RubberDandelionOmics Rubber Dandelion Multi-omics Website
More
Transcriptome Expression Annotation Rubber Pathway TF Prediction Targets Protein Network Resequencing Tools Downloads
ZH EN

How to use this page

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

TkA04G343790
Reference: TK1151 Chr: Chr04 Coordinates: 86868965-86886032 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

2887 bp · TkA04G343790|TK1151|cDNA

TAGAAGGCCCGTGCATCGGGCTTTTCCCTAGTTTCCTAGAATAGAAGAAAATTGCAACAAGCCAACAATAATACATCATACAGACACCACTACCGCCAATGATTTTGTTTTAAAGAAAATGATGCAGTAAGATCAGAGTGACGCCATCATTGTTGCCATCCTGTGTTACCGGAATCTCCATAGCTCAATCCTTCAGGCTTCAGTCACTTCCGCCGATGTACTTGTGAGAAGCGAGACGCGAGTGAGACTGTTCAGAAGTG...

CDS

Download CDS FASTA

2106 bp · TkA04G343790|TK1151|CDS

ATGTTGAAGTTAAAAAAAATAAAAGTATCACTATCACCACTAGAACATTCCATCACTATACCTGTTAAAATTCCCAAACCAAGATGGAAGGATTCTTCATTCATTGAACTTGAAAAATACGAACTAACTCTCCCACCTAACAATTCCACCATGGATCCTAAACCTATTTTGCGTTATTACACCTACACCTTACTTAAATCATCAGGTTGGTTAATTGGGAGAAGAAACAGAACCACACATTGTAAAGGTCGTGGAGAATA...

Protein

Download Protein FASTA

701 aa · TkA04G343790|TK1151|PROTEIN

MLKLKKIKVSLSPLEHSITIPVKIPKPRWKDSSFIELEKYELTLPPNNSTMDPKPILRYYTYTLLKSSGWLIGRRNRTTHCKGRGEYVFKSPEGRPIREFYRAWNMCGQTLVKDADYKTLRDDINWKDLTQFQSDLSFALTKVKEFVDSVIVTDLAHSWYLLDPFAKLVFIDKRLSLLKEGKEVKAKRSLVNGLYSKNKKPKKEKKEKCCIKDDDLLMSAIFTRKRNRSTITKKNSPVLKVVKKYNNALGVTTVLSWLIK...

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.

Download Gene (CDS) Download Protein

ID Mapping

Input IDTkA04G343790
TK1151 IDTkA04G343790
OH-1004 IDLXL04_037731
Relationship / confidenceMulti Source To Oh1004 / Complex relationship
Protein identity (%)89.100
Protein coverage (%)TK1151 96.291 / OH-1004 89.442
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 IDTkA04G343790
LocationChr04:86868965-86886032 (+)
DescriptionSimilar to IDM1: Increased DNA methylation 1
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At3g14980 Histone H3 acetyltransferase that binds methylated DNA at chromatin sites lacking histone H3K4 di- or trimethylation and catalyzes H3K18 and H3K23 acetylation.
A histone acetyltransferase regulates active DNA demethylation in Arabidopsis.2012 · DOI: 10.1126/science.1219416
Antisilencing role of the RNA-directed DNA methylation pathway and a histone acetyltransferase in Arabidopsis.2012 · DOI: 10.1073/pnas.1208557109
Regulation of active DNA demethylation by an α-crystallin domain protein in Arabidopsis.2014 · DOI: 10.1016/j.molcel.2014.06.008

Rice

No hit for this species in the current source table.

Functional annotation source
View annotation sources

Functional annotation source: OH1004 · LXL04_037731 · 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:0006325 chromatin organization Biological Process
GO:0006338 chromatin remodeling Biological Process
GO:0006351 DNA-templated transcription Biological Process
GO:0006355 regulation of DNA-templated transcription Biological Process
GO:0006955 immune response Biological Process
GO:0006959 humoral immune response Biological Process
GO:0032722 positive regulation of chemokine production Biological Process
GO:0034728 nucleosome organization Biological Process
GO:0045893 positive regulation of DNA-templated transcription Biological Process
GO:0045944 positive regulation of transcription by RNA polymerase II Biological Process
GO:0080188 gene silencing by siRNA-directed DNA methylation Biological Process
GO:0000785 chromatin Cellular Component
KEGG gene cross-reference
ath:AT3G14980
dme:Dmel_CG9594
hsa:326
mmu:11634
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.

Nucleus0.879
Rank 1 · TkA04G343790 · TK1151
Cytoplasm0.153
Rank 2 · TkA04G343790 · TK1151
Cell membrane0.036
Rank 3 · TkA04G343790 · TK1151
Endoplasmic reticulum0.020
Rank 4 · TkA04G343790 · TK1151
Plastid0.016
Rank 5 · TkA04G343790 · 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.

PF22970DUF702863-108 aa
PF22970DUF7028195-207 aa
PF16135TDBD284-334 aa
PF00628PHD291-298 aa
PF23011PHD-1st_NSD359-400 aa
PF23004PHDvar_NSD360-387 aa
PF00628PHD361-400 aa
PF23555zf-RING_Vps41376-400 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
TkA04G343790PF22970DUF7028631080.06913.8
TkA04G343790PF22970DUF70281952070.06913.8
TkA04G343790PF16135TDBD2843341.2e-1145.1
TkA04G343790PF00628PHD2912984e-0730.7
TkA04G343790PF23011PHD-1st_NSD3594000.009916.7
TkA04G343790PF23004PHDvar_NSD3603873.8e-0524.3
TkA04G343790PF00628PHD3614004e-0730.7
TkA04G343790PF23555zf-RING_Vps413764000.002118.4
TkA04G343790PF23555zf-RING_Vps414024400.002118.4
TkA04G343790PF00628PHD4144524e-0730.7
TkA04G343790PF23004PHDvar_NSD4154363.8e-0524.3
TkA04G343790PF23011PHD-1st_NSD4254350.009916.7
TkA04G343790PF23209IDM1_C5186571.3e-57194.5
TkA04G343790PF00583Acetyltransf_15466110.01416.3
TkA04G343790PF13673Acetyltransf_105486330.0004820.8
TkA04G343790PF13508Acetyltransf_75536050.1613.1

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

ProteinOrganismDescriptionIdentityDatabaseConfidence
F4IXE7Arabidopsis thalianasp|F4IXE7|IDM1_ARATH Increased DNA methylation 153.400%Swiss-ProtMedium

JBrowse

View in Genome Browser