LXL04_026459 | RubberDandelionOmics

Gene overview

LXL04_026459

Reference: OH-1004 Chr: Chr05 Coordinates: 126565993-126567960 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1041 bp · LXL04_026459|LXL04_026459|OH1004|cDNA

ATGGAAGGAACCCACGGCGGCGAGAAGACCAAAAGCCGGCTGTGCAGCATCTGCAACCAACGGAGGCCTGCTCTCAGACGACCTAAAACCCTTGAACAAATTTGCAGAGAATGCTTCTATGTGGTATTCGAGGATGAGATTCATAGTGTGATTGTAAACAACAAGCTGTTTAAGCCAGGGGAGCGCATCGCCATTGGAGCTTCTGGTGGAAAAGATTCCACGGTTCTTGCATATGTAATGTCAGAATTAAACCGGCGCCA...

CDS

Download CDS FASTA

1041 bp · LXL04_026459|LXL04_026459|OH1004|CDS

ATGGAAGGAACCCACGGCGGCGAGAAGACCAAAAGCCGGCTGTGCAGCATCTGCAACCAACGGAGGCCTGCTCTCAGACGACCTAAAACCCTTGAACAAATTTGCAGAGAATGCTTCTATGTGGTATTCGAGGATGAGATTCATAGTGTGATTGTAAACAACAAGCTGTTTAAGCCAGGGGAGCGCATCGCCATTGGAGCTTCTGGTGGAAAAGATTCCACGGTTCTTGCATATGTAATGTCAGAATTAAACCGGCGCCA...

Protein

Download Protein FASTA

346 aa · LXL04_026459|LXL04_026459|OH1004|PROTEIN

MEGTHGGEKTKSRLCSICNQRRPALRRPKTLEQICRECFYVVFEDEIHSVIVNNKLFKPGERIAIGASGGKDSTVLAYVMSELNRRHKYGLDLFLLSVDEGITGYRDDSLETVKRNEIQYGLPLKVVSYKDLYGWTMDEIVKMIGLKNNCTFCGVFRRQALDRGAALLKVDKLATGHNADDIAETVLLNILRGDIARLSRCTSIITGEDGPIPRCKPFKYTYEKEIVTYAYFKKLDYFSTECIYSPNAYRGFAREFIKDL...

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_026459`
TK1151 ID	TkA06G011040
OH-1004 ID	LXL04_026459
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.400
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_026459

Location Chr05:126565993-126567960 (-)

Description Similar to NCS6: Cytoplasmic tRNA 2-thiolation protein 1

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g44270`	Plays a central role in 2-thiolation of mcm(5)S(2)U at tRNA wobble positions of tRNA(Lys), tRNA(Glu) and tRNA(Gln).	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os02g0762300`	Plays a central role in 2-thiolation of mcm(5)S(2)U at tRNA wobble positions of tRNA(Lys), tRNA(Glu) and tRNA(Gln).	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_026459 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000302 response to reactive oxygen species Biological Process

GO:0002098 tRNA wobble uridine modification Biological Process

GO:0002143 tRNA wobble position uridine thiolation Biological Process

GO:0032447 protein urmylation Biological Process

GO:0034227 tRNA thio-modification Biological Process

GO:0080157 regulation of plant-type cell wall organization or biogenesis Biological Process

GO:0002144 cytosolic tRNA wobble base thiouridylase complex Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005739 mitochondrion Cellular Component

GO:0005829 cytosol Cellular Component

GO:0000049 tRNA binding Molecular Function

GO:0016779 nucleotidyltransferase activity Molecular Function

KEGG gene cross-reference

ath:AT2G44270

dosa:Os02g0762300

xla:779274

xtr:548460

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.

Mitochondrion0.502

Rank 1 · LXL04_026459 · OH-1004

Plastid0.245

Rank 2 · LXL04_026459 · OH-1004

Cytoplasm0.204

Rank 3 · LXL04_026459 · OH-1004

Nucleus0.093

Rank 4 · LXL04_026459 · OH-1004

Peroxisome0.033

Rank 5 · LXL04_026459 · 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.

PF01171.28ATP_bind_344-257 aa

PF16503.11zn-ribbon_14290-320 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_026459	`PF01171.28`	ATP_bind_3	44	257	7.2e-18	65.4
LXL04_026459	`PF16503.11`	zn-ribbon_14	290	320	8.4e-18	64.3

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`O64862`	Arabidopsis thaliana	Cytoplasmic tRNA 2-thiolation protein 1	86.667%	Swiss-Prot	strong database homology
`Q6Z6G6`	Oryza sativa subsp. japonica	Cytoplasmic tRNA 2-thiolation protein 1	87.117%	Swiss-Prot	strong database homology

JBrowse

View in Genome Browser

Gene Card