LXL04_001870 | RubberDandelionOmics

Gene overview

LXL04_001870

Reference: OH-1004 Chr: Chr01 Coordinates: 35421858-35423205 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

996 bp · LXL04_001870|LXL04_001870|OH1004|cDNA

ATGTATGTACTGAAACCGTATTCTTCAAACGACACCTTGCAAGAAGATCAAAAAACCGATTCAGAAAATCTGTCTGCCATGTTGGAAGATGCTATTATTTCATTTCAAAACCTTCGTCTAGAAGAAGATCAACTTCAGAAGGAATCTGAACCGGATGAATTGATGAAGGAGACCGAACTATCACAACTGGCTCCGCCTAGTTTGGAGGAGGTGGAAGAAATTACAGGTTACAGGTTTAAGAATAAGGAGTTGCTGAAGGT...

CDS

Download CDS FASTA

996 bp · LXL04_001870|LXL04_001870|OH1004|CDS

ATGTATGTACTGAAACCGTATTCTTCAAACGACACCTTGCAAGAAGATCAAAAAACCGATTCAGAAAATCTGTCTGCCATGTTGGAAGATGCTATTATTTCATTTCAAAACCTTCGTCTAGAAGAAGATCAACTTCAGAAGGAATCTGAACCGGATGAATTGATGAAGGAGACCGAACTATCACAACTGGCTCCGCCTAGTTTGGAGGAGGTGGAAGAAATTACAGGTTACAGGTTTAAGAATAAGGAGTTGCTGAAGGT...

Protein

Download Protein FASTA

331 aa · LXL04_001870|LXL04_001870|OH1004|PROTEIN

MYVLKPYSSNDTLQEDQKTDSENLSAMLEDAIISFQNLRLEEDQLQKESEPDELMKETELSQLAPPSLEEVEEITGYRFKNKELLKVAFTHGSYKADDCQSYERLEYLGDSVLNHLVAKLHYSAYPDMAPGELTRLRAANVDTEALARAALKFKLHKFLRHQKPLLQRQVNFVSFPMPPFHQRDLHDFSPTDKIQEFMEGIDEYPSHSNGMIDPPKVLADVLESLIGAIFVDTDSSMDTTWEAVKRLLHPLITPENLKLH...

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_001870`
TK1151 ID	TkA07G400860
OH-1004 ID	LXL04_001870
Relationship / confidence	Non Reciprocal Best Hit / Complex relationship
Protein identity (%)	67.000
Protein coverage (%)	TK1151 42.487 / OH-1004 26.586 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_001870

Location Chr01:35421858-35423205 (+)

Description Similar to Os06g0358800: Ribonuclease 3-like protein 3

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`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
`At3g20420`	Ribonuclease that cleaves double-stranded RNA (dsRNA).	Characterization of a ribonuclease III-like protein required for cleavage of the pre-rRNA in the 3'ETS in Arabidopsis.2008 · DOI: 10.1093/nar/gkm1130 An Arabidopsis RNase III-like protein, AtRTL2, cleaves double-stranded RNA in vitro.2011 · DOI: 10.1007/s10265-010-0382-x

Rice

Reference gene ID	Possible function	Papers / DOI
`Os06g0358800`	Cleaves double-stranded RNA (dsRNA).	No verified direct reference in this release
`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
`Os05g0271300`	Cleaves double-stranded RNA (dsRNA).	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_001870 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000911 cytokinesis by cell plate formation 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:0010228 vegetative to reproductive phase transition of meristem Biological Process

GO:0010267 ta-siRNA processing Biological Process

GO:0010599 lsiRNA processing Biological Process

GO:0030422 siRNA processing Biological Process

GO:0031053 primary miRNA processing Biological Process

GO:0035196 miRNA processing Biological Process

KEGG gene cross-reference

ath:AT1G01040

ath:AT3G20420

dosa:Os03g0121800

dosa:Os05g0271300

dosa:Os06g0358800

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.

Nucleus0.626

Rank 1 · LXL04_001870 · OH-1004

Cytoplasm0.494

Rank 2 · LXL04_001870 · OH-1004

Mitochondrion0.055

Rank 3 · LXL04_001870 · OH-1004

Cell membrane0.045

Rank 4 · LXL04_001870 · OH-1004

Endoplasmic reticulum0.035

Rank 5 · LXL04_001870 · 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.

PF14622.12Ribonucleas_3_381-163 aa

PF00636.32Ribonuclease_3103-233 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_001870	`PF14622.12`	Ribonucleas_3_3	81	163	1.8e-21	77.3
LXL04_001870	`PF00636.32`	Ribonuclease_3	103	233	2.2e-23	83.7

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
`Q9SP32`	Arabidopsis thaliana	Endoribonuclease Dicer homolog 1	33.708%	Swiss-Prot	moderate database homology
`Q9LTQ0`	Arabidopsis thaliana	Ribonuclease 3-like protein 2	36.604%	Swiss-Prot	moderate database homology
`Q69KJ0`	Oryza sativa subsp. japonica	Ribonuclease 3-like protein 3	43.396%	Swiss-Prot	moderate database homology
`Q8LMR2`	Oryza sativa subsp. japonica	Endoribonuclease Dicer homolog 1	34.831%	Swiss-Prot	moderate database homology
`Q6ATG6`	Oryza sativa subsp. japonica	Ribonuclease 3-like protein 2	35.409%	Swiss-Prot	moderate database homology

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