LXL04_018437 | RubberDandelionOmics

Gene overview

LXL04_018437

Reference: OH-1004 Chr: Chr04 Coordinates: 12938594-12939556 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

825 bp · LXL04_018437|LXL04_018437|OH1004|cDNA

ATGGCTGAGAGAGGCGGAGAACGCGGTGGATTCGGCAGGGGATTTGGTGACCGTGGCAGAGGCCGTGGTGGAGACCGTGGCAGAGGCCGCCGTCGTGGTCCTCGTCAAGCCGAAGAAGAAAAATGGGTTCCTTGCACCAAGCTCGGCCGTCTTGTGAAAGACGGTAGGATCACCAAACTCGAAGAAGTCTACCTTCACTCTCTTCCAATCAAGGAACACCAGATCATCGATCTGATCCTCCCTTCACTCAAGGACGAGGT...

CDS

Download CDS FASTA

825 bp · LXL04_018437|LXL04_018437|OH1004|CDS

ATGGCTGAGAGAGGCGGAGAACGCGGTGGATTCGGCAGGGGATTTGGTGACCGTGGCAGAGGCCGTGGTGGAGACCGTGGCAGAGGCCGCCGTCGTGGTCCTCGTCAAGCCGAAGAAGAAAAATGGGTTCCTTGCACCAAGCTCGGCCGTCTTGTGAAAGACGGTAGGATCACCAAACTCGAAGAAGTCTACCTTCACTCTCTTCCAATCAAGGAACACCAGATCATCGATCTGATCCTCCCTTCACTCAAGGACGAGGT...

Protein

Download Protein FASTA

274 aa · LXL04_018437|LXL04_018437|OH1004|PROTEIN

MAERGGERGGFGRGFGDRGRGRGGDRGRGRRRGPRQAEEEKWVPCTKLGRLVKDGRITKLEEVYLHSLPIKEHQIIDLILPSLKDEVMKIMPVQKQTRAGQRTRFKAFVVVGDSNGHVGLGVKCSKEVATAIRGAIILAKLSVIPVRRGYWGNKIGKPHTVPCKVTGKCGSVTVRLIPAPRGSGIVAARVPKKVLQMAGIDDVFTSSRGSTKTLGNFVKATFDCLLKTYGFLTPDFWRETRFSKSPFQEYTDLLAKPTTK...

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_018437`
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_018437

Location Chr04:12938594-12939556 (+)

Description Similar to RPS2D: 40S ribosomal protein S2-4

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g57490`	Small ribosomal subunit protein uS5w.	No verified direct reference in this release
`UniProt: Q93VB8`	Small ribosomal subunit protein uS5y/uS5u/uS5v.	No verified direct reference in this release
`At1g58380`	Small ribosomal subunit protein uS5z.	No verified direct reference in this release
`At2g41840`	Component of the ribosome, a large ribonucleoprotein complex responsible for the synthesis of proteins in the cell.	AtMBD6, a methyl CpG binding domain protein, maintains gene silencing in Arabidopsis by interacting with RNA binding proteins.2017 · DOI: 10.1007/s12038-016-9658-1

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_018437 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006412 translation Biological Process

GO:0031047 regulatory ncRNA-mediated gene silencing Biological Process

GO:0005634 nucleus Cellular Component

GO:0005730 nucleolus Cellular Component

GO:0005829 cytosol Cellular Component

GO:0009505 plant-type cell wall Cellular Component

GO:0009506 plasmodesma Cellular Component

GO:0022626 cytosolic ribosome Cellular Component

GO:0022627 cytosolic small ribosomal subunit Cellular Component

GO:0003723 RNA binding Molecular Function

GO:0003729 mRNA binding Molecular Function

GO:0003735 structural constituent of ribosome Molecular Function

KEGG gene cross-reference

ath:AT1G58380

ath:AT1G58684

ath:AT1G58983

ath:AT1G59359

ath:AT2G41840

ath:AT3G57490

ipu:100304556

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.

Cytoplasm0.786

Rank 1 · LXL04_018437 · OH-1004

Nucleus0.257

Rank 2 · LXL04_018437 · OH-1004

Mitochondrion0.103

Rank 3 · LXL04_018437 · OH-1004

Endoplasmic reticulum0.063

Rank 4 · LXL04_018437 · OH-1004

Cell membrane0.024

Rank 5 · LXL04_018437 · 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.

PF00333.27Ribosomal_S583-147 aa

PF03719.22Ribosomal_S5_C167-238 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_018437	`PF00333.27`	Ribosomal_S5	83	147	2.5e-30	105.0
LXL04_018437	`PF03719.22`	Ribosomal_S5_C	167	238	8.7e-26	89.9

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
`Q9SCM3`	Arabidopsis thaliana	Small ribosomal subunit protein uS5w	88.688%	Swiss-Prot	strong database homology
`Q93VB8`	Arabidopsis thaliana	Small ribosomal subunit protein uS5y/uS5u/uS5v	84.388%	Swiss-Prot	strong database homology
`Q8L8Y0`	Arabidopsis thaliana	Small ribosomal subunit protein uS5z	84.388%	Swiss-Prot	strong database homology
`P49688`	Arabidopsis thaliana	Small ribosomal subunit protein uS5x	83.122%	Swiss-Prot	strong database homology

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