DEK40 - Plant Editosome Database

Editing Details

Species

Gene ID

Organelle

Edited Gene

Position

Region

Editing Type

Codon

Amino Acid

Molecular Effect

Experiment Details

Zea mays

GRMZM2G304965

Mitochondrion

cox3

314

CDS

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	WT	No treatment	No treatment	No treatment	At 15 DAP, the WT pericarp was filled with endosperm, and the embryo had developed an obvious scutellum, coleoptile, two leaf primordia, and both shoot and root apical meristems; At 25 DAP, the WT embryos were larger and produced five or six leaf primordia	Kernel	10 DAP	RT‐PCR products were sequenced directly	95.00%	High	None	31598687
B73	dek40-ref	An SNP mutation	The SNP mutation (G to A) at base pair +1719 in the gene GRMZM2G304965 was the locus responsible for the dek40-ref phenotypes	Heterozygous	Embryo lethality; At 15 DAP, the mutant kernel embryo had only a coleoptile and an empty space between the pericarp and the endosperm; At 15 and 25 DAP, the dek40-ref mutant kernels displayed small, white, and translucent phenotypes; At 15 and 25 DAP, dek40-ref kernels had a soft texture and abnormal embryos; At 25 DAP, the mutant kernel embryos remained small and had a shoot apical meristem-like structure with one or two tiny leaf primordia; The mutant kernel and embryo were smaller than in the WT; The 100-kernel weight of dek40-ref was nearly 82.4% less than that of the WT.	Kernel	10 DAP	RT‐PCR products were sequenced directly	0.00%	Unedited	Absent	31598687
B73	dek40-1	An SNP mutation	dek40-1 had an SNP mutation (G to A) at base pair +2180, resulting in a premature stop codon in the mature transcript	Heterozygous	At 15 DAP, embryo and endosperm development were severely defective in dek40-1 kernels	Kernel	10 DAP	RT‐PCR products were sequenced directly	20.00%	Low	Decreased	31598687

Zea mays

GRMZM2G304965

Mitochondrion

nad2

CDS

C-to-U

UCC=>UUC

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	WT	No treatment	No treatment	No treatment	At 15 DAP, the WT pericarp was filled with endosperm, and the embryo had developed an obvious scutellum, coleoptile, two leaf primordia, and both shoot and root apical meristems; At 25 DAP, the WT embryos were larger and produced five or six leaf primordia	Kernel	10 DAP	RT‐PCR products were sequenced directly	100.00%	Complete	None	31598687
B73	dek40-ref	An SNP mutation	The SNP mutation (G to A) at base pair +1719 in the gene GRMZM2G304965 was the locus responsible for the dek40-ref phenotypes	Heterozygous	Embryo lethality; At 15 DAP, the mutant kernel embryo had only a coleoptile and an empty space between the pericarp and the endosperm; At 15 and 25 DAP, the dek40-ref mutant kernels displayed small, white, and translucent phenotypes; At 15 and 25 DAP, dek40-ref kernels had a soft texture and abnormal embryos; At 25 DAP, the mutant kernel embryos remained small and had a shoot apical meristem-like structure with one or two tiny leaf primordia; The mutant kernel and embryo were smaller than in the WT; The 100-kernel weight of dek40-ref was nearly 82.4% less than that of the WT.	Kernel	10 DAP	RT‐PCR products were sequenced directly	0.00%	Unedited	Absent	31598687
B73	dek40-1	An SNP mutation	dek40-1 had an SNP mutation (G to A) at base pair +2180, resulting in a premature stop codon in the mature transcript	Heterozygous	At 15 DAP, embryo and endosperm development were severely defective in dek40-1 kernels	Kernel	10 DAP	RT‐PCR products were sequenced directly	0.00%	Unedited	Absent	31598687

