TkA06G312000 | RubberDandelionOmics

Gene overview

TkA06G312000

Reference: TK1151 Chr: Chr06 Coordinates: 78252025-78259291 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

3412 bp · TkA06G312000|TK1151|cDNA

AAAACCCTTTGGTTGGAGACTTTGTAAGATACTTGCCATCGACCTACAATTTCGCATGACGTGATACATTTGCCTGAGACTCCGAACTACAAAAGAACCCTACCTTTCTTCGTGATATCGTCAAAACGAACCCGTACGCAAAGCGGCGCTCCGGACTTTTTGCAGCGGGGCACGATACATATCTTCGGCGGCGATGGGAGTACCGGCCTTTTACCGCTGGCTAGCGGAAAAGTATCCAATGGTCGTTGTTGATGTTATAG...

CDS

Download CDS FASTA

2976 bp · TkA06G312000|TK1151|CDS

ATGGGAGTACCGGCCTTTTACCGCTGGCTAGCGGAAAAGTATCCAATGGTCGTTGTTGATGTTATAGAGGAAGAAGCTGTGGATATTGACGGCATTAAAATTCCTGTCGACACAAGTAAACCTAACCCTAATCAAATTGAGTATGACAACCTGTATCTCGACATGAACGGAATAATTCATCCCTGTTTTCACCCTGAAGACCGGCCTTCTCCAACGTCTTTTAATGAGGTGTTCCAATGCATGTTTGACTACATTGATCG...

Protein

Download Protein FASTA

991 aa · TkA06G312000|TK1151|PROTEIN

MGVPAFYRWLAEKYPMVVVDVIEEEAVDIDGIKIPVDTSKPNPNQIEYDNLYLDMNGIIHPCFHPEDRPSPTSFNEVFQCMFDYIDRLFVMVRPRKLLYMAIDGVAPRAKMNQQRSRRFRAAKDAADAAAEEERLREEFEREGRKLPPKQESQTFDSNVITPGTQFMAVLSVALQYYVHQRLNNDPGWKPVKVILSDANVPGEGEHKVMSYIRLQRNLPGFDPNTRHCLYGLDADLIMLALATHEVHFSILREVVFTPGQ...

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	`TkA06G312000`
TK1151 ID	TkA06G312000
OH-1004 ID	LXL04_023513
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.900
Protein coverage (%)	TK1151 100.000 / OH-1004 100.000 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 TkA06G312000

Location Chr06:78252025-78259291 (+)

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

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

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_023513 · 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:0006281 DNA repair Biological Process

GO:0006310 DNA recombination Biological Process

GO:0006364 rRNA processing Biological Process

GO:0006369 termination of RNA polymerase II transcription Biological Process

GO:0006396 RNA processing Biological Process

GO:0006397 mRNA processing Biological Process

GO:0006401 RNA catabolic process Biological Process

GO:0007017 microtubule-based process Biological Process

GO:0007283 spermatogenesis Biological Process

GO:0010587 miRNA catabolic process Biological Process

KEGG gene cross-reference

ath:AT1G75660

ath:AT5G42540

hsa:22803

mmu:24128

pon:100173960

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.

Cytoplasm0.527

Rank 1 · TkA06G312000 · TK1151

Nucleus0.513

Rank 2 · TkA06G312000 · TK1151

Cell membrane0.062

Rank 3 · TkA06G312000 · TK1151

Endoplasmic reticulum0.059

Rank 4 · TkA06G312000 · TK1151

Golgi apparatus0.044

Rank 5 · TkA06G312000 · 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

PF00098zf-CCHC263-277 aa

PF17846XRN_M326-809 aa

PF03159XRN_N408-430 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA06G312000	`PF03159`	XRN_N	1	253	8.8e-102	340.3
TkA06G312000	`PF00098`	zf-CCHC	263	277	0.00062	20.4
TkA06G312000	`PF17846`	XRN_M	326	809	9.2e-168	559.5
TkA06G312000	`PF03159`	XRN_N	408	430	8.8e-102	340.3

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	76.300%	Swiss-Prot	High
`Q9FQ02`	Arabidopsis thaliana	sp\|Q9FQ02\|XRN2_ARATH 5'-3' exoribonuclease 2	64.200%	Swiss-Prot	High
`Q9FQ04`	Arabidopsis thaliana	sp\|Q9FQ04\|XRN4_ARATH 5'-3' exoribonuclease 4	56.400%	Swiss-Prot	High

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