LXL04_032528 | RubberDandelionOmics

Gene overview

LXL04_032528

Reference: OH-1004 Chr: Chr07 Coordinates: 24763826-24765159 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

606 bp · LXL04_032528|LXL04_032528|OH1004|cDNA

ATGGCCAACGCTACCGACGTAGATGCGCTGGACTTTGAGCCCGATGACGATGATCTCATGGACGAAGACGCAGCCGTTGACGTCGATGCTTCTTCTCCTAGGGATTCCGCTCCTATCCCTAAACTGAAATCCGCTATCACTGGTGGCTCTGTCGCCGCCGCTCCTAAGAAAACTAAAGGCCGTGGTTTCCGTGATGAAACCGACGCTGAACGTAACAACCGTATGTCCGGTCGTTTTGATTCGCTTGATTCCGATGGCGG...

CDS

Download CDS FASTA

606 bp · LXL04_032528|LXL04_032528|OH1004|CDS

ATGGCCAACGCTACCGACGTAGATGCGCTGGACTTTGAGCCCGATGACGATGATCTCATGGACGAAGACGCAGCCGTTGACGTCGATGCTTCTTCTCCTAGGGATTCCGCTCCTATCCCTAAACTGAAATCCGCTATCACTGGTGGCTCTGTCGCCGCCGCTCCTAAGAAAACTAAAGGCCGTGGTTTCCGTGATGAAACCGACGCTGAACGTAACAACCGTATGTCCGGTCGTTTTGATTCGCTTGATTCCGATGGCGG...

Protein

Download Protein FASTA

201 aa · LXL04_032528|LXL04_032528|OH1004|PROTEIN

MANATDVDALDFEPDDDDLMDEDAAVDVDASSPRDSAPIPKLKSAITGGSVAAAPKKTKGRGFRDETDAERNNRMSGRFDSLDSDGGPGPERSIEGWIILVTGVHEEAQEDDLQNAFGEFGEIKNLHLNLDRRTGFVKGYALIEYESFEEAEKAIAAMDGGELLTQTVNVDWAFSKGPFRRRNNRRRSPRGQRSRSPRRRF

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_032528`
TK1151 ID	TkA08G184890
OH-1004 ID	LXL04_032528
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
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_032528

Location Chr07:24763826-24765159 (-)

Description Similar to Y14: RNA-binding protein Y14

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g51510`	Core component of the splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junctions on mRNAs.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os05g0140500`	Core component of the splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junctions on mRNAs.	Uncovering Divergence of Rice Exon Junction Complex Core Heterodimer Gene Duplication Reveals Their Essential Role in Growth, Development, and Reproduction.2014 · DOI: 10.1104/pp.114.237958 Targeting MAGO proteins with a peptide aptamer reinforces their essential roles in multiple rice developmental pathways.2014 · DOI: 10.1111/tpj.12672
`Os03g0809900`	Core component of the splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junctions on mRNAs.	Uncovering Divergence of Rice Exon Junction Complex Core Heterodimer Gene Duplication Reveals Their Essential Role in Growth, Development, and Reproduction.2014 · DOI: 10.1104/pp.114.237958 Targeting MAGO proteins with a peptide aptamer reinforces their essential roles in multiple rice developmental pathways.2014 · DOI: 10.1111/tpj.12672

Functional annotation source

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Functional annotation source: OH1004 · LXL04_032528 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay Biological Process

GO:0000381 regulation of alternative mRNA splicing, via spliceosome Biological Process

GO:0000398 mRNA splicing, via spliceosome Biological Process

GO:0006397 mRNA processing Biological Process

GO:0006417 regulation of translation Biological Process

GO:0008380 RNA splicing Biological Process

GO:0010468 regulation of gene expression Biological Process

GO:0010628 positive regulation of gene expression Biological Process

GO:0051028 mRNA transport Biological Process

GO:0005634 nucleus Cellular Component

GO:0005654 nucleoplasm Cellular Component

GO:0005730 nucleolus Cellular Component

KEGG gene cross-reference

ath:AT1G51510

dosa:Os03g0809900

dosa:Os05g0140500

dre:503767

sasa:100196667

sasa:106581844

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.

Nucleus0.872

Rank 1 · LXL04_032528 · OH-1004

Cytoplasm0.368

Rank 2 · LXL04_032528 · OH-1004

Cell membrane0.024

Rank 3 · LXL04_032528 · OH-1004

Mitochondrion0.019

Rank 4 · LXL04_032528 · OH-1004

Endoplasmic reticulum0.017

Rank 5 · LXL04_032528 · 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.

PF00076.29RRM_199-166 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_032528	`PF00076.29`	RRM_1	99	166	1.2e-15	57.8

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
`F4I9J7`	Arabidopsis thaliana	RNA-binding protein Y14	64.062%	Swiss-Prot	strong database homology
`B7FAL5`	Oryza sativa subsp. japonica	RNA-binding protein Y14A	72.059%	Swiss-Prot	moderate database homology
`Q6ATR0`	Oryza sativa subsp. japonica	RNA-binding protein Y14B	52.410%	Swiss-Prot	strong database homology

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