LXL04_022502 | RubberDandelionOmics

Gene overview

LXL04_022502

Reference: OH-1004 Chr: Chr04 Coordinates: 151684598-151688285 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

3318 bp · LXL04_022502|LXL04_022502|OH1004|cDNA

ATGAGTAAAACAGTGCAGGTGTATGGATACCCCAATTTAGAATCTGCTGATGTAATTAAAACATCTCTGGAGAGGTATACTGGCACAGGGAGCATTTATGCTCTAGAGGTTAAAAGGTCAAACCGAGGGTCAAGATCATATGCAAAAGTACAGTTTACAACAAGGGAAAAAGCTGACTATATTCTAGAACTGGCTAATTCTAGGCGTTTGTGGTTTGGTACAACGTATTTAAAGGCTTTTGTAATGGATCATGACATTGA...

CDS

Download CDS FASTA

3318 bp · LXL04_022502|LXL04_022502|OH1004|CDS

ATGAGTAAAACAGTGCAGGTGTATGGATACCCCAATTTAGAATCTGCTGATGTAATTAAAACATCTCTGGAGAGGTATACTGGCACAGGGAGCATTTATGCTCTAGAGGTTAAAAGGTCAAACCGAGGGTCAAGATCATATGCAAAAGTACAGTTTACAACAAGGGAAAAAGCTGACTATATTCTAGAACTGGCTAATTCTAGGCGTTTGTGGTTTGGTACAACGTATTTAAAGGCTTTTGTAATGGATCATGACATTGA...

Protein

Download Protein FASTA

1105 aa · LXL04_022502|LXL04_022502|OH1004|PROTEIN

MSKTVQVYGYPNLESADVIKTSLERYTGTGSIYALEVKRSNRGSRSYAKVQFTTREKADYILELANSRRLWFGTTYLKAFVMDHDIEQRPKQFAFEMEGATLHFGCQVSKEILHVLCEMRNTSVMFGLRRLYFVVSYPTTCYKLQLSYENIWQVQLRRSRGNSSRFVVIQLYGAPRIYKKVEESVFSYYREVPDDQWVRATDFTPNFSIGQSSHLCLELPRDVDLPNLAHYFPDYEESNRQFSLVAGHSFSQNLDLVPIV...

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_022502`
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_022502

Location Chr04:151684598-151688285 (-)

Description Similar to RDR1: RNA-dependent RNA polymerase 1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g14790`	RNA-dependent direct polymerase involved in antiviral silencing.	Analysis of the involvement of an inducible Arabidopsis RNA-dependent RNA polymerase in antiviral defense.2003 · DOI: 10.1094/mpmi.2003.16.3.206 Small RNA deep sequencing reveals role for Arabidopsis thaliana RNA-dependent RNA polymerases in viral siRNA biogenesis.2009 · DOI: 10.1371/journal.pone.0004971 RNAi-mediated viral immunity requires amplification of virus-derived siRNAs in Arabidopsis thaliana.2010 · DOI: 10.1073/pnas.0904086107 Arabidopsis RNA-dependent RNA polymerases and dicer-like proteins in antiviral defense and small interfering RNA biogenesis during Turnip Mosaic Virus infection.2010 · DOI: 10.1105/tpc.109.073056
`At4g11130`	RNA-dependent direct polymerase involved in the production of small interfering RNAs (siRNAs).	Genetic and functional diversification of small RNA pathways in plants.2004 · DOI: 10.1371/journal.pbio.0020104 MicroRNA-targeted and small interfering RNA-mediated mRNA degradation is regulated by argonaute, dicer, and RNA-dependent RNA polymerase in Arabidopsis.2006 · DOI: 10.1105/tpc.106.042127 An SNF2 protein associated with nuclear RNA silencing and the spread of a silencing signal between cells in Arabidopsis.2007 · DOI: 10.1105/tpc.107.051540 Nuclear gene silencing directs reception of long-distance mRNA silencing in Arabidopsis.2007 · DOI: 10.1073/pnas.0706701104 siRNA-mediated methylation of Arabidopsis telomeres.2010 · DOI: 10.1371/journal.pgen.1000986 In vitro transcription activities of Pol IV, Pol V, and RDR2 reveal coupling of Pol IV and RDR2 for dsRNA synthesis in plant RNA silencing.2012 · DOI: 10.1016/j.molcel.2012.09.027 Structure and RNA template requirements of Arabidopsis RNA-DEPENDENT RNA POLYMERASE 2.2021 · DOI: 10.1073/pnas.2115899118
`At3g49500`	RNA-dependent RNA polymerase involved in post-transcriptional gene silencing (PTGS).	Arabidopsis SGS2 and SGS3 genes are required for posttranscriptional gene silencing and natural virus resistance.2000 · DOI: 10.1016/s0092-8674(00)80863-6 An RNA-dependent RNA polymerase gene in Arabidopsis is required for posttranscriptional gene silencing mediated by a transgene but not by a virus.2000 · DOI: 10.1016/s0092-8674(00)80864-8 Geminivirus VIGS of endogenous genes requires SGS2/SDE1 and SGS3 and defines a new branch in the genetic pathway for silencing in plants.2004 · DOI: 10.1111/j.1365-313x.2004.02103.x SGS3 and SGS2/SDE1/RDR6 are required for juvenile development and the production of trans-acting siRNAs in Arabidopsis.2004 · DOI: 10.1101/gad.1231804 The Putative RNA-dependent RNA polymerase RDR6 acts synergistically with ASYMMETRIC LEAVES1 and 2 to repress BREVIPEDICELLUS and MicroRNA165/166 in Arabidopsis leaf development.2005 · DOI: 10.1105/tpc.105.033449 A pathway for the biogenesis of trans-acting siRNAs in Arabidopsis.2005 · DOI: 10.1101/gad.1352605 Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis.2005 · DOI: 10.1016/j.cell.2005.11.035 DRB4-dependent TAS3 trans-acting siRNAs control leaf morphology through AGO7.2006 · DOI: 10.1016/j.cub.2006.03.035 Improperly terminated, unpolyadenylated mRNA of sense transgenes is targeted by RDR6-mediated RNA silencing in Arabidopsis.2007 · DOI: 10.1105/tpc.106.045724 Biochemical activities of Arabidopsis RNA-dependent RNA polymerase 6.2008 · DOI: 10.1074/jbc.m708983200 Small RNA deep sequencing reveals role for Arabidopsis thaliana RNA-dependent RNA polymerases in viral siRNA biogenesis.2009 · DOI: 10.1371/journal.pone.0004971 Unique functionality of 22-nt miRNAs in triggering RDR6-dependent siRNA biogenesis from target transcripts in Arabidopsis.2010 · DOI: 10.1038/nsmb.1866

