LXL04_010412 | RubberDandelionOmics

Gene overview

LXL04_010412

Reference: OH-1004 Chr: Chr02 Coordinates: 146211333-146213007 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

912 bp · LXL04_010412|LXL04_010412|OH1004|cDNA

TTTAACATTTTTTTGGTAAAAATATCTATCCTCTTTCTCTCTTTCGTTCATCTTTTGCTCAACTGGATAAACCCCCTACCCATAGTCTTTCTCTGTATTCCTTTGTCTCCCAACACCAATTGCTCGAGCTTCTTCAAAATGGCCACAATCTCATCAGCCATGATTTCATCAACCAGTTACCTCCATCACCACTCAACCTCTAAATCCTTCAAAACCCAGCTACCCAATTATTTCAAATTAAACCCCAACATTCCTCAAAC...

CDS

Download CDS FASTA

900 bp · LXL04_010412|LXL04_010412|OH1004|CDS

TTGGTAAAAATATCTATCCTCTTTCTCTCTTTCGTTCATCTTTTGCTCAACTGGATAAACCCCCTACCCATAGTCTTTCTCTGTATTCCTTTGTCTCCCAACACCAATTGCTCGAGCTTCTTCAAAATGGCCACAATCTCATCAGCCATGATTTCATCAACCAGTTACCTCCATCACCACTCAACCTCTAAATCCTTCAAAACCCAGCTACCCAATTATTTCAAATTAAACCCCAACATTCCTCAAACTTCCACCAGATT...

Protein

Download Protein FASTA

299 aa · LXL04_010412|LXL04_010412|OH1004|PROTEIN

MVKISILFLSFVHLLLNWINPLPIVFLCIPLSPNTNCSSFFKMATISSAMISSTSYLHHHSTSKSFKTQLPNYFKLNPNIPQTSTRFTISPVVSNPRQPTRLLSVAEEAPAAVVTLDPTSEAARRLYVGNIPRTTNNDELQKVFEEHGAVEKVEVMYDKYSGRSRRFGFVTMKTVDDVNAAIEKLNGTEIGGRKIKVNVTEKPLNGVVSILEAEETPFVDSPYKLYVGNLAKTVTSETLKTFFAEKGNVVGAKVSRVPGT...

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_010412`
TK1151 ID	TkA03G526110
OH-1004 ID	LXL04_010412
Relationship / confidence	Rbh Sequence Supported / Probable
Protein identity (%)	99.100
Protein coverage (%)	TK1151 95.473 / OH-1004 77.592 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_010412

Location Chr02:146211333-146213007 (+)

Description Similar to PSRP2: 30S ribosomal protein 2, chloroplastic

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g52150`	Component of the chloroplast ribosome (chloro-ribosome), a dedicated translation machinery responsible for the synthesis of chloroplast genome-encoded proteins, including proteins of the transcription and translation machinery and components of the photosynthetic apparatus.	Functional characterization of a plastid-specific ribosomal protein PSRP2 in Arabidopsis thaliana under abiotic stress conditions.2013 · DOI: 10.1016/j.plaphy.2013.10.027
`At3g52380`	Could be involved in splicing and/or processing of chloroplast RNAs.	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_010412 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006397 mRNA processing Biological Process

GO:0009409 response to cold Biological Process

GO:0009414 response to water deprivation Biological Process

GO:0009651 response to salt stress Biological Process

GO:0010029 regulation of seed germination Biological Process

GO:0031425 chloroplast RNA processing Biological Process

GO:0080148 negative regulation of response to water deprivation Biological Process

GO:1900140 regulation of seedling development Biological Process

GO:1901001 negative regulation of response to salt stress Biological Process

GO:1901259 chloroplast rRNA processing Biological Process

GO:0005829 cytosol Cellular Component

GO:0005840 ribosome Cellular Component

KEGG gene cross-reference

ath:AT3G52150

ath:AT3G52380

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.

Plastid0.966

Rank 1 · LXL04_010412 · OH-1004

Mitochondrion0.042

Rank 2 · LXL04_010412 · OH-1004

Nucleus0.029

Rank 3 · LXL04_010412 · OH-1004

Cytoplasm0.023

Rank 4 · LXL04_010412 · OH-1004

Cell membrane0.013

Rank 5 · LXL04_010412 · 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.

PF22976.3RRM_10124-194 aa

PF00076.29RRM_1126-196 aa

PF00076.29RRM_1225-295 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_010412	`PF22976.3`	RRM_10	124	194	3.8e-10	40.5
LXL04_010412	`PF00076.29`	RRM_1	126	196	7.5e-41	138.6
LXL04_010412	`PF00076.29`	RRM_1	225	295	7.5e-41	138.6

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
`Q8VYM4`	Arabidopsis thaliana	Small ribosomal subunit protein cS22	69.744%	Swiss-Prot	moderate database homology
`Q39061`	Arabidopsis thaliana	RNA-binding protein CP33, chloroplastic	42.458%	Swiss-Prot	moderate database homology

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