TkA02G366180 | RubberDandelionOmics

Gene overview

TkA02G366180

Reference: TK1151 Chr: Chr02 Coordinates: 93159186-93173868 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

4029 bp · TkA02G366180|TK1151|cDNA

CACGGGTCTTATAACTAGTACCCTATATACCACGTAGCCAACCCAAAAATGATTTCACAATCTTAAAAATCAAAATCGTAAAAAAGCCCATTAATTTTCAAACTCAAAACAAAACACCCCTTAAATGAATAGGGTAAATGAATGTCCGTTGCCCTCCGCCGTTCGCGTATTCTTTTCCTGTTGATTCACACAAAACAATTGCTTTGTTCTAAACTCTTGTGCAAATTTCTGAAATCTAGCTAGGGTTTAGTTATCTAGTG...

CDS

Download CDS FASTA

3873 bp · TkA02G366180|TK1151|CDS

ATGGGCGTGCCGGCGTTTTACCGGTGGTTAGCAGAGAAGTACCCAATGGTGATAGTGGATGTTATAGAGGAAGAACCGGCTGTAATCGGCGGTGTTAAAATTCCGGTGGATACAAGCAAACCTAACCCTAATAAAATCGAGTATGATAACATGTATCTCGATATGAATGGGATTATTCACCCCTGTTTCCACCCTGAAGACCGGCCTTCTCCAACCTCTTTTAGTGAGGTGTTTCAATGCGTGTTTGACTATATTGACCG...

Protein

Download Protein FASTA

1290 aa · TkA02G366180|TK1151|PROTEIN

MGVPAFYRWLAEKYPMVIVDVIEEEPAVIGGVKIPVDTSKPNPNKIEYDNMYLDMNGIIHPCFHPEDRPSPTSFSEVFQCVFDYIDRLFVMVRPRKLLYMAIDGVAPRAKMNQQRARRFKAAKDAAEAAAEEERLREEFEKEGRTLPPKKESQTFDSNVITPGTEFMAVLSVALQYYIHKRLNSDPGWKSIKVILSDANVPGEGEHKIMSYIRLQRNLPSFDPNTRHCLYGLDADLIMLGLATHEVHFSILREVVFIKGE...

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	`TkA02G366180`
TK1151 ID	TkA02G366180
OH-1004 ID	LXL04_015118
Relationship / confidence	Rbh Sequence Supported / Probable
Protein identity (%)	98.100
Protein coverage (%)	TK1151 79.225 / OH-1004 75.424 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

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Basic Information and Functional Annotation

Gene ID TkA02G366180

Location Chr02:93159186-93173868 (-)

Description Similar to XRN3: 5'-3' exoribonuclease 3

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g75660`	Possesses 5'->3' exoribonuclease activity.	Arabidopsis FIERY1, XRN2, and XRN3 are endogenous RNA silencing suppressors.2007 · DOI: 10.1105/tpc.107.055319 Arabidopsis thaliana XRN2 is required for primary cleavage in the pre-ribosomal RNA.2010 · DOI: 10.1093/nar/gkq172
`UniProt: Q9FQ02`	Possesses 5'->3' exoribonuclease activity.	No verified direct reference in this release
`At1g54490`	Possesses 5'->3' exoribonuclease activity.	AtXRN4 degrades mRNA in Arabidopsis and its substrates include selected miRNA targets.2004 · DOI: 10.1016/j.molcel.2004.06.006 A link between mRNA turnover and RNA interference in Arabidopsis.2004 · DOI: 10.1126/science.1101092 ETHYLENE-INSENSITIVE5 encodes a 5'-->3' exoribonuclease required for regulation of the EIN3-targeting F-box proteins EBF1/2.2006 · DOI: 10.1073/pnas.0605528103 The exoribonuclease XRN4 is a component of the ethylene response pathway in Arabidopsis.2006 · DOI: 10.1105/tpc.106.046508

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_015118 · 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:0000967 rRNA 5'-end processing Biological Process

GO:0006353 DNA-templated transcription termination Biological Process

GO:0006364 rRNA processing Biological Process

GO:0006369 termination of RNA polymerase II transcription Biological Process

GO:0006397 mRNA processing Biological Process

GO:0007283 spermatogenesis Biological Process

GO:0010587 miRNA catabolic process Biological Process

GO:0040034 regulation of development, heterochronic Biological Process

GO:0051984 positive regulation of chromosome segregation Biological Process

GO:0060149 negative regulation of post-transcriptional gene silencing Biological Process

GO:0060965 negative regulation of miRNA-mediated gene silencing Biological Process

KEGG gene cross-reference

ath:AT1G75660

ath:AT5G42540

cel:CELE_Y48B6A.3

gga:421236

ncr:NCU01643

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.

Nucleus0.499

Rank 1 · TkA02G366180 · TK1151

Cytoplasm0.422

Rank 2 · TkA02G366180 · TK1151

Cell membrane0.073

Rank 3 · TkA02G366180 · TK1151

Mitochondrion0.059

Rank 4 · TkA02G366180 · TK1151

Endoplasmic reticulum0.055

Rank 5 · TkA02G366180 · 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.

PF03159XRN_N1-253 aa

PF14787zf-CCHC_5139-152 aa

PF14787zf-CCHC_5261-281 aa

PF00098zf-CCHC262-278 aa

PF17846XRN_M325-817 aa

PF03159XRN_N405-436 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA02G366180	`PF03159`	XRN_N	1	253	6.3e-103	344.1
TkA02G366180	`PF14787`	zf-CCHC_5	139	152	3.4	8.2
TkA02G366180	`PF14787`	zf-CCHC_5	261	281	3.4	8.2
TkA02G366180	`PF00098`	zf-CCHC	262	278	0.0017	19.0
TkA02G366180	`PF17846`	XRN_M	325	817	2.1e-165	551.8
TkA02G366180	`PF03159`	XRN_N	405	436	6.3e-103	344.1

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
`Q9FQ03`	Arabidopsis thaliana	sp\|Q9FQ03\|XRN3_ARATH 5'-3' exoribonuclease 3	67.400%	Swiss-Prot	High
`Q9FQ02`	Arabidopsis thaliana	sp\|Q9FQ02\|XRN2_ARATH 5'-3' exoribonuclease 2	61.000%	Swiss-Prot	High
`Q9FQ04`	Arabidopsis thaliana	sp\|Q9FQ04\|XRN4_ARATH 5'-3' exoribonuclease 4	52.900%	Swiss-Prot	High

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