LXL04_001312 | RubberDandelionOmics

Gene overview

LXL04_001312

Reference: OH-1004 Chr: Chr01 Coordinates: 23906360-23910246 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

3026 bp · LXL04_001312|LXL04_001312|OH1004|cDNA

ATGGGATCGGTGAAGAGGAAGTCGTTAGAAGAAGGCCCTTCAGCTTCCACACCTCCGCCGCACAAACAACAGAAAGACAACAAGGACAATGATAGTAGATTAATGGGAGCTAACGATGAGGCGGACGCCGGGGTGGCGTGTGTTCACGATGTCTCATACCCGGAGAACTACGTTGCTGTTCCTCGGCGGTCAAATAACGAGGAAGACTCAAAGCCCGCTAAGGACTTTCCTTTTACACTCGACCCTTTCCAATCGGAGGC...

CDS

Download CDS FASTA

3006 bp · LXL04_001312|LXL04_001312|OH1004|CDS

ATGGGATCGGTGAAGAGGAAGTCGTTAGAAGAAGGCCCTTCAGCTTCCACACCTCCGCCGCACAAACAACAGAAAGACAACAAGGACAATGATAGTAGATTAATGGGAGCTAACGATGAGGCGGACGCCGGGGTGGCGTGTGTTCACGATGTCTCATACCCGGAGAACTACGTTGCTGTTCCTCGGCGGTCAAATAACGAGGAAGACTCAAAGCCCGCTAAGGACTTTCCTTTTACACTCGACCCTTTCCAATCGGAGGC...

Protein

Download Protein FASTA

1001 aa · LXL04_001312|LXL04_001312|OH1004|PROTEIN

MGSVKRKSLEEGPSASTPPPHKQQKDNKDNDSRLMGANDEADAGVACVHDVSYPENYVAVPRRSNNEEDSKPAKDFPFTLDPFQSEAISCLNAGESVMVSAHTSAGKTVVASYAIAMSLRNKQRVIYTSPIKALSNQKYREFKEEFSDVGLMTGDVTIEPNASCLVMTTEIWRSMQYKGSELTREVAWIIFDEVHYMRDRERGVVWEESIVMAPKNARFVFLSATVPNAKEFADWVAKVHQQPCHIVYTDYRPTPLQHYL...

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_001312`
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_001312

Location Chr01:23906360-23910246 (+)

Description Similar to MTR4: DExH-box ATP-dependent RNA helicase DExH9

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g59760`	ATP-dependent RNA helicase that associates with the RNA exosome complex.	MTR4, a putative RNA helicase and exosome co-factor, is required for proper rRNA biogenesis and development in Arabidopsis thaliana.2011 · DOI: 10.1111/j.1365-313x.2011.04675.x The RNA helicases AtMTR4 and HEN2 target specific subsets of nuclear transcripts for degradation by the nuclear exosome in Arabidopsis thaliana.2014 · DOI: 10.1371/journal.pgen.1004564

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_001312 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000292 RNA fragment catabolic process Biological Process

GO:0000398 mRNA splicing, via spliceosome Biological Process

GO:0000460 maturation of 5.8S rRNA Biological Process

GO:0000467 exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) Biological Process

GO:0006364 rRNA processing Biological Process

GO:0006397 mRNA processing Biological Process

GO:0006401 RNA catabolic process Biological Process

GO:0006974 DNA damage response Biological Process

GO:0008380 RNA splicing Biological Process

GO:0016075 rRNA catabolic process Biological Process

GO:0016076 snRNA catabolic process Biological Process

GO:0031125 rRNA 3'-end processing Biological Process

KEGG gene cross-reference

ath:AT1G59760

hsa:23517

mmu:72198

sce:YJL050W

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.

Nucleus0.700

Rank 1 · LXL04_001312 · OH-1004

Cytoplasm0.248

Rank 2 · LXL04_001312 · OH-1004

Mitochondrion0.065

Rank 3 · LXL04_001312 · OH-1004

Plastid0.040

Rank 4 · LXL04_001312 · OH-1004

Cell membrane0.034

Rank 5 · LXL04_001312 · 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.

PF00270.36DEAD82-231 aa

PF04851.22ResIII82-226 aa

PF22527.3DEXQc_Suv3102-213 aa

PF00271.38Helicase_C395-474 aa

PF21408.3MTR4-like_stalk528-590 aa

PF13234.13MTR4_beta-barrel592-799 aa

PF08148.18DSHCT826-996 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_001312	`PF00270.36`	DEAD	82	231	1e-27	97.6
LXL04_001312	`PF04851.22`	ResIII	82	226	4.8e-08	33.8
LXL04_001312	`PF22527.3`	DEXQc_Suv3	102	213	2.3e-08	34.5
LXL04_001312	`PF00271.38`	Helicase_C	395	474	1.1e-07	32.8
LXL04_001312	`PF21408.3`	MTR4-like_stalk	528	590	1.1e-18	67.9
LXL04_001312	`PF13234.13`	MTR4_beta-barrel	592	799	5.3e-46	158.2
LXL04_001312	`PF08148.18`	DSHCT	826	996	6.8e-54	182.9

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
`Q9XIF2`	Arabidopsis thaliana	DExH-box ATP-dependent RNA helicase DExH9	76.793%	Swiss-Prot	strong database homology

JBrowse

View in Genome Browser

Gene Card