LXL04_024446 | RubberDandelionOmics

Gene overview

LXL04_024446

Reference: OH-1004 Chr: Chr05 Coordinates: 90900139-90902815 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2403 bp · LXL04_024446|LXL04_024446|OH1004|cDNA

ATGTCGGAAATGAGAAATGAATTTACCTTGATGAAATTAAGaaagagaagagaagagaagggaagATCAGATCTCAGACCAGACCAGACGACTTTTTCTGTTACACGTACAGGAAGAACAACAGGATTCTTCTTCGATTCGATCTCATTCAAAGCTAGTTATTATATCTACTCTCTTCGTATACTTACACATATTATCAAAATTCAAAGCAAGAGAGAGGAATTTATCTGGAAAGGAGAGAAGAAAATGGTGTTAGGATG...

CDS

Download CDS FASTA

2403 bp · LXL04_024446|LXL04_024446|OH1004|CDS

ATGTCGGAAATGAGAAATGAATTTACCTTGATGAAATTAAGAAAGAGAAGAGAAGAGAAGGGAAGATCAGATCTCAGACCAGACCAGACGACTTTTTCTGTTACACGTACAGGAAGAACAACAGGATTCTTCTTCGATTCGATCTCATTCAAAGCTAGTTATTATATCTACTCTCTTCGTATACTTACACATATTATCAAAATTCAAAGCAAGAGAGAGGAATTTATCTGGAAAGGAGAGAAGAAAATGGTGTTAGGATG...

Protein

Download Protein FASTA

800 aa · LXL04_024446|LXL04_024446|OH1004|PROTEIN

MSEMRNEFTLMKLRKRREEKGRSDLRPDQTTFSVTRTGRTTGFFFDSISFKASYYIYSLRILTHIIKIQSKREEFIWKGEKKMVLGWRRAFCTSVPREGDSTSMASMDEIECEHVVDDVNSCSSTPKFGRRFGFFSSYSNPSTPPLRSQSVSSPSLRCRTTAAVPAPSSSVPVSPKLRCETKNSPRCFIRSSNPSSPRSSSPLSFLRSSLRLCTRRCGLCLQSLKRGQGMATFTAECSHCFHFPCIADHVKKQGSLACPV...

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_024446`
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_024446

Location Chr05:90900139-90902815 (-)

Description Similar to WAV3: E3 ubiquitin-protein ligase WAV3

Arabidopsis / Rice Reference Genes and Papers

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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_024446 · 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:0030212 hyaluronan metabolic process Biological Process

GO:0034097 response to cytokine Biological Process

GO:0048364 root development Biological Process

GO:0005576 extracellular region Cellular Component

GO:0005634 nucleus Cellular Component

GO:0005886 plasma membrane Cellular Component

GO:0009506 plasmodesma Cellular Component

GO:0031012 extracellular matrix Cellular Component

KEGG gene cross-reference

ath:AT2G22680

ath:AT4G37890

ath:AT5G49665

ath:AT5G65683

hsa:3700

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.

Nucleus0.392

Rank 1 · LXL04_024446 · OH-1004

Cytoplasm0.322

Rank 2 · LXL04_024446 · OH-1004

Cell membrane0.280

Rank 3 · LXL04_024446 · OH-1004

Plastid0.093

Rank 4 · LXL04_024446 · OH-1004

Endoplasmic reticulum0.069

Rank 5 · LXL04_024446 · 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_2216-261 aa

PF17123.12zf-RING_11217-246 aa

PF00092.35VWA416-522 aa

PF13768.13VWA_3416-549 aa

PF13519.13VWA_2417-521 aa

PF25243.2WAV3_C669-740 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_024446	`PF13639.13`	zf-RING_2	216	261	1.4e-07	32.4
LXL04_024446	`PF17123.12`	zf-RING_11	217	246	8.4e-07	29.3
LXL04_024446	`PF00092.35`	VWA	416	522	1.3e-12	49.0
LXL04_024446	`PF13768.13`	VWA_3	416	549	1.8e-11	45.0
LXL04_024446	`PF13519.13`	VWA_2	417	521	2.3e-15	57.8
LXL04_024446	`PF25243.2`	WAV3_C	669	740	2.3e-29	101.7

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	43.984%	Swiss-Prot	moderate database homology
`Q9ZQ46`	Arabidopsis thaliana	E3 ubiquitin-protein ligase WAVH1	43.140%	Swiss-Prot	moderate database homology
`F4JSV3`	Arabidopsis thaliana	Probable E3 ubiquitin-protein ligase EDA40	41.250%	Swiss-Prot	moderate database homology
`Q0WQX9`	Arabidopsis thaliana	Probable E3 ubiquitin-protein ligase WAVH2	39.691%	Swiss-Prot	moderate database homology

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