Zea mays

GRMZM2G304965

Mitochondrion

nad5

1901

CDS

C-to-U

UCA=>UUA

S=>L

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	WT	No treatment	No treatment	No treatment	At 15 DAP, the WT pericarp was filled with endosperm, and the embryo had developed an obvious scutellum, coleoptile, two leaf primordia, and both shoot and root apical meristems; At 25 DAP, the WT embryos were larger and produced five or six leaf primordia	Kernel	10 DAP	RT‐PCR products were sequenced directly	35.00%	Low	None	31598687
B73	dek40-ref	An SNP mutation	The SNP mutation (G to A) at base pair +1719 in the gene GRMZM2G304965 was the locus responsible for the dek40-ref phenotypes	Heterozygous	Embryo lethality; At 15 DAP, the mutant kernel embryo had only a coleoptile and an empty space between the pericarp and the endosperm; At 15 and 25 DAP, the dek40-ref mutant kernels displayed small, white, and translucent phenotypes; At 15 and 25 DAP, dek40-ref kernels had a soft texture and abnormal embryos; At 25 DAP, the mutant kernel embryos remained small and had a shoot apical meristem-like structure with one or two tiny leaf primordia; The mutant kernel and embryo were smaller than in the WT; The 100-kernel weight of dek40-ref was nearly 82.4% less than that of the WT.	Kernel	10 DAP	RT‐PCR products were sequenced directly	55.00%	Medium	Increased	31598687
B73	dek40-1	An SNP mutation	dek40-1 had an SNP mutation (G to A) at base pair +2180, resulting in a premature stop codon in the mature transcript	Heterozygous	At 15 DAP, embryo and endosperm development were severely defective in dek40-1 kernels	Kernel	10 DAP	RT‐PCR products were sequenced directly	70.00%	High	Increased	31598687

Zea mays

GRMZM2G304965

Mitochondrion

nad5

1916

CDS

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	WT	No treatment	No treatment	No treatment	At 15 DAP, the WT pericarp was filled with endosperm, and the embryo had developed an obvious scutellum, coleoptile, two leaf primordia, and both shoot and root apical meristems; At 25 DAP, the WT embryos were larger and produced five or six leaf primordia	Kernel	10 DAP	RT‐PCR products were sequenced directly	100.00%	Complete	None	31598687
B73	dek40-ref	An SNP mutation	The SNP mutation (G to A) at base pair +1719 in the gene GRMZM2G304965 was the locus responsible for the dek40-ref phenotypes	Heterozygous	Embryo lethality; At 15 DAP, the mutant kernel embryo had only a coleoptile and an empty space between the pericarp and the endosperm; At 15 and 25 DAP, the dek40-ref mutant kernels displayed small, white, and translucent phenotypes; At 15 and 25 DAP, dek40-ref kernels had a soft texture and abnormal embryos; At 25 DAP, the mutant kernel embryos remained small and had a shoot apical meristem-like structure with one or two tiny leaf primordia; The mutant kernel and embryo were smaller than in the WT; The 100-kernel weight of dek40-ref was nearly 82.4% less than that of the WT.	Kernel	10 DAP	RT‐PCR products were sequenced directly	0.00%	Unedited	Absent	31598687
B73	dek40-1	An SNP mutation	dek40-1 had an SNP mutation (G to A) at base pair +2180, resulting in a premature stop codon in the mature transcript	Heterozygous	At 15 DAP, embryo and endosperm development were severely defective in dek40-1 kernels	Kernel	10 DAP	RT‐PCR products were sequenced directly	0.00%	Unedited	Absent	31598687

Editing Factor:	DEK40
Synonym:	NA
Description:	NA
Protein Family:	PPR
Subclass:	E+
Construct Structure:	PLS-E-E+
Gene ID & Species:	GRMZM2G304965 (Zea mays)
Edited Gene(s):	cox3 nad2 nad5
Editing Type(s):	C-to-U (12)
Publication(s):	[1] Pentatricopeptide repeat protein DEK40 is required for mitochondrial function and kernel development in maize, J Exp Bot, 2019. [PMID=31598687]

Plant Editosome Database
a curated database of RNA editosome in plants

Summary

Editing Details