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Gene Card

Enter a TK1151 or OH-1004 gene ID to view sequences, annotations and analyses in the corresponding reference genome.
Flanking length, max 10000 bp
Examples TkA01G624900 LXL04_000258

Gene overview

TkA04G199410
Reference: TK1151 Chr: Chr04 Coordinates: 51323355-51329104 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

4462 bp · TkA04G199410|TK1151|cDNA

GGAACGGGCGTGAAGACAACTGAGGGAGACGCAGTCCATCATTTCGTGCATTAAATGCAAGGCTTTAAAGAAAAAGCCCGAAATACCCTCACACGCGCAGCACATGCTTTCACTTAACGGCTCATGTCGCACGGAGTTAGGCGGAGAGACCATTCATCAAAAGTTTGTTAAAGCACAATGACAATTTATAAAATTAAAAAAAGGTAGAAACTGAACTTGATATTTTGAGATCCCACATAGACAATTTATGAAGTTCTTGG...

CDS

Download CDS FASTA

3597 bp · TkA04G199410|TK1151|CDS

ATGGAAGACGCAGGACCAAGCTCCAAGGAGAAGCCGTCAAATGGATCTGTACATGTCGACATAGATGAAGAAGATGATGATGATGATATGATGGACGCACCATCAGTTAGGGATTTCGATGAGTCCTTCTTAAAGAGCTTCTGTAGAAGGGCATCCTCGTCCTTTTTCAAACACTATGGTCTTATAAGTCATCAGATCAACTCATATGACGACTTCATCAAAGTAGGAATCCAGAATGTTTTCGACTCCATTGGTGAGAT...

Protein

Download Protein FASTA

1198 aa · TkA04G199410|TK1151|PROTEIN

MEDAGPSSKEKPSNGSVHVDIDEEDDDDDMMDAPSVRDFDESFLKSFCRRASSSFFKHYGLISHQINSYDDFIKVGIQNVFDSIGEIIVEPGYDPSKKGENEWRYASIKFGKVTLERPRFYTGDKSESGNKFLDFLPRHARLQNMTYSSRMKVQFTKEVYIQELVRSDKFKTGKEKYIDKKILETEEREVYIGRIPVMVNSDTCWMSGPDRKDDCDYDQGGYFIIKGAEKTFIAQEQLGLNRLWLANSPNWRVMYRAAHK...

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.

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ID Mapping

Input IDTkA04G199410
TK1151 IDTkA04G199410
OH-1004 IDLXL04_034820
Relationship / confidenceRbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)97.700
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 versionTK1151 / 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 IDTkA04G199410
LocationChr04:51323355-51329104 (-)
DescriptionSimilar to NRPD2: DNA-directed RNA polymerases IV and V subunit 2
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At3g23780 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.
Atypical RNA polymerase subunits required for RNA-directed DNA methylation.2005 · DOI: 10.1038/ng1580
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
Transcriptional silencing induced by Arabidopsis T-DNA mutants is associated with 35S promoter siRNAs and requires genes involved in siRNA-mediated chromatin silencing.2010 · DOI: 10.1111/j.1365-313x.2010.04358.x
At3g18090 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
At4g21710 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_034820 · 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:0006354 DNA-templated transcription elongation Biological Process
GO:0006366 transcription by RNA polymerase II Biological Process
GO:0006367 transcription initiation at RNA polymerase II promoter Biological Process
GO:0030422 siRNA processing Biological Process
GO:0031047 regulatory ncRNA-mediated gene silencing Biological Process
GO:0031507 heterochromatin formation Biological Process
GO:0035194 regulatory ncRNA-mediated post-transcriptional gene silencing Biological Process
GO:0035196 miRNA processing Biological Process
GO:0050776 regulation of immune response Biological Process
GO:0050832 defense response to fungus Biological Process
GO:0080188 gene silencing by siRNA-directed DNA methylation Biological Process
GO:0141007 transposable element silencing by siRNA-mediated heterochromatin formation Biological Process
KEGG gene cross-reference
ath:AT3G18090
ath:AT3G23780
ath:AT4G21710
ddi:DDB_G0288257
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.

Nucleus0.958
Rank 1 · TkA04G199410 · TK1151
Cytoplasm0.062
Rank 2 · TkA04G199410 · TK1151
Cell membrane0.023
Rank 3 · TkA04G199410 · TK1151
Endoplasmic reticulum0.013
Rank 4 · TkA04G199410 · TK1151
Plastid0.012
Rank 5 · TkA04G199410 · 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.

PF04563RNA_pol_Rpb2_160-457 aa
PF04561RNA_pol_Rpb2_2292-423 aa
PF04565RNA_pol_Rpb2_3499-560 aa
PF04566RNA_pol_Rpb2_4504-518 aa
PF04560RNA_pol_Rpb2_7573-600 aa
PF04566RNA_pol_Rpb2_4596-657 aa
PF04567RNA_pol_Rpb2_5672-715 aa
PF00562RNA_pol_Rpb2_6724-1095 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
TkA04G199410PF04563RNA_pol_Rpb2_1604571.9e-34119.7
TkA04G199410PF04561RNA_pol_Rpb2_22924233.3e-1143.9
TkA04G199410PF04565RNA_pol_Rpb2_34995607.9e-1555.5
TkA04G199410PF04566RNA_pol_Rpb2_45045188.1e-2174.6
TkA04G199410PF04560RNA_pol_Rpb2_75736002.6e-2795.8
TkA04G199410PF04566RNA_pol_Rpb2_45966578.1e-2174.6
TkA04G199410PF04567RNA_pol_Rpb2_56727155.2e-0731.1
TkA04G199410PF00562RNA_pol_Rpb2_672410957.5e-108361.7
TkA04G199410PF04563RNA_pol_Rpb2_18398671.9e-34119.7
TkA04G199410PF04560RNA_pol_Rpb2_7109711942.6e-2795.8

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

ProteinOrganismDescriptionIdentityDatabaseConfidence
Q9LK40Arabidopsis thalianasp|Q9LK40|NRPD2_ARATH DNA-directed RNA polymerases IV and V subunit 264.300%Swiss-ProtHigh
Q9LV32Arabidopsis thalianasp|Q9LV32|RPD2B_ARATH DNA-directed RNA polymerase D subunit 2b60.800%Swiss-ProtHigh
P38420Arabidopsis thalianasp|P38420|NRPB2_ARATH DNA-directed RNA polymerase II subunit 234.300%Swiss-ProtMedium

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