LXL04_038351 | RubberDandelionOmics

Gene overview

LXL04_038351

Reference: OH-1004 Chr: Chr09 Coordinates: 38327204-38329166 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1029 bp · LXL04_038351|LXL04_038351|OH1004|cDNA

ATGACAGCCATGTCGAATCGAATCCCCAAATCAAAAAAGAGAAAAACGTCCCCATATTTACACCAAACACAATCCGAAAAAATCATACACACATACACACTCTTGGAAGAAAGTCAACCATCCGGTCAACTCATTACAGACATGGAAGATTCAATTGCGGCTATAGAATCCATATTAAGGTACAACTTCAACAACAAAAGATTGTTAGAAGCAGCCTTAACACATCCTTCTTACACCGAGAGTACCTCATATCAACACCT...

CDS

Download CDS FASTA

1029 bp · LXL04_038351|LXL04_038351|OH1004|CDS

ATGACAGCCATGTCGAATCGAATCCCCAAATCAAAAAAGAGAAAAACGTCCCCATATTTACACCAAACACAATCCGAAAAAATCATACACACATACACACTCTTGGAAGAAAGTCAACCATCCGGTCAACTCATTACAGACATGGAAGATTCAATTGCGGCTATAGAATCCATATTAAGGTACAACTTCAACAACAAAAGATTGTTAGAAGCAGCCTTAACACATCCTTCTTACACCGAGAGTACCTCATATCAACACCT...

Protein

Download Protein FASTA

342 aa · LXL04_038351|LXL04_038351|OH1004|PROTEIN

MTAMSNRIPKSKKRKTSPYLHQTQSEKIIHTYTLLEESQPSGQLITDMEDSIAAIESILRYNFNNKRLLEAALTHPSYTESTSYQHLEFVGDFVLGFAISNFVDLAYPSLDPGQLSLLRAANISTEKLARVAVRNGLYKYVRHRDTVLSDKVGKFVNVVEEEEYMVVHGGQMKAPKVLADIVESIIGAVFIDCGRDIQRLWLIIRHLLEPLVMLNVLEKQPQPITMLFEACQKEGKTVDIRHWRKGERNIASVFIDGRFF...

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_038351`
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_038351

Location Chr09:38327204-38329166 (-)

Description Similar to RTL2: Ribonuclease 3-like protein 2

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`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
`At5g45150`	Ribonuclease that cleaves double-stranded RNA (dsRNA).	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
`Os05g0271300`	Cleaves double-stranded RNA (dsRNA).	No verified direct reference in this release
`Os06g0358800`	Cleaves double-stranded RNA (dsRNA).	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_038351 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006364 rRNA processing Biological Process

GO:0030422 siRNA processing Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0003723 RNA binding Molecular Function

GO:0004525 ribonuclease III activity Molecular Function

GO:0046872 metal ion binding Molecular Function

KEGG gene cross-reference

ath:AT3G20420

ath:AT5G45150

dosa:Os05g0271300

dosa:Os06g0358800

These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.

Open Annotation Module

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.

Nucleus0.733

Rank 1 · LXL04_038351 · OH-1004

Cytoplasm0.282

Rank 2 · LXL04_038351 · OH-1004

Cell membrane0.047

Rank 3 · LXL04_038351 · OH-1004

Endoplasmic reticulum0.033

Rank 4 · LXL04_038351 · OH-1004

Plastid0.029

Rank 5 · LXL04_038351 · 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.

PF14622.12Ribonucleas_3_365-196 aa

PF00636.32Ribonuclease_385-194 aa

PF00035.33dsrm223-283 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_038351	`PF14622.12`	Ribonucleas_3_3	65	196	4.1e-18	66.5
LXL04_038351	`PF00636.32`	Ribonuclease_3	85	194	6.7e-19	69.3
LXL04_038351	`PF00035.33`	dsrm	223	283	2.6e-10	41.4

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
`Q9LTQ0`	Arabidopsis thaliana	Ribonuclease 3-like protein 2	45.768%	Swiss-Prot	moderate database homology
`Q9FKF0`	Arabidopsis thaliana	Ribonuclease 3-like protein 3	38.866%	Swiss-Prot	moderate database homology
`Q9SP32`	Arabidopsis thaliana	Endoribonuclease Dicer homolog 1	37.269%	Swiss-Prot	moderate database homology
`Q6ATG6`	Oryza sativa subsp. japonica	Ribonuclease 3-like protein 2	43.986%	Swiss-Prot	moderate database homology
`Q69KJ0`	Oryza sativa subsp. japonica	Ribonuclease 3-like protein 3	37.023%	Swiss-Prot	moderate database homology

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