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

TkA02G520890
Reference: TK1151 Chr: Chr02 Coordinates: 134331371-134339817 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

2360 bp · TkA02G520890|TK1151|cDNA

TAGATGCCTCTTTGTCTGTATCGAGCTAGAATGGTGTTGTTGTCACCTATGGATTTTATTTAATCCAATCCCACCTATTTTTCTGAAGGCCATTGCATCCGTTTTAAACACACTCTCGACTCTTCCACCAGTCCAAATCAACTGTTTCGCCTTCAATTTCGGTGCTGGTACTCGAGCAGAAGGAAGTCGTAAACTTCTGTTTGCAATAATGGCTACTGGATTCACTCCAGTTTCCTTCAGAACCCTAAAAAGCAGGGACA...

CDS

Download CDS FASTA

3429 bp · TkA02G520890|TK1151|CDS

ATGAAGATAGAAGAAGTGCAATCTACTACTAAGAAGCAGAGGATCGCTACGCACACTCATATCAAAGGCCTTGGTCTTGAGCCTACTGGAAAAGCAATCCCATTGGCGGCTGGATTTGTAGGTCAATCAGCAGCAAGAGAGGCCGGCGGCCTTGTAGTTGACATGATCCGCCAAAAAAAGATGGCTGGACGTGCACTTCTGTTTGCCGGACCTCCTGGAACTGGCAAAACCGCCCTTGCCCTTGGCATCTCCCAAGAACT...

Protein

Download Protein FASTA

1142 aa · TkA02G520890|TK1151|PROTEIN

MKIEEVQSTTKKQRIATHTHIKGLGLEPTGKAIPLAAGFVGQSAAREAGGLVVDMIRQKKMAGRALLFAGPPGTGKTALALGISQELGTKVPFCPMVGSEVYSSEVKKTEVLMENFRRAIGLRIKENKEVYEGEVTELSPEETESVTGGYGKAISHVIIGLKTVKGTKQLKLDPTIYDALIKEKVAVGDVIYIEANSGAVKRVGRSDAFATEYDLEAEEYVPLPKGEVHKKKEIVQDVTLHDLDAANARPQGGQDILSLM...

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 IDTkA02G520890
TK1151 IDTkA02G520890
OH-1004 IDLXL04_013034
Relationship / confidenceRbh Sequence Supported / Probable
Protein identity (%)94.200
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 IDTkA02G520890
LocationChr02:134331371-134339817 (-)
DescriptionSimilar to ISPG: 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase (ferredoxin), chloroplastic
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At5g60600 Enzyme of the plastid non-mevalonate pathway for isoprenoid biosynthesis that converts 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (ME-2,4cPP) into 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate.
CHLOROPLAST BIOGENESIS genes act cell and noncell autonomously in early chloroplast development.2004 · DOI: 10.1104/pp.103.036996
The Arabidopsis csb3 mutant reveals a regulatory link between salicylic acid-mediated disease resistance and the methyl-erythritol 4-phosphate pathway.2005 · DOI: 10.1111/j.1365-313x.2005.02517.x
Isoprenoid biosynthesis in plant chloroplasts via the MEP pathway: direct thylakoid/ferredoxin-dependent photoreduction of GcpE/IspG.2006 · DOI: 10.1016/j.febslet.2006.01.082
At5g22330 Proposed core component of the chromatin remodeling INO80 complex which is involved in transcriptional regulation, DNA replication and probably DNA repair. No verified direct reference in this release

Rice

Reference gene IDPossible functionPapers / DOI
Os02g0603800 Enzyme of the plastid non-mevalonate pathway for isoprenoid biosynthesis that converts 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (ME-2,4cPP) into 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate. No verified direct reference in this release
Functional annotation source
View annotation sources

Functional annotation source: OH1004 · LXL04_013034 · 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:0000492 box C/D snoRNP assembly Biological Process
GO:0006281 DNA repair Biological Process
GO:0006310 DNA recombination Biological Process
GO:0006338 chromatin remodeling Biological Process
GO:0006351 DNA-templated transcription Biological Process
GO:0006357 regulation of transcription by RNA polymerase II Biological Process
GO:0009617 response to bacterium Biological Process
GO:0009862 systemic acquired resistance, salicylic acid mediated signaling pathway Biological Process
GO:0009908 flower development Biological Process
GO:0016114 terpenoid biosynthetic process Biological Process
GO:0019288 isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway Biological Process
GO:0030154 cell differentiation Biological Process
KEGG gene cross-reference
ath:AT5G22330
ath:AT5G60600
dosa:Os02g0603800
pcu:PC_RS03560
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.

Cytoplasm0.632
Rank 1 · TkA02G520890 · TK1151
Nucleus0.253
Rank 2 · TkA02G520890 · TK1151
Mitochondrion0.146
Rank 3 · TkA02G520890 · TK1151
Cell membrane0.079
Rank 4 · TkA02G520890 · TK1151
Endoplasmic reticulum0.078
Rank 5 · TkA02G520890 · 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.

PF06068TIP4914-365 aa
PF05496RuvB_N38-91 aa
PF20030bpMoxR52-90 aa
PF02367TsaE57-90 aa
PF13245AAA_1960-86 aa
PF13481AAA_2562-95 aa
PF12775AAA_762-89 aa
PF13191AAA_1663-90 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
TkA02G520890PF06068TIP49143653e-164547.0
TkA02G520890PF05496RuvB_N38917.3e-0936.3
TkA02G520890PF20030bpMoxR52900.0513.4
TkA02G520890PF02367TsaE57900.2711.9
TkA02G520890PF13245AAA_1960860.0215.8
TkA02G520890PF13481AAA_2562950.0513.9
TkA02G520890PF12775AAA_762890.211.9
TkA02G520890PF13191AAA_1663900.0415.2
TkA02G520890PF13401AAA_22641264.7e-0627.6
TkA02G520890PF01078Mg_chelatase64840.02614.6
TkA02G520890PF00004AAA661154.2e-1040.9
TkA02G520890PF07728AAA_566900.004217.8
TkA02G520890PF13238AAA_18671270.01216.9
TkA02G520890PF13521AAA_28671200.08313.8
TkA02G520890PF13191AAA_162443090.0415.2
TkA02G520890PF13238AAA_182683490.01216.9

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
F4K0E8Arabidopsis thalianasp|F4K0E8|ISPG_ARATH 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase (ferredoxin), chloroplastic75.900%Swiss-ProtMedium
Q9FMR9Arabidopsis thalianasp|Q9FMR9|RIN1_ARATH RuvB-like protein 189.200%Swiss-ProtHigh
Q6K8J4Oryza sativa subsp. japonicasp|Q6K8J4|ISPG_ORYSJ 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase (ferredoxin), chloroplastic74.900%Swiss-ProtMedium

JBrowse

View in Genome Browser