LXL04_030585 | RubberDandelionOmics

Gene overview

LXL04_030585

Reference: OH-1004 Chr: Chr06 Coordinates: 119222029-119225583 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1554 bp · LXL04_030585|LXL04_030585|OH1004|cDNA

ATGAACATTCTTAAATTTCAGAATCTTTGCTCTGTATCTCATCTCTTCTTCTTTGTCCTCTGCCTTCGATCCACAACAAAACCCTTAAAAGATCCCACTTTCATACAAAAAGCTCCATTATTTCTTCTTTCTCTGTCTCCCTCTAATCAGATGGCAACCCAGGCAGCAAATCCTGCTGCGATTCTTCCAAGTGCTCAAGTCGTTGGCAATGCATTCGTGGAACAGTACTACCATATTCTTCATCAATCTCCTGAATTGGT...

CDS

Download CDS FASTA

1554 bp · LXL04_030585|LXL04_030585|OH1004|CDS

ATGAACATTCTTAAATTTCAGAATCTTTGCTCTGTATCTCATCTCTTCTTCTTTGTCCTCTGCCTTCGATCCACAACAAAACCCTTAAAAGATCCCACTTTCATACAAAAAGCTCCATTATTTCTTCTTTCTCTGTCTCCCTCTAATCAGATGGCAACCCAGGCAGCAAATCCTGCTGCGATTCTTCCAAGTGCTCAAGTCGTTGGCAATGCATTCGTGGAACAGTACTACCATATTCTTCATCAATCTCCTGAATTGGT...

Protein

Download Protein FASTA

517 aa · LXL04_030585|LXL04_030585|OH1004|PROTEIN

MNILKFQNLCSVSHLFFFVLCLRSTTKPLKDPTFIQKAPLFLLSLSPSNQMATQAANPAAILPSAQVVGNAFVEQYYHILHQSPELVHKFYQDSSILSRPDMNGLMSSVTTMQAIDEKIQSLDYKNYKAEIETADAQDSYQSGVIVLVTGTLTGTDKIKRKFAQTFFLAPQEKGYFVQSDVFRYVEETASLVTTSAPDNLVIPNSDNNPAMNSEPNNGPEVCDPDDNQESESGLEEQPEPEPESEPVQTRLNETSTLQKP...

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_030585`
TK1151 ID	TkA07G413700
OH-1004 ID	LXL04_030585
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	98.600
Protein coverage (%)	TK1151 99.804 / OH-1004 98.646 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

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

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Basic Information and Functional Annotation

Gene ID LXL04_030585

Location Chr06:119222029-119225583 (+)

Description Similar to NTF2: Nuclear transport factor 2

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g60980`	Involved in RNA-directed DNA methylation (RdDM).	AtMBD6, a methyl CpG binding domain protein, maintains gene silencing in Arabidopsis by interacting with RNA binding proteins.2017 · DOI: 10.1007/s12038-016-9658-1

Rice

No hit for this species in the current source table.

Functional annotation source

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Functional annotation source: OH1004 · LXL04_030585 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0007264 small GTPase-mediated signal transduction Biological Process

GO:0031047 regulatory ncRNA-mediated gene silencing Biological Process

GO:0034063 stress granule assembly Biological Process

GO:0045087 innate immune response Biological Process

GO:0051028 mRNA transport Biological Process

GO:0051260 protein homooligomerization Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005829 cytosol Cellular Component

GO:0009536 plastid Cellular Component

GO:0010494 cytoplasmic stress granule Cellular Component

GO:1990861 Ubp3-Bre5 deubiquitination complex Cellular Component

KEGG gene cross-reference

ath:AT5G60980

hsa:9908

mmu:23881

pon:100172655

spo:2541364

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.

Cytoplasm0.633

Rank 1 · LXL04_030585 · OH-1004

Nucleus0.373

Rank 2 · LXL04_030585 · OH-1004

Cell membrane0.088

Rank 3 · LXL04_030585 · OH-1004

Endoplasmic reticulum0.068

Rank 4 · LXL04_030585 · OH-1004

Golgi apparatus0.053

Rank 5 · LXL04_030585 · 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.

PF02136.27NTF268-184 aa

PF00076.29RRM_1341-409 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_030585	`PF02136.27`	NTF2	68	184	1.7e-35	122.6
LXL04_030585	`PF00076.29`	RRM_1	341	409	1e-12	48.5

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
`Q9FME2`	Arabidopsis thaliana	Nuclear transport factor 2	48.615%	Swiss-Prot	moderate database homology

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