Plant Circular RNA Database

Detail information of Zm00001d026439_circ_g.3

			
				
						 General Information
					

				
						CircRNA Name
						Zm00001d026439_circ_g.3
					

						ID in PlantcircBase
						zma_circ_003254
					

						Alias
						circ373
					

						Organism
						
							Zea mays						
					

						Position
						
							chr10: 145893642-145893755  JBrowse»						
					

						Reference genome
						
							AGPv4.38						
					

						Type  
						
							u-circRNA							
									
								

					

						Identification method
						CIRI
					

						Parent gene
						
							Zm00001d026439						
					

						Parent gene annotation
						
							Tetratricopeptide repeat (TPR)-like superfamily protein
							
					

						Parent gene strand
						+
					

						Alternative splicing
						
							NA						
					

						Support reads
						3
					

						Tissues
						seedling leaves
					

						Exon boundary  
						
							Yes-Yes							"Exon boundary" shows whether the splicing sites are on the boundary of exons or not. For example, "Yes-No" represents the donor splicing site is on the exon boundary and the accepter is not on the exon boundary.

					

						Splicing signals  
						
							GT-CA							The splicing signals of the circRNA. For example, "AG-GT" represents that the donor and the accepter splicing signal is "AG" and "GT", respectively.

					

						Number of exons covered
						Zm00001d026439_T013:1
Zm00001d026439_T038:1
Zm00001d026439_T046:1
Zm00001d026439_T061:1
Zm00001d026439_T024:1
Zm00001d026439_T066:1
Zm00001d026439_T002:1
Zm00001d026439_T089:1
Zm00001d026439_T086:1
Zm00001d026439_T075:1
Zm00001d026439_T095:1
Zm00001d026439_T029:1
Zm00001d026439_T054:1
Zm00001d026439_T080:1
Zm00001d026439_T071:1
Zm00001d026439_T031:1
Zm00001d026439_T079:1
Zm00001d026439_T026:1
Zm00001d026439_T063:1
Zm00001d026439_T058:1
Zm00001d026439_T082:1
Zm00001d026439_T072:1
Zm00001d026439_T093:1
Zm00001d026439_T068:1
Zm00001d026439_T050:1
Zm00001d026439_T052:1
Zm00001d026439_T087:1
Zm00001d026439_T044:1
Zm00001d026439_T020:1
Zm00001d026439_T022:1
Zm00001d026439_T094:1
Zm00001d026439_T074:1
Zm00001d026439_T051:1
Zm00001d026439_T057:1
Zm00001d026439_T047:1
Zm00001d026439_T092:1
Zm00001d026439_T016:1
Zm00001d026439_T078:1
Zm00001d026439_T001:1
Zm00001d026439_T027:1
Zm00001d026439_T059:1
Zm00001d026439_T014:1
Zm00001d026439_T009:1
Zm00001d026439_T083:1
Zm00001d026439_T045:1
Zm00001d026439_T067:1
Zm00001d026439_T096:1
Zm00001d026439_T036:1
Zm00001d026439_T021:1
Zm00001d026439_T049:1
Zm00001d026439_T043:1
Zm00001d026439_T091:1
Zm00001d026439_T034:1
Zm00001d026439_T018:1
Zm00001d026439_T003:1
Zm00001d026439_T060:1

					

			
		

General Information
CircRNA Name	Zm00001d026439_circ_g.3
ID in PlantcircBase	zma_circ_003254
Alias	circ373
Organism	Zea mays
Position	chr10: 145893642-145893755 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRI
Parent gene	Zm00001d026439
Parent gene annotation	Tetratricopeptide repeat (TPR)-like superfamily protein
Parent gene strand	+
Alternative splicing	NA
Support reads	3
Tissues	seedling leaves
Exon boundary	Yes-Yes "Exon boundary" shows whether the splicing sites are on the boundary of exons or not. For example, "Yes-No" represents the donor splicing site is on the exon boundary and the accepter is not on the exon boundary.
Splicing signals	GT-CA The splicing signals of the circRNA. For example, "AG-GT" represents that the donor and the accepter splicing signal is "AG" and "GT", respectively.
Number of exons covered	Zm00001d026439_T013:1 Zm00001d026439_T038:1 Zm00001d026439_T046:1 Zm00001d026439_T061:1 Zm00001d026439_T024:1 Zm00001d026439_T066:1 Zm00001d026439_T002:1 Zm00001d026439_T089:1 Zm00001d026439_T086:1 Zm00001d026439_T075:1 Zm00001d026439_T095:1 Zm00001d026439_T029:1 Zm00001d026439_T054:1 Zm00001d026439_T080:1 Zm00001d026439_T071:1 Zm00001d026439_T031:1 Zm00001d026439_T079:1 Zm00001d026439_T026:1 Zm00001d026439_T063:1 Zm00001d026439_T058:1 Zm00001d026439_T082:1 Zm00001d026439_T072:1 Zm00001d026439_T093:1 Zm00001d026439_T068:1 Zm00001d026439_T050:1 Zm00001d026439_T052:1 Zm00001d026439_T087:1 Zm00001d026439_T044:1 Zm00001d026439_T020:1 Zm00001d026439_T022:1 Zm00001d026439_T094:1 Zm00001d026439_T074:1 Zm00001d026439_T051:1 Zm00001d026439_T057:1 Zm00001d026439_T047:1 Zm00001d026439_T092:1 Zm00001d026439_T016:1 Zm00001d026439_T078:1 Zm00001d026439_T001:1 Zm00001d026439_T027:1 Zm00001d026439_T059:1 Zm00001d026439_T014:1 Zm00001d026439_T009:1 Zm00001d026439_T083:1 Zm00001d026439_T045:1 Zm00001d026439_T067:1 Zm00001d026439_T096:1 Zm00001d026439_T036:1 Zm00001d026439_T021:1 Zm00001d026439_T049:1 Zm00001d026439_T043:1 Zm00001d026439_T091:1 Zm00001d026439_T034:1 Zm00001d026439_T018:1 Zm00001d026439_T003:1 Zm00001d026439_T060:1

