LXL04_009567 | RubberDandelionOmics

Gene overview

LXL04_009567

Reference: OH-1004 Chr: Chr02 Coordinates: 129081004-129084708 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

3357 bp · LXL04_009567|LXL04_009567|OH1004|cDNA

ATGGCGGTAGAACAGAGAGACACAGCCACTGTCCGAGTCTCAAACATTCCCCGCTCAGTCACTGCCAAAGACCTCCTCGACTTCCTCGAATCCCACACCGGAAAATCCACCGTCTTCGCCTGCGAAATATCCTCCGATCACAAAAACTGGAAGTCTAGAGGCTTCGGTCGTGTCCAATTCGAAACCCTAGAATCCAAGTCCAACGCGATTGCCCTTTCCGCACAGGGCAACCTCTGCCTCAAGGGTTTCAACCTCTCCCT...

CDS

Download CDS FASTA

3357 bp · LXL04_009567|LXL04_009567|OH1004|CDS

ATGGCGGTAGAACAGAGAGACACAGCCACTGTCCGAGTCTCAAACATTCCCCGCTCAGTCACTGCCAAAGACCTCCTCGACTTCCTCGAATCCCACACCGGAAAATCCACCGTCTTCGCCTGCGAAATATCCTCCGATCACAAAAACTGGAAGTCTAGAGGCTTCGGTCGTGTCCAATTCGAAACCCTAGAATCCAAGTCCAACGCGATTGCCCTTTCCGCACAGGGCAACCTCTGCCTCAAGGGTTTCAACCTCTCCCT...

Protein

Download Protein FASTA

1118 aa · LXL04_009567|LXL04_009567|OH1004|PROTEIN

MAVEQRDTATVRVSNIPRSVTAKDLLDFLESHTGKSTVFACEISSDHKNWKSRGFGRVQFETLESKSNAIALSAQGNLCLKGFNLSLTHSLDDVIFRPVDPQNRFEQGFLRTGLLSKSDCMYVLESWGDVKAWVLPERKSLEFWVKHCGDLYRLELQFSDVLEASPCCIDSEEPTAVLLKLKHAPKLYQRLSGSKVSPRFTADRYHVCKEDFEFTWVRTTDFSSKKSIGQSSTLCLEFKHGSLALNSFKTLPFYIKDLVK...

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_009567`
TK1151 ID	TkA03G448890
OH-1004 ID	LXL04_009567
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.800
Protein coverage (%)	TK1151 100.000 / OH-1004 100.000 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_009567

Location Chr02:129081004-129084708 (-)

Description Similar to RDR2: RNA-dependent RNA polymerase 2

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`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
`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

Rice

Reference gene ID	Possible function	Papers / DOI
`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
`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
`Os01g0527600`	Involved in the RNA silencing pathway.	The small interfering RNA production pathway is required for shoot meristem initiation in rice.2007 · DOI: 10.1073/pnas.0704339104

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_009567 · 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:0009751 response to salicylic acid Biological Process

GO:0010025 wax biosynthetic process Biological Process

GO:0010492 maintenance of shoot apical meristem identity Biological Process

GO:0010495 siRNA-mediated long-distance post-transcriptional gene silencing 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:0060148 positive regulation of post-transcriptional gene silencing Biological Process

GO:0140745 siRNA transcription Biological Process

GO:0005634 nucleus Cellular Component

KEGG gene cross-reference

ath:AT1G14790

ath:AT4G11130

dosa:Os01g0527600

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.

Nucleus0.588

Rank 1 · LXL04_009567 · OH-1004

Cytoplasm0.360

Rank 2 · LXL04_009567 · OH-1004

Cell membrane0.060

Rank 3 · LXL04_009567 · OH-1004

Plastid0.037

Rank 4 · LXL04_009567 · OH-1004

Endoplasmic reticulum0.034

Rank 5 · LXL04_009567 · 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.

PF26250.1RRM_RdRP1_210-93 aa

PF24823.2PH_RDR2110-261 aa

PF26252.1RdRP_helical277-355 aa

PF05183.18RdRP378-955 aa

PF26253.1RdRP_head977-1111 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_009567	`PF26250.1`	RRM_RdRP1_2	10	93	7.2e-27	94.4
LXL04_009567	`PF24823.2`	PH_RDR2	110	261	1.7e-56	191.2
LXL04_009567	`PF26252.1`	RdRP_helical	277	355	6.5e-12	46.1
LXL04_009567	`PF05183.18`	RdRP	378	955	2.3e-186	621.7
LXL04_009567	`PF26253.1`	RdRP_head	977	1111	1.3e-36	126.7

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
`O82504`	Arabidopsis thaliana	RNA-dependent RNA polymerase 2	56.429%	Swiss-Prot	strong database homology
`Q9LQV2`	Arabidopsis thaliana	RNA-dependent RNA polymerase 1	39.982%	Swiss-Prot	moderate database homology
`Q7XM31`	Oryza sativa subsp. japonica	Probable RNA-dependent RNA polymerase 2	51.659%	Swiss-Prot	strong database homology
`Q0DXS3`	Oryza sativa subsp. japonica	Probable RNA-dependent RNA polymerase 1	44.534%	Swiss-Prot	moderate database homology
`Q8LHH9`	Oryza sativa subsp. japonica	Probable RNA-dependent RNA polymerase SHL2	36.489%	Swiss-Prot	moderate database homology

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