LXL04_032978 | RubberDandelionOmics

Gene overview

LXL04_032978

Reference: OH-1004 Chr: Chr07 Coordinates: 32608588-32613686 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2853 bp · LXL04_032978|LXL04_032978|OH1004|cDNA

ATGTCaggaagaggaagaggaagGGGCCGTGGTCGTGGACGTGGCGGCGGTCCACCGTCGGAACAGTTAACGAACCTGTCTCTTGGTTCACCGTCGCCATCGACAGCAACGCCTGCCGCTACAGTAGTTTCTACCGGTAGAGTTCCGCAGCAACCGGCAATGCAGCAGAGTTCGGTTCAAGCTCCACCGGCACCGGTGGTTACTGCACAACAGGCGTCGAACGCACCAACACCGCCGCAGGCTTTAACGGTGGCCCCTAC...

CDS

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2853 bp · LXL04_032978|LXL04_032978|OH1004|CDS

ATGTCAGGAAGAGGAAGAGGAAGGGGCCGTGGTCGTGGACGTGGCGGCGGTCCACCGTCGGAACAGTTAACGAACCTGTCTCTTGGTTCACCGTCGCCATCGACAGCAACGCCTGCCGCTACAGTAGTTTCTACCGGTAGAGTTCCGCAGCAACCGGCAATGCAGCAGAGTTCGGTTCAAGCTCCACCGGCACCGGTGGTTACTGCACAACAGGCGTCGAACGCACCAACACCGCCGCAGGCTTTAACGGTGGCCCCTAC...

Protein

Download Protein FASTA

950 aa · LXL04_032978|LXL04_032978|OH1004|PROTEIN

MSGRGRGRGRGRGRGGGPPSEQLTNLSLGSPSPSTATPAATVVSTGRVPQQPAMQQSSVQAPPAPVVTAQQASNAPTPPQALTVAPTSTKMIKAPPRTGLGTLGRKCVIRANHFRVVLGEKDPYQYDVTITPEVISKPKSREILKMLCKLYKQSHLGNMLLAYDGTKSAFTAGPLPFESKEFVVNLTEANGREKEFKVNIKFAAIKDLDYLKQFLNRRQHDNPQETIQALDVVLREAATKENRQIVGRSLFSVEFGKGVL...

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_032978`
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_032978

Location Chr07:32608588-32613686 (+)

Description Similar to AGO1: Protein argonaute 1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`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
`At2g27880`	Involved in RNA-mediated post-transcriptional gene silencing (PTGS).	Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 5' terminal nucleotide.2008 · DOI: 10.1016/j.cell.2008.02.034 The mechanism selecting the guide strand from small RNA duplexes is different among argonaute proteins.2008 · DOI: 10.1093/pcp/pcn043

Rice

Reference gene ID	Possible function	Papers / DOI
`Os03g0800200`	Essential for the progression of premeiotic mitosis and meiosis during sporogenesis.	A germ cell specific gene of the ARGONAUTE family is essential for the progression of premeiotic mitosis and meiosis during sporogenesis in rice.2007 · DOI: 10.1105/tpc.107.053199
`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_032978 · 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:0007140 male meiotic nuclear division Biological Process

GO:0007143 female meiotic nuclear division Biological Process

GO:0009561 megagametogenesis Biological Process

GO:0009615 response to virus 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:0009955 adaxial/abaxial pattern specification Biological Process

GO:0009965 leaf morphogenesis Biological Process

KEGG gene cross-reference

ath:AT1G48410

ath:AT2G27880

dosa:Os02g0672200

dosa:Os03g0800200

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.

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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.

Cytoplasm0.766

Rank 1 · LXL04_032978 · OH-1004

Nucleus0.279

Rank 2 · LXL04_032978 · OH-1004

Cell membrane0.094

Rank 3 · LXL04_032978 · OH-1004

Mitochondrion0.055

Rank 4 · LXL04_032978 · OH-1004

Endoplasmic reticulum0.047

Rank 5 · LXL04_032978 · 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.

PF16486.12ArgoN105-234 aa

PF08699.16ArgoL1246-294 aa

PF02170.29PAZ304-424 aa

PF16488.11ArgoL2434-481 aa

PF16487.11ArgoMid492-568 aa

PF02171.24Piwi587-905 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_032978	`PF16486.12`	ArgoN	105	234	1.5e-31	110.4
LXL04_032978	`PF08699.16`	ArgoL1	246	294	1.6e-17	63.6
LXL04_032978	`PF02170.29`	PAZ	304	424	4.9e-25	88.6
LXL04_032978	`PF16488.11`	ArgoL2	434	481	1.1e-13	51.9
LXL04_032978	`PF16487.11`	ArgoMid	492	568	5.6e-10	40.1
LXL04_032978	`PF02171.24`	Piwi	587	905	5.7e-111	371.3

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.

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Protein	Organism	Description	Identity	Database	Confidence
`O04379`	Arabidopsis thaliana	Protein argonaute 1	57.883%	Swiss-Prot	strong database homology
`Q9SJK3`	Arabidopsis thaliana	Protein argonaute 5	55.346%	Swiss-Prot	strong database homology
`Q851R2`	Oryza sativa subsp. japonica	Protein argonaute MEL1	59.361%	Swiss-Prot	strong database homology
`Q6EU14`	Oryza sativa subsp. japonica	Protein argonaute 1A	55.403%	Swiss-Prot	strong database homology
`Q7XSA2`	Oryza sativa subsp. japonica	Protein argonaute 1B	55.861%	Swiss-Prot	strong database homology

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