LXL04_002221 | RubberDandelionOmics

Gene overview

LXL04_002221

Reference: OH-1004 Chr: Chr01 Coordinates: 44029949-44035572 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

5082 bp · LXL04_002221|LXL04_002221|OH1004|cDNA

ATGGATGCTTCAGAGAGACCTTTAACTAACCTGATAGGTAACCTCAGATCCTGGATCCCTCGGCGGTCTGAGCCAGCTAATGTGTCGAGGGACTTTTGGATGCCCGATCAGAGTTGCAGGGTATGCTACGAGTGTGACACCCAGTTCACTTTATTCAACCGAAGACACCATTGCAGACTTTGTGGCCGAGTTTTCTGTGCCAAGTGCACTCACAACTGGATCCCTGCTAGACCTAGCTCCCAAAACATCATCAGGGAAGA...

CDS

Download CDS FASTA

5082 bp · LXL04_002221|LXL04_002221|OH1004|CDS

ATGGATGCTTCAGAGAGACCTTTAACTAACCTGATAGGTAACCTCAGATCCTGGATCCCTCGGCGGTCTGAGCCAGCTAATGTGTCGAGGGACTTTTGGATGCCCGATCAGAGTTGCAGGGTATGCTACGAGTGTGACACCCAGTTCACTTTATTCAACCGAAGACACCATTGCAGACTTTGTGGCCGAGTTTTCTGTGCCAAGTGCACTCACAACTGGATCCCTGCTAGACCTAGCTCCCAAAACATCATCAGGGAAGA...

Protein

Download Protein FASTA

1693 aa · LXL04_002221|LXL04_002221|OH1004|PROTEIN

MDASERPLTNLIGNLRSWIPRRSEPANVSRDFWMPDQSCRVCYECDTQFTLFNRRHHCRLCGRVFCAKCTHNWIPARPSSQNIIREESEKIRACNYCFKQWQQGGLAGSVDHGIPDSSLDLSTSPSAASLISTKSSGTVDSSSIAFTSVPHSVSSYQHTHYPTGLTPHQSVVMEANLEEQNDLATRGNELLLDVGTRSPNGDDFDEEFAYQLATSGGHVLQIDNGYYDELQMDDMDNEFESHKIHTDGEPHDVTSVSSCS...

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_002221`
TK1151 ID	TkA01G473660
OH-1004 ID	LXL04_002221
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.500
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

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_002221

Location Chr01:44029949-44035572 (+)

Description Similar to FAB1A: 1-phosphatidylinositol-3-phosphate 5-kinase FAB1A

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g33240`	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 Arabidopsis FAB1A/B is possibly involved in the recycling of auxin transporters.2011 · DOI: 10.4161/psb.6.4.15023
`At1g71010`	The PI(3,5)P2 regulatory complex regulates both the synthesis and turnover of phosphatidylinositol 3,5-bisphosphate (PtdIns(3,5)P2).	No verified direct reference in this release
`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
`At1g34260`	The PI(3,5)P2 regulatory complex regulates both the synthesis and turnover of phosphatidylinositol 3,5-bisphosphate (PtdIns(3,5)P2).	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_002221 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0007033 vacuole organization Biological Process

GO:0009555 pollen development Biological Process

GO:0010256 endomembrane system organization Biological Process

GO:0046854 phosphatidylinositol phosphate biosynthetic process Biological Process

GO:0090332 stomatal closure Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005739 mitochondrion Cellular Component

GO:0005768 endosome Cellular Component

GO:0010008 endosome membrane Cellular Component

GO:0000285 1-phosphatidylinositol-3-phosphate 5-kinase activity Molecular Function

GO:0005524 ATP binding Molecular Function

KEGG gene cross-reference

ath:AT1G34260

ath:AT1G71010

ath:AT3G14270

ath:AT4G33240

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.

Cytoplasm0.335

Rank 1 · LXL04_002221 · OH-1004

Cell membrane0.326

Rank 2 · LXL04_002221 · OH-1004

Nucleus0.274

Rank 3 · LXL04_002221 · OH-1004

Golgi apparatus0.106

Rank 4 · LXL04_002221 · OH-1004

Endoplasmic reticulum0.080

Rank 5 · LXL04_002221 · 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.

PF01363.28FYVE33-102 aa

PF00118.30Cpn60_TCP1405-652 aa

PF01504.25PIP5K1438-1604 aa

PF01504.25PIP5K1603-1660 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_002221	`PF01363.28`	FYVE	33	102	1e-16	61.5
LXL04_002221	`PF00118.30`	Cpn60_TCP1	405	652	1.7e-31	110.2
LXL04_002221	`PF01504.25`	PIP5K	1438	1604	8.8e-44	150.6
LXL04_002221	`PF01504.25`	PIP5K	1603	1660	8.8e-44	150.6

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q0WUR5`	Arabidopsis thaliana	1-phosphatidylinositol-3-phosphate 5-kinase FAB1A	54.141%	Swiss-Prot	strong database homology
`Q9SSJ8`	Arabidopsis thaliana	Putative 1-phosphatidylinositol-3-phosphate 5-kinase FAB1C	47.989%	Swiss-Prot	moderate database homology
`Q9LUM0`	Arabidopsis thaliana	1-phosphatidylinositol-3-phosphate 5-kinase FAB1B	64.211%	Swiss-Prot	moderate database homology
`Q9XID0`	Arabidopsis thaliana	Putative 1-phosphatidylinositol-3-phosphate 5-kinase FAB1D	35.914%	Swiss-Prot	moderate database homology

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