LXL04_009854 | RubberDandelionOmics

Gene overview

LXL04_009854

Reference: OH-1004 Chr: Chr02 Coordinates: 135000705-135011699 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

6588 bp · LXL04_009854|LXL04_009854|OH1004|cDNA

ATGGATCGTGTCGACACAGTGAAAGAGTTGCCATTCCGGGTCGGATTCACGGGTCACAGCGGCCATATTCGAATCGAGCCACTACCTCCTGTTCAACAATCCAGCTCCGTCGATTCGTTACCGGAGTTTATACTCCCTCCTGCATTCGCCAGGGAAACACCAGAATCGATCAAAAAGTTTGTGGAGGATAAATATCTCCTCCCAAGATTGGATCCTGATGAGTTTTCTGCAGAAAAAGCTGGAAGACAGTGGGAGTTTGA...

CDS

Download CDS FASTA

6588 bp · LXL04_009854|LXL04_009854|OH1004|CDS

ATGGATCGTGTCGACACAGTGAAAGAGTTGCCATTCCGGGTCGGATTCACGGGTCACAGCGGCCATATTCGAATCGAGCCACTACCTCCTGTTCAACAATCCAGCTCCGTCGATTCGTTACCGGAGTTTATACTCCCTCCTGCATTCGCCAGGGAAACACCAGAATCGATCAAAAAGTTTGTGGAGGATAAATATCTCCTCCCAAGATTGGATCCTGATGAGTTTTCTGCAGAAAAAGCTGGAAGACAGTGGGAGTTTGA...

Protein

Download Protein FASTA

2195 aa · LXL04_009854|LXL04_009854|OH1004|PROTEIN

MDRVDTVKELPFRVGFTGHSGHIRIEPLPPVQQSSSVDSLPEFILPPAFARETPESIKKFVEDKYLLPRLDPDEFSAEKAGRQWEFDWFDQAKIHLEPTMPRTVVVPAWELPFRRPQHSSDLQKWEPASIQVDVSELMVEAENSIGVRISGPPKDFVKGSINNRPFRPGGLDDSQSIGRSLPEGSCNGEWVREVLDGAPAQVIPPSCKEGMNLGDLKGHSCSWIIHEDKSVPKTTSETTLSVQFDDLFKKAWEEDVTEVP...

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_009854`
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_009854

Location Chr02:135000705-135011699 (+)

Description Similar to SKI2: DExH-box ATP-dependent RNA helicase DExH11

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g46960`	Component of the SKI complex which is thought to be involved in exosome-mediated RNA decay and associates with transcriptionally active genes in a manner dependent on PAF1 complex (PAF1C).	A DExD/H box RNA helicase is important for K+ deprivation responses and tolerance in Arabidopsis thaliana.2011 · DOI: 10.1111/j.1742-4658.2011.08147.x Context-dependent dual role of SKI8 homologs in mRNA synthesis and turnover.2012 · DOI: 10.1371/journal.pgen.1002652

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_009854 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000292 RNA fragment catabolic process Biological Process

GO:0000956 nuclear-transcribed mRNA catabolic process Biological Process

GO:0006351 DNA-templated transcription Biological Process

GO:0006402 mRNA catabolic process Biological Process

GO:0006417 regulation of translation Biological Process

GO:0006813 potassium ion transport Biological Process

GO:0016441 post-transcriptional gene silencing Biological Process

GO:0030968 endoplasmic reticulum unfolded protein response Biological Process

GO:0035864 response to potassium ion Biological Process

GO:0051607 defense response to virus Biological Process

GO:0070478 nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay Biological Process

GO:0070481 nuclear-transcribed mRNA catabolic process, non-stop decay Biological Process

KEGG gene cross-reference

ath:AT3G46960

sce:YLR398C

spo:2538841

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.

Nucleus0.445

Rank 1 · LXL04_009854 · OH-1004

Cytoplasm0.373

Rank 2 · LXL04_009854 · OH-1004

Mitochondrion0.097

Rank 3 · LXL04_009854 · OH-1004

Cell membrane0.071

Rank 4 · LXL04_009854 · OH-1004

Endoplasmic reticulum0.064

Rank 5 · LXL04_009854 · 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.

PF00270.36DEAD368-515 aa

PF03732.25PEG10_N-capsid904-973 aa

PF21408.3MTR4-like_stalk1693-1753 aa

PF13234.13MTR4_beta-barrel1760-1991 aa

PF08148.18DSHCT2017-2187 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_009854	`PF00270.36`	DEAD	368	515	4.9e-23	82.4
LXL04_009854	`PF03732.25`	PEG10_N-capsid	904	973	6.1e-06	27.2
LXL04_009854	`PF21408.3`	MTR4-like_stalk	1693	1753	2.3e-11	44.5
LXL04_009854	`PF13234.13`	MTR4_beta-barrel	1760	1991	1.2e-30	108.0
LXL04_009854	`PF08148.18`	DSHCT	2017	2187	4.7e-59	199.7

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
`F4JAA5`	Arabidopsis thaliana	DExH-box ATP-dependent RNA helicase DExH11	63.265%	Swiss-Prot	weak database homology

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