LXL04_014696 | RubberDandelionOmics

Gene overview

LXL04_014696

Reference: OH-1004 Chr: Chr03 Coordinates: 55082807-55084030 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1224 bp · LXL04_014696|LXL04_014696|OH1004|cDNA

ATGGAGGTCCAGATCGAAGTTCCATCGCATTTTCTATGCCCGATCTCTATGCAGCTCATGAACGATCCAGTGACAATATCAACTGGCATCACTTACGATCGGCAAAGCATAGAGAGATGGTTATTCACATGCAGAAGCAGCAGTTGTCCGGTCACGAAACAACCGTTGTCCGACACCGATCTAACACCTAACCACACCCTTCGCCGGTTGATTCAGTCCTGGTGTACCATGAACTCATACCATGGGTTTGATCCTATCCC...

CDS

Download CDS FASTA

1224 bp · LXL04_014696|LXL04_014696|OH1004|CDS

ATGGAGGTCCAGATCGAAGTTCCATCGCATTTTCTATGCCCGATCTCTATGCAGCTCATGAACGATCCAGTGACAATATCAACTGGCATCACTTACGATCGGCAAAGCATAGAGAGATGGTTATTCACATGCAGAAGCAGCAGTTGTCCGGTCACGAAACAACCGTTGTCCGACACCGATCTAACACCTAACCACACCCTTCGCCGGTTGATTCAGTCCTGGTGTACCATGAACTCATACCATGGGTTTGATCCTATCCC...

Protein

Download Protein FASTA

407 aa · LXL04_014696|LXL04_014696|OH1004|PROTEIN

MEVQIEVPSHFLCPISMQLMNDPVTISTGITYDRQSIERWLFTCRSSSCPVTKQPLSDTDLTPNHTLRRLIQSWCTMNSYHGFDPIPTPKKPANKSQILKLLHDAKTHPQNQIKCLRRMRSIAQSSDWNQTCMEDSGVVEFLTTVILKEKESGDSVSEACDEALIVFHHLQCTDFQLRIQLQKNESGFVDALLRVMRIGSIQSRSNAIMLLAKLFKVADPARIAGVKVELFDETVRILKNGVSIQTIKASLKLITEIIRW...

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_014696`
TK1151 ID	TkA02G404410
OH-1004 ID	LXL04_014696
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	100.000
Protein coverage (%)	TK1151 100.000 / OH-1004 96.069 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

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Basic Information and Functional Annotation

Gene ID LXL04_014696

Location Chr03:55082807-55084030 (-)

Description Similar to PUB23: E3 ubiquitin-protein ligase PUB23

Arabidopsis / Rice Reference Genes and Papers

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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_014696 · 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.

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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.

Nucleus0.659

Rank 1 · LXL04_014696 · OH-1004

Cytoplasm0.385

Rank 2 · LXL04_014696 · OH-1004

Cell membrane0.060

Rank 3 · LXL04_014696 · OH-1004

Endoplasmic reticulum0.031

Rank 4 · LXL04_014696 · OH-1004

Lysosome / Vacuole0.023

Rank 5 · LXL04_014696 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

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Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF04564.22U-box7-78 aa

PF25598.2ARM_PUB98-404 aa

PF24768.2ARM_ARMC598-298 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_014696	`PF04564.22`	U-box	7	78	2e-20	73.4
LXL04_014696	`PF25598.2`	ARM_PUB	98	404	3e-73	247.7
LXL04_014696	`PF24768.2`	ARM_ARMC5	98	298	1.7e-07	31.6

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	47.433%	Swiss-Prot	moderate database homology
`Q9SVC6`	Arabidopsis thaliana	E3 ubiquitin-protein ligase PUB22	45.287%	Swiss-Prot	moderate database homology
`Q9SF15`	Arabidopsis thaliana	E3 ubiquitin-protein ligase PUB24	34.521%	Swiss-Prot	moderate database homology
`Q9LT79`	Arabidopsis thaliana	U-box domain-containing protein 25	35.509%	Swiss-Prot	moderate database homology
`Q9FXA4`	Arabidopsis thaliana	U-box domain-containing protein 26	33.824%	Swiss-Prot	moderate database homology

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