LXL04_023965 | RubberDandelionOmics

Gene overview

LXL04_023965

Reference: OH-1004 Chr: Chr05 Coordinates: 75809278-75810364 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

468 bp · LXL04_023965|LXL04_023965|OH1004|cDNA

ATGAATCCACCAGCGATGGCTGCATGGCAGCGAATGATGATTTCCGGCAGCTCTAGAGACGGTGCTGCCCATGTGTTTGGCATTCAAAATCCATACACTGAGGGTCTTAACTATGCTATTTTACAGGTAAATTTGGAAAAGGAATATTTTGGAAAAAGGAAACAATGTATTTTGTGTCTATATGGTACAGCCCAAAATAGAAGGTTATCAGATTATCCGTTGTTCGCAAATCCATCGGTCCAAAAACATAGCAAGAAAGC...

CDS

Download CDS FASTA

402 bp · LXL04_023965|LXL04_023965|OH1004|CDS

ATGAATCCACCAGCGATGGCTGCATGGCAGCGAATGATGATTTCCGGCAGCTCTAGAGACGGTGCTGCCCATGTGTTTGGCATTCAAAATCCATACACTGAGGGTCTTAACTATGCTATTTTACAGGTAAATTTGGAAAAGGAATATTTTGGAAAAAGGAAACAATGTATTTTGTGTCTATATGGTACAGCCCAAAATAGAAGGTTATCAGATTATCCGTTGTTCGCAAATCCATCGGTCCAAAAACATAGCAAGAAAGC...

Protein

Download Protein FASTA

133 aa · LXL04_023965|LXL04_023965|OH1004|PROTEIN

MNPPAMAAWQRMMISGSSRDGAAHVFGIQNPYTEGLNYAILQVNLEKEYFGKRKQCILCLYGTAQNRRLSDYPLFANPSVQKHSKKAKISWIQSFLAGVPFIVVGYRDDSSRLVRTERLRTKDMTHRVKMKNY

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_023965`
TK1151 ID	TkA03G581210
OH-1004 ID	LXL04_023965
Relationship / confidence	Multi Candidate From Tk1151 / Complex relationship
Protein identity (%)	84.600
Protein coverage (%)	TK1151 79.817 / OH-1004 68.421 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_023965

Location Chr05:75809278-75810364 (+)

Description Similar to At4g17620: Decapping nuclease DXO homolog, chloroplastic

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g17620`	Decapping enzyme for NAD-capped RNAs: specifically hydrolyzes the nicotinamide adenine dinucleotide (NAD) cap from a subset of RNAs by removing the entire NAD moiety from the 5'-end of an NAD-capped RNA.	Arabidopsis DXO1 links RNA turnover and chloroplast function independently of its enzymatic activity.2019 · DOI: 10.1093/nar/gkz100

Rice

No hit for this species in the current source table.

Functional annotation source

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Functional annotation source: OH1004 · LXL04_023965 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000956 nuclear-transcribed mRNA catabolic process Biological Process

GO:0006402 mRNA catabolic process Biological Process

GO:0050779 RNA destabilization Biological Process

GO:0071028 nuclear mRNA surveillance Biological Process

GO:0090304 nucleic acid metabolic process Biological Process

GO:0110154 RNA decapping Biological Process

GO:0110155 NAD-cap decapping Biological Process

GO:0005634 nucleus Cellular Component

GO:0005829 cytosol Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0000166 nucleotide binding Molecular Function

GO:0000175 3'-5'-RNA exonuclease activity Molecular Function

KEGG gene cross-reference

ath:AT4G17620

xla:496313

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.

Cytoplasm0.351

Rank 1 · LXL04_023965 · OH-1004

Nucleus0.307

Rank 2 · LXL04_023965 · OH-1004

Mitochondrion0.209

Rank 3 · LXL04_023965 · OH-1004

Extracellular0.098

Rank 4 · LXL04_023965 · OH-1004

Cell membrane0.075

Rank 5 · LXL04_023965 · 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.

PF08652.18RAI180-131 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_023965	`PF08652.18`	RAI1	80	131	1.9e-11	44.6

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q8RY73`	Arabidopsis thaliana	NAD-capped RNA hydrolase DXO1	72.093%	Swiss-Prot	weak database homology

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