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

TkA04G509820
Reference: TK1151 Chr: Chr04 Coordinates: 128785379-128788967 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

2005 bp · TkA04G509820|TK1151|cDNA

AGATTAACCCGGTTCGCTTTCGATAGCTTATAGCTCCTAAATACGTCTTGGTTTCTTGCGGCTCGTCCTGTAAAGTGTAAACCCCAGAGTGGAAAAATAATAACATTTGCAACGTTGGGTTTCTCATTTCCCTCAACGCAGCAGCGAACAGCGAGGAGTGTCACAGTTCAAGGGTTTCCACAGGTTATATTCGATTGGTTTTGGTAAAAGAAAAAAAAAAAACTTGAGGGAGGGCATGAGTGGCAAACGCAGAAGGTCAT...

CDS

Download CDS FASTA

1512 bp · TkA04G509820|TK1151|CDS

ATGAGTGGCAAACGCAGAAGGTCATGGGAGAAAATGGCTCCACACTCAAAATCCAATGATGGTGGTTGGGAAGGGAACTTCAAGAATGATGACATCAGCAGAGGCAGAGATAGGAATATTCGGAGCTTTCATAATGACTGGGAAACACATTATACCACCACCACCCGCAAGCCATACAGGAGCAGGAGTAGAGGCAGAGAGTGGGAAACATATAACAAATCTTGTAGTAATGAATACAGTAGGCGTAGAGATGATGTAAG...

Protein

Download Protein FASTA

503 aa · TkA04G509820|TK1151|PROTEIN

MSGKRRRSWEKMAPHSKSNDGGWEGNFKNDDISRGRDRNIRSFHNDWETHYTTTTRKPYRSRSRGREWETYNKSCSNEYSRRRDDVRKEFYGARDQSNSKSRQISNIQCKFFAAGKCYRDDCRFSHHNPRSHDTWQPHDDDEEIHRSHNKPSWDWDDLDNKKRSWNGRPWDHDHDDNKTKSWNGEVNFRDRNDNNHNNYNNGHLNQNANVLDTSGKGQVEIEKSPKKKQEEEEEVVGNLQGRKVAENEQDGNYEKSRSTR...

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 IDTkA04G509820
TK1151 IDTkA04G509820
OH-1004 IDLXL04_039155
Relationship / confidenceRbh Sequence Supported / Probable
Protein identity (%)91.500
Protein coverage (%)TK1151 94.831 / OH-1004 98.557
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 IDTkA04G509820
LocationChr04:128785379-128788967 (+)
DescriptionSimilar to At3g18640: Zinc finger CCCH domain-containing protein 38
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At3g18640 Zinc finger CCCH domain-containing protein 38. No verified direct reference in this release
At2g33835 Transcriptional activator involved in the FRIGIDA-mediated vernalization pathway, but not in the autonomous flowering pathway.
FRIGIDA-ESSENTIAL 1 interacts genetically with FRIGIDA and FRIGIDA-LIKE 1 to promote the winter-annual habit of Arabidopsis thaliana.2005 · DOI: 10.1242/dev.02170
The FRIGIDA complex activates transcription of FLC, a strong flowering repressor in Arabidopsis, by recruiting chromatin modification factors.2011 · DOI: 10.1105/tpc.110.075911

Rice

Reference gene IDPossible functionPapers / DOI
Os08g0135800 Zinc finger CCCH domain-containing protein 55. No verified direct reference in this release
Os05g0497500 Zinc finger CCCH domain-containing protein 36. No verified direct reference in this release
Functional annotation source
View annotation sources

Functional annotation source: OH1004 · LXL04_039155 · 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:0009908 flower development Biological Process
GO:0010220 positive regulation of vernalization response Biological Process
GO:0030154 cell differentiation Biological Process
GO:0005634 nucleus Cellular Component
GO:0003677 DNA binding Molecular Function
GO:0008270 zinc ion binding Molecular Function
KEGG gene cross-reference
ath:AT2G33835
ath:AT3G18640
dosa:Os05g0497500
dosa:Os08g0135800
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.

Nucleus0.941
Rank 1 · TkA04G509820 · TK1151
Cytoplasm0.134
Rank 2 · TkA04G509820 · TK1151
Cell membrane0.030
Rank 3 · TkA04G509820 · TK1151
Endoplasmic reticulum0.016
Rank 4 · TkA04G509820 · TK1151
Mitochondrion0.012
Rank 5 · TkA04G509820 · 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.

PF29102Su_sable_N105-133 aa
PF01409tRNA-synt_2d105-129 aa
PF15663zf-CCCH_3106-128 aa
PF14608zf-CCCH_2108-126 aa
PF18044zf-CCCH_4109-126 aa
PF25261zf-CCCH_PARP12109-127 aa
PF25585zf-CCCH_DUS3L109-126 aa
PF00642zf-CCCH109-127 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
TkA04G509820PF29102Su_sable_N1051330.03615.2
TkA04G509820PF01409tRNA-synt_2d1051290.2411.6
TkA04G509820PF15663zf-CCCH_31061281.1e-0629.4
TkA04G509820PF14608zf-CCCH_21081261.2e-0732.7
TkA04G509820PF18044zf-CCCH_41091260.003417.8
TkA04G509820PF25261zf-CCCH_PARP121091270.008517.0
TkA04G509820PF25585zf-CCCH_DUS3L1091260.01615.9
TkA04G509820PF00642zf-CCCH1091270.02415.3
TkA04G509820PF22623zf-CCCH_91091270.05314.0
TkA04G509820PF18345zf_CCCH_41091260.1113.3
TkA04G509820PF22628zf-CCCH_101091260.7410.1
TkA04G509820PF17807zf-UBP_var1161332.28.8
TkA04G509820PF29102Su_sable_N3113340.03615.2
TkA04G509820PF01409tRNA-synt_2d3113280.2411.6
TkA04G509820PF15663zf-CCCH_33133821.1e-0629.4
TkA04G509820PF22623zf-CCCH_93133370.05314.0

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
Q9LIH5Arabidopsis thalianasp|Q9LIH5|C3H38_ARATH Zinc finger CCCH domain-containing protein 3853.300%Swiss-ProtLow
Q84VG7Arabidopsis thalianasp|Q84VG7|FES1_ARATH Protein FRIGIDA-ESSENTIAL 145.700%Swiss-ProtLow
Q6YYC0Oryza sativa subsp. japonicasp|Q6YYC0|C3H55_ORYSJ Zinc finger CCCH domain-containing protein 5552.200%Swiss-ProtLow
Q75K81Oryza sativa subsp. japonicasp|Q75K81|C3H36_ORYSJ Zinc finger CCCH domain-containing protein 3654.700%Swiss-ProtLow

JBrowse

View in Genome Browser