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

TkA02G477920
Reference: TK1151 Chr: Chr02 Coordinates: 121950898-121952870 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

1622 bp · TkA02G477920|TK1151|cDNA

GAGGGCGCTTTGTGTATCTCTAACGGTTTCAACGTCCACCTCAAGCAACTCTTTTCACGCCCTCTCTTAATTATTATCCCCTGTTTCTCCCTTCAATCTCCACTCTCCATCTCTCCTTTCTCAAAATCCCGTTCCAGTTCCGCGACACACTGGATTCCTATCCCACCTTCTTCTATATACTCCTCCCAACCCATCTTACATCAGCAAATTCATTTCCCAAATCCTCCATCTCTCTCTTCAAGGGGTGTAAGTTATCGGGT...

CDS

Download CDS FASTA

1350 bp · TkA02G477920|TK1151|CDS

GAGGGCGCTTTGTGTATCTCTAACGGTTTCAACGTCCACCTCAAGCAACTCTTTTCACGCCCTCTCTTAATTATTATCCCCTGTTTCTCCCTTCAATCTCCACTCTCCATCTCTCCTTTCTCAAAATCCCGTTCCAGTTCCGCGACACACTGGATTCCTATCCCACCTTCTTCTATATACTCCTCCCAACCCATCTTACATCAGCAAATTCATTTCCCAAATCCTCCATCTCTCTCTTCAAGGGGTGTAAGTTATCGGGT...

Protein

Download Protein FASTA

449 aa · TkA02G477920|TK1151|PROTEIN

EGALCISNGFNVHLKQLFSRPLLIIIPCFSLQSPLSISPFSKSRSSSATHWIPIPPSSIYSSQPILHQQIHFPNPPSLSSRGVSYRVVLSVMEMEKKEIGSSMINDSIGVDNESNNLSANLYLSSIPVPSRNDQLEFDFGSGELFNPASFCSSIFPPKFISQSQLSYSSPSECSYDDDAFSANAYATENRLSQASFILEYQQLYNCYTVCLTNLQDSVKEVDVLRQENEALRVANGDLMQRLNLFSQASMQNRLASSVRS...

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 IDTkA02G477920
TK1151 IDTkA02G477920
OH-1004 IDLXL04_039754
Relationship / confidenceNon Reciprocal Best Hit / Complex relationship
Protein identity (%)91.800
Protein coverage (%)TK1151 18.931 / OH-1004 60.284
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 IDTkA02G477920
LocationChr02:121950898-121952870 (+)
DescriptionSimilar to Os05g0576300: Zinc finger CCCH domain-containing protein 39
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At1g66810 Functions probably as a transcriptional factor that activates genes involved in secondary cell wall biosynthesis.
AtC3H14, a plant-specific tandem CCCH zinc-finger protein, binds to its target mRNAs in a sequence-specific manner and affects cell elongation in Arabidopsis thaliana.2014 · DOI: 10.1111/tpj.12667
Arabidopsis C3H14 and C3H15 have overlapping roles in the regulation of secondary wall thickening and anther development.2015 · DOI: 10.1093/jxb/erv060
At1g68200 Functions probably as a transcriptional factor that activates genes involved in secondary cell wall biosynthesis.
The Arabidopsis CALLOSE DEFECTIVE MICROSPORE1 gene is required for male fertility through regulating callose metabolism during microsporogenesis.2014 · DOI: 10.1104/pp.113.233387
Arabidopsis C3H14 and C3H15 have overlapping roles in the regulation of secondary wall thickening and anther development.2015 · DOI: 10.1093/jxb/erv060
The CCCH zinc finger protein C3H15 negatively regulates cell elongation by inhibiting brassinosteroid signaling.2022 · DOI: 10.1093/plphys/kiac046

Rice

Reference gene IDPossible functionPapers / DOI
Os05g0576300 Zinc finger CCCH domain-containing protein 39. No verified direct reference in this release
Os01g0645000 Zinc finger CCCH domain-containing protein 9. No verified direct reference in this release
Os03g0301500 Putative zinc finger CCCH domain-containing protein 21. No verified direct reference in this release
Functional annotation source
View annotation sources

