TkA01G393460 | RubberDandelionOmics

Gene overview

TkA01G393460

Reference: TK1151 Chr: Chr01 Coordinates: 98152265-98162920 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2246 bp · TkA01G393460|TK1151|cDNA

AAAAGATCATCGTTTTCTCAAAATACAAAACAAAAAGAAAGAAGAAGCGGTTGTATAATACTTGTCGTGCTATTTGGTTTCCGTGATTTTATCCCTCAGTAGGGTTTGAAAAAGTACATAAACAGAAGGTCGAAGATTTATGATTATTTTTTCTTTCGTTGTGTAATCCTGGTTTCCAAGCGCAGGTGACCTATAGCATTGCCATTTCTCATCCGATCATTGATCGAATATCAGATGATGAGTTCTAAGAGAGGCGGAGG...

CDS

Download CDS FASTA

1845 bp · TkA01G393460|TK1151|CDS

ATGATGAGTTCTAAGAGAGGCGGAGGTCAGTCTAACAGAGGCGGAGGTCAATCTAACAGAGGCGATGGCAATAAGCCTGCATCCAAGGGTAAATACATAGCCGGTGTTACTCGCTATGATGATGATCGCTTGAATCAGGCAGTCCAATATGTGAACGTGGATTGTAATTGGGAGGTTATCTCCAAAAAGAACAAAAACAGACCTGGAAATGGTGCTCCATCCAAACAGTGGGCTGCTCAAACTCCCAAACCCAACGGTGG...

Protein

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614 aa · TkA01G393460|TK1151|PROTEIN

MMSSKRGGGQSNRGGGQSNRGDGNKPASKGKYIAGVTRYDDDRLNQAVQYVNVDCNWEVISKKNKNRPGNGAPSKQWAAQTPKPNGGRGNGQARAPNNTWAAQSGGRCSGGNINYTYNPAPNAIPPPLHSGWNWNDRPANAWQLGNNIPEDVEDQNEEDVEDESETGDVNESDDDDDEFLTDESDSDKTPKTHEERKKNKWYADLFKTLEGLTLEEINEPRSYRCPACQNSPDAIHCYRTLPSLLTHAKTKESKRVKIHR...

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	`TkA01G393460`
TK1151 ID	TkA01G393460
OH-1004 ID	LXL04_003101
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.500
Protein coverage (%)	TK1151 97.068 / OH-1004 80.432 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

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SNP / Indel variants and carrier samplesCRA009020 · TK1151

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID TkA01G393460

Location Chr01:98152265-98162920 (-)

Description Similar to SGS3: Protein SUPPRESSOR OF GENE SILENCING 3

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g23570`	Required for post-transcriptional gene silencing and natural virus resistance.	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 An H3K27me3 demethylase-HSFA2 regulatory loop orchestrates transgenerational thermomemory in Arabidopsis.2019 · DOI: 10.1038/s41422-019-0145-8

Rice

Reference gene ID	Possible function	Papers / DOI
`Os12g0197500`	Required for post-transcriptional gene silencing and natural virus resistance.	No verified direct reference in this release
`UniProt: A2ZIW7`	Required for post-transcriptional gene silencing and natural virus resistance.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_003101 · 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:0009408 response to heat Biological Process

GO:0009616 RNAi-mediated antiviral immune response Biological Process

GO:0010025 wax biosynthetic process Biological Process

GO:0010050 vegetative phase change Biological Process

GO:0010267 ta-siRNA processing Biological Process

GO:0010286 heat acclimation Biological Process

GO:0030422 siRNA processing Biological Process

GO:0031047 regulatory ncRNA-mediated gene silencing Biological Process

GO:0035278 miRNA-mediated gene silencing by inhibition of translation Biological Process

GO:0042742 defense response to bacterium Biological Process

GO:0050688 regulation of defense response to virus Biological Process

GO:0051607 defense response to virus Biological Process

KEGG gene cross-reference

ath:AT5G23570

dosa:Os12g0197500

sly:100134882

zma:100037819

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.

Cytoplasm0.564

Rank 1 · TkA01G393460 · TK1151

Nucleus0.399

Rank 2 · TkA01G393460 · TK1151

Cell membrane0.120

Rank 3 · TkA01G393460 · TK1151

Endoplasmic reticulum0.065

Rank 4 · TkA01G393460 · TK1151

Mitochondrion0.045

Rank 5 · TkA01G393460 · 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.

PF16869CNDH2_M63-178 aa

PF03470zf-XS225-263 aa

PF03468XS296-410 aa

PF16869CNDH2_M449-467 aa

PF03468XS555-573 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA01G393460	`PF16869`	CNDH2_M	63	178	1.1	10.7
TkA01G393460	`PF03470`	zf-XS	225	263	7.2e-06	26.9
TkA01G393460	`PF03468`	XS	296	410	2.6e-32	112.2
TkA01G393460	`PF16869`	CNDH2_M	449	467	1.1	10.7
TkA01G393460	`PF03468`	XS	555	573	2.6e-32	112.2

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q9LDX1`	Arabidopsis thaliana	sp\|Q9LDX1\|SGS3_ARATH Protein SUPPRESSOR OF GENE SILENCING 3	48.900%	Swiss-Prot	Medium
`Q2QWE9`	Oryza sativa subsp. japonica	sp\|Q2QWE9\|SGS3_ORYSJ Protein SUPPRESSOR OF GENE SILENCING 3 homolog	55.500%	Swiss-Prot	Medium
`A2ZIW7`	Oryza sativa subsp. indica	sp\|A2ZIW7\|SGS3_ORYSI Protein SUPPRESSOR OF GENE SILENCING 3 homolog	55.500%	Swiss-Prot	Medium

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