LXL04_011778 | RubberDandelionOmics

Gene overview

LXL04_011778

Reference: OH-1004 Chr: Chr03 Coordinates: 52753-61859 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2280 bp · LXL04_011778|LXL04_011778|OH1004|cDNA

ATGGAAAGCCATGGGAATGCTACCAACTCCCTTTACTCCCACATTGGAAAGCATATGAACTTGACTGAACTTAATGACCAGCCCCGGGCCGGGCGAGATTACCTATCAGCAAACCTAACTAAAAACATGGGCATACCTGGTTTGTACCGGTGGCTAGTCGACAGATACCCCAATACACTTTGTTGCGTTGCCGAAGAGCGTTCACGCTTCTCTCACGGCCCGCCGAGCGACACCACTACACCTAATCCTAATGGCGTCGA...

CDS

Download CDS FASTA

2280 bp · LXL04_011778|LXL04_011778|OH1004|CDS

ATGGAAAGCCATGGGAATGCTACCAACTCCCTTTACTCCCACATTGGAAAGCATATGAACTTGACTGAACTTAATGACCAGCCCCGGGCCGGGCGAGATTACCTATCAGCAAACCTAACTAAAAACATGGGCATACCTGGTTTGTACCGGTGGCTAGTCGACAGATACCCCAATACACTTTGTTGCGTTGCCGAAGAGCGTTCACGCTTCTCTCACGGCCCGCCGAGCGACACCACTACACCTAATCCTAATGGCGTCGA...

Protein

Download Protein FASTA

759 aa · LXL04_011778|LXL04_011778|OH1004|PROTEIN

MESHGNATNSLYSHIGKHMNLTELNDQPRAGRDYLSANLTKNMGIPGLYRWLVDRYPNTLCCVAEERSRFSHGPPSDTTTPNPNGVEFDNLYIDMNGVIHPCFHPEGLPAPQSYDAVLRSIFRYIDRVFSIVRPRKLLFLAVDGVAPRAKMNHQRKRRFMASREAAAGAGQAAVEVGGIEDDKKLDSNVITPGTEFMDLLSCALQYYVHLRMNSDPAWRAIKVVVSDSTVVGEGEHKILSYIRSQRILPGYDPNTRHCFH...

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_011778`
TK1151 ID	TkA02G616280
OH-1004 ID	LXL04_011778
Relationship / confidence	Sequence Supported Annotation Or Model Conflict / Review
Protein identity (%)	98.800
Protein coverage (%)	TK1151 99.130 / OH-1004 45.059 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_011778

Location Chr03:52753-61859 (-)

Description Similar to XRN4: 5'-3' exoribonuclease 4

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g54490`	Possesses 5'->3' exoribonuclease activity.	AtXRN4 degrades mRNA in Arabidopsis and its substrates include selected miRNA targets.2004 · DOI: 10.1016/j.molcel.2004.06.006 A link between mRNA turnover and RNA interference in Arabidopsis.2004 · DOI: 10.1126/science.1101092 ETHYLENE-INSENSITIVE5 encodes a 5'-->3' exoribonuclease required for regulation of the EIN3-targeting F-box proteins EBF1/2.2006 · DOI: 10.1073/pnas.0605528103 The exoribonuclease XRN4 is a component of the ethylene response pathway in Arabidopsis.2006 · DOI: 10.1105/tpc.106.046508
`UniProt: Q9FQ02`	Possesses 5'->3' exoribonuclease activity.	No verified direct reference in this release
`At1g75660`	Possesses 5'->3' exoribonuclease activity.	Arabidopsis FIERY1, XRN2, and XRN3 are endogenous RNA silencing suppressors.2007 · DOI: 10.1105/tpc.107.055319 Arabidopsis thaliana XRN2 is required for primary cleavage in the pre-ribosomal RNA.2010 · DOI: 10.1093/nar/gkq172

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_011778 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000956 nuclear-transcribed mRNA catabolic process Biological Process

GO:0000967 rRNA 5'-end processing Biological Process

GO:0006397 mRNA processing Biological Process

GO:0006402 mRNA catabolic process Biological Process

GO:0009826 unidimensional cell growth Biological Process

GO:0010087 phloem or xylem histogenesis Biological Process

GO:0010286 heat acclimation Biological Process

GO:0010587 miRNA catabolic process Biological Process

GO:0031087 deadenylation-independent decapping of nuclear-transcribed mRNA Biological Process

GO:0040029 epigenetic regulation of gene expression Biological Process

GO:0051301 cell division Biological Process

GO:0060149 negative regulation of post-transcriptional gene silencing Biological Process

KEGG gene cross-reference

ath:AT1G54490

ath:AT1G75660

ath:AT5G42540

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.

Nucleus0.523

Rank 1 · LXL04_011778 · OH-1004

Cytoplasm0.382

Rank 2 · LXL04_011778 · OH-1004

Cell membrane0.083

Rank 3 · LXL04_011778 · OH-1004

Endoplasmic reticulum0.071

Rank 4 · LXL04_011778 · OH-1004

Golgi apparatus0.051

Rank 5 · LXL04_011778 · 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.

PF03159.25XRN_N43-283 aa

PF17846.7XRN_M338-419 aa

PF17846.7XRN_M420-492 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_011778	`PF03159.25`	XRN_N	43	283	1.5e-89	300.3
LXL04_011778	`PF17846.7`	XRN_M	338	419	4.2e-61	208.0
LXL04_011778	`PF17846.7`	XRN_M	420	492	4.2e-61	208.0

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
`Q9FQ04`	Arabidopsis thaliana	5'-3' exoribonuclease 4	54.369%	Swiss-Prot	weak database homology
`Q9FQ02`	Arabidopsis thaliana	5'-3' exoribonuclease 2	52.530%	Swiss-Prot	weak database homology
`Q9FQ03`	Arabidopsis thaliana	5'-3' exoribonuclease 3	52.311%	Swiss-Prot	weak database homology

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