TkA06G009000 | RubberDandelionOmics

Gene overview

TkA06G009000

Reference: TK1151 Chr: Chr06 Coordinates: 2299147-2306084 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

4851 bp · TkA06G009000|TK1151|cDNA

GTCATATGCGTAGTATTAACGAGGGAGGCTGCTCGTGTTGGTGCAATAATAAGCAGTAAGCACTCCCAATACAAAACCCTTTTGCTTCTTGGGAGTACCTCCCTTACTCTCTGCTCAAAACCCAATAAAAGATATCTTTTCTCGTTCAAGAGTTCTCCAAGATTCGATAAAAAGGGAGGTCAATAAGCAAGAAATTAAGTTTGATGGACAATGAAGTGTATGTAGAACAACAAGTGCCATCGGGTGTTCTTACAGGCATA...

CDS

Download CDS FASTA

4329 bp · TkA06G009000|TK1151|CDS

ATGGACAATGAAGTGTATGTAGAACAACAAGTGCCATCGGGTGTTCTTACAGGCATAAGATTCAAAGTTCTATCTGAAGAAGATGCCGAAAAGGCATCTGTGAAGGAAATCGTTGTACCAAATGAAGTCACAGATCCTGCATTAGGATTCCCAAATCCCGCATCACAGTGCCATACATGTGGGGCCAAAGATTATAGAACATGTGAAGGTCACATAGGCTTAATAAAATTTCCCTTCACAATACTTCATCCATATTTCTT...

Protein

Download Protein FASTA

1442 aa · TkA06G009000|TK1151|PROTEIN

MDNEVYVEQQVPSGVLTGIRFKVLSEEDAEKASVKEIVVPNEVTDPALGFPNPASQCHTCGAKDYRTCEGHIGLIKFPFTILHPYFLPEVAQLLNKICPGCKNLKKDKAKKTDVESIIEAPIICKYCDRSFKDVYPPLKFKVSMKDVFGKTAIVAESSRKPISGKNLPPDYWDFVPSDPQQEESFSSFNRRVLTHAQVYQILKDVNPSFLKGSLGKKNKIFLQSFPLTPNCHRVAEFGQNLTFDERTRAYRKMINFRGTA...

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	`TkA06G009000`
TK1151 ID	TkA06G009000
OH-1004 ID	LXL04_027604
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	27.200
Protein coverage (%)	TK1151 88.003 / OH-1004 64.035 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

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID TkA06G009000

Location Chr06:2299147-2306084 (-)

Description Similar to NRPE1: DNA-directed RNA polymerase V subunit 1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g63020`	DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates (By similarity).	Reinforcement of silencing at transposons and highly repeated sequences requires the concerted action of two distinct RNA polymerases IV in Arabidopsis.2005 · DOI: 10.1101/gad.348405 DICER-LIKE 4 is required for RNA interference and produces the 21-nucleotide small interfering RNA component of the plant cell-to-cell silencing signal.2005 · DOI: 10.1038/ng1675 Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis.2005 · DOI: 10.1016/j.cell.2005.11.035 An SNF2 protein associated with nuclear RNA silencing and the spread of a silencing signal between cells in Arabidopsis.2007 · DOI: 10.1105/tpc.107.051540 Intra- and intercellular RNA interference in Arabidopsis thaliana requires components of the microRNA and heterochromatic silencing pathways.2007 · DOI: 10.1038/ng2081 Nuclear gene silencing directs reception of long-distance mRNA silencing in Arabidopsis.2007 · DOI: 10.1073/pnas.0706701104 PolIVb influences RNA-directed DNA methylation independently of its role in siRNA biogenesis.2008 · DOI: 10.1073/pnas.0709632105 NRPD1a and NRPD1b are required to maintain post-transcriptional RNA silencing and RNA-directed DNA methylation in Arabidopsis.2008 · DOI: 10.1111/j.1365-313x.2008.03525.x
`At5g60040`	DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_027604 · 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:0006351 DNA-templated transcription Biological Process

GO:0006353 DNA-templated transcription termination Biological Process

GO:0006355 regulation of DNA-templated transcription Biological Process

GO:0006366 transcription by RNA polymerase II Biological Process

GO:0006367 transcription initiation at RNA polymerase II promoter Biological Process

GO:0006368 transcription elongation by RNA polymerase II Biological Process

GO:0006369 termination of RNA polymerase II transcription Biological Process

GO:0006370 7-methylguanosine mRNA capping Biological Process

GO:0019985 translesion synthesis Biological Process

GO:0030422 siRNA processing Biological Process

GO:0030643 intracellular phosphate ion homeostasis Biological Process

GO:0033120 positive regulation of RNA splicing Biological Process

KEGG gene cross-reference

ago:AGOS_ADR086C

ath:AT2G40030

bta:282312

hsa:5430

spo:2540292

These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.

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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.

Nucleus0.791

Rank 1 · TkA06G009000 · TK1151

Cytoplasm0.213

Rank 2 · TkA06G009000 · TK1151

Mitochondrion0.047

Rank 3 · TkA06G009000 · TK1151

Cell membrane0.032

Rank 4 · TkA06G009000 · TK1151

Endoplasmic reticulum0.020

Rank 5 · TkA06G009000 · 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.

PF04997RNA_pol_Rpb1_141-255 aa

PF00623RNA_pol_Rpb1_294-115 aa

PF00623RNA_pol_Rpb1_2309-467 aa

PF04983RNA_pol_Rpb1_3472-626 aa

PF00623RNA_pol_Rpb1_2482-516 aa

PF05000RNA_pol_Rpb1_4697-753 aa

PF04998RNA_pol_Rpb1_5826-887 aa

PF04998RNA_pol_Rpb1_51129-1204 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA06G009000	`PF04997`	RNA_pol_Rpb1_1	41	255	1.9e-08	34.7
TkA06G009000	`PF00623`	RNA_pol_Rpb1_2	94	115	5.5e-33	115.3
TkA06G009000	`PF00623`	RNA_pol_Rpb1_2	309	467	5.5e-33	115.3
TkA06G009000	`PF04983`	RNA_pol_Rpb1_3	472	626	8.1e-17	62.3
TkA06G009000	`PF00623`	RNA_pol_Rpb1_2	482	516	5.5e-33	115.3
TkA06G009000	`PF05000`	RNA_pol_Rpb1_4	697	753	6.4e-08	33.2
TkA06G009000	`PF04998`	RNA_pol_Rpb1_5	826	887	1.5e-11	45.0
TkA06G009000	`PF04998`	RNA_pol_Rpb1_5	1129	1204	1.5e-11	45.0
TkA06G009000	`PF11523`	DUF3223	1344	1417	2.5e-21	76.7

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
`Q9LQ02`	Arabidopsis thaliana	sp\|Q9LQ02\|NRPD1_ARATH DNA-directed RNA polymerase IV subunit 1	46.800%	Swiss-Prot	Medium
`F4JXF9`	Arabidopsis thaliana	sp\|F4JXF9\|NRPC1_ARATH DNA-directed RNA polymerase III subunit 1	21.400%	Swiss-Prot	Low

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