Rice

Reference gene ID	Possible function	Papers / DOI
`Os02g0736200`	Probably involved in the RNA silencing pathway and required for the generation of small interfering RNAs (siRNAs).	No verified direct reference in this release
`Os04g0465700`	Probably involved in the RNA silencing pathway and required for the generation of small interfering RNAs (siRNAs).	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_022502 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006952 defense response Biological Process

GO:0009615 response to virus Biological Process

GO:0009616 RNAi-mediated antiviral immune response Biological Process

GO:0009751 response to salicylic acid Biological Process

GO:0010025 wax biosynthetic process Biological Process

GO:0010267 ta-siRNA processing Biological Process

GO:0010495 siRNA-mediated long-distance post-transcriptional gene silencing Biological Process

GO:0016441 post-transcriptional gene silencing Biological Process

GO:0030422 siRNA processing Biological Process

GO:0031047 regulatory ncRNA-mediated gene silencing Biological Process

GO:0048366 leaf development Biological Process

GO:0048467 gynoecium development Biological Process

KEGG gene cross-reference

ath:AT1G14790

ath:AT3G49500

ath:AT4G11130

dosa:Os02g0736200

dosa:Os04g0465700

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.

Nucleus0.484

Rank 1 · LXL04_022502 · OH-1004

Cytoplasm0.432

Rank 2 · LXL04_022502 · OH-1004

Cell membrane0.099

Rank 3 · LXL04_022502 · OH-1004

Endoplasmic reticulum0.043

Rank 4 · LXL04_022502 · OH-1004

Lysosome / Vacuole0.042

Rank 5 · LXL04_022502 · 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.

PF26250.1RRM_RdRP1_24-81 aa

PF24823.2PH_RDR2102-242 aa

PF26252.1RdRP_helical267-335 aa

PF05183.18RdRP358-921 aa

PF26253.1RdRP_head942-1095 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_022502	`PF26250.1`	RRM_RdRP1_2	4	81	1.5e-16	61.3
LXL04_022502	`PF24823.2`	PH_RDR2	102	242	2.5e-37	128.9
LXL04_022502	`PF26252.1`	RdRP_helical	267	335	5.1e-10	40.0
LXL04_022502	`PF05183.18`	RdRP	358	921	1.4e-197	658.7
LXL04_022502	`PF26253.1`	RdRP_head	942	1095	1.8e-45	155.4

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
`Q9LQV2`	Arabidopsis thaliana	RNA-dependent RNA polymerase 1	61.096%	Swiss-Prot	strong database homology
`O82504`	Arabidopsis thaliana	RNA-dependent RNA polymerase 2	39.235%	Swiss-Prot	moderate database homology
`Q9SG02`	Arabidopsis thaliana	RNA-dependent RNA polymerase 6	35.671%	Swiss-Prot	moderate database homology
`Q0DXS3`	Oryza sativa subsp. japonica	Probable RNA-dependent RNA polymerase 1	65.612%	Swiss-Prot	moderate database homology
`Q7XM31`	Oryza sativa subsp. japonica	Probable RNA-dependent RNA polymerase 2	39.982%	Swiss-Prot	moderate database homology

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