TkA06G028080 | RubberDandelionOmics

Gene overview

TkA06G028080

Reference: TK1151 Chr: Chr06 Coordinates: 7601420-7603651 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2232 bp · TkA06G028080|TK1151|cDNA

ATGTATATACTTTGCAAGAAACTTGATGATGCGAACACCATCTTCCGTCAGCTTGATTTGTTCTACGCCTCGCCATGGAATTGGATGATTAGAGGGTTCACCATGATGGGGTGTTTCAATTACGCAGTCATGGTTTATTTCAAGATGCTGGGATACGGAACTTGTCCCGATAAGTACACTTTTCCATATGTCATCAAGGCTTGTGGTCAATTAGGAGGAATTCGTTTGGTTAAATCCATTCACCAAACGATTCAAACCAT...

CDS

Download CDS FASTA

2232 bp · TkA06G028080|TK1151|CDS

ATGTATATACTTTGCAAGAAACTTGATGATGCGAACACCATCTTCCGTCAGCTTGATTTGTTCTACGCCTCGCCATGGAATTGGATGATTAGAGGGTTCACCATGATGGGGTGTTTCAATTACGCAGTCATGGTTTATTTCAAGATGCTGGGATACGGAACTTGTCCCGATAAGTACACTTTTCCATATGTCATCAAGGCTTGTGGTCAATTAGGAGGAATTCGTTTGGTTAAATCCATTCACCAAACGATTCAAACCAT...

Protein

Download Protein FASTA

743 aa · TkA06G028080|TK1151|PROTEIN

MYILCKKLDDANTIFRQLDLFYASPWNWMIRGFTMMGCFNYAVMVYFKMLGYGTCPDKYTFPYVIKACGQLGGIRLVKSIHQTIQTMGFETDVYVGSSLIKLYAENGCIDNARHLFDKMPQRDDVLWNVILNGYLKHGDPKHVLSLFNQMRSSITQPGSVTYACVLSACDANIKLGTQLHGLLTKTGHVSDPQVLNTLISMYTKSQNLFDARELFNSVQEPGSVTWNVIIGGHVQNGLMEEASNLFREMISINMKPDTVT...

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	`TkA06G028080`
TK1151 ID	TkA06G028080
OH-1004 ID	LXL04_026085
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	99.700
Protein coverage (%)	TK1151 100.000 / OH-1004 89.626 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 TkA06G028080

Location Chr06:7601420-7603651 (+)

Description Similar to PCMP-E36: Pentatricopeptide repeat-containing protein At4g21300

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g21300`	Pentatricopeptide repeat-containing protein At4g21300.	No verified direct reference in this release
`At3g63370`	Involved in RNA editing event in chloroplasts.	A study of new Arabidopsis chloroplast RNA editing mutants reveals general features of editing factors and their target sites.2009 · DOI: 10.1105/tpc.109.071472
`At3g03580`	Pentatricopeptide repeat-containing protein At3g03580.	No verified direct reference in this release
`At1g11290`	Involved in multiple sites RNA editing events in chloroplasts.	Pentatricopeptide repeat proteins with the DYW motif have distinct molecular functions in RNA editing and RNA cleavage in Arabidopsis chloroplasts.2009 · DOI: 10.1105/tpc.108.064667
`At3g57430`	Involved in RNA editing events in chloroplasts.	A study of new Arabidopsis chloroplast RNA editing mutants reveals general features of editing factors and their target sites.2009 · DOI: 10.1105/tpc.109.071472

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_026085 · 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:0009451 RNA modification Biological Process

GO:0005739 mitochondrion Cellular Component

GO:0003723 RNA binding Molecular Function

GO:0003729 mRNA binding Molecular Function

GO:0008270 zinc ion binding Molecular Function

KEGG gene cross-reference

ath:AT3G03580

ath:AT4G21300

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.

Mitochondrion0.630

Rank 1 · TkA06G028080 · TK1151

Plastid0.209

Rank 2 · TkA06G028080 · TK1151

Nucleus0.050

Rank 3 · TkA06G028080 · TK1151

Cytoplasm0.034

Rank 4 · TkA06G028080 · TK1151

Peroxisome0.006

Rank 5 · TkA06G028080 · 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.

PF22330Rib_mS39_PPR8-33 aa

PF13041PPR_226-68 aa

PF01535PPR26-53 aa

PF29070MSC6_N31-117 aa

PF13812PPR_342-69 aa

PF12854PPR_155-61 aa

PF23276TPR_2463-121 aa

PF01535PPR64-88 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA06G028080	`PF22330`	Rib_mS39_PPR	8	33	0.082	13.4
TkA06G028080	`PF13041`	PPR_2	26	68	4.1e-85	280.4
TkA06G028080	`PF01535`	PPR	26	53	4.4e-81	262.4
TkA06G028080	`PF29070`	MSC6_N	31	117	1.2e-18	68.2
TkA06G028080	`PF13812`	PPR_3	42	69	2.1e-29	102.1
TkA06G028080	`PF12854`	PPR_1	55	61	4.8e-52	174.1
TkA06G028080	`PF23276`	TPR_24	63	121	7.7e-25	88.1
TkA06G028080	`PF01535`	PPR	64	88	4.4e-81	262.4
TkA06G028080	`PF17049`	AEP1	78	124	7.2e-06	26.0
TkA06G028080	`PF13812`	PPR_3	80	120	2.1e-29	102.1
TkA06G028080	`PF12854`	PPR_1	92	119	4.8e-52	174.1
TkA06G028080	`PF13041`	PPR_2	97	122	4.1e-85	280.4
TkA06G028080	`PF01535`	PPR	97	122	4.4e-81	262.4
TkA06G028080	`PF17177`	PPR_long	97	122	4.9e-05	23.5
TkA06G028080	`PF07719`	TPR_2	102	118	0.0071	17.1
TkA06G028080	`PF22330`	Rib_mS39_PPR	110	138	0.082	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
`Q9STE1`	Arabidopsis thaliana	sp\|Q9STE1\|PP333_ARATH Pentatricopeptide repeat-containing protein At4g21300	49.000%	Swiss-Prot	Medium
`Q9M1V3`	Arabidopsis thaliana	sp\|Q9M1V3\|PP296_ARATH Pentatricopeptide repeat-containing protein At3g63370, chloroplastic	36.500%	Swiss-Prot	Medium
`Q9SS60`	Arabidopsis thaliana	sp\|Q9SS60\|PP210_ARATH Pentatricopeptide repeat-containing protein At3g03580	37.000%	Swiss-Prot	Medium
`Q3E6Q1`	Arabidopsis thaliana	sp\|Q3E6Q1\|PPR32_ARATH Pentatricopeptide repeat-containing protein At1g11290, chloroplastic	36.600%	Swiss-Prot	Medium
`Q7Y211`	Arabidopsis thaliana	sp\|Q7Y211\|PP285_ARATH Pentatricopeptide repeat-containing protein At3g57430, chloroplastic	35.500%	Swiss-Prot	Medium

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