LXL04_003101 | RubberDandelionOmics

Gene overview

LXL04_003101

Reference: OH-1004 Chr: Chr01 Coordinates: 67409005-67413358 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2226 bp · LXL04_003101|LXL04_003101|OH1004|cDNA

ATGAAAtcgaaaaatcaaaagaaagaTATCAAGAGAGAGGAAGGGGATCTGCTTCCTCCGGCCACGGCGGAGAAGAAGGTAGCACACGCACCACCGGCGAAAAAGTGTTCAACCAAATCATCGATTAACGAAATTACAGGACCGGATCCGAAGGATCTTCGTAAGAATGCTATTTCTAGGGTTTTTTCCTCGTCGCTAAAGAACTCATGTGATGTTTCTCTTCCCGCTGACAAGTTTTCAGGATCTGTTGTGTTTACTCC...

CDS

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2226 bp · LXL04_003101|LXL04_003101|OH1004|CDS

ATGAAATCGAAAAATCAAAAGAAAGATATCAAGAGAGAGGAAGGGGATCTGCTTCCTCCGGCCACGGCGGAGAAGAAGGTAGCACACGCACCACCGGCGAAAAAGTGTTCAACCAAATCATCGATTAACGAAATTACAGGACCGGATCCGAAGGATCTTCGTAAGAATGCTATTTCTAGGGTTTTTTCCTCGTCGCTAAAGAACTCATGTGATGTTTCTCTTCCCGCTGACAAGTTTTCAGGATCTGTTGTGTTTACTCC...

Protein

Download Protein FASTA

741 aa · LXL04_003101|LXL04_003101|OH1004|PROTEIN

MKSKNQKKDIKREEGDLLPPATAEKKVAHAPPAKKCSTKSSINEITGPDPKDLRKNAISRVFSSSLKNSCDVSLPADKFSGSVVFTPSPPPSNLPLPTFFLRPKLSCNAEVAAAGSGIDAGATDSKLIELQMSSKRGGGQSNRGGGQSNRGDGNKPASKGKYIAGVTRYDDDRLNQAVQYVNVDCNWEVISKKNKNRPGNGAPSKQWAAQTPKPNGGRGNGQARAPNNTWAAQSGGRCSGGNINYTYNPAPNAIPPPLHS...

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_003101`
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	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_003101

Location Chr01:67409005-67413358 (+)

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

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Functional annotation source: OH1004 · LXL04_003101 · GCA_047496595.1_OSU_TarKok_2.0.

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.

Cytoplasm0.502

Rank 1 · LXL04_003101 · OH-1004

Nucleus0.419

Rank 2 · LXL04_003101 · OH-1004

Cell membrane0.155

Rank 3 · LXL04_003101 · OH-1004

Endoplasmic reticulum0.077

Rank 4 · LXL04_003101 · OH-1004

Mitochondrion0.044

Rank 5 · LXL04_003101 · 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.

PF03470.20zf-XS355-393 aa

PF03468.21XS426-540 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_003101	`PF03470.20`	zf-XS	355	393	9.4e-06	26.5
LXL04_003101	`PF03468.21`	XS	426	540	1.6e-32	112.9

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	Protein SUPPRESSOR OF GENE SILENCING 3	44.588%	Swiss-Prot	moderate database homology
`Q2QWE9`	Oryza sativa subsp. japonica	Protein SUPPRESSOR OF GENE SILENCING 3 homolog	43.005%	Swiss-Prot	moderate database homology
`A2ZIW7`	Oryza sativa subsp. indica	Protein SUPPRESSOR OF GENE SILENCING 3 homolog	49.299%	Swiss-Prot	moderate database homology

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