TkA05G438410 | RubberDandelionOmics

Gene overview

TkA05G438410

Reference: TK1151 Chr: Chr05 Coordinates: 109448812-109454105 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

975 bp · TkA05G438410|TK1151|cDNA

ATGGATCGGCCGGCGAGTTTACTCGACGAAGCTCTAGGTTTCGAAGACGGCGACTCGAAAAGCCGGCAGCCACGGGAAGGACGCGTTGTTCTACTGGAGGACTGCGTCGAAACTAGCGGCGCGTTTGTGCTACACCACCTTATAAAACGGTTTCTCTCTCCTAATCATTCGTCCTCCGACAGTGTCGTCATTTTTGTAGCATTCGCTCAACCTTTTTCTCACTACGACCGTATCCTGCGTAAGATGGGTTGCAACTTAGC...

CDS

Download CDS FASTA

975 bp · TkA05G438410|TK1151|CDS

ATGGATCGGCCGGCGAGTTTACTCGACGAAGCTCTAGGTTTCGAAGACGGCGACTCGAAAAGCCGGCAGCCACGGGAAGGACGCGTTGTTCTACTGGAGGACTGCGTCGAAACTAGCGGCGCGTTTGTGCTACACCACCTTATAAAACGGTTTCTCTCTCCTAATCATTCGTCCTCCGACAGTGTCGTCATTTTTGTAGCATTCGCTCAACCTTTTTCTCACTACGACCGTATCCTGCGTAAGATGGGTTGCAACTTAGC...

Protein

Download Protein FASTA

324 aa · TkA05G438410|TK1151|PROTEIN

MDRPASLLDEALGFEDGDSKSRQPREGRVVLLEDCVETSGAFVLHHLIKRFLSPNHSSSDSVVIFVAFAQPFSHYDRILRKMGCNLAVQRENKRLIFFDMLMLECPDDDGTEGGLLALYGNIHKAVEFNSLNKNITIIIDDISLLEVAANGSTKDVLNFMHYCHTLTTQFGCTIITVIHDDIYSSEDGFTLPTQLEYLADITIKAEPLVTGLAADIHGQLTVLNKGLGRWKGKIRNFHYRVPSASNGDLSNYLKTIVALQ...

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	`TkA05G438410`
TK1151 ID	TkA05G438410
OH-1004 ID	LXL04_021998
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	97.000
Protein coverage (%)	TK1151 99.691 / OH-1004 74.041 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 TkA05G438410

Location Chr05:109448812-109454105 (-)

Description Similar to ELP6: Elongator complex protein 6

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g10090`	Component of the elongator complex which is required for multiple tRNA modifications, including mcm5U (5-methoxycarbonylmethyl uridine), mcm5s2U (5-methoxycarbonylmethyl-2-thiouridine), and ncm5U (5-carbamoylmethyl uridine) (By similarity).	No verified direct reference in this release
`At1g58440`	May catalyze stereospecific oxidation of squalene to (S)-2,3-epoxysqualene in sterol biosynthesis.	Arabidopsis thaliana squalene epoxidase 1 is essential for root and seed development.2007 · DOI: 10.1074/jbc.m611831200 Identification of the Arabidopsis dry2/sqe1-5 mutant reveals a central role for sterols in drought tolerance and regulation of reactive oxygen species.2009 · DOI: 10.1111/j.1365-313x.2009.03849.x Analysis of the arabidopsis dry2/sqe1-5 mutant suggests a role for sterols in signaling.2009 · DOI: 10.4161/psb.4.9.9425
`At4g37760`	May catalyze stereospecific oxidation of squalene to (S)-2,3-epoxysqualene in sterol biosynthesis.	Arabidopsis thaliana squalene epoxidase 1 is essential for root and seed development.2007 · DOI: 10.1074/jbc.m611831200

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_021998 · 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:0002098 tRNA wobble uridine modification Biological Process

GO:0002238 response to molecule of fungal origin Biological Process

GO:0006979 response to oxidative stress Biological Process

GO:0008284 positive regulation of cell population proliferation Biological Process

GO:0009414 response to water deprivation Biological Process

GO:0009723 response to ethylene Biological Process

GO:0009725 response to hormone Biological Process

GO:0009751 response to salicylic acid Biological Process

GO:0009753 response to jasmonic acid Biological Process

GO:0009926 auxin polar transport Biological Process

GO:0010015 root morphogenesis Biological Process

GO:0010016 shoot system morphogenesis Biological Process

KEGG gene cross-reference

ath:AT1G58440

ath:AT2G22830

ath:AT4G10090

These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.

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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.

Cytoplasm0.559

Rank 1 · TkA05G438410 · TK1151

Nucleus0.304

Rank 2 · TkA05G438410 · TK1151

Peroxisome0.171

Rank 3 · TkA05G438410 · TK1151

Mitochondrion0.086

Rank 4 · TkA05G438410 · TK1151

Endoplasmic reticulum0.059

Rank 5 · TkA05G438410 · TK1151

LocPro · Direct prediction · Computational prediction, not experimental localization

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Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF09807ELP622-241 aa

PF10483Elong_Iki129-210 aa

PF06745ATPase50-204 aa

PF16836PSY3129-179 aa

PF08491SE239-323 aa

PF01494FAD_binding_3274-322 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA05G438410	`PF09807`	ELP6	22	241	8.6e-30	104.7
TkA05G438410	`PF10483`	Elong_Iki1	29	210	1.1e-05	25.8
TkA05G438410	`PF06745`	ATPase	50	204	0.0017	18.5
TkA05G438410	`PF16836`	PSY3	129	179	0.015	15.6
TkA05G438410	`PF08491`	SE	239	323	2.5e-30	106.2
TkA05G438410	`PF01494`	FAD_binding_3	274	322	0.19	11.7

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q8L9Y2`	Arabidopsis thaliana	sp\|Q8L9Y2\|ELP6_ARATH Elongator complex protein 6	53.800%	Swiss-Prot	High
`Q9SM02`	Arabidopsis thaliana	sp\|Q9SM02\|ERG14_ARATH Squalene epoxidase 1	70.200%	Swiss-Prot	Low
`Q8VYH2`	Arabidopsis thaliana	sp\|Q8VYH2\|ERG16_ARATH Squalene epoxidase 3	61.900%	Swiss-Prot	Low

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