TkA03G548080 | RubberDandelionOmics

Gene overview

TkA03G548080

Reference: TK1151 Chr: Chr03 Coordinates: 138263472-138265769 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1093 bp · TkA03G548080|TK1151|cDNA

TGCCCTTATAATTGTTCAATTAACAAAACCCTACAAACAACAAAACAAAAGAATCGGCCGACTTCGCGACCTCCACACAGCTTCTTCTCGGCCGACATCCAGCTCCGTCAACCGTGGTCAGGTTATTGTTGCTCTACAGAAATGGAGTATGTGAGCCCCGAAGGACTCCGTTTGGATGGACGACGTCCCTTGGAGATGAGACAGCTTCGAGCAGAATTAGGCGCTGTTTCCAGAGCTGATGGGTCGGCAGTTTTTGAGAT...

CDS

Download CDS FASTA

867 bp · TkA03G548080|TK1151|CDS

TGCCCTTATAATTGTTCAATTAACAAAACCCTACAAACAACAAAACAAAAGAATCGGCCGACTTCGCGACCTCCACACAGCTTCTTCTCGGCCGACATCCAGCTCCGTCAACCGTGGTCAGGTTATTGTTGCTCTACAGAAATGGAGTATGTGAGCCCCGAAGGACTCCGTTTGGATGGACGACGTCCCTTGGAGATGAGACAGCTTCGAGCAGAATTAGGCGCTGTTTCCAGAGCTGATGGGTCGGCAGTTTTTGAGAT...

Protein

Download Protein FASTA

288 aa · TkA03G548080|TK1151|PROTEIN

CPYNCSINKTLQTTKQKNRPTSRPPHSFFSADIQLRQPWSGYCCSTEMEYVSPEGLRLDGRRPLEMRQLRAELGAVSRADGSAVFEMGNTKVIAAVYGPREVQQRSQQLNDKALIRCEYTMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGTRSACINAATLALADAGIPMRDLVTSCSAGYLNTTPLLDLNYVEDSAGGPDVTVGILPKLDKVTLLQMDAKLPMDIFENVMQLA...

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	`TkA03G548080`
TK1151 ID	TkA03G548080
OH-1004 ID	LXL04_013061
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	30.500
Protein coverage (%)	TK1151 80.903 / OH-1004 87.109 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 TkA03G548080

Location Chr03:138263472-138265769 (+)

Description Similar to RRP41L: Exosome complex component RRP41-like

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g61620`	Non-catalytic component of the RNA exosome complex which has 3'->5' exoribonuclease activity and participates in a multitude of cellular RNA processing, maturation and degradation events.	Poly(A) tail-dependent exonuclease AtRrp41p from Arabidopsis thaliana rescues 5.8 S rRNA processing and mRNA decay defects of the yeast ski6 mutant and is found in an exosome-sized complex in plant and yeast cells.2000 · DOI: 10.1074/jbc.m005493200

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_013061 · 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:0000956 nuclear-transcribed mRNA catabolic process Biological Process

GO:0006364 rRNA processing Biological Process

GO:0009845 seed germination Biological Process

GO:0010467 gene expression Biological Process

GO:0016075 rRNA catabolic process Biological Process

GO:0034475 U4 snRNA 3'-end processing Biological Process

GO:0071028 nuclear mRNA surveillance Biological Process

GO:0071051 poly(A)-dependent snoRNA 3'-end processing Biological Process

GO:0090351 seedling development Biological Process

GO:0000176 nuclear exosome (RNase complex) Cellular Component

GO:0000177 cytoplasmic exosome (RNase complex) Cellular Component

GO:0000178 exosome (RNase complex) Cellular Component

KEGG gene cross-reference

ath:AT4G27490

dre:326786

pfu:PF1568

pho:PH1549

xtr:549770

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.

Nucleus0.623

Rank 1 · TkA03G548080 · TK1151

Cytoplasm0.475

Rank 2 · TkA03G548080 · TK1151

Mitochondrion0.090

Rank 3 · TkA03G548080 · TK1151

Endoplasmic reticulum0.035

Rank 4 · TkA03G548080 · TK1151

Cell membrane0.035

Rank 5 · TkA03G548080 · 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.

PF01138RNase_PH65-195 aa

PF03725RNase_PH_C198-263 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA03G548080	`PF01138`	RNase_PH	65	195	3.8e-41	141.2
TkA03G548080	`PF03725`	RNase_PH_C	198	263	4.1e-12	46.6

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
`Q9SP08`	Arabidopsis thaliana	sp\|Q9SP08\|RRP41_ARATH Exosome complex component RRP41 homolog	81.700%	Swiss-Prot	High

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