TkA04G392820 | RubberDandelionOmics

Gene overview

TkA04G392820

Reference: TK1151 Chr: Chr04 Coordinates: 98795792-98799020 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1681 bp · TkA04G392820|TK1151|cDNA

TGAACGAGGCAAGTGGAGCCTTCTATCATCCATTAAATTTGTACTTGACTCATCTCGTTTTCGTTTTAGTATTGTTCGTTGCTCTTTCTTCACTCTTTTCGAGCCCGTCGGCGTTCTCTTCTCCAATCTCTTCTGACACCATAATCTTTACGCCACTGTAGATGCGGAATCCTGCCTCAAGTTTTCACCAACGCAAACTATCTGTTCGATGAAATGCCTGAACGATGATGTTGTTTATCGCCTCCACAACTCCGCATCAT...

CDS

Download CDS FASTA

1284 bp · TkA04G392820|TK1151|CDS

ATGATGTTGTTTATCGCCTCCACAACTCCGCATCATTTGATTTTCCCCGTTGTTCCCATTCTTGGTCTGGGAACTAACTTCAAGATCAGGCCGCGAGTTTCCTTGATTTTGGTGAAAAGGGGTCGAGGTTTGAAAGAAACAAGAACAAGAAGCGGGATTTCGTGTAAAGGGTATTCGGACAGTGAAGCAGAGTTGGCTTTAGAGAGGGAAATTTTGAATTTCATGAAGAATTCGAGTAACCCAAACGAGTTTCCGACTAA...

Protein

Download Protein FASTA

427 aa · TkA04G392820|TK1151|PROTEIN

MMLFIASTTPHHLIFPVVPILGLGTNFKIRPRVSLILVKRGRGLKETRTRSGISCKGYSDSEAELALEREILNFMKNSSNPNEFPTKKQLLDAGRVDLVDGISKTGGWLALGWDYSDDENDSESDDLNDKRELQTRVESFQQRQDPYGHSSSFHTSSHQPASPSGRSLETEADEDTGVEGILSRLKKHRSLTFDSHMEKNTHYTYPRKQFLDFQPAEIDYRKEELKSNTDLQVEDGNNRPDDIRSRLKEMQLELSSALGS...

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	`TkA04G392820`
TK1151 ID	TkA04G392820
OH-1004 ID	LXL04_006972
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	40.800
Protein coverage (%)	TK1151 21.780 / OH-1004 33.677 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 TkA04G392820

Location Chr04:98795792-98799020 (-)

Description Similar to PTST: Protein PTST, chloroplastic

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g27070`	Involved in starch granule initiation in leaf chloroplasts.	Homologs of PROTEIN TARGETING TO STARCH Control Starch Granule Initiation in Arabidopsis Leaves.2017 · DOI: 10.1105/tpc.17.00222 Two Plastidial Coiled-Coil Proteins Are Essential for Normal Starch Granule Initiation in Arabidopsis.2018 · DOI: 10.1105/tpc.18.00219
`At5g39790`	Involved in targeting GBSS1 to the starch granule.	Arabidopsis At5g39790 encodes a chloroplast-localized, carbohydrate-binding, coiled-coil domain-containing putative scaffold protein.2008 · DOI: 10.1186/1471-2229-8-120
`At5g03420`	Involved in starch granule initiation in leaf chloroplasts.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os03g0686900`	Involved in compound starch granule formation and starch synthesis in endosperm.	FLOURY ENDOSPERM6 encodes a CBM48 domain-containing protein involved in compound granule formation and starch synthesis in rice endosperm.2014 · DOI: 10.1111/tpj.12444

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_006972 · 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:0006633 fatty acid biosynthetic process Biological Process

GO:0010581 regulation of starch biosynthetic process Biological Process

GO:0019252 starch biosynthetic process Biological Process

GO:2000014 regulation of endosperm development Biological Process

GO:0005737 cytoplasm Cellular Component

GO:0005739 mitochondrion Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0009535 chloroplast thylakoid membrane Cellular Component

GO:0009569 chloroplast starch grain Cellular Component

GO:0009570 chloroplast stroma Cellular Component

GO:0030247 polysaccharide binding Molecular Function

GO:2001066 amylopectin binding Molecular Function

KEGG gene cross-reference

ath:AT1G27070

ath:AT5G03420

ath:AT5G39790

dosa:Os03g0686900

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.

Plastid0.937

Rank 1 · TkA04G392820 · TK1151

Nucleus0.066

Rank 2 · TkA04G392820 · TK1151

Cytoplasm0.055

Rank 3 · TkA04G392820 · TK1151

Mitochondrion0.043

Rank 4 · TkA04G392820 · TK1151

Peroxisome0.037

Rank 5 · TkA04G392820 · TK1151

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.

PF20355DUF6650164-202 aa

PF20355DUF6650251-310 aa

PF16561AMPK1_CBM347-424 aa

PF02922CBM_48348-405 aa

PF16760CBM53354-395 aa

PF22058X25_BaPul_like367-404 aa

PF19662DUF6165388-425 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA04G392820	`PF20355`	DUF6650	164	202	0.035	14.7
TkA04G392820	`PF20355`	DUF6650	251	310	0.035	14.7
TkA04G392820	`PF16561`	AMPK1_CBM	347	424	2.6e-19	69.9
TkA04G392820	`PF02922`	CBM_48	348	405	0.00026	22.0
TkA04G392820	`PF16760`	CBM53	354	395	0.023	15.7
TkA04G392820	`PF22058`	X25_BaPul_like	367	404	0.078	13.8
TkA04G392820	`PF19662`	DUF6165	388	425	0.078	13.4

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
`Q9LFY0`	Arabidopsis thaliana	sp\|Q9LFY0\|PTST2_ARATH Protein PTST homolog 2, chloroplastic	37.900%	Swiss-Prot	Medium
`Q94AX2`	Arabidopsis thaliana	sp\|Q94AX2\|PTST_ARATH Protein PTST, chloroplastic	36.400%	Swiss-Prot	Low
`F4KFB3`	Arabidopsis thaliana	sp\|F4KFB3\|PTST3_ARATH Protein PTST homolog 3, chloroplastic	38.500%	Swiss-Prot	Low
`Q10F03`	Oryza sativa subsp. japonica	sp\|Q10F03\|FLO6_ORYSJ Protein FLOURY ENDOSPERM 6, chloroplastic	36.500%	Swiss-Prot	Medium

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