TkA03G559400 | RubberDandelionOmics

Gene overview

TkA03G559400

Reference: TK1151 Chr: Chr03 Coordinates: 141807771-141811255 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2766 bp · TkA03G559400|TK1151|cDNA

ATCCAATCCCTCGGAGGACCCTACCGAAGTTCCGTCGGGGGTGCCCGGTGAATAAAACCAACCATACCTTCTTATATCCCTTTCTGAGTGGAATTCGGCTCCAGTTCGTCATGGCAGAAATAGCAGCGCCATATCCTCAACTGAGCTTCCTTCGTTTTGATAAAAGTGCAATTACGCCTCCTAATTATGCCCAAAGACTACATTTTTCATCTAGGTTTCTGACAAGTGTTCCTGATGTCACCGGAAAACGGAGAAGAATC...

CDS

Download CDS FASTA

2676 bp · TkA03G559400|TK1151|CDS

CCAATCCCTCGGAGGACCCTACCGAAGTTCCGTCGGGGGTGCCCGGTGAATAAAACCAACCATACCTTCTTATATCCCTTTCTGAGTGGAATTCGGCTCCAGTTCGTCATGGCAGAAATAGCAGCGCCATATCCTCAACTGAGCTTCCTTCGTTTTGATAAAAGTGCAATTACGCCTCCTAATTATGCCCAAAGACTACATTTTTCATCTAGGTTTCTGACAAGTGTTCCTGATGTCACCGGAAAACGGAGAAGAATCAT...

Protein

Download Protein FASTA

891 aa · TkA03G559400|TK1151|PROTEIN

PIPRRTLPKFRRGCPVNKTNHTFLYPFLSGIRLQFVMAEIAAPYPQLSFLRFDKSAITPPNYAQRLHFSSRFLTSVPDVTGKRRRIIKIAVVRAKSGTVIEKEQEFKPSFEEYLKAMETVKSRREKRKVSTETPPSPSPSPSRSPSRKIDEGSFELKDSQDQITPRKVGNLEQGEVKKTWHRKKSDPKEPQLAANVKDINISPTIDEKHSKLQGQSFNTKRGSHINSVSSHDYARDTAVHDQSRVLLNSKQNEAMKKWTR...

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	`TkA03G559400`
TK1151 ID	TkA03G559400
OH-1004 ID	LXL04_010977
Relationship / confidence	Rbh Sequence Supported / Probable
Protein identity (%)	98.300
Protein coverage (%)	TK1151 93.939 / OH-1004 70.220 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

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · TK1151

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID TkA03G559400

Location Chr03:141807771-141811255 (+)

Description Similar to EMB2279: Pentatricopeptide repeat-containing protein At1g30610, chloroplastic

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g30610`	May play a role in embryogenesis.	No verified direct reference in this release
`At5g67570`	Involved in the regulation of early chloroplast development and chloroplast gene expression in a SIGF-dependent manner.	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_010977 · 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:0005976 polysaccharide metabolic process Biological Process

GO:0009658 chloroplast organization Biological Process

GO:0009793 embryo development ending in seed dormancy Biological Process

GO:0010239 chloroplast mRNA processing Biological Process

GO:0016042 lipid catabolic process Biological Process

GO:0042793 plastid transcription Biological Process

GO:0000325 plant-type vacuole Cellular Component

GO:0005576 extracellular region Cellular Component

GO:0005886 plasma membrane Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0003729 mRNA binding Molecular Function

GO:0016788 hydrolase activity, acting on ester bonds Molecular Function

KEGG gene cross-reference

ath:AT1G28570

ath:AT1G28580

ath:AT1G28590

ath:AT1G30610

ath:AT5G67570

These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.

Open Annotation Module

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.

Plastid0.768

Rank 1 · TkA03G559400 · TK1151

Mitochondrion0.127

Rank 2 · TkA03G559400 · TK1151

Nucleus0.093

Rank 3 · TkA03G559400 · TK1151

Cytoplasm0.031

Rank 4 · TkA03G559400 · TK1151

Cell membrane0.016

Rank 5 · TkA03G559400 · 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.

PF13812PPR_3195-206 aa

PF16736sCache_like233-306 aa

PF23276TPR_24374-428 aa

PF13812PPR_3389-412 aa

PF13041PPR_2390-414 aa

PF01535PPR391-409 aa

PF13041PPR_2425-463 aa

PF01535PPR426-451 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA03G559400	`PF13812`	PPR_3	195	206	1.1e-21	77.4
TkA03G559400	`PF16736`	sCache_like	233	306	0.054	14.6
TkA03G559400	`PF23276`	TPR_24	374	428	5.9e-09	36.6
TkA03G559400	`PF13812`	PPR_3	389	412	1.1e-21	77.4
TkA03G559400	`PF13041`	PPR_2	390	414	5.2e-39	132.8
TkA03G559400	`PF01535`	PPR	391	409	1.6e-33	113.3
TkA03G559400	`PF13041`	PPR_2	425	463	5.2e-39	132.8
TkA03G559400	`PF01535`	PPR	426	451	1.6e-33	113.3
TkA03G559400	`PF14559`	TPR_19	436	460	0.034	15.2
TkA03G559400	`PF13041`	PPR_2	457	486	5.2e-39	132.8
TkA03G559400	`PF13812`	PPR_3	457	485	1.1e-21	77.4
TkA03G559400	`PF23276`	TPR_24	460	487	5.9e-09	36.6
TkA03G559400	`PF01535`	PPR	469	486	1.6e-33	113.3
TkA03G559400	`PF23276`	TPR_24	497	554	5.9e-09	36.6
TkA03G559400	`PF13812`	PPR_3	505	554	1.1e-21	77.4
TkA03G559400	`PF12854`	PPR_1	505	534	2.5e-18	66.2

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
`Q9SA76`	Arabidopsis thaliana	sp\|Q9SA76\|PPR64_ARATH Pentatricopeptide repeat-containing protein At1g30610, chloroplastic	53.500%	Swiss-Prot	Medium
`Q9FJW6`	Arabidopsis thaliana	sp\|Q9FJW6\|PP451_ARATH Pentatricopeptide repeat-containing protein At5g67570, chloroplastic	31.700%	Swiss-Prot	Medium

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