TkA03G113260 | RubberDandelionOmics

Gene overview

TkA03G113260

Reference: TK1151 Chr: Chr03 Coordinates: 28976585-28982656 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

3053 bp · TkA03G113260|TK1151|cDNA

ATCCAACTCTCCCTCGAGTCCCGTCTCATAATCATAGATTCATAGGTAAGAAACAAAACAAACGCCATAGGCGAAGAAAGCCCTAATCTGCTCTTGTTTGTTTTGCTCTCCCAAATCATCAAATGAAGACCTTGTAATTAGAAGATCTCAACTTGTAGATTCTCCCCACTGGTGAATTTTCCTTTGCTGTAGATTCTGTGGCTGTATGGAAAGGAACAGTGGGCCCCCATTCAAGAAACGCCCAAACCCCCGTTTCAACA...

CDS

Download CDS FASTA

1458 bp · TkA03G113260|TK1151|CDS

ATGCTTGTTCCTAATAATACGGTTGGGTGTCTTTTGGGGAAAGGTGGTGAGGTTATTAAGAGATTGAGGGGGGAGACTGGTGCGGTTATTCGCCTTTTGCCTGCTGATCAGCTTCCTACTTGTGCTATGGAAACTGATGAATTATTGCAGATATCAGGCATACCAGACGTAACAAGAAAAGCCCTAGCCAAAGTCTCAACATTATTACACCAAAACCCCCGCAAAGACGAACCGCCATCAAACAGCCGCCCCGTGGGGGC...

Protein

Download Protein FASTA

485 aa · TkA03G113260|TK1151|PROTEIN

MLVPNNTVGCLLGKGGEVIKRLRGETGAVIRLLPADQLPTCAMETDELLQISGIPDVTRKALAKVSTLLHQNPRKDEPPSNSRPVGAPRSFHPGAPPPPPERGPYTYGAPPLPWRGYGNEPPRFGPPPPPPPVIEPVEDTPIEFPMKILCGEGKIGGVVGRNGISLRQFQQETGTSISVEEPLVGSDERVILVSSFDAIQKPRSRTIDAILLLQDKTSEHNEKGLITTRVLIPSSKVGCILGQGGMIINEMRRRIKADIR...

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.

ID Mapping

Input ID	`TkA03G113260`
TK1151 ID	TkA03G113260
OH-1004 ID	LXL04_007088
Relationship / confidence	Sequence Supported Annotation Or Model Conflict / Review
Protein identity (%)	95.500
Protein coverage (%)	TK1151 100.000 / OH-1004 36.727 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 version	TK1151 / 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 ID TkA03G113260

Location Chr03:28976585-28982656 (+)

Description Similar to At4g18375: KH domain-containing protein At4g18375

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / 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

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_007088 · 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:0010286 heat acclimation Biological Process

GO:0010468 regulation of gene expression Biological Process

GO:0031053 primary miRNA processing Biological Process

GO:1900150 regulation of defense response to fungus Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0010445 nuclear dicing body Cellular Component

KEGG gene cross-reference

ath:AT4G18375

ath:AT5G53060

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.

Nucleus0.847

Rank 1 · TkA03G113260 · TK1151

Cytoplasm0.325

Rank 2 · TkA03G113260 · TK1151

Cell membrane0.027

Rank 3 · TkA03G113260 · TK1151

Endoplasmic reticulum0.019

Rank 4 · TkA03G113260 · TK1151

Mitochondrion0.015

Rank 5 · TkA03G113260 · 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.

PF00013KH_11-65 aa

PF22675KH-I_KHDC4-BBP6-32 aa

PF07650KH_28-31 aa

PF20777KH_SLS1_217-61 aa

PF00013KH_1147-200 aa

PF07650KH_2151-180 aa

PF22675KH-I_KHDC4-BBP156-179 aa

PF20777KH_SLS1_2166-204 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA03G113260	`PF00013`	KH_1	1	65	2e-35	121.1
TkA03G113260	`PF22675`	KH-I_KHDC4-BBP	6	32	0.00026	21.5
TkA03G113260	`PF07650`	KH_2	8	31	1.8e-06	28.4
TkA03G113260	`PF20777`	KH_SLS1_2	17	61	0.083	14.0
TkA03G113260	`PF00013`	KH_1	147	200	2e-35	121.1
TkA03G113260	`PF07650`	KH_2	151	180	1.8e-06	28.4
TkA03G113260	`PF22675`	KH-I_KHDC4-BBP	156	179	0.00026	21.5
TkA03G113260	`PF20777`	KH_SLS1_2	166	204	0.083	14.0
TkA03G113260	`PF00013`	KH_1	227	295	2e-35	121.1
TkA03G113260	`PF07650`	KH_2	227	262	1.8e-06	28.4
TkA03G113260	`PF22675`	KH-I_KHDC4-BBP	237	262	0.00026	21.5

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

Protein	Organism	Description	Identity	Database	Confidence
`Q8W4B1`	Arabidopsis thaliana	sp\|Q8W4B1\|RCF3_ARATH RNA-binding KH domain-containing protein RCF3	30.200%	Swiss-Prot	Medium

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