LXL04_021538 | RubberDandelionOmics

Gene overview

LXL04_021538

Reference: OH-1004 Chr: Chr04 Coordinates: 132066564-132068511 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

993 bp · LXL04_021538|LXL04_021538|OH1004|cDNA

ATGGAGCAGGCTGTTCTCGATGATATAATCCAGAGGCTGATTCAAGTTAAAGGCAAACCTGGTAAGCAGGTGCAACTCACTGAACCGGAAATCAAGCAACTTTGTGTTGTTTCTAAAGAGATCTTCTTACGCCAGCCTAATTTGCTGGAAATCGAAGCACCCATCAAGATTTGTGGCGATGTCCATGGTCAATACTCCGACCTTCTACGTCTTTTTGAGTACGGCGGATTACCTCCGGAAGCCAATTACTTGTTCCTTGG...

CDS

Download CDS FASTA

993 bp · LXL04_021538|LXL04_021538|OH1004|CDS

ATGGAGCAGGCTGTTCTCGATGATATAATCCAGAGGCTGATTCAAGTTAAAGGCAAACCTGGTAAGCAGGTGCAACTCACTGAACCGGAAATCAAGCAACTTTGTGTTGTTTCTAAAGAGATCTTCTTACGCCAGCCTAATTTGCTGGAAATCGAAGCACCCATCAAGATTTGTGGCGATGTCCATGGTCAATACTCCGACCTTCTACGTCTTTTTGAGTACGGCGGATTACCTCCGGAAGCCAATTACTTGTTCCTTGG...

Protein

Download Protein FASTA

330 aa · LXL04_021538|LXL04_021538|OH1004|PROTEIN

MEQAVLDDIIQRLIQVKGKPGKQVQLTEPEIKQLCVVSKEIFLRQPNLLEIEAPIKICGDVHGQYSDLLRLFEYGGLPPEANYLFLGDYVDRGKQSLETICLLLAYKIKYPDNFFLLRGNHECASINRIYGFYDECKRRFNVKLWKTFSDCFNCLPVAALIDDKILCMHGGLSPDLNNLDQIRNLRRPTDIPDSGLLCDLLWSDPCTEVKGWGMNDRGVSYTFGADIVTEFLQKHDLDLVCRAHQVVEDGYEFFADRQLV...

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_021538`
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_021538

Location Chr04:132066564-132068511 (+)

Description Similar to Os03g0268000: Serine/threonine-protein phosphatase PP1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g39840`	Serine/threonine-protein phosphatase that possesses phosphatase activity toward para-nitrophenyl phosphate (pNPP) in vitro.	Arabidopsis DELLA protein degradation is controlled by a type-one protein phosphatase, TOPP4.2014 · DOI: 10.1371/journal.pgen.1004464 TYPE-ONE PROTEIN PHOSPHATASE4 regulates pavement cell interdigitation by modulating PIN-FORMED1 polarity and trafficking in Arabidopsis.2015 · DOI: 10.1104/pp.114.249904 TOPP4 Regulates the Stability of PHYTOCHROME INTERACTING FACTOR5 during Photomorphogenesis in Arabidopsis.2016 · DOI: 10.1104/pp.15.01729
`At2g29400`	Serine/threonine-protein phosphatase that possesses phosphatase activity toward para-nitrophenyl phosphate (pNPP) in vitro.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os03g0268000`	Serine/threonine-protein phosphatase PP1.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_021538 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006468 protein phosphorylation Biological Process

GO:0006470 protein dephosphorylation Biological Process

GO:0009740 gibberellic acid mediated signaling pathway Biological Process

GO:0010161 red light signaling pathway Biological Process

GO:0016311 dephosphorylation Biological Process

GO:0000164 protein phosphatase type 1 complex Cellular Component

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0004722 protein serine/threonine phosphatase activity Molecular Function

GO:0046872 metal ion binding Molecular Function

KEGG gene cross-reference

ath:AT2G29400

ath:AT2G39840

dosa:Os03g0268000

nta:107829724

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.

Cytoplasm0.665

Rank 1 · LXL04_021538 · OH-1004

Nucleus0.490

Rank 2 · LXL04_021538 · OH-1004

Cell membrane0.066

Rank 3 · LXL04_021538 · OH-1004

Mitochondrion0.064

Rank 4 · LXL04_021538 · OH-1004

Endoplasmic reticulum0.048

Rank 5 · LXL04_021538 · 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.

PF16891.11STPPase_N6-52 aa

PF00149.34Metallophos54-247 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_021538	`PF16891.11`	STPPase_N	6	52	1.4e-20	74.2
LXL04_021538	`PF00149.34`	Metallophos	54	247	6.8e-52	177.5

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
`P48484`	Arabidopsis thaliana	Serine/threonine-protein phosphatase PP1 isozyme 4	86.093%	Swiss-Prot	strong database homology
`P30366`	Arabidopsis thaliana	Serine/threonine-protein phosphatase PP1 isozyme 1	83.553%	Swiss-Prot	strong database homology
`P48489`	Oryza sativa subsp. japonica	Serine/threonine-protein phosphatase PP1	85.762%	Swiss-Prot	strong database homology

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