LXL04_022780 | RubberDandelionOmics

Gene overview

LXL04_022780

Reference: OH-1004 Chr: Chr05 Coordinates: 8931449-8934235 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1479 bp · LXL04_022780|LXL04_022780|OH1004|cDNA

ATGGATAAGCTCGAAAAGGCACCAAAAGAGGTTCTGGTGGACATCGTGAAGCTGGCACAAAAGCGAGAAATGAAAGGCAGTAATGGAGGCTGGAAGGAGTTTTTGACTGTTTACGACAAGAAAGTTGGGGTCAGCTTGAGTGATCCAGCAAGAAGGTCCCCTGAAGCATTGCTTGCTTTCTTGAATACATTCACTAACGTTGATGATTTAAAGTTCTTTGATAAAGTCGCGGAGAAACATTTCAGCAATGAGCATATCGA...

CDS

Download CDS FASTA

1479 bp · LXL04_022780|LXL04_022780|OH1004|CDS

ATGGATAAGCTCGAAAAGGCACCAAAAGAGGTTCTGGTGGACATCGTGAAGCTGGCACAAAAGCGAGAAATGAAAGGCAGTAATGGAGGCTGGAAGGAGTTTTTGACTGTTTACGACAAGAAAGTTGGGGTCAGCTTGAGTGATCCAGCAAGAAGGTCCCCTGAAGCATTGCTTGCTTTCTTGAATACATTCACTAACGTTGATGATTTAAAGTTCTTTGATAAAGTCGCGGAGAAACATTTCAGCAATGAGCATATCGA...

Protein

Download Protein FASTA

492 aa · LXL04_022780|LXL04_022780|OH1004|PROTEIN

MDKLEKAPKEVLVDIVKLAQKREMKGSNGGWKEFLTVYDKKVGVSLSDPARRSPEALLAFLNTFTNVDDLKFFDKVAEKHFSNEHIEKKTDKLSPEQELVYKTVGHPQYAQSYSFPSYEEGWVTTKERKKAKANRSNEMVAIDCEMVLCEDGTDALVRVCVVDRELKVKLDELVKPDKPVADYKTNITGVTAKDLEHVTCSLEDIQGSMRKLLSRGTILIGHSLNNDLQVLKIDHSRVIDTSLVFKYWSGSNFRRPSLND...

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_022780`
Source version	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_022780

Location Chr05:8931449-8934235 (-)

Description Similar to SDN1: Small RNA degrading nuclease 1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g67240`	3'-5' exonuclease degrading single-stranded small RNAs.	No verified direct reference in this release
`At3g50100`	3'-5' exonuclease degrading single-stranded small RNAs.	Degradation of microRNAs by a family of exoribonucleases in Arabidopsis.2008 · DOI: 10.1126/science.1163728
`At5g05540`	3'-5' exonuclease degrading single-stranded small RNAs.	No verified direct reference in this release
`At3g50090`	Putative 3'-5' exonuclease degrading single-stranded small RNAs.	No verified direct reference in this release
`At5g25800`	Probable 3'-5' exonuclease degrading single-stranded small 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_022780 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006351 DNA-templated transcription Biological Process

GO:0010587 miRNA catabolic process Biological Process

GO:0031125 rRNA 3'-end processing Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0016592 mediator complex Cellular Component

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

GO:0003676 nucleic acid binding Molecular Function

GO:0003723 RNA binding Molecular Function

GO:0004527 exonuclease activity Molecular Function

GO:0008408 3'-5' exonuclease activity Molecular Function

GO:0035198 miRNA binding Molecular Function

KEGG gene cross-reference

ath:AT3G50100

ath:AT5G05540

ath:AT5G67240

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.

Nucleus0.637

Rank 1 · LXL04_022780 · OH-1004

Cytoplasm0.340

Rank 2 · LXL04_022780 · OH-1004

Mitochondrion0.076

Rank 3 · LXL04_022780 · OH-1004

Cell membrane0.057

Rank 4 · LXL04_022780 · OH-1004

Endoplasmic reticulum0.036

Rank 5 · LXL04_022780 · 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.

PF00929.32RNase_T140-289 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_022780	`PF00929.32`	RNase_T	140	289	2.3e-09	38.7

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
`Q8RXK2`	Arabidopsis thaliana	Small RNA degrading nuclease 3	50.679%	Swiss-Prot	strong database homology
`A3KPE8`	Arabidopsis thaliana	Small RNA degrading nuclease 1	52.323%	Swiss-Prot	strong database homology
`Q9FFG1`	Arabidopsis thaliana	Small RNA degrading nuclease 2	49.000%	Swiss-Prot	moderate database homology
`Q9SN09`	Arabidopsis thaliana	Putative small RNA degrading nuclease 4	46.372%	Swiss-Prot	moderate database homology
`Q8L7M4`	Arabidopsis thaliana	Small RNA degrading nuclease 5	45.181%	Swiss-Prot	weak database homology

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