LXL04_038811 | RubberDandelionOmics

Gene overview

LXL04_038811

Reference: OH-1004 Chr: Chr09 Coordinates: 50992561-50995499 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1389 bp · LXL04_038811|LXL04_038811|OH1004|cDNA

ATGAAGGGTTCGTTGGATCGAACGAAGGTTGTGCTTCGGCACTTGCCACACAACATTTCTCAGTCAGCGCTCGTGGAACAAATTGATGCCCGTTTTTCCGGTCGTTACAACTGGTTCTGTTTCCGTTCCGGGAAAAACAGTCTGAAGTATCAATCTTATGCAAGAGCCTACATCGACTTTAAGCACCCTGATGATGTCATCGAGTTTGCAGAGTTCTTTGATGGACACGTGTTTGTTAATGAAAAGGGCACCCAATTCAA...

CDS

Download CDS FASTA

1389 bp · LXL04_038811|LXL04_038811|OH1004|CDS

ATGAAGGGTTCGTTGGATCGAACGAAGGTTGTGCTTCGGCACTTGCCACACAACATTTCTCAGTCAGCGCTCGTGGAACAAATTGATGCCCGTTTTTCCGGTCGTTACAACTGGTTCTGTTTCCGTTCCGGGAAAAACAGTCTGAAGTATCAATCTTATGCAAGAGCCTACATCGACTTTAAGCACCCTGATGATGTCATCGAGTTTGCAGAGTTCTTTGATGGACACGTGTTTGTTAATGAAAAGGGCACCCAATTCAA...

Protein

Download Protein FASTA

462 aa · LXL04_038811|LXL04_038811|OH1004|PROTEIN

MKGSLDRTKVVLRHLPHNISQSALVEQIDARFSGRYNWFCFRSGKNSLKYQSYARAYIDFKHPDDVIEFAEFFDGHVFVNEKGTQFKTIVEYAPSQRVPKQWSKKDGREGTIDKDPEYLEFLELISKPVENLPSAEIQLERKEAERAGTAKEAPVVTPLMEFIRQKRAAKGGPRRSMPNGKLMRRGSGASSSSNSNSNSNSNSPALKRGSERRRTSTTMYVPRDNSGKGSRSGKEKSTYVQVNKRDDQQQSGSVVLEEGR...

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_038811`
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_038811

Location Chr09:50992561-50995499 (-)

Description Similar to UPF3: Regulator of nonsense transcripts UPF3

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g33980`	Recruits UPF2 at the cytoplasmic side of the nuclear envelope and the subsequent formation of an UPF1-UPF2-UPF3 surveillance complex (including UPF1 bound to release factors at the stalled ribosome) is believed to activate NMD.	UPF3 suppresses aberrant spliced mRNA in Arabidopsis.2005 · DOI: 10.1111/j.1365-313x.2005.02473.x Genome-wide suppression of aberrant mRNA-like noncoding RNAs by NMD in Arabidopsis.2009 · DOI: 10.1073/pnas.0808902106 Extensive coupling of alternative splicing of pre-mRNAs of serine/arginine (SR) genes with nonsense-mediated decay.2010 · DOI: 10.1111/j.1469-8137.2009.03065.x Nonsense-mediated mRNA decay factors, UPF1 and UPF3, contribute to plant defense.2011 · DOI: 10.1093/pcp/pcr144 Alternative splicing and nonsense-mediated decay modulate expression of important regulatory genes in Arabidopsis.2012 · DOI: 10.1093/nar/gkr932 Arabidopsis plants having defects in nonsense-mediated mRNA decay factors UPF1, UPF2, and UPF3 show photoperiod-dependent phenotypes in development and stress responses.2012 · DOI: 10.1111/j.1744-7909.2012.01093.x

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_038811 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

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

GO:0009611 response to wounding Biological Process

GO:0009863 salicylic acid mediated signaling pathway Biological Process

GO:0009867 jasmonic acid mediated signaling pathway Biological Process

GO:0042742 defense response to bacterium Biological Process

GO:0045727 positive regulation of translation Biological Process

GO:0048571 long-day photoperiodism Biological Process

GO:0051028 mRNA transport Biological Process

GO:2000623 negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay Biological Process

GO:0005634 nucleus Cellular Component

GO:0005654 nucleoplasm Cellular Component

GO:0005730 nucleolus Cellular Component

KEGG gene cross-reference

ath:AT1G33980

dre:393929

dre:566608

hsa:65109

hsa:65110

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.

Nucleus0.763

Rank 1 · LXL04_038811 · OH-1004

Cytoplasm0.278

Rank 2 · LXL04_038811 · OH-1004

Cell membrane0.086

Rank 3 · LXL04_038811 · OH-1004

Endoplasmic reticulum0.038

Rank 4 · LXL04_038811 · OH-1004

Golgi apparatus0.012

Rank 5 · LXL04_038811 · 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.

PF03467.22Smg4_UPF37-168 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_038811	`PF03467.22`	Smg4_UPF3	7	168	1.8e-54	185.1

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
`Q9FVW4`	Arabidopsis thaliana	Regulator of nonsense transcripts UPF3	41.468%	Swiss-Prot	moderate database homology

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