TkA08G037650 | RubberDandelionOmics

Gene overview

TkA08G037650

Reference: TK1151 Chr: Chr08 Coordinates: 9594837-9595420 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

564 bp · TkA08G037650|TK1151|cDNA

TAATCTTCAAAACTCAATTCACCAACTTCACGCGCAGCTTTTCATCTCTCCCAAACCTCACACAATGCGTTTCGTCCCTCCAATCATCTGCCAAACATGCCAACTTACAGGAAGGAAAGAAACTCCATTCCTACATGCTCATCAATGGCTTCCTCACCTCCCCGGTCTCCATCACCAGCCTCATCAACATGTACTCCAAATGCAACTCCATCTCCGACGCCTTTCTACTTTTCACTTCGTCGTCAACTTCTCACCTCAAT...

CDS

Download CDS FASTA

468 bp · TkA08G037650|TK1151|CDS

ATGCCAACTTACAGGAAGGAAAGAAACTCCATTCCTACATGCTCATCAATGGCTTCCTCACCTCCCCGGTCTCCATCACCAGCCTCATCAACATGTACTCCAAATGCAACTCCATCTCCGACGCCTTTCTACTTTTCACTTCGTCGTCAACTTCTCACCTCAATGTTTTCGCCTACAACGCAATCATCGCTGGCTTTATCTTCAACGAATTGCCAAAACCCGCATTACAGGTCTACGAAACAGATGGATAAATACACATT...

Protein

Download Protein FASTA

156 aa · TkA08G037650|TK1151|PROTEIN

MPTYRKERNSIPTCSSMASSPPRSPSPASSTCTPNATPSPTPFYFSLRRQLLTSMFSPTTQSSLALSSTNCQNPHYRSTKQMDKYTFPCVVTAFSGCGDVVGLKIVHGLVFKFGMDHDLFVGSAAVHGYLKFGLMADAQRVFDEMPDRDIVLWNAM

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	`TkA08G037650`
TK1151 ID	TkA08G037650
OH-1004 ID	LXL04_017959
Relationship / confidence	Non Reciprocal Best Hit / Complex relationship
Protein identity (%)	100.000
Protein coverage (%)	TK1151 48.077 / OH-1004 12.255 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 TkA08G037650

Location Chr08:9594837-9595420 (+)

Description Similar to PCMP-E31: Pentatricopeptide repeat-containing protein At3g14730

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g14730`	Pentatricopeptide repeat-containing protein At3g14730.	No verified direct reference in this release
`At2g13600`	Pentatricopeptide repeat-containing protein At2g13600.	No verified direct reference in this release
`At1g15510`	Regulates the RNA editing of the chloroplast transcript accD, and is essential for the early stages of chloroplast biogenesis.	AtECB2, a pentatricopeptide repeat protein, is required for chloroplast transcript accD RNA editing and early chloroplast biogenesis in Arabidopsis thaliana.2009 · DOI: 10.1111/j.1365-313x.2009.03930.x Editing of accD and ndhF chloroplast transcripts is partially affected in the Arabidopsis vanilla cream1 mutant.2010 · DOI: 10.1007/s11103-010-9616-5 A point mutation in the pentatricopeptide repeat motif of the AtECB2 protein causes delayed chloroplast development.2011 · DOI: 10.1111/j.1744-7909.2011.01030.x
`At4g35130`	Pentatricopeptide repeat-containing protein At4g35130, chloroplastic.	No verified direct reference in this release
`At3g50420`	Pentatricopeptide repeat-containing protein At3g50420.	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_017959 · 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:0006397 mRNA processing Biological Process

GO:0009451 RNA modification Biological Process

GO:0010087 phloem or xylem histogenesis Biological Process

GO:0010182 sugar mediated signaling pathway Biological Process

GO:0010305 leaf vascular tissue pattern formation Biological Process

GO:0010588 cotyledon vascular tissue pattern formation Biological Process

GO:0048366 leaf development Biological Process

GO:0080156 mitochondrial mRNA modification Biological Process

GO:1900865 chloroplast RNA modification Biological Process

GO:0005739 mitochondrion Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0003723 RNA binding Molecular Function

KEGG gene cross-reference

ath:AT2G13600

ath:AT3G14730

ath:AT4G18750

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.

Mitochondrion0.675

Rank 1 · TkA08G037650 · TK1151

Nucleus0.132

Rank 2 · TkA08G037650 · TK1151

Plastid0.089

Rank 3 · TkA08G037650 · TK1151

Cytoplasm0.059

Rank 4 · TkA08G037650 · TK1151

Extracellular0.010

Rank 5 · TkA08G037650 · 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.

PF13041PPR_282-94 aa

PF01535PPR126-149 aa

PF12854PPR_1126-145 aa

PF13041PPR_2127-150 aa

PF01535PPR151-156 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA08G037650	`PF13041`	PPR_2	82	94	0.011	16.5
TkA08G037650	`PF01535`	PPR	126	149	0.0057	17.5
TkA08G037650	`PF12854`	PPR_1	126	145	0.062	13.8
TkA08G037650	`PF13041`	PPR_2	127	150	0.011	16.5
TkA08G037650	`PF01535`	PPR	151	156	0.0057	17.5

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`Q9LUC2`	Arabidopsis thaliana	sp\|Q9LUC2\|PP231_ARATH Pentatricopeptide repeat-containing protein At3g14730	54.100%	Swiss-Prot	Low
`Q9SIT7`	Arabidopsis thaliana	sp\|Q9SIT7\|PP151_ARATH Pentatricopeptide repeat-containing protein At2g13600	44.000%	Swiss-Prot	Low
`Q9M9E2`	Arabidopsis thaliana	sp\|Q9M9E2\|PPR45_ARATH Pentatricopeptide repeat-containing protein At1g15510, chloroplastic	43.200%	Swiss-Prot	Low
`O49619`	Arabidopsis thaliana	sp\|O49619\|PP350_ARATH Pentatricopeptide repeat-containing protein At4g35130, chloroplastic	38.000%	Swiss-Prot	Low
`Q9SCT2`	Arabidopsis thaliana	sp\|Q9SCT2\|PP277_ARATH Pentatricopeptide repeat-containing protein At3g50420	39.200%	Swiss-Prot	Medium

JBrowse

View in Genome Browser

Gene Card