DEK40 - Plant Editosome Database - BIG Data Center

Summary

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]

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
B73WTNo treatmentNo treatmentNo treatmentAt 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 primordiaKernel10 DAPRT‐PCR products were sequenced directly95.00%HighNone31598687
B73dek40-refAn SNP mutationThe SNP mutation (G to A) at base pair +1719 in the gene GRMZM2G304965 was the locus responsible for the dek40-ref phenotypesHeterozygousEmbryo 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.Kernel10 DAPRT‐PCR products were sequenced directly0.00%UneditedAbsent31598687
B73dek40-1An SNP mutationdek40-1 had an SNP mutation (G to A) at base pair +2180, resulting in a premature stop codon in the mature transcriptHeterozygousAt 15 DAP, embryo and endosperm development were severely defective in dek40-1 kernelsKernel10 DAPRT‐PCR products were sequenced directly20.00%LowDecreased31598687
Zea mays GRMZM2G304965 Mitochondrion nad2 26 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
B73WTNo treatmentNo treatmentNo treatmentAt 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 primordiaKernel10 DAPRT‐PCR products were sequenced directly100.00%CompleteNone31598687
B73dek40-refAn SNP mutationThe SNP mutation (G to A) at base pair +1719 in the gene GRMZM2G304965 was the locus responsible for the dek40-ref phenotypesHeterozygousEmbryo 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.Kernel10 DAPRT‐PCR products were sequenced directly0.00%UneditedAbsent31598687
B73dek40-1An SNP mutationdek40-1 had an SNP mutation (G to A) at base pair +2180, resulting in a premature stop codon in the mature transcriptHeterozygousAt 15 DAP, embryo and endosperm development were severely defective in dek40-1 kernelsKernel10 DAPRT‐PCR products were sequenced directly0.00%UneditedAbsent31598687
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
B73WTNo treatmentNo treatmentNo treatmentAt 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 primordiaKernel10 DAPRT‐PCR products were sequenced directly35.00%LowNone31598687
B73dek40-refAn SNP mutationThe SNP mutation (G to A) at base pair +1719 in the gene GRMZM2G304965 was the locus responsible for the dek40-ref phenotypesHeterozygousEmbryo 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.Kernel10 DAPRT‐PCR products were sequenced directly55.00%MediumIncreased31598687
B73dek40-1An SNP mutationdek40-1 had an SNP mutation (G to A) at base pair +2180, resulting in a premature stop codon in the mature transcriptHeterozygousAt 15 DAP, embryo and endosperm development were severely defective in dek40-1 kernelsKernel10 DAPRT‐PCR products were sequenced directly70.00%HighIncreased31598687
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
B73WTNo treatmentNo treatmentNo treatmentAt 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 primordiaKernel10 DAPRT‐PCR products were sequenced directly100.00%CompleteNone31598687
B73dek40-refAn SNP mutationThe SNP mutation (G to A) at base pair +1719 in the gene GRMZM2G304965 was the locus responsible for the dek40-ref phenotypesHeterozygousEmbryo 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.Kernel10 DAPRT‐PCR products were sequenced directly0.00%UneditedAbsent31598687
B73dek40-1An SNP mutationdek40-1 had an SNP mutation (G to A) at base pair +2180, resulting in a premature stop codon in the mature transcriptHeterozygousAt 15 DAP, embryo and endosperm development were severely defective in dek40-1 kernelsKernel10 DAPRT‐PCR products were sequenced directly0.00%UneditedAbsent31598687
Last update: Jul 2021 (version 1.0)