LXL04_030352 | RubberDandelionOmics

Gene overview

LXL04_030352

Reference: OH-1004 Chr: Chr06 Coordinates: 114795015-114796033 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

672 bp · LXL04_030352|LXL04_030352|OH1004|cDNA

ATGGAATCAATTTCATGGTCATCTTCTCACATTTACCTCAGTAACAGAACCCCTGTCTCTCTTTCCTTCCACTTGTCGTCAACGAATCCTTCAACCCTCTCTTTCCCTCATCGTCACACGACGTTTTCCGCCTTGAAAACTAGTAGAGGTGATTTCAGCCCCCAGCAGGGTGGAGCTTCTTACTCTGCGGCTGATTTAGTGAGAAAGCCGACCGTAGATGTGAAGGACTATGGTAGGGGGTTTCCGAAAGTGGAATCAGA...

CDS

Download CDS FASTA

672 bp · LXL04_030352|LXL04_030352|OH1004|CDS

ATGGAATCAATTTCATGGTCATCTTCTCACATTTACCTCAGTAACAGAACCCCTGTCTCTCTTTCCTTCCACTTGTCGTCAACGAATCCTTCAACCCTCTCTTTCCCTCATCGTCACACGACGTTTTCCGCCTTGAAAACTAGTAGAGGTGATTTCAGCCCCCAGCAGGGTGGAGCTTCTTACTCTGCGGCTGATTTAGTGAGAAAGCCGACCGTAGATGTGAAGGACTATGGTAGGGGGTTTCCGAAAGTGGAATCAGA...

Protein

Download Protein FASTA

223 aa · LXL04_030352|LXL04_030352|OH1004|PROTEIN

MESISWSSSHIYLSNRTPVSLSFHLSSTNPSTLSFPHRHTTFSALKTSRGDFSPQQGGASYSAADLVRKPTVDVKDYGRGFPKVESEIEDDGGMDRGGEAWVDWEDRILEDTVPLVGFVRMILHSGKYESGERLSSEHENIILQRVLAHHPESEKKIGSGIDYIMVGNHPDFESSRCLFIVRKNGEMVDFSYWKCVKAFIRKKYPLQADSFINQHFQRRRRHD

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_030352`
TK1151 ID	TkAUNG001790
OH-1004 ID	LXL04_030352
Relationship / confidence	Sequence Supported Annotation Or Model Conflict / Review
Protein identity (%)	100.000
Protein coverage (%)	TK1151 100.000 / OH-1004 58.296 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_030352

Location Chr06:114795015-114796033 (+)

Description Similar to DCL: Protein DCL, chloroplastic

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g45230`	Required for normal plastid function and plant development.	No verified direct reference in this release
`At2g40030`	DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.	Atypical RNA polymerase subunits required for RNA-directed DNA methylation.2005 · DOI: 10.1038/ng1580 Reinforcement of silencing at transposons and highly repeated sequences requires the concerted action of two distinct RNA polymerases IV in Arabidopsis.2005 · DOI: 10.1101/gad.348405 The Arabidopsis chromatin-modifying nuclear siRNA pathway involves a nucleolar RNA processing center.2006 · DOI: 10.1016/j.cell.2006.05.031 PolIVb influences RNA-directed DNA methylation independently of its role in siRNA biogenesis.2008 · DOI: 10.1073/pnas.0709632105 NRPD1a and NRPD1b are required to maintain post-transcriptional RNA silencing and RNA-directed DNA methylation in Arabidopsis.2008 · DOI: 10.1111/j.1365-313x.2008.03525.x
`At5g62440`	May play a role in ribosome biogenesis and in determining the rate of cell division.	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_030352 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006351 DNA-templated transcription Biological Process

GO:0009658 chloroplast organization Biological Process

GO:0009793 embryo development ending in seed dormancy Biological Process

GO:0017126 nucleologenesis Biological Process

GO:0030422 siRNA processing Biological Process

GO:0035194 regulatory ncRNA-mediated post-transcriptional gene silencing Biological Process

GO:0050832 defense response to fungus Biological Process

GO:0051302 regulation of cell division Biological Process

GO:1901259 chloroplast rRNA processing Biological Process

GO:0000418 RNA polymerase IV complex Cellular Component

GO:0000419 RNA polymerase V complex Cellular Component

GO:0005634 nucleus Cellular Component

KEGG gene cross-reference

ath:AT1G45230

ath:AT2G40030

ath:AT5G62440

sly:544019

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.

Plastid0.924

Rank 1 · LXL04_030352 · OH-1004

Nucleus0.089

Rank 2 · LXL04_030352 · OH-1004

Mitochondrion0.043

Rank 3 · LXL04_030352 · OH-1004

Cytoplasm0.024

Rank 4 · LXL04_030352 · OH-1004

Cell membrane0.013

Rank 5 · LXL04_030352 · 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.

PF11523.14DUF3223120-196 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_030352	`PF11523.14`	DUF3223	120	196	1.5e-30	106.3

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
`Q9C642`	Arabidopsis thaliana	Protein DCL homolog, chloroplastic	72.000%	Swiss-Prot	moderate database homology
`Q5D869`	Arabidopsis thaliana	DNA-directed RNA polymerase V subunit 1	37.931%	Swiss-Prot	moderate database homology
`Q8L557`	Arabidopsis thaliana	Protein EMBRYO DEFECTIVE 514	41.667%	Swiss-Prot	weak database homology

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