			
						 Experimental Information
					
						Sanger sequencing for BSS  
						
							NA							Sanger sequencing for back-splicing site (BSS) validation. "Yes" represents Sanger sequencing has been performed to valid the back-splicing site, "No" represents the opposite, "NA" represents "not available".

						PCR primers for BSS   
						
							NA							PCR primers used in back-splicing site (BSS) validation.

						Sanger sequencing for FL   
						
							NA							Sanger sequencing for full-length (FL) sequence validation of circRNAs. "Yes" represents Sanger sequencing has been performed to valid the full-length of circRNA, "No" represents the opposite.

						PCR primers for FL   
						
							NA							 PCR primers used in full-length (FL) sequence validation.

Experimental Information
Sanger sequencing for BSS	NA Sanger sequencing for back-splicing site (BSS) validation. "Yes" represents Sanger sequencing has been performed to valid the back-splicing site, "No" represents the opposite, "NA" represents "not available".
PCR primers for BSS	NA PCR primers used in back-splicing site (BSS) validation.
Sanger sequencing for FL	NA Sanger sequencing for full-length (FL) sequence validation of circRNAs. "Yes" represents Sanger sequencing has been performed to valid the full-length of circRNA, "No" represents the opposite.
PCR primers for FL	NA PCR primers used in full-length (FL) sequence validation.

			
						 Sequences
					
						Splice junction sequence  
						
							GGCTCGAAGAGGCATGCCAAAACCTGATTCATCTATTGCAAGTAAAGGACATCTTAGggatgct
gctgcatggctagaatattttgagtcaaaagcattagaacaacaagaggc

						Assembled circRNA sequence  
						
							NA
The sequence of a circRNA based on assembly using circseq-cup (Ye et al., 2016) or CIRI-full (Zheng and Zhao, 2018) or CIRCexplorer2 (Zhang et al., 2016).

						Full-length trsnacripts
						
							NA						
					
						Genomic sequence
						
							GGATGCTGCTGCATGGCTAGAATATTTTGAGTCAAAAGCATTAGAACAACAAGAGGCGGCTCGA
AGAGGCATGCCAAAACCTGATTCATCTATTGCAAGTAAAGGACATCTTAG

Sequences
Splice junction sequence	GGCTCGAAGAGGCATGCCAAAACCTGATTCATCTATTGCAAGTAAAGGACATCTTAGggatgct gctgcatggctagaatattttgagtcaaaagcattagaacaacaagaggc
Assembled circRNA sequence	NA The sequence of a circRNA based on assembly using circseq-cup (Ye et al., 2016) or CIRI-full (Zheng and Zhao, 2018) or CIRCexplorer2 (Zhang et al., 2016).
Full-length trsnacripts	NA
Genomic sequence	GGATGCTGCTGCATGGCTAGAATATTTTGAGTCAAAAGCATTAGAACAACAAGAGGCGGCTCGA AGAGGCATGCCAAAACCTGATTCATCTATTGCAAGTAAAGGACATCTTAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.358116228

Conservation Information
Conserved circRNAs	NA
PMCS	0.358116228

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							145893713-145893752(+)
145893715-145893644(-)
145893732-145893754(-)
						
						Potential amino acid sequence
						
							MPKPDSSIASKGHLRDAAAWLEYFESKALEQQEAARRGMPKPDSSIASKGHLRDAAAWLEYFES
KALEQQEAARRGMPKPDSSIASKGHLRDAAAWLEYFESKALEQQEAARRGMPKPDSSIASKGHL
(+)
MPLRAASCCSNAFDSKYSSHAAASLRCPLLAIDESGFGMPLRAASCCSNAFDSKYSSHAAASLR
CPLLAIDESGFGMPLRAASCCSNAFDSKYSSHAAASLRCPLLAIDESGFGMPLRAASCCSNAFD
SKYSSHAAAS(-)
MNQVLACLFEPPLVVLMLLTQNILAMQQHP*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	145893713-145893752(+) 145893715-145893644(-) 145893732-145893754(-)
Potential amino acid sequence	MPKPDSSIASKGHLRDAAAWLEYFESKALEQQEAARRGMPKPDSSIASKGHLRDAAAWLEYFES KALEQQEAARRGMPKPDSSIASKGHLRDAAAWLEYFESKALEQQEAARRGMPKPDSSIASKGHL (+) MPLRAASCCSNAFDSKYSSHAAASLRCPLLAIDESGFGMPLRAASCCSNAFDSKYSSHAAASLR CPLLAIDESGFGMPLRAASCCSNAFDSKYSSHAAASLRCPLLAIDESGFGMPLRAASCCSNAFD SKYSSHAAAS(-) MNQVLACLFEPPLVVLMLLTQNILAMQQHP*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chen et al., 2017b

circRNA

Detail information of Zm00001d026439_circ_g.3

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