LXL04_032360 | RubberDandelionOmics

Gene overview

LXL04_032360

Reference: OH-1004 Chr: Chr07 Coordinates: 21315857-21319524 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

3597 bp · LXL04_032360|LXL04_032360|OH1004|cDNA

ATGGAGTCCGAAAGAAATGACAAGGAAATGGTGGTCACCCAGGTCAGCATAGGTGGATTTGACACCAATGTCACAGCAAAACAGCTATTAGACTTCATAGAAAGAAAAGCAGGACTAGTTTTCAGGTGTAGACTAAAAAAATCCTCAACACCTCCCGACACATACCCGGAGTTTGATGCTGACCTGGACACCATTCAAAAACTCAATGACTACGAGAAGGTGGAACCCCATGCCTTTGTCCATTTCGTTGACCCTGATTC...

CDS

Download CDS FASTA

3597 bp · LXL04_032360|LXL04_032360|OH1004|CDS

ATGGAGTCCGAAAGAAATGACAAGGAAATGGTGGTCACCCAGGTCAGCATAGGTGGATTTGACACCAATGTCACAGCAAAACAGCTATTAGACTTCATAGAAAGAAAAGCAGGACTAGTTTTCAGGTGTAGACTAAAAAAATCCTCAACACCTCCCGACACATACCCGGAGTTTGATGCTGACCTGGACACCATTCAAAAACTCAATGACTACGAGAAGGTGGAACCCCATGCCTTTGTCCATTTCGTTGACCCTGATTC...

Protein

Download Protein FASTA

1198 aa · LXL04_032360|LXL04_032360|OH1004|PROTEIN

MESERNDKEMVVTQVSIGGFDTNVTAKQLLDFIERKAGLVFRCRLKKSSTPPDTYPEFDADLDTIQKLNDYEKVEPHAFVHFVDPDSVNSIKEAEGMCDLILDNNPLKVNLGPENPYKMNERRRTKLPFKLSNVVVEIGLLASRDQFLVGWRGPSSGVDFLIDPFDCSCKFLFTKDTAFSFKGTKDYAVIKCNYKVEFLARDVNDIKEYMDYSQSSMVLVFQLSSAPLITYRTADDDIEITHPSEMLDDDDPWIRTTDFT...

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_032360`
TK1151 ID	TkA08G169360
OH-1004 ID	LXL04_032360
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.700
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

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_032360

Location Chr07:21315857-21319524 (+)

Description Similar to RDR6: RNA-dependent RNA polymerase 6

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`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
`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
`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
`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

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_032360 · 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:0010492 maintenance of shoot apical meristem identity 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:0035194 regulatory ncRNA-mediated post-transcriptional gene silencing Biological Process

GO:0048366 leaf development Biological Process

KEGG gene cross-reference

ath:AT1G14790

ath:AT3G49500

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.

Nucleus0.565

Rank 1 · LXL04_032360 · OH-1004

Cytoplasm0.359

Rank 2 · LXL04_032360 · OH-1004

Cell membrane0.075

Rank 3 · LXL04_032360 · OH-1004

Endoplasmic reticulum0.037

Rank 4 · LXL04_032360 · OH-1004

Mitochondrion0.034

Rank 5 · LXL04_032360 · 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.

PF24572.2RBD_RDR610-110 aa

PF24577.2RDR6_2nd130-295 aa

PF24823.2PH_RDR2193-288 aa

PF26252.1RdRP_helical319-401 aa

PF05183.18RdRP419-1002 aa

PF26253.1RdRP_head1024-1179 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_032360	`PF24572.2`	RBD_RDR6	10	110	1e-27	97.2
LXL04_032360	`PF24577.2`	RDR6_2nd	130	295	8.9e-78	260.3
LXL04_032360	`PF24823.2`	PH_RDR2	193	288	3e-07	31.2
LXL04_032360	`PF26252.1`	RdRP_helical	319	401	1.9e-21	76.6
LXL04_032360	`PF05183.18`	RdRP	419	1002	6.5e-197	656.5
LXL04_032360	`PF26253.1`	RdRP_head	1024	1179	3.7e-42	144.7

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
`Q9SG02`	Arabidopsis thaliana	RNA-dependent RNA polymerase 6	62.948%	Swiss-Prot	strong database homology
`Q9LQV2`	Arabidopsis thaliana	RNA-dependent RNA polymerase 1	35.609%	Swiss-Prot	moderate database homology
`Q8LHH9`	Oryza sativa subsp. japonica	Probable RNA-dependent RNA polymerase SHL2	57.024%	Swiss-Prot	strong database homology
`Q7XM31`	Oryza sativa subsp. japonica	Probable RNA-dependent RNA polymerase 2	36.931%	Swiss-Prot	moderate database homology
`Q0DXS3`	Oryza sativa subsp. japonica	Probable RNA-dependent RNA polymerase 1	41.069%	Swiss-Prot	moderate database homology

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