LXL04_032494 | RubberDandelionOmics

Gene overview

LXL04_032494

Reference: OH-1004 Chr: Chr07 Coordinates: 24096088-24097059 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

972 bp · LXL04_032494|LXL04_032494|OH1004|cDNA

ATGAAAACCCACCACCCGAAACTTAAACCTCCACCTCGGCCACTCTTCTCTTGTGGCTTCTTTCGCTACTGCACTCAATCTGTAATCAGCCCCACCAATCCGAGTCCACCGGTGCTCCCTCATTCAGAACCCacgccaccgccaccgccaccaccaccgcaaACCCACTCCgagtcttcttcttcttccaatACTTCACAAAGCTTTACTCAATGGAGATTCTCTCACACACCCAATTCCCTAACAGACCCATATCCAGA...

CDS

Download CDS FASTA

972 bp · LXL04_032494|LXL04_032494|OH1004|CDS

ATGAAAACCCACCACCCGAAACTTAAACCTCCACCTCGGCCACTCTTCTCTTGTGGCTTCTTTCGCTACTGCACTCAATCTGTAATCAGCCCCACCAATCCGAGTCCACCGGTGCTCCCTCATTCAGAACCCACGCCACCGCCACCGCCACCACCACCGCAAACCCACTCCGAGTCTTCTTCTTCTTCCAATACTTCACAAAGCTTTACTCAATGGAGATTCTCTCACACACCCAATTCCCTAACAGACCCATATCCAGA...

Protein

Download Protein FASTA

323 aa · LXL04_032494|LXL04_032494|OH1004|PROTEIN

MKTHHPKLKPPPRPLFSCGFFRYCTQSVISPTNPSPPVLPHSEPTPPPPPPPPQTHSESSSSSNTSQSFTQWRFSHTPNSLTDPYPETTKMHHQSPPPPPPPPPVVISDLQELFHVAELQLSTGLDSDRVKAIYMLQHSLVNPRATAEGGDLVSCPPAVMRGVLGCLRDKEVAKPATRVLLALCLGECNRHVAVEEGAVGKVVEALVDLDGGAVAERALAALELLCTVAEGAAELRSHALVGPMMVEVMRRMETTRGREN...

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_032494`
TK1151 ID	TkA08G181750
OH-1004 ID	LXL04_032494
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.700
Protein coverage (%)	TK1151 100.000 / OH-1004 100.000 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_032494

Location Chr07:24096088-24097059 (+)

Description Similar to PUB26: U-box domain-containing protein 26

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g49780`	Functions as an E3 ubiquitin ligase.	No verified direct reference in this release
`At3g19380`	Functions as an E3 ubiquitin ligase.	No verified direct reference in this release
`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
`At3g54850`	Functions as an E3 ubiquitin ligase with specific E2 ubiquitin-conjugating enzymes.	Structure and biochemical function of a prototypical Arabidopsis U-box domain.2004 · DOI: 10.1074/jbc.m405057200
`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

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_032494 · 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

GO:0070696 transmembrane receptor protein serine/threonine kinase binding Molecular Function

KEGG gene cross-reference

ath:AT1G49780

ath:AT2G35930

ath:AT3G19380

ath:AT3G52450

ath:AT3G54850

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.

Nucleus0.492

Rank 1 · LXL04_032494 · OH-1004

Cytoplasm0.479

Rank 2 · LXL04_032494 · OH-1004

Cell membrane0.148

Rank 3 · LXL04_032494 · OH-1004

Endoplasmic reticulum0.081

Rank 4 · LXL04_032494 · OH-1004

Golgi apparatus0.029

Rank 5 · LXL04_032494 · 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.

PF25598.2ARM_PUB156-314 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_032494	`PF25598.2`	ARM_PUB	156	314	8.9e-19	68.7

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
`Q9FXA4`	Arabidopsis thaliana	U-box domain-containing protein 26	30.366%	Swiss-Prot	moderate database homology
`Q9LT79`	Arabidopsis thaliana	U-box domain-containing protein 25	26.250%	Swiss-Prot	weak database homology
`Q84TG3`	Arabidopsis thaliana	E3 ubiquitin-protein ligase PUB23	27.861%	Swiss-Prot	weak database homology
`Q8VZ40`	Arabidopsis thaliana	U-box domain-containing protein 14	32.877%	Swiss-Prot	weak database homology
`Q9SVC6`	Arabidopsis thaliana	E3 ubiquitin-protein ligase PUB22	28.931%	Swiss-Prot	weak database homology

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