Plant Circular RNA Database

Detail information of Zm00001d001978_circ_g.3

			
				
						 General Information
					

				
						CircRNA Name
						Zm00001d001978_circ_g.3
					

						ID in PlantcircBase
						zma_circ_007020
					

						Alias
						zma_circ_0001040, GRMZM2G017654_C2
					

						Organism
						
							Zea mays						
					

						Position
						
							chr2: 3814970-3815553  JBrowse»						
					

						Reference genome
						
							AGPv4.38						
					

						Type  
						
							u-circRNA							
									
								

					

						Identification method
						find_circ, CIRI2
					

						Parent gene
						
							Zm00001d001978						
					

						Parent gene annotation
						
							MAP3K epsilon protein kinase 1
							
					

						Parent gene strand
						+
					

						Alternative splicing
						
							Zm00001d001978_circ_g.2 						
					

						Support reads
						NA
					

						Tissues
						leaf, root
					

						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-AG							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
						Zm00001d001978_T022:2
Zm00001d001978_T007:2
Zm00001d001978_T103:2
Zm00001d001978_T030:2
Zm00001d001978_T014:2
Zm00001d001978_T107:2
Zm00001d001978_T005:2
Zm00001d001978_T130:2
Zm00001d001978_T096:2
Zm00001d001978_T031:2
Zm00001d001978_T111:2
Zm00001d001978_T008:2
Zm00001d001978_T009:2
Zm00001d001978_T089:2
Zm00001d001978_T117:2
Zm00001d001978_T037:2
Zm00001d001978_T012:2
Zm00001d001978_T122:2
Zm00001d001978_T074:2
Zm00001d001978_T033:2
Zm00001d001978_T039:2
Zm00001d001978_T002:2
Zm00001d001978_T018:2
Zm00001d001978_T084:2
Zm00001d001978_T020:2
Zm00001d001978_T011:2
Zm00001d001978_T026:2
Zm00001d001978_T077:2
Zm00001d001978_T088:2
Zm00001d001978_T042:2
Zm00001d001978_T101:2
Zm00001d001978_T016:2
Zm00001d001978_T080:2
Zm00001d001978_T118:2
Zm00001d001978_T120:2
Zm00001d001978_T079:2
Zm00001d001978_T104:2
Zm00001d001978_T133:2
Zm00001d001978_T017:2
Zm00001d001978_T060:2
Zm00001d001978_T114:2
Zm00001d001978_T058:2
Zm00001d001978_T015:2
Zm00001d001978_T019:2
Zm00001d001978_T087:2
Zm00001d001978_T081:2
Zm00001d001978_T075:2
Zm00001d001978_T013:2
Zm00001d001978_T109:2
Zm00001d001978_T121:2
Zm00001d001978_T125:2
Zm00001d001978_T073:2
Zm00001d001978_T115:2
Zm00001d001978_T131:2
Zm00001d001978_T071:2
Zm00001d001978_T006:2
Zm00001d001978_T124:2
Zm00001d001978_T028:2
Zm00001d001978_T091:2
Zm00001d001978_T055:2
Zm00001d001978_T049:2
Zm00001d001978_T076:2
Zm00001d001978_T010:2
Zm00001d001978_T090:2

					

			
		

