LXL04_020917 | RubberDandelionOmics

Gene overview

LXL04_020917

Reference: OH-1004 Chr: Chr04 Coordinates: 114931945-114934014 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2070 bp · LXL04_020917|LXL04_020917|OH1004|cDNA

ATGTGTGATGCACACACTCGCCGGATTTTAACTTTTCCGGCGATTCGTCCAAGCGAAACAGCAGCTCCGGCGACCCTTCTTTTCTCTCTGATCACCCTTTCGGATACCATATCTTCATACAAATCCAAACCCATTTACTCCAATGCTCGAAATGCAAAAGATTCTTTTCGTCTTGTCAGCAATATCCTCGTCATCCTCGAAGAGATCCGACGAGATCAGACATGTCTGTCATGCGcgatggttctctcactctcGGAGCT...

CDS

Download CDS FASTA

2070 bp · LXL04_020917|LXL04_020917|OH1004|CDS

ATGTGTGATGCACACACTCGCCGGATTTTAACTTTTCCGGCGATTCGTCCAAGCGAAACAGCAGCTCCGGCGACCCTTCTTTTCTCTCTGATCACCCTTTCGGATACCATATCTTCATACAAATCCAAACCCATTTACTCCAATGCTCGAAATGCAAAAGATTCTTTTCGTCTTGTCAGCAATATCCTCGTCATCCTCGAAGAGATCCGACGAGATCAGACATGTCTGTCATGCGCGATGGTTCTCTCACTCTCGGAGCT...

Protein

Download Protein FASTA

689 aa · LXL04_020917|LXL04_020917|OH1004|PROTEIN

MCDAHTRRILTFPAIRPSETAAPATLLFSLITLSDTISSYKSKPIYSNARNAKDSFRLVSNILVILEEIRRDQTCLSCAMVLSLSELHYVFQKLRFLLEDCTKSDARMWMLTRSEKVSNQFRAIFRSISVALDVLPLDSVDVSVEVRELVGLVKTQALNSKLGFRPEDQRALEHLRSILDQLEHQMVPDPNNLKQVLDHLGICSWTGCNKEIKFLDSEIGSEKSTSKKSDLGILSSLMGLMIYNRCTVFTTVDGERFTIS...

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_020917`
TK1151 ID	TkA05G333000
OH-1004 ID	LXL04_020917
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	95.000
Protein coverage (%)	TK1151 86.022 / OH-1004 80.987 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

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_020917

Location Chr04:114931945-114934014 (-)

Description Similar to PUB19: U-box domain-containing protein 19

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g60190`	Functions as an E3 ubiquitin ligase.	No verified direct reference in this release
`At1g10560`	Functions as an E3 ubiquitin ligase (By similarity).	The N-Terminal UND Motif of the Arabidopsis U-Box E3 Ligase PUB18 Is Critical for the Negative Regulation of ABA-Mediated Stomatal Movement and Determines Its Ubiquitination Specificity for Exocyst Subunit Exo70B1.2016 · DOI: 10.1105/tpc.16.00347
`At1g29340`	Functions as an E3 ubiquitin ligase.	The E3 ubiquitin ligase activity of arabidopsis PLANT U-BOX17 and its functional tobacco homolog ACRE276 are required for cell death and defense.2006 · DOI: 10.1105/tpc.105.039198
`At3g46510`	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_020917 · 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:0009738 abscisic acid-activated signaling pathway Biological Process

GO:0009787 regulation of abscisic acid-activated signaling pathway Biological Process

GO:0009877 nodulation Biological Process

GO:0010029 regulation of seed germination Biological Process

GO:0010119 regulation of stomatal movement Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0036377 arbuscular mycorrhizal association Biological Process

GO:0042742 defense response to bacterium Biological Process

KEGG gene cross-reference

ath:AT1G10560

ath:AT1G29340

ath:AT1G60190

ath:AT3G46510

mtr:11430446

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.

Cytoplasm0.559

Rank 1 · LXL04_020917 · OH-1004

Nucleus0.362

Rank 2 · LXL04_020917 · OH-1004

Cell membrane0.186

Rank 3 · LXL04_020917 · OH-1004

Endoplasmic reticulum0.057

Rank 4 · LXL04_020917 · OH-1004

Lysosome / Vacuole0.043

Rank 5 · LXL04_020917 · 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.

PF25368.2PUB10_N57-156 aa

PF04564.22U-box278-346 aa

PF11789.15zf-Nse279-320 aa

PF13445.13zf-RING_UBOX282-318 aa

PF25598.2ARM_PUB386-662 aa

PF24768.2ARM_ARMC5395-564 aa

PF00514.30Arm415-451 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_020917	`PF25368.2`	PUB10_N	57	156	9.3e-12	46.4
LXL04_020917	`PF04564.22`	U-box	278	346	7.1e-16	58.9
LXL04_020917	`PF11789.15`	zf-Nse	279	320	2.4e-06	28.0
LXL04_020917	`PF13445.13`	zf-RING_UBOX	282	318	2.3e-07	31.4
LXL04_020917	`PF25598.2`	ARM_PUB	386	662	3.5e-13	50.4
LXL04_020917	`PF24768.2`	ARM_ARMC5	395	564	3.4e-09	37.2
LXL04_020917	`PF00514.30`	Arm	415	451	6.1e-15	55.4

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
`O80742`	Arabidopsis thaliana	U-box domain-containing protein 19	43.103%	Swiss-Prot	moderate database homology
`Q9XIJ5`	Arabidopsis thaliana	U-box domain-containing protein 18	42.775%	Swiss-Prot	moderate database homology
`Q9C7R6`	Arabidopsis thaliana	U-box domain-containing protein 17	33.278%	Swiss-Prot	moderate database homology
`Q9SNC6`	Arabidopsis thaliana	U-box domain-containing protein 13	31.674%	Swiss-Prot	moderate database homology

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