TkA01G489640 | RubberDandelionOmics

Gene overview

TkA01G489640

Reference: TK1151 Chr: Chr01 Coordinates: 122526380-122527386 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

783 bp · TkA01G489640|TK1151|cDNA

ATGAATAAATGCGGAGAATCTCAAGCTCTCGAACAAGCTATAGAAGTCCACGATCATCTCACAAGGTCAATACCCAATCTCGATGTTCACATTCACAACAAAATCCTTGAAATGTACTCAAAATGCGGTTCCATGGAAGCCGCATTTCACGTATTTGACGAGATGCCGAGACGAAATCTCACATCGTGGGACACCATGATAACATGGCTGGCAGAAAACGCAATCGACATGTTCACAAAATTCAAAATTACCGGATTAAA...

CDS

Download CDS FASTA

783 bp · TkA01G489640|TK1151|CDS

ATGAATAAATGCGGAGAATCTCAAGCTCTCGAACAAGCTATAGAAGTCCACGATCATCTCACAAGGTCAATACCCAATCTCGATGTTCACATTCACAACAAAATCCTTGAAATGTACTCAAAATGCGGTTCCATGGAAGCCGCATTTCACGTATTTGACGAGATGCCGAGACGAAATCTCACATCGTGGGACACCATGATAACATGGCTGGCAGAAAACGCAATCGACATGTTCACAAAATTCAAAATTACCGGATTAAA...

Protein

Download Protein FASTA

260 aa · TkA01G489640|TK1151|PROTEIN

MNKCGESQALEQAIEVHDHLTRSIPNLDVHIHNKILEMYSKCGSMEAAFHVFDEMPRRNLTSWDTMITWLAENAIDMFTKFKITGLKPDNQINDLNFSQMREELFPIAVLWRSVSLQINDLNFYNRRFHRPPLQNNNFHGWIRGDEDVMELLWQNGQVVMQNQNQRSAGNKKPETRSSLASREIRSSVADKETGPSHLFMKEDDLLYPTPPSSAPLTTDSRSLPPPPPPSIMIPSPCILDQGYAQVVADGRKEKKYMVML

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	`TkA01G489640`
TK1151 ID	TkA01G489640
OH-1004 ID	LXL04_005489
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	82.700
Protein coverage (%)	TK1151 60.385 / OH-1004 96.000 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

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Basic Information and Functional Annotation

Gene ID TkA01G489640

Location Chr01:122526380-122527386 (+)

Description Protein of unknown function

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g29230`	Pentatricopeptide repeat-containing protein At3g29230.	No verified direct reference in this release
`At1g29710`	Pentatricopeptide repeat-containing protein At1g29710, mitochondrial.	No verified direct reference in this release
`At2g03880`	Pentatricopeptide repeat-containing protein At2g03880, mitochondrial.	No verified direct reference in this release
`At1g06143`	Pentatricopeptide repeat-containing protein At1g06143.	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

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_005489 · 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) No functional description available

KEGG gene cross-reference No functional description available

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.

Nucleus0.377

Rank 1 · TkA01G489640 · TK1151

Cytoplasm0.251

Rank 2 · TkA01G489640 · TK1151

Plastid0.129

Rank 3 · TkA01G489640 · TK1151

Mitochondrion0.129

Rank 4 · TkA01G489640 · TK1151

Cell membrane0.095

Rank 5 · TkA01G489640 · 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.

PF17177PPR_long1-71 aa

PF13041PPR_24-18 aa

PF23276TPR_244-61 aa

PF01535PPR10-18 aa

PF13041PPR_228-60 aa

PF12854PPR_128-55 aa

PF19967VMAP-M531-54 aa

PF01535PPR33-59 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA01G489640	`PF17177`	PPR_long	1	71	0.011	15.9
TkA01G489640	`PF13041`	PPR_2	4	18	2.8e-07	31.2
TkA01G489640	`PF23276`	TPR_24	4	61	0.021	15.5
TkA01G489640	`PF01535`	PPR	10	18	0.0003	21.5
TkA01G489640	`PF13041`	PPR_2	28	60	2.8e-07	31.2
TkA01G489640	`PF12854`	PPR_1	28	55	0.073	13.5
TkA01G489640	`PF19967`	VMAP-M5	31	54	0.15	12.9
TkA01G489640	`PF01535`	PPR	33	59	0.0003	21.5
TkA01G489640	`PF13041`	PPR_2	62	90	2.8e-07	31.2
TkA01G489640	`PF01535`	PPR	62	72	0.0003	21.5
TkA01G489640	`PF19967`	VMAP-M5	74	123	0.15	12.9

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
`Q9LS72`	Arabidopsis thaliana	sp\|Q9LS72\|PP261_ARATH Pentatricopeptide repeat-containing protein At3g29230	35.200%	Swiss-Prot	Low
`Q9C6G2`	Arabidopsis thaliana	sp\|Q9C6G2\|PPR63_ARATH Pentatricopeptide repeat-containing protein At1g29710, mitochondrial	40.000%	Swiss-Prot	Low
`Q9SI53`	Arabidopsis thaliana	sp\|Q9SI53\|PP147_ARATH Pentatricopeptide repeat-containing protein At2g03880, mitochondrial	34.000%	Swiss-Prot	Low
`Q56X05`	Arabidopsis thaliana	sp\|Q56X05\|PPR15_ARATH Pentatricopeptide repeat-containing protein At1g06143	36.200%	Swiss-Prot	Low
`Q9M9E2`	Arabidopsis thaliana	sp\|Q9M9E2\|PPR45_ARATH Pentatricopeptide repeat-containing protein At1g15510, chloroplastic	34.000%	Swiss-Prot	Low

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