LXL04_031592 | RubberDandelionOmics

Gene overview

LXL04_031592

Reference: OH-1004 Chr: Chr07 Coordinates: 8039424-8041893 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2067 bp · LXL04_031592|LXL04_031592|OH1004|cDNA

ATGTCCTCTGCTGGCGCCGCCGCCACTATATCCACCACGACTCTCACAACACATCTCACTATCCTCGCCTTCCTCTCCGCCACCACCGTCTACTGCTTCTATAAGTCCCGCCGCCTCCGCCACCTTAAACTATCATCCCCTTCCTCAAACCCTAATCTCTCCTCTGCTACTAGAAAAGGAAAACTCTTCTTCATCTCTCAAACAGGCACCTCTAAGACTCTAGCTCAACGTCTCTTCAACCAACTGACCTCCAATAACCT...

CDS

Download CDS FASTA

2067 bp · LXL04_031592|LXL04_031592|OH1004|CDS

ATGTCCTCTGCTGGCGCCGCCGCCACTATATCCACCACGACTCTCACAACACATCTCACTATCCTCGCCTTCCTCTCCGCCACCACCGTCTACTGCTTCTATAAGTCCCGCCGCCTCCGCCACCTTAAACTATCATCCCCTTCCTCAAACCCTAATCTCTCCTCTGCTACTAGAAAAGGAAAACTCTTCTTCATCTCTCAAACAGGCACCTCTAAGACTCTAGCTCAACGTCTCTTCAACCAACTGACCTCCAATAACCT...

Protein

Download Protein FASTA

688 aa · LXL04_031592|LXL04_031592|OH1004|PROTEIN

MSSAGAAATISTTTLTTHLTILAFLSATTVYCFYKSRRLRHLKLSSPSSNPNLSSATRKGKLFFISQTGTSKTLAQRLFNQLTSNNLPFDLVDPNVYEPEDLHQENLVLIIASTWEDGNPPSNGVFLSNWLSESAEDFRVGSLLLSKCKFAVFGVGSRAYGDNFNAVGRGISTKMRSLGASEILPLSEGDVDEGELDKAFGNWSKEVIKVLKAGELRGNVSELNGDENGYEMSDGSDYEDDDYEDEENETESDIVDLEDI...

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_031592`
TK1151 ID	TkA08G115370
OH-1004 ID	LXL04_031592
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	95.200
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_031592

Location Chr07:8039424-8041893 (-)

Description Similar to TYW1: S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g75200`	Probable component of the wybutosine biosynthesis pathway.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os03g0775300`	Probable component of the wybutosine biosynthesis pathway.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_031592 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0031591 wybutosine biosynthetic process Biological Process

GO:0005739 mitochondrion Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0010181 FMN binding Molecular Function

GO:0046872 metal ion binding Molecular Function

GO:0051539 4 iron, 4 sulfur cluster binding Molecular Function

GO:0102521 tRNA-4-demethylwyosine synthase activity Molecular Function

KEGG gene cross-reference

ath:AT1G75200

dosa:Os03g0775300

hsa:55253

pon:100171721

xla:735035

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.

Mitochondrion0.248

Rank 1 · LXL04_031592 · OH-1004

Cytoplasm0.191

Rank 2 · LXL04_031592 · OH-1004

Nucleus0.174

Rank 3 · LXL04_031592 · OH-1004

Endoplasmic reticulum0.156

Rank 4 · LXL04_031592 · OH-1004

Plastid0.150

Rank 5 · LXL04_031592 · 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.

PF00258.31Flavodoxin_162-203 aa

PF04055.28Radical_SAM344-502 aa

PF08608.18Wyosine_form555-618 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_031592	`PF00258.31`	Flavodoxin_1	62	203	1.1e-24	87.9
LXL04_031592	`PF04055.28`	Radical_SAM	344	502	2.7e-09	38.1
LXL04_031592	`PF08608.18`	Wyosine_form	555	618	2.4e-25	89.3

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
`Q8RXN5`	Arabidopsis thaliana	S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase	69.733%	Swiss-Prot	strong database homology
`Q8H8N3`	Oryza sativa subsp. japonica	S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase	62.614%	Swiss-Prot	strong database homology

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