LXL04_019033 | RubberDandelionOmics

Gene overview

LXL04_019033

Reference: OH-1004 Chr: Chr04 Coordinates: 22397432-22402957 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

3246 bp · LXL04_019033|LXL04_019033|OH1004|cDNA

ATGGAAGGTGTGGCAGAAGTTCTACTTCCATTTTCAATAGAAAGGTTGCTCGAAGAGATATGTCTCCAGAAGGGTCTAGAGATGCCGGACGTTGCTGCTCGGAAGACTCTTTCGAGAATCAGCGAAGAGTCTGCCATTGATGTAATGAAAAGAGTAAGTTCGACTAGAACACCGATATATAACTTGAGTGGATACATTGTTCATTTGGTGAACAGACACGGATCAGTGGCTTCTACTTCTGCTCGCGGTGATGTTGAGAG...

CDS

Download CDS FASTA

3246 bp · LXL04_019033|LXL04_019033|OH1004|CDS

ATGGAAGGTGTGGCAGAAGTTCTACTTCCATTTTCAATAGAAAGGTTGCTCGAAGAGATATGTCTCCAGAAGGGTCTAGAGATGCCGGACGTTGCTGCTCGGAAGACTCTTTCGAGAATCAGCGAAGAGTCTGCCATTGATGTAATGAAAAGAGTAAGTTCGACTAGAACACCGATATATAACTTGAGTGGATACATTGTTCATTTGGTGAACAGACACGGATCAGTGGCTTCTACTTCTGCTCGCGGTGATGTTGAGAG...

Protein

Download Protein FASTA

1081 aa · LXL04_019033|LXL04_019033|OH1004|PROTEIN

MEGVAEVLLPFSIERLLEEICLQKGLEMPDVAARKTLSRISEESAIDVMKRVSSTRTPIYNLSGYIVHLVNRHGSVASTSARGDVESMRLSSPYPSSPSSSASSTPRRTAYYDSPSSKQFFESPCSCKSASPVIPQYRAPTNGSHGSPVQEHTSSFSCSSLKGALPNYWPSVDQPTTSPTSSSKGTNPNHVSQRYSGPENSSQTDSPSYYISDQALVLSGLEFRRLFMVHSYIGSKKLEDALSLKDAVEIDSMKTMTMFE...

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_019033`
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_019033

Location Chr04:22397432-22402957 (+)

Description Similar to RDR3: Probable RNA-dependent RNA polymerase 3

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g19910`	Probably involved in the RNA silencing pathway and required for the generation of small interfering RNAs (siRNAs).	No verified direct reference in this release
`At2g19930`	Probably involved in the RNA silencing pathway and required for the generation of small interfering RNAs (siRNAs).	No verified direct reference in this release
`At2g19920`	Probably involved in the RNA silencing pathway and required for the generation of small interfering RNAs (siRNAs).	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os01g0197900`	Probably involved in the RNA silencing pathway and required for the generation of small interfering RNAs (siRNAs).	No verified direct reference in this release
`Os01g0198000`	Probably involved in the RNA silencing pathway and required for the generation of small interfering RNAs (siRNAs).	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_019033 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0030422 siRNA processing Biological Process

GO:0009507 chloroplast Cellular Component

GO:0031380 nuclear RNA-directed RNA polymerase complex Cellular Component

GO:0003723 RNA binding Molecular Function

GO:0003968 RNA-directed RNA polymerase activity Molecular Function

KEGG gene cross-reference

ath:AT2G19910

ath:AT2G19920

ath:AT2G19930

dosa:Os01g0197900

dosa:Os01g0198000

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.

Nucleus0.763

Rank 1 · LXL04_019033 · OH-1004

Cytoplasm0.243

Rank 2 · LXL04_019033 · OH-1004

Cell membrane0.055

Rank 3 · LXL04_019033 · OH-1004

Mitochondrion0.032

Rank 4 · LXL04_019033 · OH-1004

Endoplasmic reticulum0.029

Rank 5 · LXL04_019033 · 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.

PF26249.14HB_RdRP3_N6-76 aa

PF26252.1RdRP_helical219-285 aa

PF05183.18RdRP304-933 aa

PF26253.1RdRP_head982-1061 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_019033	`PF26249.1`	4HB_RdRP3_N	6	76	6.1e-10	39.9
LXL04_019033	`PF26252.1`	RdRP_helical	219	285	6.2e-08	33.3
LXL04_019033	`PF05183.18`	RdRP	304	933	4e-102	343.5
LXL04_019033	`PF26253.1`	RdRP_head	982	1061	2.5e-13	51.2

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
`O82190`	Arabidopsis thaliana	Probable RNA-dependent RNA polymerase 3	41.743%	Swiss-Prot	moderate database homology
`O82188`	Arabidopsis thaliana	Probable RNA-dependent RNA polymerase 5	47.381%	Swiss-Prot	moderate database homology
`O82189`	Arabidopsis thaliana	Probable RNA-dependent RNA polymerase 4	45.620%	Swiss-Prot	moderate database homology
`Q5QMN5`	Oryza sativa subsp. japonica	Probable RNA-dependent RNA polymerase 3	38.079%	Swiss-Prot	moderate database homology
`Q5QMN4`	Oryza sativa subsp. japonica	Probable RNA-dependent RNA polymerase 4	38.185%	Swiss-Prot	moderate database homology

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