LXL04_009501 | RubberDandelionOmics

Gene overview

LXL04_009501

Reference: OH-1004 Chr: Chr02 Coordinates: 127577474-127580837 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1920 bp · LXL04_009501|LXL04_009501|OH1004|cDNA

ATGAATCATTACGACTCCAGAATTGCGGACACTGGTTCTTACCATCAACGTCGGAGTGATTTTATGGGATTACCGCATTCGGCGGGACCCCCTGCCGGTGCTGCTTCAAACTATGTCCGCGGCGGACCGGCACCATTCAGAGGTCCACCAGGACCACCACCGTCTTTTGGCGGCCGTGGAAGTGGTTACCCTCCCTTCGAACCTGGTGTTAGGGGAGGTTTTAGTGTAGGCGTAGGTGGGAATGGAAGAGGAGGGAGAGG...

CDS

Download CDS FASTA

1920 bp · LXL04_009501|LXL04_009501|OH1004|CDS

ATGAATCATTACGACTCCAGAATTGCGGACACTGGTTCTTACCATCAACGTCGGAGTGATTTTATGGGATTACCGCATTCGGCGGGACCCCCTGCCGGTGCTGCTTCAAACTATGTCCGCGGCGGACCGGCACCATTCAGAGGTCCACCAGGACCACCACCGTCTTTTGGCGGCCGTGGAAGTGGTTACCCTCCCTTCGAACCTGGTGTTAGGGGAGGTTTTAGTGTAGGCGTAGGTGGGAATGGAAGAGGAGGGAGAGG...

Protein

Download Protein FASTA

639 aa · LXL04_009501|LXL04_009501|OH1004|PROTEIN

MNHYDSRIADTGSYHQRRSDFMGLPHSAGPPAGAASNYVRGGPAPFRGPPGPPPSFGGRGSGYPPFEPGVRGGFSVGVGGNGRGGRGFSSGRGGGGRTSNGGFDSGRSRGGRDFDSGRGSSRGGSSGGRGFDRGYRGGGRGGGRDGGRGGRGGGRGGRGGGSKGDLYSIALPKQDFINLVPFEKNFYRESPSVSDMTDQEVAVYRGRREITVEGHDVPKPIRMFHEAGFPGYCLDVIARLGFIEPTPIQAQGWPMALKGR...

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_009501`
Source version	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_009501

Location Chr02:127577474-127580837 (+)

Description Similar to RH30: DEAD-box ATP-dependent RNA helicase 30

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g63120`	ATP-dependent RNA helicase involved nonsense-mediated mRNA decay and ribosome biogenesis through rRNA processing.	No verified direct reference in this release
`At1g55150`	ATP-dependent RNA helicase involved nonsense-mediated mRNA decay and ribosome biogenesis through rRNA processing.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os01g0197200`	ATP-dependent RNA helicase involved nonsense-mediated mRNA decay and ribosome biogenesis through rRNA processing.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_009501 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay Biological Process

GO:0000380 alternative mRNA splicing, via spliceosome Biological Process

GO:0006364 rRNA processing Biological Process

GO:0006369 termination of RNA polymerase II transcription Biological Process

GO:0009616 RNAi-mediated antiviral immune response Biological Process

GO:0071042 nuclear polyadenylation-dependent mRNA catabolic process Biological Process

GO:0005634 nucleus Cellular Component

GO:0005730 nucleolus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:1990904 ribonucleoprotein complex Cellular Component

GO:0002151 G-quadruplex RNA binding Molecular Function

GO:0003723 RNA binding Molecular Function

KEGG gene cross-reference

ani:ANIA_05931

ath:AT1G55150

ath:AT5G63120

kla:KLLA0_F23716g

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.

Nucleus0.682

Rank 1 · LXL04_009501 · OH-1004

Cytoplasm0.541

Rank 2 · LXL04_009501 · OH-1004

Endoplasmic reticulum0.038

Rank 3 · LXL04_009501 · OH-1004

Cell membrane0.032

Rank 4 · LXL04_009501 · OH-1004

Mitochondrion0.029

Rank 5 · LXL04_009501 · 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.

PF00270.36DEAD246-416 aa

PF00271.38Helicase_C453-562 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_009501	`PF00270.36`	DEAD	246	416	1.9e-50	171.6
LXL04_009501	`PF00271.38`	Helicase_C	453	562	1.1e-32	113.2

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`Q8W4R3`	Arabidopsis thaliana	DEAD-box ATP-dependent RNA helicase 30	73.975%	Swiss-Prot	strong database homology
`Q9C718`	Arabidopsis thaliana	DEAD-box ATP-dependent RNA helicase 20	73.378%	Swiss-Prot	moderate database homology
`Q5QMN3`	Oryza sativa subsp. japonica	DEAD-box ATP-dependent RNA helicase 20	75.000%	Swiss-Prot	moderate database homology

JBrowse

View in Genome Browser

Gene Card