LXL04_037956 | RubberDandelionOmics

Gene overview

LXL04_037956

Reference: OH-1004 Chr: Chr09 Coordinates: 26826833-26829929 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1264 bp · LXL04_037956|LXL04_037956|OH1004|cDNA

ATGCTTGGGAGATCAACTACTGAGGCAATTGATAATAATGGTGACCGGGATAGCCGTGGAGTAAAAATCCCATGGCCCGAAGCTGAATCGATTCCCAGAGAGAAGGGCAGAAAGAAGatagagatagagagagagagagaactagagatagagagagagatggGAGAGGAAGATGGGCCAGGGCTATTCCATCACAAGAAACAAACACTAATCGATGAAATCTCCGGTAAGATCATCAACGGTGATCTCCTCACCAAGAT...

CDS

Download CDS FASTA

1257 bp · LXL04_037956|LXL04_037956|OH1004|CDS

ATGCTTGGGAGATCAACTACTGAGGCAATTGATAATAATGGTGACCGGGATAGCCGTGGAGTAAAAATCCCATGGCCCGAAGCTGAATCGATTCCCAGAGAGAAGGGCAGAAAGAAGATAGAGATAGAGAGAGAGAGAGAACTAGAGATAGAGAGAGAGATGGGAGAGGAAGATGGGCCAGGGCTATTCCATCACAAGAAACAAACACTAATCGATGAAATCTCCGGTAAGATCATCAACGGTGATCTCCTCACCAAGAT...

Protein

Download Protein FASTA

418 aa · LXL04_037956|LXL04_037956|OH1004|PROTEIN

MLGRSTTEAIDNNGDRDSRGVKIPWPEAESIPREKGRKKIEIERERELEIEREMGEEDGPGLFHHKKQTLIDEISGKIINGDLLTKIQAAREIRSMIRNRISSDKIRTKLAAAGVIQPLVLMLYSRNHDAREVSLLALLNLASRNERNKEQIVTCGGIPPLVDLLKFQNTNTLRELATAAILTLSTASPNKKTIIDSGVIPLLIQILSCGTVQGRVDSVTALHNLLTSQQQQQPPLIPDSKAIPPLINLLKECKKSSKFA...

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_037956`
TK1151 ID	TkA04G367870
OH-1004 ID	LXL04_037956
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	100.000
Protein coverage (%)	TK1151 100.000 / OH-1004 87.321 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_037956

Location Chr09:26826833-26829929 (-)

Description Similar to PUB3: U-box domain-containing protein 3

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g54790`	Functions as an E3 ubiquitin ligase.	No verified direct reference in this release
`At3g46510`	Functions as an E3 ubiquitin ligase.	No verified direct reference in this release
`At1g24330`	Functions as an E3 ubiquitin ligase.	No verified direct reference in this release
`At1g23030`	Functions as an E3 ubiquitin ligase.	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_037956 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0002237 response to molecule of bacterial origin Biological Process

GO:0007166 cell surface receptor signaling pathway Biological Process

GO:0009609 response to symbiotic bacterium Biological Process

GO:0009610 response to symbiotic fungus Biological Process

GO:0009877 nodulation Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0036377 arbuscular mycorrhizal association Biological Process

GO:0042742 defense response to bacterium Biological Process

GO:0050777 negative regulation of immune response Biological Process

GO:0051865 protein autoubiquitination Biological Process

GO:0090333 regulation of stomatal closure Biological Process

GO:2000028 regulation of photoperiodism, flowering Biological Process

KEGG gene cross-reference

ath:AT1G23030

ath:AT1G24330

ath:AT3G46510

ath:AT3G54790

mtr:11430446

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.

Cytoplasm0.534

Rank 1 · LXL04_037956 · OH-1004

Nucleus0.389

Rank 2 · LXL04_037956 · OH-1004

Cell membrane0.178

Rank 3 · LXL04_037956 · OH-1004

Endoplasmic reticulum0.051

Rank 4 · LXL04_037956 · OH-1004

Lysosome / Vacuole0.037

Rank 5 · LXL04_037956 · 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.

PF24768.2ARM_ARMC595-182 aa

PF00514.30Arm145-179 aa

PF24768.2ARM_ARMC5184-358 aa

PF00514.30Arm188-226 aa

PF25598.2ARM_PUB197-363 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_037956	`PF24768.2`	ARM_ARMC5	95	182	2e-14	54.4
LXL04_037956	`PF00514.30`	Arm	145	179	1.9e-28	98.2
LXL04_037956	`PF24768.2`	ARM_ARMC5	184	358	2e-14	54.4
LXL04_037956	`PF00514.30`	Arm	188	226	1.9e-28	98.2
LXL04_037956	`PF25598.2`	ARM_PUB	197	363	3e-17	63.7

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
`Q8GWV5`	Arabidopsis thaliana	U-box domain-containing protein 3	36.029%	Swiss-Prot	moderate database homology
`Q9SNC6`	Arabidopsis thaliana	U-box domain-containing protein 13	33.684%	Swiss-Prot	moderate database homology
`O48700`	Arabidopsis thaliana	U-box domain-containing protein 6	29.514%	Swiss-Prot	weak database homology
`Q8GUG9`	Arabidopsis thaliana	U-box domain-containing protein 11	31.522%	Swiss-Prot	moderate database homology

JBrowse

View in Genome Browser

Gene Card