DEK39 - Plant Editosome Database - CNCB-NGDC

DEK39 - Plant Editosome Database - CNCB-NGDC

Summary

Editing Factor:	DEK39
Synonym:	Defective Kernel39
Description:	Encoding a PPR protein required for seed development in maize
Protein Family:	PPR
Subclass:	E
Physical Interaction:	NA
Construct Structure:	PLS-E1-E2
Gene ID & Species:	GRMZM2G345128 (Zea mays)
Edited Gene(s):	nad3
Editing Type(s):	C-to-U (10)
Publication(s):	[1] Defective Kernel 39 encodes a PPR protein required for seed development in maize., Journal of integrative plant biology, 2018. [PMID=28981206]

Editing Details

Species

Gene ID

Organelle

Edited Gene

Position

Region

Nuclear Genome

Organelle Genome

Other Position Region

Other Position

Editing Type

Codon

Amino Acid

Molecular Effect

Experiment Details

Zea mays

GRMZM2G345128

Mitochondrion

247

CDS

MaizeGDB

B73_RefGen_v4

NA

NA

C-to-U

CCU=>UCU

P=>S

Recoding

**Experiment Details**
Genotype (Ecotype)	Allele	Treatment	Treatment Detail	Mutant Type	Phenotype	Tissue	Development Stage	Detection Method	Editing Frequency	Editing Extent	Mutant Effect	PMID
B73	dek39	EMS Mutation	A G-to-A alteration results in Trp being converted to a stop codon	Homozygous	Delayed embryogenesis and endosperm development, reduced kernel size, and seedling lethality	Endosperm	12 DAP	RNA-Seq	40.00%	Medium	Decreased	28981206
siblings of the mutant or B73	WT	Control	Control	Control	Normal	Endosperm	12 DAP	RNA-Seq	80.00%	High	None	28981206
B73	dek39	EMS Mutation	A G-to-A alteration results in Trp being converted to a stop codon	Homozygous	Delayed embryogenesis and endosperm development, reduced kernel size, and seedling lethality	Endosperm	12 DAP	Direct Sequencing of PCR Products	50.70%	Medium	Decreased	28981206
siblings of the mutant or B73	WT	Control	Control	Control	Normal	Endosperm	12 DAP	Direct Sequencing of PCR Products	68.40%	High	None	28981206
B73	com	Complementation	dek39 + ProDek39::Dek39-MYC	Confirm presence of DEK39 transcripts	Similar growth phenotype as wild-type	Endosperm	12 DAP	Direct Sequencing of PCR Products	68.20%	High	Restored	28981206

Zea mays

GRMZM2G345128

Mitochondrion

275

CDS

MaizeGDB

B73_RefGen_v4

NA

NA

C-to-U

UCU=>UUU

S=>F

Recoding

**Experiment Details**
Genotype (Ecotype)	Allele	Treatment	Treatment Detail	Mutant Type	Phenotype	Tissue	Development Stage	Detection Method	Editing Frequency	Editing Extent	Mutant Effect	PMID
B73	dek39	EMS Mutation	A G-to-A alteration results in Trp being converted to a stop codon	Homozygous	Delayed embryogenesis and endosperm development, reduced kernel size, and seedling lethality	Endosperm	12 DAP	RNA-Seq	4.40%	Poor	Decreased	28981206
siblings of the mutant or B73	WT	Control	Control	Control	Normal	Endosperm	12 DAP	RNA-Seq	64.00%	High	None	28981206
B73	dek39	EMS Mutation	A G-to-A alteration results in Trp being converted to a stop codon	Homozygous	Delayed embryogenesis and endosperm development, reduced kernel size, and seedling lethality	Endosperm	12 DAP	Direct Sequencing of PCR Products	0.00%	Unedited	Absent	28981206
siblings of the mutant or B73	WT	Control	Control	Control	Normal	Endosperm	12 DAP	Direct Sequencing of PCR Products	59.60%	Medium	None	28981206
B73	com	Complementation	dek39 + ProDek39::Dek39-MYC	Confirm presence of DEK39 transcripts	Similar growth phenotype as wild-type	Endosperm	12 DAP	Direct Sequencing of PCR Products	60.30%	High	Restored	28981206

Last update: Feb 2026 (version 2.0)