TkA04G339880 | RubberDandelionOmics

Gene overview

TkA04G339880

Reference: TK1151 Chr: Chr04 Coordinates: 85862780-85869403 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2052 bp · TkA04G339880|TK1151|cDNA

TTTCAGGAGTTACCTGAAGGCAATTGGTATTGTTCAAATTGCTGTTGTTGGAGTTGTGGGGATGTAATCAATCATATCGAGGCTTCAGAGTCTTATAATTCTCTCAAATGTTTGCAGTGTGAACATAAATATCATTTGGAATGTGTCGAAGGGAATGGAATCGAGGGAGGGTCGGTGGGTCCCACCTGGTTCTGTGGAGAAACCTGTAAAAAGATACACTGGAGTCTTCGTTCCCAGATTGGGTGTCGGAATCCACTTTC...

CDS

Download CDS FASTA

834 bp · TkA04G339880|TK1151|CDS

TTTCAGGAGTTACCTGAAGGCAATTGGTATTGTTCAAATTGCTGTTGTTGGAGTTGTGGGGATGTAATCAATCATATCGAGGCTTCAGAGTCTTATAATTCTCTCAAATGTTTGCAGTGTGAACATAAATATCATTTGGAATGTGTCGAAGGGAATGGAATCGAGGGAGGGTCGGTGGGTCCCACCTGGTTCTGTGGAGAAACCTGTAAAAAGATACACTGGAGTCTTCGTTCCCAGATTGGGTGTCGGAATCCACTTTC...

Protein

Download Protein FASTA

277 aa · TkA04G339880|TK1151|PROTEIN

FQELPEGNWYCSNCCCWSCGDVINHIEASESYNSLKCLQCEHKYHLECVEGNGIEGGSVGPTWFCGETCKKIHWSLRSQIGCRNPLSDGFSWTLLKCIHGEQKVNSNPAFIALKAECNLKLAVALTIMEECFLPMVDTRTGIYMISHVVYNWGSEFVRLNYEGFYTMVLEKNDILLCVASIRIHGTTVAEMPLIGTCTKYRRQGMCRRLMNAIEQMLKSFKVETLVVSAIPSLVDTWTGGFGFLRLEDDERKSLGKLTSW...

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	`TkA04G339880`
TK1151 ID	TkA04G339880
OH-1004 ID	LXL04_037731
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	74.600
Protein coverage (%)	TK1151 92.058 / OH-1004 39.620 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 TkA04G339880

Location Chr04:85862780-85869403 (+)

Description Similar to IDM1: Increased DNA methylation 1

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / 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.

Nucleus0.545

Rank 1 · TkA04G339880 · TK1151

Cytoplasm0.443

Rank 2 · TkA04G339880 · TK1151

Cell membrane0.065

Rank 3 · TkA04G339880 · TK1151

Endoplasmic reticulum0.053

Rank 4 · TkA04G339880 · TK1151

Golgi apparatus0.036

Rank 5 · TkA04G339880 · 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.

PF00628PHD3-14 aa

PF06044DpnI8-51 aa

PF23555zf-RING_Vps4116-54 aa

PF00628PHD21-66 aa

PF06044DpnI64-133 aa

PF23209IDM1_C132-256 aa

PF00583Acetyltransf_1160-225 aa

PF13673Acetyltransf_10162-248 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA04G339880	`PF00628`	PHD	3	14	0.077	13.7
TkA04G339880	`PF06044`	DpnI	8	51	0.82	10.0
TkA04G339880	`PF23555`	zf-RING_Vps41	16	54	0.002	18.4
TkA04G339880	`PF00628`	PHD	21	66	0.077	13.7
TkA04G339880	`PF06044`	DpnI	64	133	0.82	10.0
TkA04G339880	`PF23209`	IDM1_C	132	256	3.2e-52	177.0
TkA04G339880	`PF00583`	Acetyltransf_1	160	225	0.004	18.1
TkA04G339880	`PF13673`	Acetyltransf_10	162	248	0.00011	23.0
TkA04G339880	`PF13508`	Acetyltransf_7	167	219	0.049	14.7

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
`F4IXE7`	Arabidopsis thaliana	sp\|F4IXE7\|IDM1_ARATH Increased DNA methylation 1	55.900%	Swiss-Prot	High

JBrowse

View in Genome Browser

Gene Card