LXL04_030237	`PF13768.13`	VWA_3	365	490	1.4e-12	48.7
LXL04_030237	`PF13519.13`	VWA_2	366	472	5.9e-19	69.4
LXL04_030237	`PF25243.2`	WAV3_C	639	710	3.1e-31	107.7

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
`Q9LTA6`	Arabidopsis thaliana	E3 ubiquitin-protein ligase WAV3	49.938%	Swiss-Prot	moderate database homology
`Q9ZQ46`	Arabidopsis thaliana	E3 ubiquitin-protein ligase WAVH1	40.503%	Swiss-Prot	moderate database homology
`F4JSV3`	Arabidopsis thaliana	Probable E3 ubiquitin-protein ligase EDA40	44.084%	Swiss-Prot	moderate database homology
`Q0WQX9`	Arabidopsis thaliana	Probable E3 ubiquitin-protein ligase WAVH2	38.568%	Swiss-Prot	moderate database homology

JBrowse

View in Genome Browser

Gene Card