General Information
CircRNA Name	Zm00001d001978_circ_g.3
ID in PlantcircBase	zma_circ_007020
Alias	zma_circ_0001040, GRMZM2G017654_C2
Organism	Zea mays
Position	chr2: 3814970-3815553 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	find_circ, CIRI2
Parent gene	Zm00001d001978
Parent gene annotation	MAP3K epsilon protein kinase 1
Parent gene strand	+
Alternative splicing	Zm00001d001978_circ_g.2
Support reads	NA
Tissues	leaf, root
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-AG 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	Zm00001d001978_T022:2 Zm00001d001978_T007:2 Zm00001d001978_T103:2 Zm00001d001978_T030:2 Zm00001d001978_T014:2 Zm00001d001978_T107:2 Zm00001d001978_T005:2 Zm00001d001978_T130:2 Zm00001d001978_T096:2 Zm00001d001978_T031:2 Zm00001d001978_T111:2 Zm00001d001978_T008:2 Zm00001d001978_T009:2 Zm00001d001978_T089:2 Zm00001d001978_T117:2 Zm00001d001978_T037:2 Zm00001d001978_T012:2 Zm00001d001978_T122:2 Zm00001d001978_T074:2 Zm00001d001978_T033:2 Zm00001d001978_T039:2 Zm00001d001978_T002:2 Zm00001d001978_T018:2 Zm00001d001978_T084:2 Zm00001d001978_T020:2 Zm00001d001978_T011:2 Zm00001d001978_T026:2 Zm00001d001978_T077:2 Zm00001d001978_T088:2 Zm00001d001978_T042:2 Zm00001d001978_T101:2 Zm00001d001978_T016:2 Zm00001d001978_T080:2 Zm00001d001978_T118:2 Zm00001d001978_T120:2 Zm00001d001978_T079:2 Zm00001d001978_T104:2 Zm00001d001978_T133:2 Zm00001d001978_T017:2 Zm00001d001978_T060:2 Zm00001d001978_T114:2 Zm00001d001978_T058:2 Zm00001d001978_T015:2 Zm00001d001978_T019:2 Zm00001d001978_T087:2 Zm00001d001978_T081:2 Zm00001d001978_T075:2 Zm00001d001978_T013:2 Zm00001d001978_T109:2 Zm00001d001978_T121:2 Zm00001d001978_T125:2 Zm00001d001978_T073:2 Zm00001d001978_T115:2 Zm00001d001978_T131:2 Zm00001d001978_T071:2 Zm00001d001978_T006:2 Zm00001d001978_T124:2 Zm00001d001978_T028:2 Zm00001d001978_T091:2 Zm00001d001978_T055:2 Zm00001d001978_T049:2 Zm00001d001978_T076:2 Zm00001d001978_T010:2 Zm00001d001978_T090:2

			
						 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  
						
							GCCAAGTAAGATAGAGCTGGAGAATAAAGAAAGTTCAACTGTTGAGGATGGTGATGTATTCTCA
TTTCAGGCTGGAAGACAGAATATTGACTTCCAAATGgaatatcgacggggatgatgaaagctca
agaggggacaataactcgggtttttgcgacacaccaggagatacccgagcaactattgcttcta
atgttgac

						Assembled circRNA sequence  
						
							Yes
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
						
							Transcript length: 448
Transcript exons: 3814970-3815072,3815209-3815553
GAATATCGACGGGGATGATGAAAGCTCAAGAGGGGACAATAACTCGGGTTTTTGCGACACACCA
GGAGATACCCGAGCAACTATTGCTTCTAATGTTGACCAGGTGAATGGGAGGAACGGACCAAATA
TGGACTCTGCTGCGCAAAGTAAATCTGAAGAGCTTCATGATGGAAATTTAGAACTTACAGAGGG
CATTAGTTCGAACAATGTGGCGCTTGTGAAAGATAATGTGGTCCTTAATAAAGATCCGACACTA
GTTTTACATGAGAAGTTACCGGTGGAATCTTCATTTGGAGATGCTGATTTGAATGGCAAAGTAA
TGGCACATGAACTATTGCAAGGTGGTCTGCCAAGTAAGATAGAGCTGGAGAATAAAGAAAGTTC
AACTGTTGAGGATGGTGATGTATTCTCATTTCAGGCTGGAAGACAGAATATTGACTTCCAAATG
						
						Genomic sequence
						
							GAATATCGACGGGGATGATGAAAGCTCAAGAGGGGACAATAACTCGGGTTTTTGCGACACACCA
GGAGATACCCGAGCAACTATTGCTTCTAATGTTGACCAGGTAACACTGTCAGGGTTTTTTACAC
ATCATGTTTAGCTCAGGGATTGATCCTCCCAAATCTTCTGCAGTGCACCCACTATGTTCTTAGC
CTCTGAGGCTTGCAAATTATAAATCATTTTTATTTATGCTGCTCTAGGTGAATGGGAGGAACGG
ACCAAATATGGACTCTGCTGCGCAAAGTAAATCTGAAGAGCTTCATGATGGAAATTTAGAACTT
ACAGAGGGCATTAGTTCGAACAATGTGGCGCTTGTGAAAGATAATGTGGTCCTTAATAAAGATC
CGACACTAGTTTTACATGAGAAGTTACCGGTGGAATCTTCATTTGGAGATGCTGATTTGAATGG
CAAAGTAATGGCACATGAACTATTGCAAGGTGGTCTGCCAAGTAAGATAGAGCTGGAGAATAAA
GAAAGTTCAACTGTTGAGGATGGTGATGTATTCTCATTTCAGGCTGGAAGACAGAATATTGACT
TCCAAATG

