LXL04_014961 | RubberDandelionOmics

Gene overview

LXL04_014961

Reference: OH-1004 Chr: Chr03 Coordinates: 60485818-60490751 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

3279 bp · LXL04_014961|LXL04_014961|OH1004|cDNA

ATGGTGAGGAAGAAGAGGACTGAAACTTCAGGGGAGGGCTCTCAGCCTCAGGAGTTTGCTTCTGGACAAGGTAGTGGTGCTCAAAGGCCGCCACCTCAGCAACAACAGcagggtggtggtggtggttacCAGGGAAGAGGACAGGGTGGTTATCAAGGCAGAGGGCAGGGTGGTGGTTATCAAGGAGGACAAGGACAAGGCGGTGGTTACCAAGGTGGAGGAGGACAAGGTGGTTACCAAGGCGGACCACCTCAAGGTGG...

CDS

Download CDS FASTA

3279 bp · LXL04_014961|LXL04_014961|OH1004|CDS

ATGGTGAGGAAGAAGAGGACTGAAACTTCAGGGGAGGGCTCTCAGCCTCAGGAGTTTGCTTCTGGACAAGGTAGTGGTGCTCAAAGGCCGCCACCTCAGCAACAACAGCAGGGTGGTGGTGGTGGTTACCAGGGAAGAGGACAGGGTGGTTATCAAGGCAGAGGGCAGGGTGGTGGTTATCAAGGAGGACAAGGACAAGGCGGTGGTTACCAAGGTGGAGGAGGACAAGGTGGTTACCAAGGCGGACCACCTCAAGGTGG...

Protein

Download Protein FASTA

1092 aa · LXL04_014961|LXL04_014961|OH1004|PROTEIN

MVRKKRTETSGEGSQPQEFASGQGSGAQRPPPQQQQQGGGGGYQGRGQGGYQGRGQGGGYQGGQGQGGGYQGGGGQGGYQGGPPQGGGGYQGGQQPQGGRGWVQRGGPPPQRGGPPQQYYGGPPDQGQQQRPPRGTAPPQRRGGPSRPSVPELYQATQTPQQPVATLQPTPHADVHHGESSSMSSTDQMADESAAQFQQLSVQQEEPLPIQAPPASSKSMRFPQRPGKGSTGIRCIVKANHFFAELPDKDLHQYDVTITP...

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_014961`
TK1151 ID	TkA02G380650
OH-1004 ID	LXL04_014961
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	97.600
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

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_014961

Location Chr03:60485818-60490751 (-)

Description Similar to AGO1B: Protein argonaute 1B

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

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

Rice

Reference gene ID	Possible function	Papers / DOI
`Os04g0566500`	Involved in the RNA silencing pathway, especially during antiviral responses.	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
`Os06g0729300`	Probably involved in the RNA silencing pathway.	No verified direct reference in this release
`Os02g0831600`	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_014961 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006351 DNA-templated transcription 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

GO:0010218 response to far red light Biological Process

GO:0010267 ta-siRNA processing Biological Process

GO:0010305 leaf vascular tissue pattern formation Biological Process

GO:0010589 leaf proximal/distal pattern formation Biological Process

GO:0016441 post-transcriptional gene silencing Biological Process

KEGG gene cross-reference

ath:AT1G48410

dosa:Os02g0672200

dosa:Os02g0831600

dosa:Os06g0729300

These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.

Open Annotation Module

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.

Cytoplasm0.721

Rank 1 · LXL04_014961 · OH-1004

Nucleus0.385

Rank 2 · LXL04_014961 · OH-1004

Cell membrane0.079

Rank 3 · LXL04_014961 · OH-1004

Endoplasmic reticulum0.065

Rank 4 · LXL04_014961 · OH-1004

Mitochondrion0.057

Rank 5 · LXL04_014961 · 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.

PF12764.13Gly-rich_Ago1101-206 aa

PF16486.12ArgoN235-368 aa

PF08699.16ArgoL1378-428 aa

PF02170.29PAZ434-560 aa

PF16488.11ArgoL2570-616 aa

PF16487.11ArgoMid627-701 aa

PF02171.24Piwi721-1040 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_014961	`PF12764.13`	Gly-rich_Ago1	101	206	2.4e-07	32.1
LXL04_014961	`PF16486.12`	ArgoN	235	368	4.7e-37	128.3
LXL04_014961	`PF08699.16`	ArgoL1	378	428	5e-22	78.0
LXL04_014961	`PF02170.29`	PAZ	434	560	4.9e-30	104.7
LXL04_014961	`PF16488.11`	ArgoL2	570	616	1.3e-16	61.3
LXL04_014961	`PF16487.11`	ArgoMid	627	701	4.6e-12	46.7
LXL04_014961	`PF02171.24`	Piwi	721	1040	1.7e-115	386.2

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`O04379`	Arabidopsis thaliana	Protein argonaute 1	74.544%	Swiss-Prot	strong database homology
`Q7XSA2`	Oryza sativa subsp. japonica	Protein argonaute 1B	81.590%	Swiss-Prot	strong database homology
`Q6EU14`	Oryza sativa subsp. japonica	Protein argonaute 1A	72.252%	Swiss-Prot	strong database homology
`Q5Z5B2`	Oryza sativa subsp. japonica	Protein argonaute 1D	74.639%	Swiss-Prot	strong database homology
`Q6K972`	Oryza sativa subsp. japonica	Protein argonaute 1C	75.924%	Swiss-Prot	strong database homology

JBrowse

View in Genome Browser

Gene Card