TkA01G390800 | RubberDandelionOmics

Gene overview

TkA01G390800

Reference: TK1151 Chr: Chr01 Coordinates: 97590906-97592184 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

863 bp · TkA01G390800|TK1151|cDNA

ACTTCACTGTCGAATGATGCTTTTTCTCTGGCGTCAGGCGACACAAAGGTGATTGCAGCTGTTTACGGACCGAAAGCTGGAACTAGGAAAAATGAAAACCCCGGAAAGGCTTGCATTGAAGTCATTTGGAAGCCAAAAACCGGTCAGAGTGGGAAATCAGAGAGGGAGATGGTACTTAAGAAGACGTTACAAAGCATCTGCCTTTTGAATGGTCATCCCAATACAACAACTTCAATTGTCATCCAGGTTGTCAATGACGA...

CDS

Download CDS FASTA

450 bp · TkA01G390800|TK1151|CDS

ACTTCACTGTCGAATGATGCTTTTTCTCTGGCGTCAGGCGACACAAAGGTGATTGCAGCTGTTTACGGACCGAAAGCTGGAACTAGGAAAAATGAAAACCCCGGAAAGGCTTGCATTGAAGTCATTTGGAAGCCAAAAACCGGTCAGAGTGGGAAATCAGAGAGGGAGATGGTACTTAAGAAGACGTTACAAAGCATCTGCCTTTTGAATGGTCATCCCAATACAACAACTTCAATTGTCATCCAGGTTGTCAATGACGA...

Protein

Download Protein FASTA

149 aa · TkA01G390800|TK1151|PROTEIN

TSLSNDAFSLASGDTKVIAAVYGPKAGTRKNENPGKACIEVIWKPKTGQSGKSEREMVLKKTLQSICLLNGHPNTTTSIVIQVVNDDGALLPCAINAACAALEDAGTPLKHLAVAICSCMAENGKILLDPSKIEEQKLRRLYIWYFQIP

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	`TkA01G390800`
TK1151 ID	TkA01G390800
OH-1004 ID	LXL04_032480
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	92.100
Protein coverage (%)	TK1151 91.946 / OH-1004 52.060 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 TkA01G390800

Location Chr01:97590906-97592184 (+)

Description Similar to RRP46: Exosome complex exonuclease RRP46 homolog

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g46210`	Probable component of the exosome 3'->5' exoribonuclease complex, a complex that degrades inherently unstable mRNAs containing AU-rich elements (AREs) within their 3'-untranslated regions.	No verified direct reference in this release
`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

Reference gene ID	Possible function	Papers / DOI
`Os03g0854200`	May participate in RNA processing and degradation.	Structural and biochemical characterization of CRN-5 and Rrp46: an exosome component participating in apoptotic DNA degradation.2010 · DOI: 10.1261/rna.2180810

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_032480 · 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:0006396 RNA processing Biological Process

GO:0006401 RNA catabolic process Biological Process

GO:0006402 mRNA catabolic process 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:0045006 DNA deamination Biological Process

GO:0051607 defense response to virus Biological Process

GO:0071028 nuclear mRNA surveillance Biological Process

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

KEGG gene cross-reference

ath:AT3G46210

dosa:Os03g0854200

hbu:Hbut_0571

hsa:56915

mmu:27998

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.

Nucleus0.748

Rank 1 · TkA01G390800 · TK1151

Cytoplasm0.352

Rank 2 · TkA01G390800 · TK1151

Mitochondrion0.038

Rank 3 · TkA01G390800 · TK1151

Cell membrane0.024

Rank 4 · TkA01G390800 · TK1151

Endoplasmic reticulum0.022

Rank 5 · TkA01G390800 · 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_PH11-108 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA01G390800	`PF01138`	RNase_PH	11	108	2.1e-18	67.7

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
`Q9LX74`	Arabidopsis thaliana	sp\|Q9LX74\|EXOS5_ARATH Exosome complex exonuclease RRP46 homolog	72.000%	Swiss-Prot	High
`Q9SP08`	Arabidopsis thaliana	sp\|Q9SP08\|RRP41_ARATH Exosome complex component RRP41 homolog	34.800%	Swiss-Prot	Medium
`Q84T68`	Oryza sativa subsp. japonica	sp\|Q84T68\|EXOS5_ORYSJ Exosome complex exonuclease RRP46 homolog	67.900%	Swiss-Prot	High

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