LXL04_003893 | RubberDandelionOmics

Gene overview

LXL04_003893

Reference: OH-1004 Chr: Chr01 Coordinates: 112428497-112439445 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1791 bp · LXL04_003893|LXL04_003893|OH1004|cDNA

ATGAAAGTCCGGAGAGGGAAACGATCTGAGGCATTTTGGCCATCAATTGTGATGAAAAAATGGTTGAATATTCCGCCAAAGAATAATGATTTTAGTGAAGATGAAATCGATCCAGAAACAGAAAGTGAAGAAGATGTCTGCTCCAGCTCCGTAAAAGAGGAACCAATGAATTTTAAGGAGGAGCATGCTTGCAAAATGTCTCCATTCTCGAGTCAAACCTCAAACGCTACGCCCTCAAAGAGGTTGGTAAAACACAAGAG...

CDS

Download CDS FASTA

1791 bp · LXL04_003893|LXL04_003893|OH1004|CDS

ATGAAAGTCCGGAGAGGGAAACGATCTGAGGCATTTTGGCCATCAATTGTGATGAAAAAATGGTTGAATATTCCGCCAAAGAATAATGATTTTAGTGAAGATGAAATCGATCCAGAAACAGAAAGTGAAGAAGATGTCTGCTCCAGCTCCGTAAAAGAGGAACCAATGAATTTTAAGGAGGAGCATGCTTGCAAAATGTCTCCATTCTCGAGTCAAACCTCAAACGCTACGCCCTCAAAGAGGTTGGTAAAACACAAGAG...

Protein

Download Protein FASTA

596 aa · LXL04_003893|LXL04_003893|OH1004|PROTEIN

MKVRRGKRSEAFWPSIVMKKWLNIPPKNNDFSEDEIDPETESEEDVCSSSVKEEPMNFKEEHACKMSPFSSQTSNATPSKRLVKHKRWNSESVHSTKTKDVRITIGTWNVAGRPPYDGLDIDNWLCLHEPADIYVLGFQEVVPLNVGNVLGAETREPTSKWDTIIRKSLNKSHKPESIPKSYSAPTSPGTDSMNNDESFSTEITSPDRKEITMMIKSPRFYGLDWSTYELNVKKDICISGKKLRKVLSSSDRVRNDWVTN...

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_003893`
TK1151 ID	TkA06G022970
OH-1004 ID	LXL04_003893
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	60.500
Protein coverage (%)	TK1151 100.000 / OH-1004 99.664 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_003893

Location Chr01:112428497-112439445 (-)

Description Similar to IP5P2: Type I inositol polyphosphate 5-phosphatase 2

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g18010`	Has phosphatase activity toward Ins(1,4,5)P3 and Ins(1,3,4,5)P4.	No verified direct reference in this release
`At1g34120`	Has phosphatase activity toward Ins(1,4,5)P3 and Ins(1,3,4,5)P4, but not toward Ins(1,4)P2, Ins(1)P.	No verified direct reference in this release
`At2g32010`	Has phosphatase activity toward PtdIns(4,5)P₂ and, more weakly, PtdIns(3,4,5)P₃, but not Ins(1,4,5)P₃.	CVP2- and CVL1-mediated phosphoinositide signaling as a regulator of the ARF GAP SFC/VAN3 in establishment of foliar vein patterns.2009 · DOI: 10.1111/j.1365-313x.2009.03920.x Primary root protophloem differentiation requires balanced phosphatidylinositol-4,5-biphosphate levels and systemically affects root branching.2015 · DOI: 10.1242/dev.118364
`At3g63240`	Type I inositol polyphosphate 5-phosphatase 4.	No verified direct reference in this release
`At1g05470`	May have phosphatase activity toward PtdIns(4,5)P₂ and PtdIns(3,4,5)P₃.	Genetic regulation of vascular tissue patterning in Arabidopsis.1999 · DOI: 10.1105/tpc.11.11.2123 Cotyledon vascular pattern2-mediated inositol (1,4,5) triphosphate signal transduction is essential for closed venation patterns of Arabidopsis foliar organs.2004 · DOI: 10.1105/tpc.021030 CVP2- and CVL1-mediated phosphoinositide signaling as a regulator of the ARF GAP SFC/VAN3 in establishment of foliar vein patterns.2009 · DOI: 10.1111/j.1365-313x.2009.03920.x Primary root protophloem differentiation requires balanced phosphatidylinositol-4,5-biphosphate levels and systemically affects root branching.2015 · DOI: 10.1242/dev.118364

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_003893 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009737 response to abscisic acid Biological Process

GO:0009738 abscisic acid-activated signaling pathway Biological Process

GO:0009845 seed germination Biological Process

GO:0010305 leaf vascular tissue pattern formation Biological Process

GO:0032957 inositol trisphosphate metabolic process Biological Process

GO:0043647 inositol phosphate metabolic process Biological Process

GO:0046856 phosphatidylinositol dephosphorylation Biological Process

GO:0071472 cellular response to salt stress Biological Process

GO:0090351 seedling development Biological Process

GO:2000377 regulation of reactive oxygen species metabolic process Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

KEGG gene cross-reference

ath:AT1G34120

ath:AT2G32010

ath:AT3G63240

ath:AT4G18010

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.

Cytoplasm0.413

Rank 1 · LXL04_003893 · OH-1004

Nucleus0.295

Rank 2 · LXL04_003893 · OH-1004

Cell membrane0.244

Rank 3 · LXL04_003893 · OH-1004

Golgi apparatus0.078

Rank 4 · LXL04_003893 · OH-1004

Plastid0.075

Rank 5 · LXL04_003893 · 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.

PF22669.3Exo_endo_phos2106-174 aa

PF22669.3Exo_endo_phos2329-557 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_003893	`PF22669.3`	Exo_endo_phos2	106	174	1.1e-69	235.8
LXL04_003893	`PF22669.3`	Exo_endo_phos2	329	557	1.1e-69	235.8

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
`Q9FUR2`	Arabidopsis thaliana	Type I inositol polyphosphate 5-phosphatase 2	47.678%	Swiss-Prot	moderate database homology
`Q84MA2`	Arabidopsis thaliana	Type I inositol polyphosphate 5-phosphatase 1	36.705%	Swiss-Prot	moderate database homology
`Q0WQ41`	Arabidopsis thaliana	Type IV inositol polyphosphate 5-phosphatase 7	38.687%	Swiss-Prot	moderate database homology
`Q8GTS0`	Arabidopsis thaliana	Type I inositol polyphosphate 5-phosphatase 4	57.261%	Swiss-Prot	weak database homology
`Q9LR47`	Arabidopsis thaliana	Type IV inositol polyphosphate 5-phosphatase 6	54.237%	Swiss-Prot	weak database homology

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