LXL04_009204 | RubberDandelionOmics

Gene overview

LXL04_009204

Reference: OH-1004 Chr: Chr02 Coordinates: 120394911-120395685 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

408 bp · LXL04_009204|LXL04_009204|OH1004|cDNA

ATGAACGTGGCGCCTTCCCCTCCACCGCCTACCGGAGAAGATGATAATAGGAACAGTAGGACCTCCGCGAAAACTCCGCCGTCGTCACTCGATTCTCTACCAAGTAGTTCGCCCTCCTCCCCTATTCTCCGAGGTCCGATCAAATTGACGGCGAGATCATGCTTGTACGAGATATGCACGAAAAGTCACTGGAAACGTCCGGTATTCACTTGTTGCAGCGAAATAGGGCCGAGTAACCTCAGATCATTCACCTACAAAGC...

CDS

Download CDS FASTA

408 bp · LXL04_009204|LXL04_009204|OH1004|CDS

ATGAACGTGGCGCCTTCCCCTCCACCGCCTACCGGAGAAGATGATAATAGGAACAGTAGGACCTCCGCGAAAACTCCGCCGTCGTCACTCGATTCTCTACCAAGTAGTTCGCCCTCCTCCCCTATTCTCCGAGGTCCGATCAAATTGACGGCGAGATCATGCTTGTACGAGATATGCACGAAAAGTCACTGGAAACGTCCGGTATTCACTTGTTGCAGCGAAATAGGGCCGAGTAACCTCAGATCATTCACCTACAAAGC...

Protein

Download Protein FASTA

135 aa · LXL04_009204|LXL04_009204|OH1004|PROTEIN

MNVAPSPPPPTGEDDNRNSRTSAKTPPSSLDSLPSSSPSSPILRGPIKLTARSCLYEICTKSHWKRPVFTCCSEIGPSNLRSFTYKAVVEMIEGPKSNTVVECIGKPQSTKKNAADSAAEGVLWYLVHLGYPKKP

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_009204`
TK1151 ID	TkA03G408870
OH-1004 ID	LXL04_009204
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.300
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

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

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Basic Information and Functional Annotation

Gene ID LXL04_009204

Location Chr02:120394911-120395685 (+)

Description Similar to DCL4: Endoribonuclease Dicer homolog 4

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g20320`	Ribonuclease (RNase) III involved in RNA-mediated post- transcriptional gene silencing (PTGS).	Partially redundant functions of Arabidopsis DICER-like enzymes and a role for DCL4 in producing trans-acting siRNAs.2005 · DOI: 10.1016/j.cub.2005.07.024 DICER-LIKE 4 functions in trans-acting small interfering RNA biogenesis and vegetative phase change in Arabidopsis thaliana.2005 · DOI: 10.1073/pnas.0506426102 A pathway for the biogenesis of trans-acting siRNAs in Arabidopsis.2005 · DOI: 10.1101/gad.1352605 DICER-LIKE 4 is required for RNA interference and produces the 21-nucleotide small interfering RNA component of the plant cell-to-cell silencing signal.2005 · DOI: 10.1038/ng1675 DRB4-dependent TAS3 trans-acting siRNAs control leaf morphology through AGO7.2006 · DOI: 10.1016/j.cub.2006.03.035 An antagonistic function for Arabidopsis DCL2 in development and a new function for DCL4 in generating viral siRNAs.2006 · DOI: 10.1038/sj.emboj.7601217 Suppression of antiviral silencing by cucumber mosaic virus 2b protein in Arabidopsis is associated with drastically reduced accumulation of three classes of viral small interfering RNAs.2007 · DOI: 10.1105/tpc.106.047449 Transitivity in Arabidopsis can be primed, requires the redundant action of the antiviral Dicer-like 4 and Dicer-like 2, and is compromised by viral-encoded suppressor proteins.2007 · DOI: 10.1261/rna.541307 A novel class of bacteria-induced small RNAs in Arabidopsis.2007 · DOI: 10.1101/gad.1595107 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
`At1g80650`	Ribonuclease 3-like protein 1.	No verified direct reference in this release
`At1g01040`	Ribonuclease (RNase) III involved in RNA-mediated post- transcriptional gene silencing (PTGS).	Specific interactions between Dicer-like proteins and HYL1/DRB-family dsRNA-binding proteins in Arabidopsis thaliana.2005 · DOI: 10.1007/s11103-004-6853-5 Partially redundant functions of Arabidopsis DICER-like enzymes and a role for DCL4 in producing trans-acting siRNAs.2005 · DOI: 10.1016/j.cub.2005.07.024 The interaction between DCL1 and HYL1 is important for efficient and precise processing of pri-miRNA in plant microRNA biogenesis.2006 · DOI: 10.1261/rna.2146906 A novel class of bacteria-induced small RNAs in Arabidopsis.2007 · DOI: 10.1101/gad.1595107 The RNA-binding proteins HYL1 and SE promote accurate in vitro processing of pri-miRNA by DCL1.2008 · DOI: 10.1073/pnas.0803356105 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

