TkA02G532480 | RubberDandelionOmics

Gene overview

TkA02G532480

Reference: TK1151 Chr: Chr02 Coordinates: 137238591-137241628 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1393 bp · TkA02G532480|TK1151|cDNA

AGCGAACTGAAAGAATCTCTCATCACATTCAGTAGCTTATGCCTAGGATTTAAAAACAATAACAACATGAATTGCCTTACAAATCTTTCAAGATCCTTTTCGGCTTTGCCTTTAGGTAGCTTCAAATGTACAGCTTCAACTTATCCGCGCTTTGTCAATATGAAGGGATTGGTGAACGCAACTGCTCTTCGAGAAAGTTGTTTAGTTAAGGCCACTTCTAGTTCTACACCTAGTACCAACATGGATGGTACCAAAGAAGA...

CDS

Download CDS FASTA

1119 bp · TkA02G532480|TK1151|CDS

ATGAATTGCCTTACAAATCTTTCAAGATCCTTTTCGGCTTTGCCTTTAGGTAGCTTCAAATGTACAGCTTCAACTTATCCGCGCTTTGTCAATATGAAGGGATTGGTGAACGCAACTGCTCTTCGAGAAAGTTGTTTAGTTAAGGCCACTTCTAGTTCTACACCTAGTACCAACATGGATGGTACCAAAGAAGAGGAGAAATCTGATGTTTACAGCACAAACATGACTGAAGCAATGGGTGCTGTTTTGACTTATAGGCA...

Protein

Download Protein FASTA

372 aa · TkA02G532480|TK1151|PROTEIN

MNCLTNLSRSFSALPLGSFKCTASTYPRFVNMKGLVNATALRESCLVKATSSSTPSTNMDGTKEEEKSDVYSTNMTEAMGAVLTYRHELGMNYNFILPDLIVGSCLQTPADVDKLRSINVKTIYCLQQDSDLEYFGVDINAIREYASTFDDIQHLRAEIRDFDSTDLRVRLPAVVSKLHKAVKRNGGVTYIHCTAGLGRAPATALAYMFWVQGYKLNDALNIILRNRKCFPKVDAIKSATADILTGLKTRSITLTWNGDN...

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	`TkA02G532480`
TK1151 ID	TkA02G532480
OH-1004 ID	LXL04_012167
Relationship / confidence	Non Reciprocal Best Hit / Complex relationship
Protein identity (%)	42.200
Protein coverage (%)	TK1151 49.731 / OH-1004 66.090 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	TK1151 / GWHBCHF00000000

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SNP / Indel variants and carrier samplesCRA009020 · TK1151

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID TkA02G532480

Location Chr02:137238591-137241628 (-)

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
`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
`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

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. These OH1004 annotations are retrieved through ID mapping; the Arabidopsis/rice table below uses protein alignments from the query reference.

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.

Plastid0.947

Rank 1 · TkA02G532480 · TK1151

Mitochondrion0.067

Rank 2 · TkA02G532480 · TK1151

Cytoplasm0.056

Rank 3 · TkA02G532480 · TK1151

Nucleus0.036

Rank 4 · TkA02G532480 · TK1151

Peroxisome0.028

Rank 5 · TkA02G532480 · TK1151

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.

PF00782DSPc72-96 aa

PF22784PTP-SAK98-218 aa

PF22785Tc-R-P111-210 aa

PF00782DSPc135-230 aa

PF16561AMPK1_CBM252-336 aa

PF22058X25_BaPul_like281-321 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA02G532480	`PF00782`	DSPc	72	96	3.6e-13	50.2
TkA02G532480	`PF22784`	PTP-SAK	98	218	5.6e-06	27.2
TkA02G532480	`PF22785`	Tc-R-P	111	210	3.9e-05	24.8
TkA02G532480	`PF00782`	DSPc	135	230	3.6e-13	50.2
TkA02G532480	`PF16561`	AMPK1_CBM	252	336	6.8e-18	65.4
TkA02G532480	`PF22058`	X25_BaPul_like	281	321	0.015	16.1

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
`Q9FEB5`	Arabidopsis thaliana	sp\|Q9FEB5\|DSPG4_ARATH Phosphoglucan phosphatase DSP4, chloroplastic	59.300%	Swiss-Prot	High
`Q9SRK5`	Arabidopsis thaliana	sp\|Q9SRK5\|LSF2_ARATH Phosphoglucan phosphatase LSF2, chloroplastic	42.100%	Swiss-Prot	Medium

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