Plant Circular RNA Database

Detail information of Zm00001d013274_circ_g.3

			
				
						 General Information
					

				
						CircRNA Name
						Zm00001d013274_circ_g.3
					

						ID in PlantcircBase
						zma_circ_001883
					

						Alias
						circ868
					

						Organism
						
							Zea mays						
					

						Position
						
							chr5: 7555405-7555767  JBrowse»						
					

						Reference genome
						
							AGPv4.38						
					

						Type  
						
							ui-circRNA							
									
								

					

						Identification method
						CIRI
					

						Parent gene
						
							Zm00001d013274						
					

						Parent gene annotation
						
							Probable helicase MAGATAMA 3
							
					

						Parent gene strand
						-
					

						Alternative splicing
						
							Zm00001d013274_circ_ag.1 Zm00001d013274_circ_g.1 Zm00001d013274_circ_ag.2 						
					

						Support reads
						4
					

						Tissues
						seedling leaves
					

						Exon boundary  
						
							No-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  
						
							CT-AA							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
						Zm00001d013274_T016:2
Zm00001d013274_T063:2
Zm00001d013274_T024:2
Zm00001d013274_T043:2
Zm00001d013274_T032:2
Zm00001d013274_T034:2
Zm00001d013274_T073:2
Zm00001d013274_T022:2
Zm00001d013274_T060:2
Zm00001d013274_T048:2
Zm00001d013274_T065:2
Zm00001d013274_T078:2
Zm00001d013274_T041:2
Zm00001d013274_T039:2
Zm00001d013274_T011:2
Zm00001d013274_T066:2
Zm00001d013274_T044:2
Zm00001d013274_T072:2
Zm00001d013274_T037:2
Zm00001d013274_T021:2
Zm00001d013274_T001:2
Zm00001d013274_T070:2
Zm00001d013274_T007:2
Zm00001d013274_T075:2
Zm00001d013274_T040:2
Zm00001d013274_T020:2
Zm00001d013274_T042:2
Zm00001d013274_T080:2
Zm00001d013274_T057:2
Zm00001d013274_T006:2
Zm00001d013274_T061:2
Zm00001d013274_T049:2
Zm00001d013274_T081:2
Zm00001d013274_T068:2
Zm00001d013274_T064:2
Zm00001d013274_T026:2
Zm00001d013274_T079:2
Zm00001d013274_T059:2
Zm00001d013274_T028:2
Zm00001d013274_T053:2
Zm00001d013274_T003:2
Zm00001d013274_T036:2
Zm00001d013274_T013:2
Zm00001d013274_T050:2
Zm00001d013274_T074:2
Zm00001d013274_T052:2
Zm00001d013274_T012:2
Zm00001d013274_T038:2
Zm00001d013274_T004:2
Zm00001d013274_T035:2
Zm00001d013274_T025:2
Zm00001d013274_T009:2
Zm00001d013274_T076:2
Zm00001d013274_T023:2
Zm00001d013274_T033:2

					

			
		

