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

TkA04G393910
Reference: TK1151 Chr: Chr04 Coordinates: 99056751-99058483 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

1194 bp · TkA04G393910|TK1151|cDNA

TTAATGCTAAGCTCCAGTTTCCCAAAATCAAAAAACATGATGCGCACTGCGCACTCCCCACCCCCGATCAAAACTCCATTCCTTTTTCAGACGCTTGCTTGCATCCCGACCATTTGCTAAAACCTAGGGTTTGTACTTATCTTCTCTCAATCCACCCCAATTGCTCTACAATCCCGCACATTTACCTTCTTTCCGCCATTTTCATCATCGTTTCAAGCTCCTATTTCGTTACTTTTCCCAATATTTCGCCTTCAATTTAT...

CDS

Download CDS FASTA

642 bp · TkA04G393910|TK1151|CDS

ATGGCGAAGACAAAGCCTGGAAAGAAAGATTTAGATACTTACACTATCAAAGGAACCAACAAACTCGTTAGACCTGGAGACTGTGTGTTGATGAGGCCTGCTGATTCCGATAAGCCACCGTACGTAGCGCGTGTGGAGAAGCTGGAGGCTGATCACCGGAACAATGTGAAGGTGAGAGTTAGGTGGTATTACCGGCCAGAGGAGTCACTCGGAGGAAGACGCCAGTTTCACGGCGTTAAGGAGCTGTTTTTATCCGATCA...

Protein

Download Protein FASTA

213 aa · TkA04G393910|TK1151|PROTEIN

MAKTKPGKKDLDTYTIKGTNKLVRPGDCVLMRPADSDKPPYVARVEKLEADHRNNVKVRVRWYYRPEESLGGRRQFHGVKELFLSDHYDMQSAHTIEGKCIVHSFKNYTKLDNVGTEDYFCRFEYKAATGGFTPDRVAVYCKCEMPYNPDDLMVQCEGCKDWFHPSCMGMTIEEAKKLEQFLCSDCSSDDDTKGFPISQSTDPKMEVKRRKQR

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 IDTkA04G393910
TK1151 IDTkA04G393910
OH-1004 IDLXL04_038124
Relationship / confidenceMulti Source To Oh1004 / Complex relationship
Protein identity (%)99.100
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 IDTkA04G393910
LocationChr04:99056751-99058483 (+)
DescriptionSimilar to EBS: Chromatin remodeling protein EBS
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At4g22140 Chromatin remodeling factor that binds to methylated histone (e.g. H3K4me2/3) to prevent their acetylation (e.g. H3K9K14Ac), likely by recruiting histone deacetylase (HDAC) complexes, and thus regulating the transcription of target genes. No verified direct reference in this release
At4g39100 Chromatin remodeling factor that binds to methylated histone (e.g. H3K4me2/3) to prevent their acetylation (e.g. H3K9K14Ac), likely by recruiting histone deacetylase (HDAC) complexes, and thus regulate the transcription of target genes. No verified direct reference in this release
At4g04260 Chromatin remodeling factor that binds to methylated histone (e.g. H3K4me2/3) to prevent their acetylation (e.g. H3K9K14Ac), likely by recruiting histone deacetylase (HDAC) complexes, and thus regulate the transcription of target genes. 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_038124 · 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:0006351 DNA-templated transcription Biological Process
GO:0009791 post-embryonic development Biological Process
GO:0009845 seed germination Biological Process
GO:0009908 flower development Biological Process
GO:0010228 vegetative to reproductive phase transition of meristem Biological Process
GO:0045814 negative regulation of gene expression, epigenetic Biological Process
GO:0048579 negative regulation of long-day photoperiodism, flowering Biological Process
GO:2000028 regulation of photoperiodism, flowering Biological Process
GO:0005634 nucleus Cellular Component
GO:0000976 transcription cis-regulatory region binding Molecular Function
GO:0003682 chromatin binding Molecular Function
KEGG gene cross-reference
ath:AT4G04260
ath:AT4G22140
ath:AT4G39100
hsa:57597
mmu:268515
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.

Nucleus0.919
Rank 1 · TkA04G393910 · TK1151
Cytoplasm0.185
Rank 2 · TkA04G393910 · TK1151
Cell membrane0.032
Rank 3 · TkA04G393910 · TK1151
Endoplasmic reticulum0.024
Rank 4 · TkA04G393910 · TK1151
Mitochondrion0.023
Rank 5 · TkA04G393910 · 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.

PF01426BAH23-134 aa
PF00628PHD99-122 aa
PF30811PHD_UBR7-like139-188 aa
PF20826PHD_5139-186 aa
PF31197PHD_JHD1140-171 aa
PF00628PHD141-186 aa
PF27108PHD_Pygo142-179 aa
PF23011PHD-1st_NSD148-186 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
TkA04G393910PF01426BAH231342.4e-2589.5
TkA04G393910PF00628PHD991222e-0938.0
TkA04G393910PF30811PHD_UBR7-like1391883.2e-1040.5
TkA04G393910PF20826PHD_51391861e-0629.4
TkA04G393910PF31197PHD_JHD11401710.00119.6
TkA04G393910PF00628PHD1411862e-0938.0
TkA04G393910PF27108PHD_Pygo1421790.0001122.9
TkA04G393910PF23011PHD-1st_NSD1481860.1512.9
TkA04G393910PF15446zf-PHD-like1491710.02614.8
TkA04G393910PF13831PHD_21511860.0002221.4
TkA04G393910PF21257PHD_ash2p_like1531750.09113.4
TkA04G393910PF16866PHD_41531830.4111.3
TkA04G393910PF15446zf-PHD-like1802120.02614.8
TkA04G393910PF31197PHD_JHD11831930.00119.6

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
F4JL28Arabidopsis thalianasp|F4JL28|EBS_ARATH Chromatin remodeling protein EBS76.300%Swiss-ProtHigh
Q9FEN9Arabidopsis thalianasp|Q9FEN9|SHL_ARATH Chromatin remodeling protein SHL67.000%Swiss-ProtHigh
F4JGB7Arabidopsis thalianasp|F4JGB7|EBSL_ARATH Chromatin remodeling protein At4g0426061.900%Swiss-ProtHigh

JBrowse

View in Genome Browser