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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

TkA02G551230
Reference: TK1151 Chr: Chr02 Coordinates: 142246476-142248852 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

1254 bp · TkA02G551230|TK1151|cDNA

CGTAGCAAGTATGGTGGGGTATCCGTAGGCACGTGGTGTCGTGTGAAAAGAGGGAAATACATGGGAGATTTAGCTCAGGTTCATTTTTATTCCACCCTTATTTTGGGTTATTTTGGGTTTTCGTTGTTTTATTTATATGGATATGATGCAGGTTGTGAATGTGAATGAGTTTCAGAGGAAAGCCACTGTTAAGCTTCTCCCGAGAATAGATCTACAAGCCATGGTTAAAAAATACAGTGGAGTTGCGGACTACCAGTATA...

CDS

Download CDS FASTA

1251 bp · TkA02G551230|TK1151|CDS

ATGGCGGGTAATGGCAGAGGAACCGCTGGAGATTATTTATCGGGGAAACGGACGCATGACGGAGACCGGAGGACGGTATATGGGAGTGACTATCGGTTCAGTTCTTGTAACGTGGAAGATAATCGCGCTTTTCGTAAGGATTACCATGGCCCAGATCTCGAAGCTAGGGCTGAACCAAAGACGCCTAACTTTCCTGGGTTTCCCAAAAATGAAGCGATGCATGAAGAGGAAGTAGAGAAGTTTGTTGAAGAGCATTATAA...

Protein

Download Protein FASTA

416 aa · TkA02G551230|TK1151|PROTEIN

MAGNGRGTAGDYLSGKRTHDGDRRTVYGSDYRFSSCNVEDNRAFRKDYHGPDLEARAEPKTPNFPGFPKNEAMHEEEVEKFVEEHYKPFRSKYGGVSVGTWCRVKRGKYMGDLAQVVNVNEFQRKATVKLLPRIDLQAMVKKYSGVADYQYTSPAPRLITSGELNAYRLRVRQSLDPDTGDLYEVFDGMKLKDGYVFKKLALDSLNFSNFKPSEAELMKFNGKPDESNYVNNKQTMNNNNQVGEGLSSSYMNNNFEVPDR...

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 IDTkA02G551230
TK1151 IDTkA02G551230
OH-1004 IDLXL04_012591
Relationship / confidenceRbh High Identity Coverage Synteny / Strict
Protein identity (%)100.000
Protein coverage (%)TK1151 97.356 / OH-1004 86.538
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 IDTkA02G551230
LocationChr02:142246476-142248852 (-)
DescriptionSimilar to RDM3: Protein RNA-directed DNA methylation 3
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At5g04290 Effector of RNA-directed DNA methylation (RdDM) triggered by small interfering RNAs (siRNAs, 24-nt RNAs).
An effector of RNA-directed DNA methylation in arabidopsis is an ARGONAUTE 4- and RNA-binding protein.2009 · DOI: 10.1016/j.cell.2009.04.028
Identification of genes required for de novo DNA methylation in Arabidopsis.2011 · DOI: 10.4161/epi.6.3.14242
Independent chromatin binding of ARGONAUTE4 and SPT5L/KTF1 mediates transcriptional gene silencing.2011 · DOI: 10.1371/journal.pgen.1002120
At2g34210 May regulate transcription elongation by RNA polymerase II. No verified direct reference in this release
At4g08350 May regulate transcription elongation by RNA polymerase II. 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_012591 · 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:0006357 regulation of transcription by RNA polymerase II Biological Process
GO:0006368 transcription elongation by RNA polymerase II Biological Process
GO:0006397 mRNA processing Biological Process
GO:0006412 translation Biological Process
GO:0030422 siRNA processing Biological Process
GO:0031507 heterochromatin formation Biological Process
GO:0032784 regulation of DNA-templated transcription elongation Biological Process
GO:0080188 gene silencing by siRNA-directed DNA methylation Biological Process
GO:0000785 chromatin Cellular Component
GO:0005634 nucleus Cellular Component
GO:0005654 nucleoplasm Cellular Component
GO:0005840 ribosome Cellular Component
KEGG gene cross-reference
ath:AT2G34210
ath:AT4G08350
ath:AT5G04290
cne:CNA06210
uma:UMAG_10033
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.

Nucleus0.907
Rank 1 · TkA02G551230 · TK1151
Cytoplasm0.135
Rank 2 · TkA02G551230 · TK1151
Cell membrane0.033
Rank 3 · TkA02G551230 · TK1151
Endoplasmic reticulum0.018
Rank 4 · TkA02G551230 · TK1151
Plastid0.018
Rank 5 · TkA02G551230 · 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.

PF23042KOW1_SPT597-220 aa
PF00467KOW98-123 aa
PF10303DUF2408211-239 aa
PF01093Clusterin308-367 aa
PF10303DUF2408308-392 aa
PF09727CortBP2313-382 aa
PF24423OVT1314-361 aa
PF29075NOCA1_mid319-382 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
TkA02G551230PF23042KOW1_SPT5972202.9e-2383.6
TkA02G551230PF00467KOW981237.3e-0523.2
TkA02G551230PF10303DUF24082112390.3312.2
TkA02G551230PF01093Clusterin3083670.006416.3
TkA02G551230PF10303DUF24083083920.3312.2
TkA02G551230PF09727CortBP23133820.1912.5
TkA02G551230PF24423OVT13143610.212.8
TkA02G551230PF29075NOCA1_mid3193820.02815.0
TkA02G551230PF07813LTXXQ3233510.1513.5
TkA02G551230PF23042KOW1_SPT53473762.9e-2383.6
TkA02G551230PF07813LTXXQ3543830.1513.5

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
F4JW79Arabidopsis thalianasp|F4JW79|RDM3_ARATH Protein RNA-directed DNA methylation 350.000%Swiss-ProtLow
O80770Arabidopsis thalianasp|O80770|SPT52_ARATH Putative transcription elongation factor SPT5 homolog 240.900%Swiss-ProtLow
Q9STN3Arabidopsis thalianasp|Q9STN3|SPT51_ARATH Putative transcription elongation factor SPT5 homolog 142.800%Swiss-ProtLow

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