TkA02G023350 | RubberDandelionOmics

Gene overview

TkA02G023350

Reference: TK1151 Chr: Chr02 Coordinates: 5520679-5527458 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

3107 bp · TkA02G023350|TK1151|cDNA

CTGCCGATGTTTGGGGGGCGCAGTAGCTACCAGCAGACAGCAGCAGTACTACTGAATTCACTCCCGTCATTCGGCACTGGGGCGCACGAAGAACGCGTCACTGTTTCTTCTTCATTCTTCCTTAAAACCCTAATTTCATCATCGTTAAAGGATTCTTGTGGATGTAAAAGATGGAGAAAGTAAACAGTGAAGACGCTAGCGGTTCACCACCACCCTCACCACCACCGCCAGATGTCACACAACCTGATGCCATAACAGAG...

CDS

Download CDS FASTA

2355 bp · TkA02G023350|TK1151|CDS

ATGGTATCCATTAGTTCCGAAGATAACAGAGCAATTGAAAACAAAGTTTTAGGAAGAAAAATTCTTGAAAAACTTCACCAAACATATTCAATACAACTTTCTGGTAAGAAATTTGCATATGATGGAGAAAAGAGTCTTTACACTGTTGGACCTCTTCCACAAAACATGTTTGAATTCATGGTTGTATTAATAGATTCACATGCAACACGTGAAAGTCCTTCTGATGAAGGAACGGGTAAAAGGGCAAGACGGTCTTTTCA...

Protein

Download Protein FASTA

784 aa · TkA02G023350|TK1151|PROTEIN

MVSISSEDNRAIENKVLGRKILEKLHQTYSIQLSGKKFAYDGEKSLYTVGPLPQNMFEFMVVLIDSHATRESPSDEGTGKRARRSFQEKTFKVEIKFAAEIPLKSIFLALQGEEPEKLQDSLRVLDIILRQQAAQRGCLLVKQSFFHNDSRNFVDIGGGVSGCRGFHSSFHPTHGGFSLNMDVSTTMILTPGPVIDFLKSNQNAREIRSLDWLKARKMLKNMRIKTSHSNMEFKITGMSEKPCNQLLFPLRVRKEDGTYD...

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	`TkA02G023350`
TK1151 ID	TkA02G023350
OH-1004 ID	LXL04_023143
Relationship / confidence	Non Reciprocal Best Hit / Complex relationship
Protein identity (%)	63.400
Protein coverage (%)	TK1151 96.046 / OH-1004 83.644 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	TK1151 / GWHBCHF00000000

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · TK1151

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Basic Information and Functional Annotation

Gene ID TkA02G023350

Location Chr02:5520679-5527458 (-)

Description Similar to AGO4: Protein argonaute 4

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g32940`	Involved in transcriptional gene silencing (TGS).	Role of Arabidopsis AGO6 in siRNA accumulation, DNA methylation and transcriptional gene silencing.2007 · DOI: 10.1038/sj.emboj.7601603 The Arabidopsis RNA-directed DNA methylation argonautes functionally diverge based on their expression and interaction with target loci.2010 · DOI: 10.1105/tpc.109.072199
`At2g27040`	Together with RDM3, required for transcriptional gene silencing (TGS) by DNA methylation and repressive histone modifications (H3K9me2) of several chromatin loci.	ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone methylation.2003 · DOI: 10.1126/science.1079695 Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats.2004 · DOI: 10.1016/j.cub.2004.06.055 The Arabidopsis chromatin-modifying nuclear siRNA pathway involves a nucleolar RNA processing center.2006 · DOI: 10.1016/j.cell.2006.05.031 An ARGONAUTE4-containing nuclear processing center colocalized with Cajal bodies in Arabidopsis thaliana.2006 · DOI: 10.1016/j.cell.2006.05.032 Distinct catalytic and non-catalytic roles of ARGONAUTE4 in RNA-directed DNA methylation.2006 · DOI: 10.1038/nature05198 Reiterated WG/GW motifs form functionally and evolutionarily conserved ARGONAUTE-binding platforms in RNAi-related components.2007 · DOI: 10.1101/gad.451207 ARGONAUTE4 is required for resistance to Pseudomonas syringae in Arabidopsis.2007 · DOI: 10.1105/tpc.107.054494 Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 5' terminal nucleotide.2008 · DOI: 10.1016/j.cell.2008.02.034 Viral genome methylation as an epigenetic defense against geminiviruses.2008 · DOI: 10.1128/jvi.00719-08 RNA polymerase V transcription guides ARGONAUTE4 to chromatin.2009 · DOI: 10.1038/ng.365 The Arabidopsis RNA-directed DNA methylation argonautes functionally diverge based on their expression and interaction with target loci.2010 · DOI: 10.1105/tpc.109.072199 Independent chromatin binding of ARGONAUTE4 and SPT5L/KTF1 mediates transcriptional gene silencing.2011 · DOI: 10.1371/journal.pgen.1002120

