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

TkA04G328600
Reference: TK1151 Chr: Chr04 Coordinates: 83008531-83012425 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

2834 bp · TkA04G328600|TK1151|cDNA

GTTTTCCCGTAAAAAAGCCCTAATTTTCCCCCCTCAACCTTTCAAAAAGATGATACCAAGTTACCAACAATTCAACTTCCGGGCACAAATGGTCGGCGTTCCTTACAATTGGACTCATGTTGCTCGATGTTACGTCCGAGAGCAGTCAATTCATGCATTCCGTAAGTGAGATATTCATCATAAATTCAACGAAGCTTTAGCAATTGATGTCAAAAGCTAGTTTCTAGAGGATTTTCCTCCATGCGTCTTTGATTTTTTAT...

CDS

Download CDS FASTA

1440 bp · TkA04G328600|TK1151|CDS

ATGGAAACTCCAGCTTCCAAGCGTCCGCTAAGAAAAAAACCCCTCTCTAGAAGCTACGATGAAAACCTAATGGACGATTACCTCGACAAGCAACTCGGTAACACCCCAAGGAAACGGATGAGAACAAAGAAAGAACTCGAAAAAGAAACAGAAAAAGAAGCCATGATCGCCCTTTCTCTAGGGTTCCCCATTGACGCCCTTCTAGAAGAAGAAATCAAAGCCAACGTTGTCTCAGAACTCCACGGAAAACAACAAAACGA...

Protein

Download Protein FASTA

479 aa · TkA04G328600|TK1151|PROTEIN

METPASKRPLRKKPLSRSYDENLMDDYLDKQLGNTPRKRMRTKKELEKETEKEAMIALSLGFPIDALLEEEIKANVVSELHGKQQNDYIVVRNHILSRWRSNVHAWLSKGEIKETVSNEFNHLLHSAYDFLHFNGYINFGVSPSFKPQIPEETTEKSVIIIGAGLAGLAAARQLLSFGFKVIVLEGRNRPGGRVYTQKMGLNLGHNQGQNGNYAMVDLGGSVITGIHANPLGVLARQLSIPLHKIKDECPLYNPEGKPVA...

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 IDTkA04G328600
TK1151 IDTkA04G328600
OH-1004 IDLXL04_037604
Relationship / confidenceSequence Supported Annotation Or Model Conflict / Review
Protein identity (%)98.900
Protein coverage (%)TK1151 97.077 / OH-1004 59.189
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 IDTkA04G328600
LocationChr04:83008531-83012425 (-)
DescriptionSimilar to LDL2: Lysine-specific histone demethylase 1 homolog 2
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At3g13682 Probable histone demethylase that reduces the levels of histone H3 'Lys-4' methylation in chromatin of the floral repressor FLOWERING LOCUS C (FLC) and the sporophytically silenced floral repressor FWA.
Arabidopsis relatives of the human lysine-specific Demethylase1 repress the expression of FWA and FLOWERING LOCUS C and thus promote the floral transition.2007 · DOI: 10.1105/tpc.107.052373
Arabidopsis histone demethylases LDL1 and LDL2 control primary seed dormancy by regulating DELAY OF GERMINATION 1 and ABA signaling-related genes.2015 · DOI: 10.3389/fpls.2015.00159
At3g10390 Probable histone demethylase that promotes flowering independently of the photoperiod and vernalization pathways by repressing FLOWERING LOCUS C (FLC), a floral repressor that blocks the transition from vegetative to reproductive development. No verified direct reference in this release

Rice

Reference gene IDPossible functionPapers / DOI
Os08g0143400 Probable histone demethylase. No verified direct reference in this release
Os04g0560300 Probable histone demethylase. No verified direct reference in this release
UniProt: Q01H90 Probable histone demethylase. No verified direct reference in this release
Functional annotation source
View annotation sources

Functional annotation source: OH1004 · LXL04_037604 · 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:0009627 systemic acquired resistance Biological Process
GO:0010228 vegetative to reproductive phase transition of meristem Biological Process
GO:0045892 negative regulation of DNA-templated transcription Biological Process
GO:0046208 spermine catabolic process Biological Process
GO:0048364 root development Biological Process
GO:0048510 regulation of timing of transition from vegetative to reproductive phase Biological Process
GO:1903602 thermospermine catabolic process Biological Process
GO:1904629 response to diterpene Biological Process
GO:2000028 regulation of photoperiodism, flowering Biological Process
GO:0005634 nucleus Cellular Component
KEGG gene cross-reference
ath:AT1G62830
ath:AT3G10390
ath:AT3G13682
dosa:Os04g0560300
dosa:Os08g0143400
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.

Cytoplasm0.487
Rank 1 · TkA04G328600 · TK1151
Nucleus0.470
Rank 2 · TkA04G328600 · TK1151
Mitochondrion0.110
Rank 3 · TkA04G328600 · TK1151
Peroxisome0.041
Rank 4 · TkA04G328600 · TK1151
Cell membrane0.040
Rank 5 · TkA04G328600 · 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.

PF13478XdhC_C37-80 aa
PF01593Amino_oxidase64-105 aa
PF04433SWIRM68-139 aa
PF01488Shikimate_DH151-189 aa
PF028262-Hacid_dh_C151-189 aa
PF01946Thi4153-195 aa
PF01262AlaDh_PNT_C155-188 aa
PF21799MurD-like_N156-192 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
TkA04G328600PF13478XdhC_C37800.3212.3
TkA04G328600PF01593Amino_oxidase641057.5e-43148.1
TkA04G328600PF04433SWIRM681391.2e-1351.8
TkA04G328600PF01488Shikimate_DH1511890.004617.8
TkA04G328600PF028262-Hacid_dh_C1511890.0115.9
TkA04G328600PF01946Thi41531952.4e-0524.4
TkA04G328600PF01262AlaDh_PNT_C1551880.001219.1
TkA04G328600PF21799MurD-like_N1561920.01716.1
TkA04G328600PF07992Pyr_redox_21572074.7e-0730.2
TkA04G328600PF03486HI0933_like1572050.0001122.5
TkA04G328600PF01494FAD_binding_31571880.0006319.8
TkA04G328600PF00070Pyr_redox1572000.01116.9
TkA04G328600PF01266DAO1581923.1e-0627.7
TkA04G328600PF12831FAD_oxidored1582205.4e-0523.4
TkA04G328600PF00890FAD_binding_21581907.4e-0522.8
TkA04G328600PF01134GIDA1581840.00218.0

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
Q9LID0Arabidopsis thalianasp|Q9LID0|LDL2_ARATH Lysine-specific histone demethylase 1 homolog 265.700%Swiss-ProtHigh
Q9CAE3Arabidopsis thalianasp|Q9CAE3|FLD_ARATH Protein FLOWERING LOCUS D52.500%Swiss-ProtHigh
Q6YYZ1Oryza sativa subsp. japonicasp|Q6YYZ1|LDL2_ORYSJ Lysine-specific histone demethylase 1 homolog 251.500%Swiss-ProtHigh
Q7XUR2Oryza sativa subsp. japonicasp|Q7XUR2|LDL3_ORYSJ Lysine-specific histone demethylase 1 homolog 353.200%Swiss-ProtHigh
Q01H90Oryza sativa subsp. indicasp|Q01H90|LDL3_ORYSI Lysine-specific histone demethylase 1 homolog 352.900%Swiss-ProtHigh

JBrowse

View in Genome Browser