LXL04_012167 | RubberDandelionOmics

Gene overview

LXL04_012167

Reference: OH-1004 Chr: Chr03 Coordinates: 7650900-7652528 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

870 bp · LXL04_012167|LXL04_012167|OH1004|cDNA

ATGAAATCTCTTGCTCCCTCtcccttttcttcttcatctttcaTCTATGCATCTTCACCGCTCAAATTCAAAGTTACATTGTCAAATCCAAACAATAGAAAACCCCAATTCAATCTCAATCTCACTCCAACAAATCTCAAACCAGACACAGTTTACTGTAAAGCAACACAAAATGATATCGATGGAACCCCACAAAGCCGTCAAAGCTCAACAAACCACAAAATGGAGGATTACAACACTGCCATGAAGAGAATGATGAG...

CDS

Download CDS FASTA

870 bp · LXL04_012167|LXL04_012167|OH1004|CDS

ATGAAATCTCTTGCTCCCTCTCCCTTTTCTTCTTCATCTTTCATCTATGCATCTTCACCGCTCAAATTCAAAGTTACATTGTCAAATCCAAACAATAGAAAACCCCAATTCAATCTCAATCTCACTCCAACAAATCTCAAACCAGACACAGTTTACTGTAAAGCAACACAAAATGATATCGATGGAACCCCACAAAGCCGTCAAAGCTCAACAAACCACAAAATGGAGGATTACAACACTGCCATGAAGAGAATGATGAG...

Protein

Download Protein FASTA

289 aa · LXL04_012167|LXL04_012167|OH1004|PROTEIN

MKSLAPSPFSSSSFIYASSPLKFKVTLSNPNNRKPQFNLNLTPTNLKPDTVYCKATQNDIDGTPQSRQSSTNHKMEDYNTAMKRMMRNPYEYHHDLGMNYNLITENLIVGSQPQKPEDIDHLKNEQNVAYILNLQQDGDIAYWGINLESIVKRCQQLGVRHMRRPARDFDPDSLRSMLPKAVSSLEWAISEGKGRVYVHCTAGLGRAPAVSIAYMFWFLDMDLNTAYDMLTEKRPCGPNKKAIRGATYDLAKNDPGKEPF...

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_012167`
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_012167

Location Chr03:7650900-7652528 (-)

Description Similar to LSF2: Phosphoglucan phosphatase LSF2, chloroplastic

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g10940`	Starch-associated phosphoglucan phosphatase that selectively dephosphorylates the glucan C3 position.	The phosphoglucan phosphatase like sex Four2 dephosphorylates starch at the C3-position in Arabidopsis.2011 · DOI: 10.1105/tpc.111.092155 Structure of the Arabidopsis glucan phosphatase like sex four2 reveals a unique mechanism for starch dephosphorylation.2013 · DOI: 10.1105/tpc.113.112706
`At3g52180`	Starch granule-associated phosphoglucan phosphatase involved in the control of starch accumulation.	Similar protein phosphatases control starch metabolism in plants and glycogen metabolism in mammals.2006 · DOI: 10.1074/jbc.m600519200 A chloroplast-localized dual-specificity protein phosphatase in Arabidopsis contains a phylogenetically dispersed and ancient carbohydrate-binding domain, which binds the polysaccharide starch.2006 · DOI: 10.1111/j.1365-313x.2006.02704.x STARCH-EXCESS4 is a laforin-like Phosphoglucan phosphatase required for starch degradation in Arabidopsis thaliana.2009 · DOI: 10.1105/tpc.108.064360 The Laforin-like dual-specificity phosphatase SEX4 from Arabidopsis hydrolyzes both C6- and C3-phosphate esters introduced by starch-related dikinases and thereby affects phase transition of alpha-glucans.2010 · DOI: 10.1104/pp.109.149914 The phosphoglucan phosphatase like sex Four2 dephosphorylates starch at the C3-position in Arabidopsis.2011 · DOI: 10.1105/tpc.111.092155 Engineering starch accumulation by manipulation of phosphate metabolism of starch.2012 · DOI: 10.1111/j.1467-7652.2012.00684.x Phosphoglucan-bound structure of starch phosphatase Starch Excess4 reveals the mechanism for C6 specificity.2014 · DOI: 10.1073/pnas.1400757111
`At3g01510`	Starch granule-associated phosphoglucan phosphatase involved in the control of starch accumulation.	A putative phosphatase, LSF1, is required for normal starch turnover in Arabidopsis leaves.2010 · DOI: 10.1104/pp.109.148981

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_012167 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0005977 glycogen metabolic process Biological Process

GO:0005978 glycogen biosynthetic process Biological Process

GO:0005982 starch metabolic process Biological Process

GO:0005983 starch catabolic process Biological Process

GO:0006914 autophagy Biological Process

GO:0009892 negative regulation of metabolic process Biological Process

GO:0016311 dephosphorylation Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005829 cytosol Cellular Component

GO:0005886 plasma membrane Cellular Component

GO:0009501 amyloplast Cellular Component

KEGG gene cross-reference

ath:AT3G01510

ath:AT3G10940

ath:AT3G52180

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.

Plastid0.973

Rank 1 · LXL04_012167 · OH-1004

Mitochondrion0.041

Rank 2 · LXL04_012167 · OH-1004

Cytoplasm0.024

Rank 3 · LXL04_012167 · OH-1004

Nucleus0.023

Rank 4 · LXL04_012167 · OH-1004

Cell membrane0.014

Rank 5 · LXL04_012167 · 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.

PF22784.2PTP-SAK105-217 aa

PF00782.26DSPc122-239 aa

PF22785.2Tc-R-P124-217 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_012167	`PF22784.2`	PTP-SAK	105	217	3e-06	28.1
LXL04_012167	`PF00782.26`	DSPc	122	239	5.1e-15	56.2
LXL04_012167	`PF22785.2`	Tc-R-P	124	217	6.1e-06	27.4

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
`Q9SRK5`	Arabidopsis thaliana	Phosphoglucan phosphatase LSF2, chloroplastic	74.806%	Swiss-Prot	strong database homology
`Q9FEB5`	Arabidopsis thaliana	Phosphoglucan phosphatase DSP4, chloroplastic	41.294%	Swiss-Prot	moderate database homology
`F4J117`	Arabidopsis thaliana	Phosphoglucan phosphatase LSF1, chloroplastic	38.503%	Swiss-Prot	moderate database homology

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