Rice

Reference gene ID	Possible function	Papers / DOI
`Os07g0265600`	Probably involved in the RNA silencing pathway.	No verified direct reference in this release
`Os01g0275600`	Probably involved in the RNA silencing pathway.	No verified direct reference in this release
`Os04g0151800`	Probably involved in the RNA silencing pathway.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_023143 · GCA_047496595.1_OSU_TarKok_2.0. These OH1004 annotations are retrieved through ID mapping; the Arabidopsis/rice table below uses protein alignments from the query reference.

GO annotations (OH1004 source)

GO:0006351 DNA-templated transcription Biological Process

GO:0006417 regulation of translation Biological Process

GO:0009554 megasporogenesis Biological Process

GO:0010526 transposable element silencing Biological Process

GO:0030422 siRNA processing Biological Process

GO:0031047 regulatory ncRNA-mediated gene silencing Biological Process

GO:0031048 regulatory ncRNA-mediated heterochromatin formation Biological Process

GO:0031507 heterochromatin formation Biological Process

GO:0042742 defense response to bacterium Biological Process

GO:0048481 plant ovule development Biological Process

GO:0051607 defense response to virus Biological Process

GO:0080188 gene silencing by siRNA-directed DNA methylation Biological Process

KEGG gene cross-reference

ath:AT2G27040

ath:AT5G21150

dosa:Os01g0275600

dosa:Os04g0151800

dosa:Os07g0265600

osa:4324438

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.

Cytoplasm0.702

Rank 1 · TkA02G023350 · TK1151

Nucleus0.329

Rank 2 · TkA02G023350 · TK1151

Mitochondrion0.078

Rank 3 · TkA02G023350 · TK1151

Cell membrane0.073

Rank 4 · TkA02G023350 · TK1151

Endoplasmic reticulum0.050

Rank 5 · TkA02G023350 · TK1151

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.

PF16486ArgoN15-129 aa

PF08699ArgoL1141-188 aa

PF16488ArgoL2180-192 aa

PF02170PAZ195-326 aa

PF01660Vmethyltransf210-333 aa

PF16486ArgoN299-328 aa

PF16488ArgoL2337-381 aa

PF16487ArgoMid390-435 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA02G023350	`PF16486`	ArgoN	15	129	4e-19	70.1
TkA02G023350	`PF08699`	ArgoL1	141	188	1.3e-16	60.6
TkA02G023350	`PF16488`	ArgoL2	180	192	1.8e-12	48.0
TkA02G023350	`PF02170`	PAZ	195	326	2.6e-28	99.2
TkA02G023350	`PF01660`	Vmethyltransf	210	333	0.074	12.8
TkA02G023350	`PF16486`	ArgoN	299	328	4e-19	70.1
TkA02G023350	`PF16488`	ArgoL2	337	381	1.8e-12	48.0
TkA02G023350	`PF16487`	ArgoMid	390	435	4.6e-07	30.7
TkA02G023350	`PF02171`	Piwi	480	758	5.4e-87	292.6
TkA02G023350	`PF16488`	ArgoL2	537	545	1.8e-12	48.0

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
`O48771`	Arabidopsis thaliana	sp\|O48771\|AGO6_ARATH Protein argonaute 6	62.600%	Swiss-Prot	High
`Q9ZVD5`	Arabidopsis thaliana	sp\|Q9ZVD5\|AGO4_ARATH Protein argonaute 4	58.700%	Swiss-Prot	High
`Q6YSJ5`	Oryza sativa subsp. japonica	sp\|Q6YSJ5\|AGO16_ORYSJ Protein argonaute 16	65.000%	Swiss-Prot	High
`Q9SDG8`	Oryza sativa subsp. japonica	sp\|Q9SDG8\|AGO4A_ORYSJ Protein argonaute 4A	58.900%	Swiss-Prot	High
`Q0JF58`	Oryza sativa subsp. japonica	sp\|Q0JF58\|AGO4B_ORYSJ Protein argonaute 4B	58.500%	Swiss-Prot	High

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