LXL04_018885 | RubberDandelionOmics

Gene overview

LXL04_018885

Reference: OH-1004 Chr: Chr04 Coordinates: 19606503-19610016 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1014 bp · LXL04_018885|LXL04_018885|OH1004|cDNA

ATGAAATTCTGCAAGAAATACCAGGAATACATGCAAACGCAAGATGAGAAGAAATTACCTGCTGTGGGTTTTAAAAATCTCAAAAAGATATTGAAGCGCTGCCGCACTGATACGATTCGTTCACAAAATTCTCGTCGATCACAATCGCCGACGCCTCTTAACGATTCTCCTCACGGCAGCTCCGCCATTTGTCCTCATCATTGCGCCGTGTGCGATGGAACTTTCTTTCCTTCCCTTTTCAAAGAAATGTCCGCAGTGGT...

CDS

Download CDS FASTA

1014 bp · LXL04_018885|LXL04_018885|OH1004|CDS

ATGAAATTCTGCAAGAAATACCAGGAATACATGCAAACGCAAGATGAGAAGAAATTACCTGCTGTGGGTTTTAAAAATCTCAAAAAGATATTGAAGCGCTGCCGCACTGATACGATTCGTTCACAAAATTCTCGTCGATCACAATCGCCGACGCCTCTTAACGATTCTCCTCACGGCAGCTCCGCCATTTGTCCTCATCATTGCGCCGTGTGCGATGGAACTTTCTTTCCTTCCCTTTTCAAAGAAATGTCCGCAGTGGT...

Protein

Download Protein FASTA

337 aa · LXL04_018885|LXL04_018885|OH1004|PROTEIN

MKFCKKYQEYMQTQDEKKLPAVGFKNLKKILKRCRTDTIRSQNSRRSQSPTPLNDSPHGSSAICPHHCAVCDGTFFPSLFKEMSAVVGCFNKRAQKLLDIHLATGFRKYYVWCKDKLQGKNGTFLVEEGKDLVSYAIINAIAMRKILKKYDKIHYLKHGQAFRSQVQSMHMDILQSPWLCELIAFHINLRETKVDTRKTSELFEGCSLVFNEGKPSLSCELSDTLKLEIGLTCSICLDTVFDSVALTCGHIFCYMCACKS...

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_018885`
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_018885

Location Chr04:19606503-19610016 (-)

Description Similar to BAH1: E3 ubiquitin-protein ligase BAH1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g02860`	E3 ubiquitin-protein ligase that mediates E2-dependent protein ubiquitination.	BAH1/NLA, a RING-type ubiquitin E3 ligase, regulates the accumulation of salicylic acid and immune responses to Pseudomonas syringae DC3000.2008 · DOI: 10.1104/pp.108.124529

Rice

Reference gene ID	Possible function	Papers / DOI
`UniProt: B8B5U8`	Probable E3 ubiquitin-protein ligase BAH1-like 1.	No verified direct reference in this release
`Os07g0673200`	Probable E3 ubiquitin-protein ligase BAH1-like 2.	No verified direct reference in this release
`Os03g0650900`	Probable E3 ubiquitin-protein ligase BAH1-like 1.	No verified direct reference in this release
`UniProt: A2XK56`	Probable E3 ubiquitin-protein ligase BAH1-like 1.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_018885 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009626 plant-type hypersensitive response Biological Process

GO:0009627 systemic acquired resistance Biological Process

GO:0009697 salicylic acid biosynthetic process Biological Process

GO:0009751 response to salicylic acid Biological Process

GO:0010167 response to nitrate Biological Process

GO:0010337 regulation of salicylic acid metabolic process Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0042742 defense response to bacterium Biological Process

GO:0080021 response to benzoic acid Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005739 mitochondrion Cellular Component

KEGG gene cross-reference

ath:AT1G02860

dosa:Os03g0650900

dosa:Os07g0673200

osa:4333590

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.

Cytoplasm0.518

Rank 1 · LXL04_018885 · OH-1004

Nucleus0.382

Rank 2 · LXL04_018885 · OH-1004

Cell membrane0.184

Rank 3 · LXL04_018885 · OH-1004

Lysosome / Vacuole0.077

Rank 4 · LXL04_018885 · OH-1004

Endoplasmic reticulum0.069

Rank 5 · LXL04_018885 · 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.

PF03105.25SPX132-155 aa

PF24921.2RING_XB3-XBAT31232-284 aa

PF00097.32zf-C3HC4233-281 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_018885	`PF03105.25`	SPX	132	155	2.3e-08	35.2
LXL04_018885	`PF24921.2`	RING_XB3-XBAT31	232	284	3.3e-07	31.0
LXL04_018885	`PF00097.32`	zf-C3HC4	233	281	4.9e-06	27.0

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
`Q9SRX9`	Arabidopsis thaliana	E3 ubiquitin-protein ligase NLA	60.694%	Swiss-Prot	strong database homology
`B8B5U8`	Oryza sativa subsp. indica	Probable E3 ubiquitin-protein ligase BAH1-like 1	61.538%	Swiss-Prot	strong database homology
`Q7XI73`	Oryza sativa subsp. japonica	Probable E3 ubiquitin-protein ligase BAH1-like 2	61.243%	Swiss-Prot	strong database homology
`Q7XZZ3`	Oryza sativa subsp. japonica	Probable E3 ubiquitin-protein ligase BAH1-like 1	42.363%	Swiss-Prot	moderate database homology
`A2XK56`	Oryza sativa subsp. indica	Probable E3 ubiquitin-protein ligase BAH1-like 1	42.363%	Swiss-Prot	moderate database homology

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