LXL04_002960 | RubberDandelionOmics

Gene overview

LXL04_002960

Reference: OH-1004 Chr: Chr01 Coordinates: 62649733-62652006 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

543 bp · LXL04_002960|LXL04_002960|OH1004|cDNA

ATGCAGAGCCAAATCGTATGCAGCGGTTGTCGGAGCATATTGCTTTATCCAAGAGGAGCTTCTAATGTGTGCTGTGCATTGTGTAATGCCGTTACCTCGGTTCCTCCTCCCGGCATGGAAATGGACCAACTTATTTGTGGAGGTTGCCGCACATTGCTAATGTACACACGTGGTGCTACAAGTGTCAGATGTTCCTGTTGTCATACAGTCAATCTTGCACCAGTTTCTAACCAAGTTGCTCAAGTAAGTTGTGGAAATTG...

CDS

Download CDS FASTA

543 bp · LXL04_002960|LXL04_002960|OH1004|CDS

ATGCAGAGCCAAATCGTATGCAGCGGTTGTCGGAGCATATTGCTTTATCCAAGAGGAGCTTCTAATGTGTGCTGTGCATTGTGTAATGCCGTTACCTCGGTTCCTCCTCCCGGCATGGAAATGGACCAACTTATTTGTGGAGGTTGCCGCACATTGCTAATGTACACACGTGGTGCTACAAGTGTCAGATGTTCCTGTTGTCATACAGTCAATCTTGCACCAGTTTCTAACCAAGTTGCTCAAGTAAGTTGTGGAAATTG...

Protein

Download Protein FASTA

180 aa · LXL04_002960|LXL04_002960|OH1004|PROTEIN

MQSQIVCSGCRSILLYPRGASNVCCALCNAVTSVPPPGMEMDQLICGGCRTLLMYTRGATSVRCSCCHTVNLAPVSNQVAQVSCGNCRTMLMYPFGAPSVKCAICHYITNVNTSNGRVPVPMRPNGTTTTSGSLPPVSTAMPHSHNQTVVVENPMSVDESGKLVSNVVVGVTTEKKKAIK

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_002960`
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_002960

Location Chr01:62649733-62652006 (+)

Description Similar to LOL3: Protein LOL3

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g20380`	Negative regulator of reactive oxygen-induced cell death, cold stress-induced cell death, pathogen-induced hypersensitive response (HR), basal disease resistance.	The Arabidopsis LSD1 gene plays an important role in the regulation of low temperature-dependent cell death.2010 · DOI: 10.1111/j.1469-8137.2010.03275.x
`At1g32540`	Positive regulator of reactive oxygen-induced cell death.	Antagonistic control of oxidative stress-induced cell death in Arabidopsis by two related, plant-specific zinc finger proteins.2003 · DOI: 10.1073/pnas.1130421100

Rice

Reference gene ID	Possible function	Papers / DOI
`Os03g0639600`	Putative zinc finger that may be involved in programmed cell death and defense response.	No verified direct reference in this release
`Os12g0611000`	Putative zinc finger that may be involved in programmed cell death and defense response.	No verified direct reference in this release
`Os08g0159500`	Negative regulator of programmed cell death and hypersensitive response (HR).	OsLSD1, a rice zinc finger protein, regulates programmed cell death and callus differentiation.2005 · DOI: 10.1094/mpmi-18-0375

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_002960 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000303 response to superoxide Biological Process

GO:0001666 response to hypoxia Biological Process

GO:0002240 response to molecule of oomycetes origin Biological Process

GO:0009626 plant-type hypersensitive response Biological Process

GO:0009862 systemic acquired resistance, salicylic acid mediated signaling pathway Biological Process

GO:0010104 regulation of ethylene-activated signaling pathway Biological Process

GO:0010310 regulation of hydrogen peroxide metabolic process Biological Process

GO:0010602 regulation of 1-aminocyclopropane-1-carboxylate metabolic process Biological Process

GO:0010618 aerenchyma formation Biological Process

GO:0030154 cell differentiation Biological Process

GO:0031348 negative regulation of defense response Biological Process

GO:0034051 negative regulation of plant-type hypersensitive response Biological Process

KEGG gene cross-reference

ath:AT1G32540

ath:AT4G20380

dosa:Os03g0639600

dosa:Os08g0159500

dosa:Os12g0611000

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.

Cytoplasm0.561

Rank 1 · LXL04_002960 · OH-1004

Nucleus0.490

Rank 2 · LXL04_002960 · OH-1004

Cell membrane0.109

Rank 3 · LXL04_002960 · OH-1004

Lysosome / Vacuole0.055

Rank 4 · LXL04_002960 · OH-1004

Endoplasmic reticulum0.047

Rank 5 · LXL04_002960 · 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.

PF06943.18zf-LSD17-31 aa

PF06943.18zf-LSD146-70 aa

PF06943.18zf-LSD184-108 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_002960	`PF06943.18`	zf-LSD1	7	31	9.7e-40	134.8
LXL04_002960	`PF06943.18`	zf-LSD1	46	70	9.7e-40	134.8
LXL04_002960	`PF06943.18`	zf-LSD1	84	108	9.7e-40	134.8

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
`P94077`	Arabidopsis thaliana	Protein LSD1	63.298%	Swiss-Prot	strong database homology
`Q93ZB1`	Arabidopsis thaliana	Protein LOL1	70.796%	Swiss-Prot	moderate database homology
`Q6ASS2`	Oryza sativa subsp. japonica	Protein LOL3	62.766%	Swiss-Prot	strong database homology
`Q2QMB3`	Oryza sativa subsp. japonica	Protein LOL2	64.045%	Swiss-Prot	strong database homology
`Q0J7V9`	Oryza sativa subsp. japonica	Protein LSD1	66.667%	Swiss-Prot	moderate database homology

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