TkA01G028270 | RubberDandelionOmics

Gene overview

TkA01G028270

Reference: TK1151 Chr: Chr01 Coordinates: 7250242-7253533 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2221 bp · TkA01G028270|TK1151|cDNA

CCCCGGTTTAGTTTTTCAATTTGGTTTTGAATTGTATCCGGTTTTCTTCGCCCCCGGCGGATTGTGGGGTGGAATATACCGCAAGACATCACTTTCAGTCGCCGTCTCCGGTCCGAATGAGCTCTCGCCTACCTCCTATCCTCCTCCGCAACCTCCATTCTTCTCTAGACGTCTCCTCCATGGCGGCGGCCGGTTTCATCTTCCGAACCCTCTCCACACACTCACTCTCGGCCTCATCCAAACTCTCATCGTTACCTTCA...

CDS

Download CDS FASTA

1131 bp · TkA01G028270|TK1151|CDS

ATGAGCTCTCGCCTACCTCCTATCCTCCTCCGCAACCTCCATTCTTCTCTAGACGTCTCCTCCATGGCGGCGGCCGGTTTCATCTTCCGAACCCTCTCCACACACTCACTCTCGGCCTCATCCAAACTCTCATCGTTACCTTCACTGGTCTCTCATTGTCGCTCCAATCTTTCCTATTCTACTACCTCTTCTTCTCCGTTGCTTGGTGGTTTATTCAGTGCTCACCGTAGCATAGATGGAGATTGGATGCATTCGAGAAG...

Protein

Download Protein FASTA

376 aa · TkA01G028270|TK1151|PROTEIN

MSSRLPPILLRNLHSSLDVSSMAAAGFIFRTLSTHSLSASSKLSSLPSLVSHCRSNLSYSTTSSSPLLGGLFSAHRSIDGDWMHSRRLGGKVSASQRGYRKVRGRPAARKKEKGKELELDVRICLEEQLPDDPEILDIAEMLRLNVPMAMKLAFDSLKDSEHKTRDPSVDDVGQFESVELSILLCNDEFIRELNKDWRNEDHATDVLSMSQHVPELKLPLLMLGDIIISVETAARQAEERGHTLLDEIRVLMVHGLLHLL...

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	`TkA01G028270`
TK1151 ID	TkA01G028270
OH-1004 ID	LXL04_005609
Relationship / confidence	Sequence Supported Annotation Or Model Conflict / Review
Protein identity (%)	100.000
Protein coverage (%)	TK1151 100.000 / OH-1004 48.958 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 TkA01G028270

Location Chr01:7250242-7253533 (+)

Description Similar to YBEY: Endoribonuclease YBEY, chloroplastic

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g25870`	Endoribonuclease required for chloroplast ribosomal RNA (rRNA) processing and essential for normal growth and development.	The conserved endoribonuclease YbeY is required for chloroplast ribosomal RNA processing in Arabidopsis.2015 · DOI: 10.1104/pp.114.255000

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_005609 · 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:0006364 rRNA processing Biological Process

GO:0009658 chloroplast organization Biological Process

GO:1901259 chloroplast rRNA processing Biological Process

GO:0005737 cytoplasm Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0009570 chloroplast stroma Cellular Component

GO:0004222 metalloendopeptidase activity Molecular Function

GO:0004521 RNA endonuclease activity Molecular Function

GO:0008270 zinc ion binding Molecular Function

GO:0046872 metal ion binding Molecular Function

KEGG gene cross-reference

aae:aq_1354

ade:Adeh_2719

ath:AT2G25870

hmo:HM1_2448

sul:SYO3AOP1_0254

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.

Plastid0.919

Rank 1 · TkA01G028270 · TK1151

Mitochondrion0.086

Rank 2 · TkA01G028270 · TK1151

Nucleus0.049

Rank 3 · TkA01G028270 · TK1151

Cytoplasm0.036

Rank 4 · TkA01G028270 · TK1151

Cell membrane0.012

Rank 5 · TkA01G028270 · 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.

PF12710HAD142-207 aa

PF02130YbeY176-285 aa

PF00702Hydrolase249-249 aa

PF12710HAD253-271 aa

PF08282Hydrolase_3329-372 aa

PF00702Hydrolase329-351 aa

PF13344Hydrolase_6329-368 aa

PF12710HAD329-343 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA01G028270	`PF12710`	HAD	142	207	0.087	13.9
TkA01G028270	`PF02130`	YbeY	176	285	8.8e-36	123.7
TkA01G028270	`PF00702`	Hydrolase	249	249	0.0038	18.4
TkA01G028270	`PF12710`	HAD	253	271	0.087	13.9
TkA01G028270	`PF08282`	Hydrolase_3	329	372	5.9e-13	49.9
TkA01G028270	`PF00702`	Hydrolase	329	351	0.0038	18.4
TkA01G028270	`PF13344`	Hydrolase_6	329	368	0.0062	17.3
TkA01G028270	`PF12710`	HAD	329	343	0.087	13.9
TkA01G028270	`PF04312`	DUF460	331	372	0.086	13.3
TkA01G028270	`PF00702`	Hydrolase	349	374	0.0038	18.4
TkA01G028270	`PF12710`	HAD	350	372	0.087	13.9

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`Q8L5Z4`	Arabidopsis thaliana	sp\|Q8L5Z4\|YBEY_ARATH Endoribonuclease YBEY, chloroplastic	69.600%	Swiss-Prot	High

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