LXL04_024681 | RubberDandelionOmics

Gene overview

LXL04_024681

Reference: OH-1004 Chr: Chr05 Coordinates: 96600695-96602902 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1581 bp · LXL04_024681|LXL04_024681|OH1004|cDNA

ATGCATCCTCAAAACGAGATGAATTATGCATCACCATCGTCGTATTACAATTACCACCAATCTGACATCCAAAACCCTATAGCTAATCCCCCGTTCGATCAATTTCCTTCTACAACTGCTGCATCTGCCCCTCCAGATCCTTCAATTTACCATTTCCCCGATTACTCGACCAATCACCCCTCTACTTATTACCATAACGATCATCAGAGTGGAACGGTTCAGAATTTTGATTCGGGTAATCCTGGTTATGATCCGCAGTC...

CDS

Download CDS FASTA

1581 bp · LXL04_024681|LXL04_024681|OH1004|CDS

ATGCATCCTCAAAACGAGATGAATTATGCATCACCATCGTCGTATTACAATTACCACCAATCTGACATCCAAAACCCTATAGCTAATCCCCCGTTCGATCAATTTCCTTCTACAACTGCTGCATCTGCCCCTCCAGATCCTTCAATTTACCATTTCCCCGATTACTCGACCAATCACCCCTCTACTTATTACCATAACGATCATCAGAGTGGAACGGTTCAGAATTTTGATTCGGGTAATCCTGGTTATGATCCGCAGTC...

Protein

Download Protein FASTA

526 aa · LXL04_024681|LXL04_024681|OH1004|PROTEIN

MHPQNEMNYASPSSYYNYHQSDIQNPIANPPFDQFPSTTAASAPPDPSIYHFPDYSTNHPSTYYHNDHQSGTVQNFDSGNPGYDPQSMPSWYHHQSYDHNQNQNQAAVPFGGAIVDQSVYAYTGGNTGRQGESSKVPEVSFDDYGRPLGLSDGGKKQQVGSTEVLRNEKGNESIYAYTGGNNGRKDESSSRMPALRFDDYGRPITFGSEGGNGHMGSVSQLDSAKIVKATPKVQVNEDVQNGVQKFRVILLSEVGGMQGD...

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_024681`
TK1151 ID	TkA06G117610
OH-1004 ID	LXL04_024681
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	97.500
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

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

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Basic Information and Functional Annotation

Gene ID LXL04_024681

Location Chr05:96600695-96602902 (+)

Description Similar to FREE1: Protein FREE1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g20110`	Endosomal sorting complex required for transport (ESCRT) component regulating multivesicular body (MVB) protein sorting and plant growth.	A unique plant ESCRT component, FREE1, regulates multivesicular body protein sorting and plant growth.2014 · DOI: 10.1016/j.cub.2014.09.014 Dual roles of an Arabidopsis ESCRT component FREE1 in regulating vacuolar protein transport and autophagic degradation.2015 · DOI: 10.1073/pnas.1421271112 FYVE1 is essential for vacuole biogenesis and intracellular trafficking in Arabidopsis.2015 · DOI: 10.1104/pp.114.253377 FYVE1/FREE1 Interacts with the PYL4 ABA Receptor and Mediates Its Delivery to the Vacuolar Degradation Pathway.2016 · DOI: 10.1105/tpc.16.00178 The effect of ABRE BINDING FACTOR 4-mediated FYVE1 on salt stress tolerance in Arabidopsis.2020 · DOI: 10.1016/j.plantsci.2020.110489
`At3g14270`	The PI(3,5)P2 regulatory complex regulates both the synthesis and turnover of phosphatidylinositol 3,5-bisphosphate (PtdIns(3,5)P2).	Arabidopsis FAB1/PIKfyve proteins are essential for development of viable pollen.2009 · DOI: 10.1104/pp.109.146159 Loss-of-function and gain-of-function mutations in FAB1A/B impair endomembrane homeostasis, conferring pleiotropic developmental abnormalities in Arabidopsis.2011 · DOI: 10.1104/pp.110.167981

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_024681 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0007033 vacuole organization Biological Process

GO:0009555 pollen development Biological Process

GO:0009738 abscisic acid-activated signaling pathway Biological Process

GO:0009788 negative regulation of abscisic acid-activated signaling pathway Biological Process

GO:0010256 endomembrane system organization Biological Process

GO:0015031 protein transport Biological Process

GO:0035973 aggrephagy Biological Process

GO:0036258 multivesicular body assembly Biological Process

GO:0042059 negative regulation of epidermal growth factor receptor signaling pathway Biological Process

GO:0046854 phosphatidylinositol phosphate biosynthetic process Biological Process

GO:0060586 multicellular organismal-level iron ion homeostasis Biological Process

GO:0070676 intralumenal vesicle formation Biological Process

KEGG gene cross-reference

ath:AT1G20110

ath:AT3G14270

cbr:CBG_14460

hsa:23001

mmu:72145

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.

Cytoplasm0.521

Rank 1 · LXL04_024681 · OH-1004

Cell membrane0.299

Rank 2 · LXL04_024681 · OH-1004

Nucleus0.265

Rank 3 · LXL04_024681 · OH-1004

Golgi apparatus0.101

Rank 4 · LXL04_024681 · OH-1004

Lysosome / Vacuole0.075

Rank 5 · LXL04_024681 · 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.

PF01363.28FYVE375-439 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_024681	`PF01363.28`	FYVE	375	439	1.1e-20	74.3

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
`Q9ASS2`	Arabidopsis thaliana	Protein FREE1	54.433%	Swiss-Prot	strong database homology
`Q9LUM0`	Arabidopsis thaliana	1-phosphatidylinositol-3-phosphate 5-kinase FAB1B	27.586%	Swiss-Prot	weak database homology

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