LXL04_032820 | RubberDandelionOmics

Gene overview

LXL04_032820

Reference: OH-1004 Chr: Chr07 Coordinates: 29814560-29815798 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1239 bp · LXL04_032820|LXL04_032820|OH1004|cDNA

ATGGGCGATCTCGAAAGCGATGTCGAAGTTCCTCGGTTTTTCTTGTGCCCAATTTCACTTGAGATCATGAAAGACCCTGTAATCCTCTCCACCGGAATCACATATGATCGTGATAGCATCGAGAAATGGTTGTTTTCTCAGAAGAATGACGTTTGTCCGGTAACCAAACAAGTCGTCGTCGATATTGATCTCACCCCTAATCACACTCTTCGCCGTTTAATCCAATCTTGGTGCACCATTAACGCGTCATCCGGCATCGA...

CDS

Download CDS FASTA

1239 bp · LXL04_032820|LXL04_032820|OH1004|CDS

ATGGGCGATCTCGAAAGCGATGTCGAAGTTCCTCGGTTTTTCTTGTGCCCAATTTCACTTGAGATCATGAAAGACCCTGTAATCCTCTCCACCGGAATCACATATGATCGTGATAGCATCGAGAAATGGTTGTTTTCTCAGAAGAATGACGTTTGTCCGGTAACCAAACAAGTCGTCGTCGATATTGATCTCACCCCTAATCACACTCTTCGCCGTTTAATCCAATCTTGGTGCACCATTAACGCGTCATCCGGCATCGA...

Protein

Download Protein FASTA

412 aa · LXL04_032820|LXL04_032820|OH1004|PROTEIN

MGDLESDVEVPRFFLCPISLEIMKDPVILSTGITYDRDSIEKWLFSQKNDVCPVTKQVVVDIDLTPNHTLRRLIQSWCTINASSGIERFPTPRLPISKPEIVRLLKDTKSPQLQLKSLKRLKTIVMENEKNKRLVESVSAADYLAGILSTGAGEISGVDGFVSTGVDEAICILYHLKLSGNGLKSLFGITENFVETLTRVMQRSASYESRAYAVMLLKSMFEVAEPIQVTSLSTEFFKELVHILVDQISQKATKAALKLL...

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_032820`
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_032820

Location Chr07:29814560-29815798 (+)

Description Similar to PUB23: E3 ubiquitin-protein ligase PUB23

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g35930`	E3 ubiquitin-protein ligase that negatively regulates water stress response.	Arabidopsis PUB22 and PUB23 are homologous U-Box E3 ubiquitin ligases that play combinatory roles in response to drought stress.2008 · DOI: 10.1105/tpc.108.060699 Negative regulation of PAMP-triggered immunity by an E3 ubiquitin ligase triplet in Arabidopsis.2008 · DOI: 10.1016/j.cub.2008.07.085
`At3g52450`	E3 ubiquitin-protein ligase that negatively regulates water stress response.	Arabidopsis PUB22 and PUB23 are homologous U-Box E3 ubiquitin ligases that play combinatory roles in response to drought stress.2008 · DOI: 10.1105/tpc.108.060699 Negative regulation of PAMP-triggered immunity by an E3 ubiquitin ligase triplet in Arabidopsis.2008 · DOI: 10.1016/j.cub.2008.07.085 The ubiquitin ligase PUB22 targets a subunit of the exocyst complex required for PAMP-triggered responses in Arabidopsis.2012 · DOI: 10.1105/tpc.112.104463
`At3g11840`	E3 ubiquitin-protein ligase that acts as a negative regulator of the immunity triggered by the pathogen-associated molecular patterns (PAMPs), in association with PUB22 and PUB23.	Negative regulation of PAMP-triggered immunity by an E3 ubiquitin ligase triplet in Arabidopsis.2008 · DOI: 10.1016/j.cub.2008.07.085
`At3g19380`	Functions as an E3 ubiquitin ligase.	No verified direct reference in this release
`At1g49780`	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_032820 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0002679 respiratory burst involved in defense response Biological Process

GO:0006952 defense response Biological Process

GO:0009414 response to water deprivation Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0051865 protein autoubiquitination Biological Process

GO:0098542 defense response to other organism Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005829 cytosol Cellular Component

GO:0004842 ubiquitin-protein transferase activity Molecular Function

GO:0061630 ubiquitin protein ligase activity Molecular Function

KEGG gene cross-reference

ath:AT1G49780

ath:AT2G35930

ath:AT3G11840

ath:AT3G19380

ath:AT3G52450

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.

Nucleus0.624

Rank 1 · LXL04_032820 · OH-1004

Cytoplasm0.383

Rank 2 · LXL04_032820 · OH-1004

Cell membrane0.081

Rank 3 · LXL04_032820 · OH-1004

Endoplasmic reticulum0.041

Rank 4 · LXL04_032820 · OH-1004

Lysosome / Vacuole0.024

Rank 5 · LXL04_032820 · 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.

PF04564.22U-box10-79 aa

PF25598.2ARM_PUB100-410 aa

PF24768.2ARM_ARMC5210-366 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_032820	`PF04564.22`	U-box	10	79	7.7e-21	74.7
LXL04_032820	`PF25598.2`	ARM_PUB	100	410	9.4e-80	269.0
LXL04_032820	`PF24768.2`	ARM_ARMC5	210	366	2.3e-08	34.5

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
`Q84TG3`	Arabidopsis thaliana	E3 ubiquitin-protein ligase PUB23	56.731%	Swiss-Prot	strong database homology
`Q9SVC6`	Arabidopsis thaliana	E3 ubiquitin-protein ligase PUB22	54.587%	Swiss-Prot	strong database homology
`Q9SF15`	Arabidopsis thaliana	E3 ubiquitin-protein ligase PUB24	35.857%	Swiss-Prot	moderate database homology
`Q9LT79`	Arabidopsis thaliana	U-box domain-containing protein 25	32.992%	Swiss-Prot	moderate database homology
`Q9FXA4`	Arabidopsis thaliana	U-box domain-containing protein 26	30.751%	Swiss-Prot	moderate database homology

JBrowse

View in Genome Browser

Gene Card