LXL04_039103 | RubberDandelionOmics

Gene overview

LXL04_039103

Reference: OH-1004 Chr: Chr09 Coordinates: 59326418-59332743 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2886 bp · LXL04_039103|LXL04_039103|OH1004|cDNA

ATGCCCACAAGGCAAATCAAAGAAGTAGTGGAACAACACCTTGTGATCAAACCGAAATCAAACTTACAAAATCAGATGCAAAAAACCCCCAACGTATTCCCAGAAGAAAATGGGAGTTGTCCACCTTGTACGACTCACGAAAACCACCATCATCAGCCACACAGGAACAAAGcaagaagaagaggaagaggaagaggTGGCCGGAAATCATCTGATCAAGAAACCCGGCGGCCATGTGCGGTGGCTGCTTCACCAAATCC...

CDS

Download CDS FASTA

2886 bp · LXL04_039103|LXL04_039103|OH1004|CDS

ATGCCCACAAGGCAAATCAAAGAAGTAGTGGAACAACACCTTGTGATCAAACCGAAATCAAACTTACAAAATCAGATGCAAAAAACCCCCAACGTATTCCCAGAAGAAAATGGGAGTTGTCCACCTTGTACGACTCACGAAAACCACCATCATCAGCCACACAGGAACAAAGCAAGAAGAAGAGGAAGAGGAAGAGGTGGCCGGAAATCATCTGATCAAGAAACCCGGCGGCCATGTGCGGTGGCTGCTTCACCAAATCC...

Protein

Download Protein FASTA

961 aa · LXL04_039103|LXL04_039103|OH1004|PROTEIN

MPTRQIKEVVEQHLVIKPKSNLQNQMQKTPNVFPEENGSCPPCTTHENHHHQPHRNKARRRGRGRGGRKSSDQETRRPCAVAASPNPADTQDKISEMGFPWSNKSLRFAPRPGYGQTGTVCIVKANHFMAQLPDKDLNQYDVSIFPEVTSKSWNRAIMGELVKRYKESDLGMRLPAYDGRKCLYTAGELPFVWKEFRIKMVDEDDGINSPKREREYKVVIRFVAHVNLHHLGQFLAGKRADGSQEAIQILDIVLKELSTK...

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_039103`
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_039103

Location Chr09:59326418-59332743 (+)

Description Similar to AGO10: Protein argonaute 10

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g43810`	Involved in RNA-mediated post-transcriptional gene silencing (PTGS).	Redundant and specific roles of the ARGONAUTE proteins AGO1 and ZLL in development and small RNA-directed gene silencing.2009 · DOI: 10.1371/journal.pgen.1000646 microRNA-directed cleavage and translational repression of the copper chaperone for superoxide dismutase mRNA in Arabidopsis.2010 · DOI: 10.1111/j.1365-313x.2010.04162.x
`At1g48410`	Involved in RNA-mediated post-transcriptional gene silencing (PTGS).	Arabidopsis ARGONAUTE1 is an RNA Slicer that selectively recruits microRNAs and short interfering RNAs.2005 · DOI: 10.1073/pnas.0505461102 Cucumber mosaic virus-encoded 2b suppressor inhibits Arabidopsis Argonaute1 cleavage activity to counter plant defense.2006 · DOI: 10.1101/gad.1495506 Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 5' terminal nucleotide.2008 · DOI: 10.1016/j.cell.2008.02.034 Arabidopsis DRB4, AGO1, AGO7, and RDR6 participate in a DCL4-initiated antiviral RNA silencing pathway negatively regulated by DCL1.2008 · DOI: 10.1073/pnas.0805760105 Redundant and specific roles of the ARGONAUTE proteins AGO1 and ZLL in development and small RNA-directed gene silencing.2009 · DOI: 10.1371/journal.pgen.1000646 The Arabidopsis thaliana double-stranded RNA binding protein DRB1 directs guide strand selection from microRNA duplexes.2009 · DOI: 10.1261/rna.1646909 Unique functionality of 22-nt miRNAs in triggering RDR6-dependent siRNA biogenesis from target transcripts in Arabidopsis.2010 · DOI: 10.1038/nsmb.1866 AGO1 defines a novel locus of Arabidopsis controlling leaf development.1998 · DOI: 10.1093/emboj/17.1.170

Rice

Reference gene ID	Possible function	Papers / DOI
`Os06g0597400`	Probably involved in the RNA silencing pathway.	No verified direct reference in this release
`Os02g0672200`	Involved in the RNA silencing pathway, especially during antiviral responses.	No verified direct reference in this release
`Os04g0566500`	Involved in the RNA silencing pathway, especially during antiviral responses.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_039103 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006351 DNA-templated transcription Biological Process

GO:0006417 regulation of translation Biological Process

GO:0009616 RNAi-mediated antiviral immune response Biological Process

GO:0009733 response to auxin Biological Process

GO:0009753 response to jasmonic acid Biological Process

GO:0009850 auxin metabolic process Biological Process

GO:0009934 regulation of meristem structural organization Biological Process

GO:0009955 adaxial/abaxial pattern specification Biological Process

GO:0009965 leaf morphogenesis Biological Process

GO:0010072 primary shoot apical meristem specification Biological Process

GO:0010218 response to far red light Biological Process

GO:0010267 ta-siRNA processing Biological Process

KEGG gene cross-reference

ath:AT1G48410

ath:AT5G43810

dosa:Os02g0672200

osa:9269490

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.

Cytoplasm0.657

Rank 1 · LXL04_039103 · OH-1004

Nucleus0.358

Rank 2 · LXL04_039103 · OH-1004

Mitochondrion0.077

Rank 3 · LXL04_039103 · OH-1004

Cell membrane0.073

Rank 4 · LXL04_039103 · OH-1004

Endoplasmic reticulum0.050

Rank 5 · LXL04_039103 · 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.

PF16486.12ArgoN121-254 aa

PF08699.16ArgoL1264-314 aa

PF02170.29PAZ347-450 aa

PF16488.11ArgoL2460-506 aa

PF16487.11ArgoMid517-594 aa

PF02171.24Piwi609-928 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_039103	`PF16486.12`	ArgoN	121	254	1.4e-33	117.0
LXL04_039103	`PF08699.16`	ArgoL1	264	314	9.4e-20	70.7
LXL04_039103	`PF02170.29`	PAZ	347	450	5.6e-29	101.3
LXL04_039103	`PF16488.11`	ArgoL2	460	506	1.9e-16	60.7
LXL04_039103	`PF16487.11`	ArgoMid	517	594	3.6e-14	53.5
LXL04_039103	`PF02171.24`	Piwi	609	928	5.4e-116	387.8

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
`Q9XGW1`	Arabidopsis thaliana	Protein argonaute 10	83.908%	Swiss-Prot	strong database homology
`O04379`	Arabidopsis thaliana	Protein argonaute 1	72.398%	Swiss-Prot	strong database homology
`Q69VD5`	Oryza sativa subsp. japonica	Protein argonaute PNH1	79.358%	Swiss-Prot	strong database homology
`Q6EU14`	Oryza sativa subsp. japonica	Protein argonaute 1A	72.666%	Swiss-Prot	strong database homology
`Q7XSA2`	Oryza sativa subsp. japonica	Protein argonaute 1B	73.198%	Swiss-Prot	strong database homology

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