LXL04_019732 | RubberDandelionOmics

Gene overview

LXL04_019732

Reference: OH-1004 Chr: Chr04 Coordinates: 38837839-38840708 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2004 bp · LXL04_019732|LXL04_019732|OH1004|cDNA

ATGGAAGCGACGGCGAAGGAGCTTACCGTTGGACAACCACCCAATATTCCGACCGAGCCACCTCCGTTGGCCAGAAAGCCGGTGACTGAAATGTCAGCGGAAGAGATGGTGGCGAAATCTATAGTTCCGGTGAAGAAGGAATTTATCTATCCTGTACCTAACCGACTTAATAGTGATAACAATGGACCACCAACTGACGCTGTTCCTGCCTCCACCACCTCCTCCGCACCTGTCAGTAACGAGAAGAAATCGAAAAGACA...

CDS

Download CDS FASTA

2004 bp · LXL04_019732|LXL04_019732|OH1004|CDS

ATGGAAGCGACGGCGAAGGAGCTTACCGTTGGACAACCACCCAATATTCCGACCGAGCCACCTCCGTTGGCCAGAAAGCCGGTGACTGAAATGTCAGCGGAAGAGATGGTGGCGAAATCTATAGTTCCGGTGAAGAAGGAATTTATCTATCCTGTACCTAACCGACTTAATAGTGATAACAATGGACCACCAACTGACGCTGTTCCTGCCTCCACCACCTCCTCCGCACCTGTCAGTAACGAGAAGAAATCGAAAAGACA...

Protein

Download Protein FASTA

667 aa · LXL04_019732|LXL04_019732|OH1004|PROTEIN

MEATAKELTVGQPPNIPTEPPPLARKPVTEMSAEEMVAKSIVPVKKEFIYPVPNRLNSDNNGPPTDAVPASTTSSAPVSNEKKSKRQLKRERNQEKQSTRNLCPMVAKTGITDSCPYNEKCRFSHNIEAFKAQKPADLEGNCPFEGNEEGPCPYGLGCRFLGTHKTNSASGIPNGLKNSEINGLKKDVQRLLWKNKMKFPKADAQLKVLGLMGPTKSKKTPIPNNEEENGCGEMGTDPIVQIQVPEKAESNNNGDDPRPQ...

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_019732`
TK1151 ID	TkA05G081920
OH-1004 ID	LXL04_019732
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

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

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Basic Information and Functional Annotation

Gene ID LXL04_019732

Location Chr04:38837839-38840708 (-)

Description Similar to At4g38890: tRNA-dihydrouridine(47) synthase [NAD(P)(+)]-like

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g38890`	Catalyzes the synthesis of dihydrouridine, a modified base found in the D-loop of most tRNAs.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os04g0117600`	Catalyzes the synthesis of dihydrouridine, a modified base found in the D-loop of most tRNAs.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_019732 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0002943 tRNA dihydrouridine synthesis Biological Process

GO:0006397 mRNA processing Biological Process

GO:0006417 regulation of translation Biological Process

GO:0005634 nucleus Cellular Component

GO:0005773 vacuole Cellular Component

GO:0003723 RNA binding Molecular Function

GO:0008270 zinc ion binding Molecular Function

GO:0017150 tRNA dihydrouridine synthase activity Molecular Function

GO:0050660 flavin adenine dinucleotide binding Molecular Function

GO:0102265 tRNA-dihydrouridine47 synthase activity Molecular Function

GO:0106414 mRNA dihydrouridine synthase activity Molecular Function

KEGG gene cross-reference

ath:AT4G38890

dosa:Os04g0117600

hsa:56931

xla:379349

xtr:394959

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.

Nucleus0.688

Rank 1 · LXL04_019732 · OH-1004

Cytoplasm0.342

Rank 2 · LXL04_019732 · OH-1004

Mitochondrion0.084

Rank 3 · LXL04_019732 · OH-1004

Cell membrane0.035

Rank 4 · LXL04_019732 · OH-1004

Endoplasmic reticulum0.023

Rank 5 · LXL04_019732 · 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.

PF25585.2zf-CCCH_DUS3L101-133 aa

PF25585.2zf-CCCH_DUS3L135-166 aa

PF01207.24Dus318-554 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_019732	`PF25585.2`	zf-CCCH_DUS3L	101	133	3.3e-16	59.6
LXL04_019732	`PF25585.2`	zf-CCCH_DUS3L	135	166	3.3e-16	59.6
LXL04_019732	`PF01207.24`	Dus	318	554	4.8e-50	171.2

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
`Q9T0J6`	Arabidopsis thaliana	tRNA-dihydrouridine(47) synthase [NAD(P)(+)]-like	61.045%	Swiss-Prot	strong database homology
`Q7XT07`	Oryza sativa subsp. japonica	tRNA-dihydrouridine(47) synthase [NAD(P)(+)]-like	57.594%	Swiss-Prot	strong database homology

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