LXL04_017373 | RubberDandelionOmics

Gene overview

LXL04_017373

Reference: OH-1004 Chr: Chr03 Coordinates: 147741696-147744577 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1440 bp · LXL04_017373|LXL04_017373|OH1004|cDNA

ATGGCGGTCCATTCTCTCCTCCGGCGAGTCCTATTCAGATCACCACCGATTATTCCGTCATCAGCCGGCGTCAGAACTGCAGCCGCACCGTACCACGACGTTCAAATGAAAAACTACTCAACCGAATTCACCAAAGCGGAAGATCAGAACACCGAGAACAAGAAAGGAAAGTGGTTAACTTTGCCGCCTTTCAGTATTACCGTTAACGGTGCTTCATTGGGAAAAGATATTGTCGGAAGACGGCAGTCGACCAGTGAAGG...

CDS

Download CDS FASTA

1440 bp · LXL04_017373|LXL04_017373|OH1004|CDS

ATGGCGGTCCATTCTCTCCTCCGGCGAGTCCTATTCAGATCACCACCGATTATTCCGTCATCAGCCGGCGTCAGAACTGCAGCCGCACCGTACCACGACGTTCAAATGAAAAACTACTCAACCGAATTCACCAAAGCGGAAGATCAGAACACCGAGAACAAGAAAGGAAAGTGGTTAACTTTGCCGCCTTTCAGTATTACCGTTAACGGTGCTTCATTGGGAAAAGATATTGTCGGAAGACGGCAGTCGACCAGTGAAGG...

Protein

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479 aa · LXL04_017373|LXL04_017373|OH1004|PROTEIN

MAVHSLLRRVLFRSPPIIPSSAGVRTAAAPYHDVQMKNYSTEFTKAEDQNTENKKGKWLTLPPFSITVNGASLGKDIVGRRQSTSEGDANASTTTALKWVTQCCPQLPRSLVQKLFRLRQVRRETSEDSFSDQDVQAPVSRVKRVAAKDSMKPGDTIHLPISVQSSPIEKPECICSEEELKFLHDLELYKDSAIIVINKPPGMPVQGGIGIKRSLDELVGTYLRHDFSEPPRLVHRLDRDSSGILVLGRTQLSATVLHSV...

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_017373`
TK1151 ID	TkA02G046720
OH-1004 ID	LXL04_017373
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.800
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_017373

Location Chr03:147741696-147744577 (+)

Description Similar to At3g19440: RNA pseudouridine synthase 4, mitochondrial

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g19440`	RNA pseudouridine synthase 4, mitochondrial.	No verified direct reference in this release
`At1g78910`	RNA pseudouridine synthase 3, mitochondrial.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os08g0520100`	RNA pseudouridine synthase 3, mitochondrial.	No verified direct reference in this release
`Os09g0103500`	RNA pseudouridine synthase 4, mitochondrial.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_017373 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000455 enzyme-directed rRNA pseudouridine synthesis Biological Process

GO:0005634 nucleus Cellular Component

GO:0005739 mitochondrion Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0003723 RNA binding Molecular Function

GO:0009982 pseudouridine synthase activity Molecular Function

GO:0160141 23S rRNA pseudouridine(955/2504/2580) synthase activity Molecular Function

KEGG gene cross-reference

ath:AT1G78910

ath:AT3G19440

dosa:Os08g0520100

dosa:Os09g0103500

rty:RT0249

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.

Mitochondrion0.867

Rank 1 · LXL04_017373 · OH-1004

Nucleus0.083

Rank 2 · LXL04_017373 · OH-1004

Cytoplasm0.079

Rank 3 · LXL04_017373 · OH-1004

Plastid0.055

Rank 4 · LXL04_017373 · OH-1004

Cell membrane0.017

Rank 5 · LXL04_017373 · 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.

PF00849.28PseudoU_synth_2194-364 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_017373	`PF00849.28`	PseudoU_synth_2	194	364	5.3e-25	89.1

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
`Q9LT72`	Arabidopsis thaliana	RNA pseudouridine synthase 4, mitochondrial	53.942%	Swiss-Prot	strong database homology
`Q5XET6`	Arabidopsis thaliana	RNA pseudouridine synthase 3, mitochondrial	39.801%	Swiss-Prot	moderate database homology
`Q0J4D4`	Oryza sativa subsp. japonica	RNA pseudouridine synthase 3, mitochondrial	41.730%	Swiss-Prot	moderate database homology
`Q69K07`	Oryza sativa subsp. japonica	RNA pseudouridine synthase 4, mitochondrial	54.135%	Swiss-Prot	moderate database homology

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