General Information
CircRNA Name	Zm00001d013274_circ_g.3
ID in PlantcircBase	zma_circ_001883
Alias	circ868
Organism	Zea mays
Position	chr5: 7555405-7555767 JBrowse»
Reference genome	AGPv4.38
Type	ui-circRNA
Identification method	CIRI
Parent gene	Zm00001d013274
Parent gene annotation	Probable helicase MAGATAMA 3
Parent gene strand	-
Alternative splicing	Zm00001d013274_circ_ag.1 Zm00001d013274_circ_g.1 Zm00001d013274_circ_ag.2
Support reads	4
Tissues	seedling leaves
Exon boundary	No-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	CT-AA 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	Zm00001d013274_T016:2 Zm00001d013274_T063:2 Zm00001d013274_T024:2 Zm00001d013274_T043:2 Zm00001d013274_T032:2 Zm00001d013274_T034:2 Zm00001d013274_T073:2 Zm00001d013274_T022:2 Zm00001d013274_T060:2 Zm00001d013274_T048:2 Zm00001d013274_T065:2 Zm00001d013274_T078:2 Zm00001d013274_T041:2 Zm00001d013274_T039:2 Zm00001d013274_T011:2 Zm00001d013274_T066:2 Zm00001d013274_T044:2 Zm00001d013274_T072:2 Zm00001d013274_T037:2 Zm00001d013274_T021:2 Zm00001d013274_T001:2 Zm00001d013274_T070:2 Zm00001d013274_T007:2 Zm00001d013274_T075:2 Zm00001d013274_T040:2 Zm00001d013274_T020:2 Zm00001d013274_T042:2 Zm00001d013274_T080:2 Zm00001d013274_T057:2 Zm00001d013274_T006:2 Zm00001d013274_T061:2 Zm00001d013274_T049:2 Zm00001d013274_T081:2 Zm00001d013274_T068:2 Zm00001d013274_T064:2 Zm00001d013274_T026:2 Zm00001d013274_T079:2 Zm00001d013274_T059:2 Zm00001d013274_T028:2 Zm00001d013274_T053:2 Zm00001d013274_T003:2 Zm00001d013274_T036:2 Zm00001d013274_T013:2 Zm00001d013274_T050:2 Zm00001d013274_T074:2 Zm00001d013274_T052:2 Zm00001d013274_T012:2 Zm00001d013274_T038:2 Zm00001d013274_T004:2 Zm00001d013274_T035:2 Zm00001d013274_T025:2 Zm00001d013274_T009:2 Zm00001d013274_T076:2 Zm00001d013274_T023:2 Zm00001d013274_T033:2

			
						 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  
						
							ACAATCTTCTGAAACCGGTCCATGGTGGAGGTGGTGGAGGGAGTTGATGTGCCGCTGCTGGACT
TCTCCACCGCCATTGGAAGGGTGGCCACTTGTGTGCccttcctcgtcgttactgcgtccctgga
tgatctgtgccttgacctcctcaaagagcagtggctcaaagacaccaaggtactcagccaccga
gacgtatg

						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
						
							CCTTCCTCGTCGTTACTGCGTCCCTGGATGATCTGTGCCTTGACCTCCTCAAAGAGCAGTGGCT
CAAAGACACCAAGGTACTCAGCCACCGAGACGTATGTGTTCTTCACATGCTGCAGCACCTTGGC
CTGCTTGCCGCCCTGACCCCCATGACCAGAAAAGGTTAGGGATTTAGAAGGTATGTCAGACGGG
TGGCGGGTGTGGTGAGTTGATGTGCATGTACCTTGGATTCAGCGATGAGACGGAGGTAATCCCA
GCTTAGGACAATCTTCTGAAACCGGTCCATGGTGGAGGTGGTGGAGGGAGTTGATGTGCCGCTG
CTGGACTTCTCCACCGCCATTGGAAGGGTGGCCACTTGTGTGC

Sequences
Splice junction sequence	ACAATCTTCTGAAACCGGTCCATGGTGGAGGTGGTGGAGGGAGTTGATGTGCCGCTGCTGGACT TCTCCACCGCCATTGGAAGGGTGGCCACTTGTGTGCccttcctcgtcgttactgcgtccctgga tgatctgtgccttgacctcctcaaagagcagtggctcaaagacaccaaggtactcagccaccga gacgtatg
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	CCTTCCTCGTCGTTACTGCGTCCCTGGATGATCTGTGCCTTGACCTCCTCAAAGAGCAGTGGCT CAAAGACACCAAGGTACTCAGCCACCGAGACGTATGTGTTCTTCACATGCTGCAGCACCTTGGC CTGCTTGCCGCCCTGACCCCCATGACCAGAAAAGGTTAGGGATTTAGAAGGTATGTCAGACGGG TGGCGGGTGTGGTGAGTTGATGTGCATGTACCTTGGATTCAGCGATGAGACGGAGGTAATCCCA GCTTAGGACAATCTTCTGAAACCGGTCCATGGTGGAGGTGGTGGAGGGAGTTGATGTGCCGCTG CTGGACTTCTCCACCGCCATTGGAAGGGTGGCCACTTGTGTGC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.552183219

Conservation Information
Conserved circRNAs	NA
PMCS	0.552183219

			
						 Functional Information
					
						Coding potential
						N
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	N
Potential coding position	NA
Potential amino acid sequence	NA
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chen et al., 2017b

circRNA

Detail information of Zm00001d013274_circ_g.3

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