LXL04_029355 | RubberDandelionOmics

Gene overview

LXL04_029355

Reference: OH-1004 Chr: Chr06 Coordinates: 88285724-88287485 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

444 bp · LXL04_029355|LXL04_029355|OH1004|cDNA

ATGCCAGTTCCCTTAGCTCCATACCCAACTCCTCATGTACCATTTACACCACCTGCTGCAACTGGTTCTGAAAGCCAACTAGTGTGTTCCGGATGTCGAAATCTTCTTCTTTACCCAATGGGAGCAACTACAGTTTGCTGTGCTGTTTGCAATTCCGTCACCGCTGTACCTCTTCCCGGTACCGAAATGGCACAATTAGTATGTGGAGGTTGCCACACTTTACTCATGTACATTCGTGGGGCTGCAAGTGTACAATGTTC...

CDS

Download CDS FASTA

444 bp · LXL04_029355|LXL04_029355|OH1004|CDS

ATGCCAGTTCCCTTAGCTCCATACCCAACTCCTCATGTACCATTTACACCACCTGCTGCAACTGGTTCTGAAAGCCAACTAGTGTGTTCCGGATGTCGAAATCTTCTTCTTTACCCAATGGGAGCAACTACAGTTTGCTGTGCTGTTTGCAATTCCGTCACCGCTGTACCTCTTCCCGGTACCGAAATGGCACAATTAGTATGTGGAGGTTGCCACACTTTACTCATGTACATTCGTGGGGCTGCAAGTGTACAATGTTC...

Protein

Download Protein FASTA

147 aa · LXL04_029355|LXL04_029355|OH1004|PROTEIN

MPVPLAPYPTPHVPFTPPAATGSESQLVCSGCRNLLLYPMGATTVCCAVCNSVTAVPLPGTEMAQLVCGGCHTLLMYIRGAASVQCSCCHTINLALEENQVIAHINCGNCKMLLMYPYGARSVKCAVCQFVTSIGASASNIEQKSIA

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_029355`
TK1151 ID	TkA07G306560
OH-1004 ID	LXL04_029355
Relationship / confidence	Rbh Sequence Supported / Probable
Protein identity (%)	93.900
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

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_029355

Location Chr06:88285724-88287485 (+)

Description Similar to LOL1: Protein LOL1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`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
`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

Rice

Reference gene ID	Possible function	Papers / DOI
`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
`Os12g0611000`	Putative zinc finger that may be involved in programmed cell death and defense response.	No verified direct reference in this release
`Os03g0639600`	Putative zinc finger that may be involved in programmed cell death and defense response.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_029355 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009626 plant-type hypersensitive response 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

GO:0034052 positive regulation of plant-type hypersensitive response Biological Process

GO:0043068 positive regulation of programmed cell death Biological Process

GO:0045595 regulation of cell differentiation Biological Process

GO:0098542 defense response to other organism Biological Process

GO:2000121 regulation of removal of superoxide radicals Biological Process

GO:0005576 extracellular region Cellular Component

GO:0005634 nucleus Cellular Component

GO:0003677 DNA binding Molecular Function

KEGG gene cross-reference

ath:AT1G32540

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.

Nucleus0.523

Rank 1 · LXL04_029355 · OH-1004

Cytoplasm0.514

Rank 2 · LXL04_029355 · OH-1004

Cell membrane0.086

Rank 3 · LXL04_029355 · OH-1004

Endoplasmic reticulum0.063

Rank 4 · LXL04_029355 · OH-1004

Mitochondrion0.056

Rank 5 · LXL04_029355 · 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-LSD129-53 aa

PF06943.18zf-LSD168-92 aa

PF06943.18zf-LSD1107-131 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_029355	`PF06943.18`	zf-LSD1	29	53	6.6e-37	125.8
LXL04_029355	`PF06943.18`	zf-LSD1	68	92	6.6e-37	125.8
LXL04_029355	`PF06943.18`	zf-LSD1	107	131	6.6e-37	125.8

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
`Q93ZB1`	Arabidopsis thaliana	Protein LOL1	80.153%	Swiss-Prot	strong database homology
`P94077`	Arabidopsis thaliana	Protein LSD1	56.250%	Swiss-Prot	strong database homology
`Q0J7V9`	Oryza sativa subsp. japonica	Protein LSD1	75.862%	Swiss-Prot	strong database homology
`Q2QMB3`	Oryza sativa subsp. japonica	Protein LOL2	61.062%	Swiss-Prot	strong database homology
`Q6ASS2`	Oryza sativa subsp. japonica	Protein LOL3	57.895%	Swiss-Prot	strong database homology

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