Rice

Reference gene ID	Possible function	Papers / DOI
`Os04g0509300`	Involved in the RNA silencing pathway.	The small interfering RNA production pathway is required for shoot meristem initiation in rice.2007 · DOI: 10.1073/pnas.0704339104 Oryza sativa dicer-like4 reveals a key role for small interfering RNA silencing in plant development.2007 · DOI: 10.1105/tpc.107.052209
`Os03g0121800`	Involved in the RNA silencing pathway.	Loss of function of OsDCL1 affects microRNA accumulation and causes developmental defects in rice.2005 · DOI: 10.1104/pp.105.063420 Genome-wide analysis for discovery of rice microRNAs reveals natural antisense microRNAs (nat-miRNAs).2008 · DOI: 10.1073/pnas.0708743105

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_009204 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000911 cytokinesis by cell plate formation Biological Process

GO:0006353 DNA-templated transcription termination Biological Process

GO:0006364 rRNA processing Biological Process

GO:0006396 RNA processing Biological Process

GO:0009616 RNAi-mediated antiviral immune response Biological Process

GO:0009880 embryonic pattern specification Biological Process

GO:0009908 flower development Biological Process

GO:0009944 polarity specification of adaxial/abaxial axis Biological Process

GO:0010050 vegetative phase change Biological Process

GO:0010228 vegetative to reproductive phase transition of meristem Biological Process

GO:0010267 ta-siRNA processing Biological Process

GO:0010492 maintenance of shoot apical meristem identity Biological Process

KEGG gene cross-reference

ath:AT1G01040

ath:AT1G80650

ath:AT5G20320

dosa:Os03g0121800

dosa:Os04g0509300

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.

Nucleus0.796

Rank 1 · LXL04_009204 · OH-1004

Cytoplasm0.304

Rank 2 · LXL04_009204 · OH-1004

Cell membrane0.052

Rank 3 · LXL04_009204 · OH-1004

Endoplasmic reticulum0.045

Rank 4 · LXL04_009204 · OH-1004

Plastid0.014

Rank 5 · LXL04_009204 · 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.

PF14709.14DND1_DSRM50-126 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_009204	`PF14709.14`	DND1_DSRM	50	126	7.5e-21	74.9

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`P84634`	Arabidopsis thaliana	Dicer-like protein 4	42.708%	Swiss-Prot	moderate database homology
`Q9M8N2`	Arabidopsis thaliana	Ribonuclease 3-like protein 1	50.000%	Swiss-Prot	moderate database homology
`Q9SP32`	Arabidopsis thaliana	Endoribonuclease Dicer homolog 1	35.294%	Swiss-Prot	moderate database homology
`A7LFZ6`	Oryza sativa subsp. japonica	Endoribonuclease Dicer homolog 4	40.650%	Swiss-Prot	moderate database homology
`Q8LMR2`	Oryza sativa subsp. japonica	Endoribonuclease Dicer homolog 1	32.955%	Swiss-Prot	moderate database homology

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