Functional annotation source: OH1004 · LXL04_039754 · 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:0006351 DNA-templated transcription Biological Process
GO:0006355 regulation of DNA-templated transcription Biological Process
GO:0009742 brassinosteroid mediated signaling pathway Biological Process
GO:0045893 positive regulation of DNA-templated transcription Biological Process
GO:0051511 negative regulation of unidimensional cell growth Biological Process
GO:1901347 negative regulation of secondary cell wall biogenesis Biological Process
GO:0005634 nucleus Cellular Component
GO:0005737 cytoplasm Cellular Component
GO:0000976 transcription cis-regulatory region binding Molecular Function
GO:0003677 DNA binding Molecular Function
GO:0003700 DNA-binding transcription factor activity Molecular Function
GO:0003729 mRNA binding Molecular Function
KEGG gene cross-reference
ath:AT1G66810
ath:AT1G68200
dosa:Os01g0645000
dosa:Os05g0576300
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.

Cytoplasm0.495
Rank 1 · TkA02G477920 · TK1151
Nucleus0.466
Rank 2 · TkA02G477920 · TK1151
Cell membrane0.099
Rank 3 · TkA02G477920 · TK1151
Endoplasmic reticulum0.057
Rank 4 · TkA02G477920 · TK1151
Plastid0.043
Rank 5 · TkA02G477920 · 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.

PF23261zf-CCCH_11169-177 aa
PF16131Torus333-347 aa
PF20992CBP66_2nd362-410 aa
PF00642zf-CCCH374-398 aa
PF25585zf-CCCH_DUS3L374-397 aa
PF25427zf-CCCH_UNK374-404 aa
PF23035zf-CCCH_UNK-like_4th374-382 aa
PF16131Torus375-401 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
TkA02G477920PF23261zf-CCCH_111691779.36.6
TkA02G477920PF16131Torus3333470.03315.5
TkA02G477920PF20992CBP66_2nd3624100.09913.4
TkA02G477920PF00642zf-CCCH3743985.7e-1761.9
TkA02G477920PF25585zf-CCCH_DUS3L3743972.1e-0937.9
TkA02G477920PF25427zf-CCCH_UNK3744042.8e-0524.6
TkA02G477920PF23035zf-CCCH_UNK-like_4th3743824.37.6
TkA02G477920PF16131Torus3754010.03315.5
TkA02G477920PF14625Lustrin_cystein3753960.05814.4
TkA02G477920PF18044zf-CCCH_43773971.3e-1041.5
TkA02G477920PF25542zf-CCCH_123773980.00816.6
TkA02G477920PF25261zf-CCCH_PARP123774000.03814.9
TkA02G477920PF18345zf_CCCH_43783973.8e-0730.7
TkA02G477920PF14608zf-CCCH_23783980.0006720.8
TkA02G477920PF22623zf-CCCH_93783974.47.8
TkA02G477920PF23261zf-CCCH_113794009.36.6

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
Q9C9N3Arabidopsis thalianasp|Q9C9N3|C3H14_ARATH Zinc finger CCCH domain-containing protein 1437.400%Swiss-ProtMedium
Q9C9F5Arabidopsis thalianasp|Q9C9F5|C3H15_ARATH Zinc finger CCCH domain-containing protein 1541.200%Swiss-ProtMedium
Q6L5G1Oryza sativa subsp. japonicasp|Q6L5G1|C3H39_ORYSJ Zinc finger CCCH domain-containing protein 3942.900%Swiss-ProtMedium
A2ZVY5Oryza sativa subsp. japonicasp|A2ZVY5|C3H9_ORYSJ Zinc finger CCCH domain-containing protein 937.000%Swiss-ProtMedium
Q10MN8Oryza sativa subsp. japonicasp|Q10MN8|C3H21_ORYSJ Putative zinc finger CCCH domain-containing protein 2141.300%Swiss-ProtLow

JBrowse

View in Genome Browser