LXL04_016972 | RubberDandelionOmics

Gene overview

LXL04_016972

Reference: OH-1004 Chr: Chr03 Coordinates: 138189086-138193388 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1425 bp · LXL04_016972|LXL04_016972|OH1004|cDNA

ATGAAGGGTCCGTTAGATCGGACGAAAATTGTGCTTCGGCACTTGCCGCATACGATTTCGCAGTCGGCGCTCATGGAGCAAATTGACGCCCGTTTTTCTGGTCGATACAATTGGTTTAGTTTCCGTTCCGGAAAGCAAAGCCTGAAGTGTCAATCATATTCCAGAGCCTATATTGACTTTAAGCAGCCAGAGGATGTCATTGAGTTTGCAGAGTTCTTTGATGGACATGTTTTTGTTAACGAGAAGGGTACCCAATTCAA...

CDS

Download CDS FASTA

1425 bp · LXL04_016972|LXL04_016972|OH1004|CDS

ATGAAGGGTCCGTTAGATCGGACGAAAATTGTGCTTCGGCACTTGCCGCATACGATTTCGCAGTCGGCGCTCATGGAGCAAATTGACGCCCGTTTTTCTGGTCGATACAATTGGTTTAGTTTCCGTTCCGGAAAGCAAAGCCTGAAGTGTCAATCATATTCCAGAGCCTATATTGACTTTAAGCAGCCAGAGGATGTCATTGAGTTTGCAGAGTTCTTTGATGGACATGTTTTTGTTAACGAGAAGGGTACCCAATTCAA...

Protein

Download Protein FASTA

474 aa · LXL04_016972|LXL04_016972|OH1004|PROTEIN

MKGPLDRTKIVLRHLPHTISQSALMEQIDARFSGRYNWFSFRSGKQSLKCQSYSRAYIDFKQPEDVIEFAEFFDGHVFVNEKGTQFKTIVEYAPSQRVPKQWSKKDGREGTIVKDPEYLEFLESVSKPVENLPSAEIQLERKEAERAGAGKEAPIVTALMDFIRQKRAAKGGPRRSLPNGKLMRRGTNASSSNSNSTGVKRGSEKRTSTMYVLREGGKNSNGKEKSTYVKRAEKSSTQSGSVVLDEEKASDIGKKKILLL...

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_016972`
TK1151 ID	TkA02G086670
OH-1004 ID	LXL04_016972
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.600
Protein coverage (%)	TK1151 100.000 / OH-1004 100.000 Coverage and evidence Coverage is the aligned span of the best-scoring HSP divided by representative protein length. A homolog match does not establish functional validation.
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_016972

Location Chr03:138189086-138193388 (-)

Description Similar to UPF3: Regulator of nonsense transcripts UPF3

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

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_016972 · 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.

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.

Nucleus0.807

Rank 1 · LXL04_016972 · OH-1004

Cytoplasm0.236

Rank 2 · LXL04_016972 · OH-1004

Cell membrane0.072

Rank 3 · LXL04_016972 · OH-1004

Endoplasmic reticulum0.035

Rank 4 · LXL04_016972 · OH-1004

Golgi apparatus0.013

Rank 5 · LXL04_016972 · 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.

PF03467.22Smg4_UPF37-168 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_016972	`PF03467.22`	Smg4_UPF3	7	168	8.7e-53	179.6

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
`Q9FVW4`	Arabidopsis thaliana	Regulator of nonsense transcripts UPF3	44.553%	Swiss-Prot	moderate database homology

JBrowse

View in Genome Browser

Gene Card