TkA03G607590 | RubberDandelionOmics

Gene overview

TkA03G607590

Reference: TK1151 Chr: Chr03 Coordinates: 154330493-154331556 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

926 bp · TkA03G607590|TK1151|cDNA

CCTCTCTCTCTCTCTCTCTAATCCTCCTAATCCCTTCTTGATGTGTGAATCGGCCTATGCAAATCTGTAGGCGCTGAAGTTTTTGAGGATCGACTTCAATTGGAATCTCTTCTATTAAAACGAAGGTGATATCTATCCAGAAAATTGCAGCTTAAATCATCACAAAATCAGAAAATTGCTTCAAATTTTAGGCGCTGAAGTTTTTGAGGATCGACTTCAAATTTCAGTCGCTGAAGTTTTTGAGGATCAACTTCCGGCAT...

CDS

Download CDS FASTA

570 bp · TkA03G607590|TK1151|CDS

ATGGCTGGGCAAAGAAGTAGCAGTCATGGAAAACGCTCACACTCTCAATCCGACTACAGTGACCATGGAAGAAGCAGCAAAAGACGTAACAACAGTGATGACAGAGGCCAAAACTCAATCGGATCAGATGGCATAGTGTACCGTTACTTATGCCCTAGTAAGAGAATCGGAAGCATAATGGGACGTGGTGGGGATATAATCAAACAATTGAGATCTGAAAGCAAGTCCAAAATCAGAATTGGGGAGACTGTTGACCTAGC...

Protein

Download Protein FASTA

189 aa · TkA03G607590|TK1151|PROTEIN

MAGQRSSSHGKRSHSQSDYSDHGRSSKRRNNSDDRGQNSIGSDGIVYRYLCPSKRIGSIMGRGGDIIKQLRSESKSKIRIGETVDLADDQDPEETPQVTVRLLVPSDQIGCVIGKGGQIVQNIRTGTGAQVRIVKDNHLPACALSSDELVQVYILSSGRVRGCDYEKGERRNKEPKRGKIRARKREGER

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	`TkA03G607590`
TK1151 ID	TkA03G607590
OH-1004 ID	LXL04_006309
Relationship / confidence	Non Reciprocal Best Hit / Complex relationship
Protein identity (%)	71.900
Protein coverage (%)	TK1151 80.423 / OH-1004 36.499 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

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SNP / Indel variants and carrier samplesCRA009020 · TK1151

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Basic Information and Functional Annotation

Gene ID TkA03G607590

Location Chr03:154330493-154331556 (-)

Description Similar to At4g18375: KH domain-containing protein At4g18375

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`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
`At4g18375`	KH domain-containing protein At4g18375.	No verified direct reference in this release
`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_006309 · 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.

Nucleus0.908

Rank 1 · TkA03G607590 · TK1151

Cytoplasm0.215

Rank 2 · TkA03G607590 · TK1151

Cell membrane0.026

Rank 3 · TkA03G607590 · TK1151

Mitochondrion0.015

Rank 4 · TkA03G607590 · TK1151

Endoplasmic reticulum0.014

Rank 5 · TkA03G607590 · 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-B41-71 aa

PF00013KH_147-83 aa

PF07650KH_254-80 aa

PF22891KH_PNO1_2nd54-82 aa

PF13184KH_NusA_1st55-80 aa

PF22675KH-I_KHDC4-BBP56-80 aa

PF13083KH_KhpA-B93-125 aa

PF07650KH_298-137 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA03G607590	`PF13083`	KH_KhpA-B	41	71	6.9e-06	26.6
TkA03G607590	`PF00013`	KH_1	47	83	1.1e-23	83.5
TkA03G607590	`PF07650`	KH_2	54	80	4.2e-06	27.2
TkA03G607590	`PF22891`	KH_PNO1_2nd	54	82	0.6	10.7
TkA03G607590	`PF13184`	KH_NusA_1st	55	80	0.0016	19.3
TkA03G607590	`PF22675`	KH-I_KHDC4-BBP	56	80	9.2e-06	26.1
TkA03G607590	`PF13083`	KH_KhpA-B	93	125	6.9e-06	26.6
TkA03G607590	`PF07650`	KH_2	98	137	4.2e-06	27.2
TkA03G607590	`PF26594`	KH_NusA_2nd	98	118	0.092	13.3
TkA03G607590	`PF00013`	KH_1	99	152	1.1e-23	83.5
TkA03G607590	`PF13184`	KH_NusA_1st	107	135	0.0016	19.3
TkA03G607590	`PF22891`	KH_PNO1_2nd	108	135	0.6	10.7
TkA03G607590	`PF22675`	KH-I_KHDC4-BBP	109	133	9.2e-06	26.1

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
`F4KDN0`	Arabidopsis thaliana	sp\|F4KDN0\|HEN4_ARATH KH domain-containing protein HEN4	49.100%	Swiss-Prot	Low
`P58223`	Arabidopsis thaliana	sp\|P58223\|Y4837_ARATH KH domain-containing protein At4g18375	29.100%	Swiss-Prot	Low
`Q8W4B1`	Arabidopsis thaliana	sp\|Q8W4B1\|RCF3_ARATH RNA-binding KH domain-containing protein RCF3	38.600%	Swiss-Prot	Low

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