LXL04_029860 | RubberDandelionOmics

Gene overview

LXL04_029860

Reference: OH-1004 Chr: Chr06 Coordinates: 102333915-102337485 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1819 bp · LXL04_029860|LXL04_029860|OH1004|cDNA

TGCGAATCCGCCTGTTCGCTCACAAAATCACACCCAAATTTTACAGCTCTTCCCCCTTTCTTtcgactctctctctcttcccCCCGACATTACTTCACAAATCGAACTTTCCAATTCACAGCACCGAACCCACCAAAGATCGAACAACACTTCCAGAAAAATCCGTAAATTCTGACGGCCCCCATTCATGGATTTATCGGAGCAAGAGGTAGACTTGTTCGGTGATTTGGAATTCGAAAATGAAGATACCCATAAAAAGG...

CDS

Download CDS FASTA

1632 bp · LXL04_029860|LXL04_029860|OH1004|CDS

ATGGATTTATCGGAGCAAGAGGTAGACTTGTTCGGTGATTTGGAATTCGAAAATGAAGATACCCATAAAAAGGAAGAAGATAGCCAACAATCCTCGTCATCTTCATCGTCATCGTCATCTGGTGGGTCGTCTTCCTCGTATTCATCTTCCAATCGCAGCAGTAGCGGAGGAGCGGGAAGTGGCAGTGGCAGTGATAGCAGCGGCGGTTCCGCCAGTCGTGGCGCTGCTGGCGGCGATGCTGGTGGTGCGGCTGTGGCTGG...

Protein

Download Protein FASTA

543 aa · LXL04_029860|LXL04_029860|OH1004|PROTEIN

MDLSEQEVDLFGDLEFENEDTHKKEEDSQQSSSSSSSSSSGGSSSSYSSSNRSSSGGAGSGSGSDSSGGSASRGAAGGDAGGAAVAGAEEVEEEEDNGEVKSSYYNQQYGYDDDYNVVEEDKDLFGSDNDEYVKTQIASPFPVPVLPQPPARNTNNPSRGGYGRGGRWQNDRGGAGILPRPGGGPFPQRQNYGYGSKFYAPRNDERFVSELKFSKSEETLSRKVIAFQEPSELGCYSRVESGEVYFDDSSLRLFKRLITE...

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_029860`
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_029860

Location Chr06:102333915-102337485 (+)

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

View annotation sources

Functional annotation source: OH1004 · LXL04_029860 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000448 cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) Biological Process

GO:0000956 nuclear-transcribed mRNA catabolic process Biological Process

GO:0006397 mRNA processing Biological Process

GO:0006402 mRNA catabolic process Biological Process

GO:0030846 termination of RNA polymerase II transcription, poly(A)-coupled Biological Process

GO:0031087 deadenylation-independent decapping of nuclear-transcribed mRNA Biological Process

GO:0050779 RNA destabilization Biological Process

GO:0071028 nuclear mRNA surveillance Biological Process

GO:0071035 nuclear polyadenylation-dependent rRNA catabolic process Biological Process

GO:0090304 nucleic acid metabolic process Biological Process

GO:0110154 RNA decapping Biological Process

GO:0110155 NAD-cap decapping Biological Process

KEGG gene cross-reference

afm:AFUA_6G05060

ani:ANIA_06514

ath:AT4G17620

ncr:NCU04191

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.

Cytoplasm0.525

Rank 1 · LXL04_029860 · OH-1004

Nucleus0.477

Rank 2 · LXL04_029860 · OH-1004

Mitochondrion0.090

Rank 3 · LXL04_029860 · OH-1004

Endoplasmic reticulum0.062

Rank 4 · LXL04_029860 · OH-1004

Cell membrane0.056

Rank 5 · LXL04_029860 · 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.

PF08652.18RAI1228-530 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_029860	`PF08652.18`	RAI1	228	530	3.7e-87	293.4

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	68.750%	Swiss-Prot	strong database homology

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