LXL04_011238 | RubberDandelionOmics

Gene overview

LXL04_011238

Reference: OH-1004 Chr: Chr02 Coordinates: 160616108-160619231 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1764 bp · LXL04_011238|LXL04_011238|OH1004|cDNA

ATGGAGAGATTTGCTCCGGTGGGGATGACGGTCTCGGCGTTTGTGAAGTGGGAAGAAGTTTTTTCTACAAACCATAGAGGAAGAAGAGAGGTACGGTATTATCTGAAACGGCGGGATGGGACTTCCGATTTGGCAGTTGTCGGCAAAGAGAAGAAATCAGGGTCCAAAATGAAGACGTCTCCGTTGGTCTCTTCTTCCTATCGTTATCGATACGCAATTCGTGACAAATCGCTCTTTCCGTCATCTGAAATTTTTACCAA...

CDS

Download CDS FASTA

1764 bp · LXL04_011238|LXL04_011238|OH1004|CDS

ATGGAGAGATTTGCTCCGGTGGGGATGACGGTCTCGGCGTTTGTGAAGTGGGAAGAAGTTTTTTCTACAAACCATAGAGGAAGAAGAGAGGTACGGTATTATCTGAAACGGCGGGATGGGACTTCCGATTTGGCAGTTGTCGGCAAAGAGAAGAAATCAGGGTCCAAAATGAAGACGTCTCCGTTGGTCTCTTCTTCCTATCGTTATCGATACGCAATTCGTGACAAATCGCTCTTTCCGTCATCTGAAATTTTTACCAA...

Protein

Download Protein FASTA

587 aa · LXL04_011238|LXL04_011238|OH1004|PROTEIN

MERFAPVGMTVSAFVKWEEVFSTNHRGRREVRYYLKRRDGTSDLAVVGKEKKSGSKMKTSPLVSSSYRYRYAIRDKSLFPSSEIFTKLRSRRQVIDWLSSLVTDGSFSQPPKIIEAGDTLKSKSENFQDVHLHKSIIHQTPDLQWVGSFTFKKKRKHYEAYTRSGVKISVDDFVYVLAEEDKRLVAHLEDLYQDSKGNKVAVVRWFHKVDEVFGIDHHHKPHNPYYNINNNHKEIFFSLCAQDLNIECIDGPATVLTPQH...

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_011238`
TK1151 ID	TkA03G575500
OH-1004 ID	LXL04_011238
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	100.000
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_011238

Location Chr02:160616108-160619231 (-)

Description Similar to DUF3: DUF724 domain-containing protein 3

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g17330`	May regulate root reactive oxygen species accumulation and cell-wall integrity under salt stress.	SWO1 modulates cell wall integrity under salt stress by interacting with importin ɑ in Arabidopsis.2021 · DOI: 10.1007/s44154-021-00010-5
`At1g26540`	May be involved in the polar growth of plant cells via transportation of RNAs.	Characterization of DUF724 gene family in Arabidopsis thaliana.2010 · DOI: 10.1007/s11103-009-9551-5
`At1g09320`	Heterochromatin-binding protein that preferentially occupies long transposons and specifically recognizes the histone H3 'Lys-9' methylation (H3K9me) marks, with a stronger affinity for dimethylated H3K9 (H3K9me2).	Arabidopsis AGDP1 links H3K9me2 to DNA methylation in heterochromatin.2018 · DOI: 10.1038/s41467-018-06965-w Plant HP1 protein ADCP1 links multivalent H3K9 methylation readout to heterochromatin formation.2019 · DOI: 10.1038/s41422-018-0104-9
`At1g11420`	May be involved in the polar growth of plant cells via transportation of RNAs.	No verified direct reference in this release
`At2g47230`	May be involved in the polar growth of plant cells via transportation of RNAs.	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_011238 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006346 DNA methylation-dependent constitutive heterochromatin formation Biological Process

GO:0009651 response to salt stress Biological Process

GO:0009934 regulation of meristem structural organization Biological Process

GO:0010468 regulation of gene expression Biological Process

GO:0071555 cell wall organization Biological Process

GO:2000280 regulation of root development Biological Process

GO:0000325 plant-type vacuole Cellular Component

GO:0000775 chromosome, centromeric region Cellular Component

GO:0000792 heterochromatin Cellular Component

GO:0005634 nucleus Cellular Component

GO:0009506 plasmodesma Cellular Component

GO:0042393 histone binding Molecular Function

KEGG gene cross-reference

ath:AT1G09320

ath:AT1G11420

ath:AT1G26540

ath:AT4G17330

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.

Nucleus0.969

Rank 1 · LXL04_011238 · OH-1004

Cytoplasm0.067

Rank 2 · LXL04_011238 · OH-1004

Cell membrane0.026

Rank 3 · LXL04_011238 · OH-1004

Endoplasmic reticulum0.017

Rank 4 · LXL04_011238 · OH-1004

Plastid0.014

Rank 5 · LXL04_011238 · 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.

PF01426.25BAH167-285 aa

PF05641.19Agenet341-414 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_011238	`PF01426.25`	BAH	167	285	3.9e-08	33.9
LXL04_011238	`PF05641.19`	Agenet	341	414	9.4e-18	65.2

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
`F4JP43`	Arabidopsis thaliana	Protein SWOLLEN 1	28.105%	Swiss-Prot	weak database homology
`Q9FZD9`	Arabidopsis thaliana	DUF724 domain-containing protein 3	29.730%	Swiss-Prot	weak database homology
`Q500V5`	Arabidopsis thaliana	Protein AGENET DOMAIN (AGD)-CONTAINING P1	30.667%	Swiss-Prot	weak database homology
`F4I8W1`	Arabidopsis thaliana	DUF724 domain-containing protein 2	29.814%	Swiss-Prot	weak database homology
`O22897`	Arabidopsis thaliana	DUF724 domain-containing protein 6	29.054%	Swiss-Prot	weak database homology

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