TkA04G469890 | RubberDandelionOmics

Gene overview

TkA04G469890

Reference: TK1151 Chr: Chr04 Coordinates: 118653550-118655931 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2233 bp · TkA04G469890|TK1151|cDNA

ACCACGGCTGCTTCCTTCAACATCCAGTCTCCATCTCTCCCATCTCAAACAGCAAACCCTAACTTCCTAATCCCTGTTAGATCCTTCGCCTTTTCTTCAGCCGAGGAAGCTGCGGCCGAACGCCGACGCCGCAAACGTCGCCTCCGTATCGAGCCCCCGTTACACGCCCTCCAGCGTGATCCCAATGCTCCACGCCCTAGACGTGACCCTAATCAACCTGACACTACATCAGCTCTCGTTGGACCTCGACTCAGTCTCCA...

CDS

Download CDS FASTA

2112 bp · TkA04G469890|TK1151|CDS

ACCACGGCTGCTTCCTTCAACATCCAGTCTCCATCTCTCCCATCTCAAACAGCAAACCCTAACTTCCTAATCCCTGTTAGATCCTTCGCCTTTTCTTCAGCCGAGGAAGCTGCGGCCGAACGCCGACGCCGCAAACGTCGCCTCCGTATCGAGCCCCCGTTACACGCCCTCCAGCGTGATCCCAATGCTCCACGCCCTAGACGTGACCCTAATCAACCTGACACTACATCAGCTCTCGTTGGACCTCGACTCAGTCTCCA...

Protein

Download Protein FASTA

703 aa · TkA04G469890|TK1151|PROTEIN

TTAASFNIQSPSLPSQTANPNFLIPVRSFAFSSAEEAAAERRRRKRRLRIEPPLHALQRDPNAPRPRRDPNQPDTTSALVGPRLSLHNRVQSLIRAGDLDNASVVARQSVFSSTRPTVFTCNAIIGSMYRAKRYLDAIALFAYFFKQCNIVPNVVSYNFLIVSHCENGEVDKALEVYQHIKDNAPFSPSAVTFRHLTKGLIDAGRINEAVEMLWKMVGDGHGADSQVFNNIISGFLNLNNLEKANEFFDELKGRCMVYDG...

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	`TkA04G469890`
TK1151 ID	TkA04G469890
OH-1004 ID	LXL04_038833
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.000
Protein coverage (%)	TK1151 84.211 / OH-1004 84.091 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 TkA04G469890

Location Chr04:118653550-118655931 (+)

Description Similar to GRP23: Pentatricopeptide repeat-containing protein At1g10270

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g10270`	May function as a transcriptional regulator essential for early embryogenesis.	Arabidopsis GLUTAMINE-RICH PROTEIN23 is essential for early embryogenesis and encodes a novel nuclear PPR motif protein that interacts with RNA polymerase II subunit III.2006 · DOI: 10.1105/tpc.105.039495
`At3g60980`	Pentatricopeptide repeat-containing protein At3g60980, mitochondrial.	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_038833 · 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:0006351 DNA-templated transcription Biological Process

GO:0006979 response to oxidative stress Biological Process

GO:0009793 embryo development ending in seed dormancy Biological Process

GO:0009960 endosperm development Biological Process

GO:0051301 cell division Biological Process

GO:0005634 nucleus Cellular Component

GO:0005739 mitochondrion Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0003729 mRNA binding Molecular Function

GO:0005524 ATP binding Molecular Function

KEGG gene cross-reference

ath:AT1G09900

ath:AT1G10270

ath:AT3G49240

ath:AT3G60960

ath:AT3G60980

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.

Plastid0.635

Rank 1 · TkA04G469890 · TK1151

Mitochondrion0.314

Rank 2 · TkA04G469890 · TK1151

Nucleus0.051

Rank 3 · TkA04G469890 · TK1151

Cytoplasm0.036

Rank 4 · TkA04G469890 · TK1151

Cell membrane0.016

Rank 5 · TkA04G469890 · 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.

PF13428TPR_1488-108 aa

PF13424TPR_1294-141 aa

PF12854PPR_195-105 aa

PF13812PPR_3115-161 aa

PF13041PPR_2116-142 aa

PF12854PPR_1116-141 aa

PF01535PPR119-141 aa

PF23276TPR_24120-142 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA04G469890	`PF13428`	TPR_14	88	108	2.7e-07	31.3
TkA04G469890	`PF13424`	TPR_12	94	141	0.0008	20.3
TkA04G469890	`PF12854`	PPR_1	95	105	1e-37	128.2
TkA04G469890	`PF13812`	PPR_3	115	161	1.1e-14	55.0
TkA04G469890	`PF13041`	PPR_2	116	142	1.9e-49	166.3
TkA04G469890	`PF12854`	PPR_1	116	141	1e-37	128.2
TkA04G469890	`PF01535`	PPR	119	141	5.1e-39	130.5
TkA04G469890	`PF23276`	TPR_24	120	142	3e-16	60.2
TkA04G469890	`PF29070`	MSC6_N	121	248	6e-19	69.1
TkA04G469890	`PF07719`	TPR_2	128	141	0.00017	22.2
TkA04G469890	`PF25575`	TPR_BSK1_C	129	175	0.0012	19.4
TkA04G469890	`PF30154`	TPR_YpiA	129	142	0.0033	18.1
TkA04G469890	`PF13432`	TPR_16	130	188	0.0011	20.1
TkA04G469890	`PF17177`	PPR_long	139	182	5.8e-11	42.9
TkA04G469890	`PF13812`	PPR_3	148	194	1.1e-14	55.0
TkA04G469890	`PF12854`	PPR_1	149	177	1e-37	128.2

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
`Q9SY69`	Arabidopsis thaliana	sp\|Q9SY69\|PPR29_ARATH Pentatricopeptide repeat-containing protein At1g10270	39.700%	Swiss-Prot	Medium
`Q9LEX5`	Arabidopsis thaliana	sp\|Q9LEX5\|PP290_ARATH Pentatricopeptide repeat-containing protein At3g60980, mitochondrial	38.300%	Swiss-Prot	Low

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