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

TkA01G441590
Reference: TK1151 Chr: Chr01 Coordinates: 110418094-110421020 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

2378 bp · TkA01G441590|TK1151|cDNA

AGAGCCCTAATGTTTAGGGACTAAAATAGATAAAAACCAACTAAAATACTTAATTTACTCTTCGATAAGAAAAAGTGGAAGGGTCGGAACGGAAAATAAAATTTAACCTGCAGAGTCGACAGTTGAGAGCTACCAGACGACGGCGGCGGTTTCTTCTTCTGAGTTCTACCAAGCTATGGATATGAGATTCGTTGTTGATTGAATTAATAATTAGGTTACTTGTATGTCAATGGATGGTTCCTTTCCAAATAAGCGTCTCT...

CDS

Download CDS FASTA

1791 bp · TkA01G441590|TK1151|CDS

ATGTCAATGGATGGTTCCTTTCCAAATAAGCGTCTCTTCGACCATTCTACCTCCGACAGGTCCGACCATCCTCACCTTACACCGACCTCTTCTAACAAGCGGCGCCACCAACACCACCACCCTCATCCATCCTCCCCTGCCACTCCTCAATCTAACAACAATAATCCTTTTCGCGCCTCTCTCAAACTCTCCTCCGGCGAAACCCTATTCCGTATTCTATGCCCTTCTGCAAAGACCGGCGGTGTCATCGGCAAGGGCGG...

Protein

Download Protein FASTA

597 aa · TkA01G441590|TK1151|PROTEIN

MSMDGSFPNKRLFDHSTSDRSDHPHLTPTSSNKRRHQHHHPHPSSPATPQSNNNNPFRASLKLSSGETLFRILCPSAKTGGVIGKGGAIIRQFREETGAKIRIDDYTHGSEERVIVIVAECTHKNKDIPNNNNDDSNSEESGNSNCEESPAQKALIRIFERILRVDEERSKMSKEESDNGEDNSTEGSGGVPQGPVVCRMLAASNQIGCVLGRGGKIIEKIRQESGAQVRVLPKDQLPECASPGDELIQMAGKFSAVKKA...

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 IDTkA01G441590
TK1151 IDTkA01G441590
OH-1004 IDLXL04_002239
Relationship / confidenceMulti Source To Oh1004 / Complex relationship
Protein identity (%)97.800
Protein coverage (%)TK1151 98.995 / OH-1004 79.183
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 IDTkA01G441590
LocationChr01:110418094-110421020 (-)
DescriptionSimilar to RCF3: RNA-binding KH domain-containing protein RCF3
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At5g53060 Acts as a negative regulator of osmotic stress-induced gene expression.
HOS5-a negative regulator of osmotic stress-induced gene expression in Arabidopsis thaliana.1999 · DOI: 10.1046/j.1365-313x.1999.00558.x
A KH domain-containing putative RNA-binding protein is critical for heat stress-responsive gene regulation and thermotolerance in Arabidopsis.2013 · DOI: 10.1093/mp/sss119
The arabidopsis RNA binding protein with K homology motifs, SHINY1, interacts with the C-terminal domain phosphatase-like 1 (CPL1) to repress stress-inducible gene expression.2013 · DOI: 10.1371/journal.pgen.1003625
A KH-domain RNA-binding protein interacts with FIERY2/CTD phosphatase-like 1 and splicing factors and is important for pre-mRNA splicing in Arabidopsis.2013 · DOI: 10.1371/journal.pgen.1003875
The Arabidopsis KH-Domain RNA-Binding Protein ESR1 Functions in Components of Jasmonate Signalling, Unlinking Growth Restraint and Resistance to Stress.2015 · DOI: 10.1371/journal.pone.0126978
The RNA-binding protein HOS5 and serine/arginine-rich proteins RS40 and RS41 participate in miRNA biogenesis in Arabidopsis.2015 · DOI: 10.1093/nar/gkv751
KH domain protein RCF3 is a tissue-biased regulator of the plant miRNA biogenesis cofactor HYL1.2015 · DOI: 10.1073/pnas.1512865112
At4g18375 KH domain-containing protein At4g18375. No verified direct reference in this release
At5g64390 Functions in floral reproductive organ identity in the third whorl and floral determinacy specification by specifically promoting the processing of AGAMOUS (AG) pre-mRNA. 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_002239 · 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:0006396 RNA processing Biological Process
GO:0006397 mRNA processing Biological Process
GO:0006970 response to osmotic stress Biological Process
GO:0008380 RNA splicing Biological Process
GO:0009867 jasmonic acid mediated signaling pathway Biological Process
GO:0009911 positive regulation of flower development Biological Process
GO:0010093 specification of floral organ identity Biological Process
GO:0010286 heat acclimation Biological Process
GO:0010468 regulation of gene expression Biological Process
GO:0030154 cell differentiation Biological Process
GO:0031053 primary miRNA processing Biological Process
GO:0048497 maintenance of floral organ identity Biological Process
KEGG gene cross-reference
ath:AT4G18375
ath:AT5G53060
ath:AT5G64390
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.

Nucleus0.910
Rank 1 · TkA01G441590 · TK1151
Cytoplasm0.204
Rank 2 · TkA01G441590 · TK1151
Cell membrane0.029
Rank 3 · TkA01G441590 · TK1151
Endoplasmic reticulum0.016
Rank 4 · TkA01G441590 · TK1151
Lysosome / Vacuole0.010
Rank 5 · TkA01G441590 · 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.

PF13083KH_KhpA-B64-91 aa
PF00013KH_170-118 aa
PF07650KH_276-102 aa
PF13184KH_NusA_1st79-103 aa
PF22891KH_PNO1_2nd79-106 aa
PF22675KH-I_KHDC4-BBP81-105 aa
PF03254XG_FTase88-156 aa
PF00013KH_1198-264 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
TkA01G441590PF13083KH_KhpA-B64912.9e-0834.2
TkA01G441590PF00013KH_1701189e-59195.8
TkA01G441590PF07650KH_2761021.7e-0938.1
TkA01G441590PF13184KH_NusA_1st791030.001519.5
TkA01G441590PF22891KH_PNO1_2nd791060.003318.0
TkA01G441590PF22675KH-I_KHDC4-BBP811051.8e-1041.2
TkA01G441590PF03254XG_FTase881560.0002420.5
TkA01G441590PF00013KH_11982649e-59195.8
TkA01G441590PF13083KH_KhpA-B2022222.9e-0834.2
TkA01G441590PF07650KH_22032341.7e-0938.1
TkA01G441590PF22891KH_PNO1_2nd2042310.003318.0
TkA01G441590PF22675KH-I_KHDC4-BBP2052311.8e-1041.2
TkA01G441590PF13184KH_NusA_1st2052330.001519.5
TkA01G441590PF13083KH_KhpA-B3063352.9e-0834.2
TkA01G441590PF00013KH_13113609e-59195.8
TkA01G441590PF22675KH-I_KHDC4-BBP3163451.8e-1041.2

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
Q8W4B1Arabidopsis thalianasp|Q8W4B1|RCF3_ARATH RNA-binding KH domain-containing protein RCF331.700%Swiss-ProtMedium
P58223Arabidopsis thalianasp|P58223|Y4837_ARATH KH domain-containing protein At4g1837529.500%Swiss-ProtLow
F4KDN0Arabidopsis thalianasp|F4KDN0|HEN4_ARATH KH domain-containing protein HEN442.400%Swiss-ProtLow

JBrowse

View in Genome Browser