Sequences
Splice junction sequence	GCCAAGTAAGATAGAGCTGGAGAATAAAGAAAGTTCAACTGTTGAGGATGGTGATGTATTCTCA TTTCAGGCTGGAAGACAGAATATTGACTTCCAAATGgaatatcgacggggatgatgaaagctca agaggggacaataactcgggtttttgcgacacaccaggagatacccgagcaactattgcttcta atgttgac
Assembled circRNA sequence	Yes 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	Transcript length: 448 Transcript exons: 3814970-3815072,3815209-3815553 GAATATCGACGGGGATGATGAAAGCTCAAGAGGGGACAATAACTCGGGTTTTTGCGACACACCA GGAGATACCCGAGCAACTATTGCTTCTAATGTTGACCAGGTGAATGGGAGGAACGGACCAAATA TGGACTCTGCTGCGCAAAGTAAATCTGAAGAGCTTCATGATGGAAATTTAGAACTTACAGAGGG CATTAGTTCGAACAATGTGGCGCTTGTGAAAGATAATGTGGTCCTTAATAAAGATCCGACACTA GTTTTACATGAGAAGTTACCGGTGGAATCTTCATTTGGAGATGCTGATTTGAATGGCAAAGTAA TGGCACATGAACTATTGCAAGGTGGTCTGCCAAGTAAGATAGAGCTGGAGAATAAAGAAAGTTC AACTGTTGAGGATGGTGATGTATTCTCATTTCAGGCTGGAAGACAGAATATTGACTTCCAAATG
Genomic sequence	GAATATCGACGGGGATGATGAAAGCTCAAGAGGGGACAATAACTCGGGTTTTTGCGACACACCA GGAGATACCCGAGCAACTATTGCTTCTAATGTTGACCAGGTAACACTGTCAGGGTTTTTTACAC ATCATGTTTAGCTCAGGGATTGATCCTCCCAAATCTTCTGCAGTGCACCCACTATGTTCTTAGC CTCTGAGGCTTGCAAATTATAAATCATTTTTATTTATGCTGCTCTAGGTGAATGGGAGGAACGG ACCAAATATGGACTCTGCTGCGCAAAGTAAATCTGAAGAGCTTCATGATGGAAATTTAGAACTT ACAGAGGGCATTAGTTCGAACAATGTGGCGCTTGTGAAAGATAATGTGGTCCTTAATAAAGATC CGACACTAGTTTTACATGAGAAGTTACCGGTGGAATCTTCATTTGGAGATGCTGATTTGAATGG CAAAGTAATGGCACATGAACTATTGCAAGGTGGTCTGCCAAGTAAGATAGAGCTGGAGAATAAA GAAAGTTCAACTGTTGAGGATGGTGATGTATTCTCATTTCAGGCTGGAAGACAGAATATTGACT TCCAAATG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.132150161

Conservation Information
Conserved circRNAs	NA
PMCS	0.132150161

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							3815234-3814984(+)
3815502-3814984(+)
						
						Potential amino acid sequence
						
							MDSAAQSKSEELHDGNLELTEGISSNNVALVKDNVVLNKDPTLVLHEKLPVESSFGDADLNGKV
MAHELLQGGLPSKIELENKESSTVEDGDVFSFQAGRQNIDFQMEYRRG*(+)
MVMYSHFRLEDRILTSKWNIDGDDESSRGDNNSGFCDTPGDTRATIASNVDQVNGRNGPNMDSA
AQSKSEELHDGNLELTEGISSNNVALVKDNVVLNKDPTLVLHEKLPVESSFGDADLNGKVMAHE
LLQGGLPSKIELENKESSTVEDGDVFSFQAGRQNIDFQMEYRRG*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to drought stress

Functional Information
Coding potential	Y
Potential coding position	3815234-3814984(+) 3815502-3814984(+)
Potential amino acid sequence	MDSAAQSKSEELHDGNLELTEGISSNNVALVKDNVVLNKDPTLVLHEKLPVESSFGDADLNGKV MAHELLQGGLPSKIELENKESSTVEDGDVFSFQAGRQNIDFQMEYRRG(+) MVMYSHFRLEDRILTSKWNIDGDDESSRGDNNSGFCDTPGDTRATIASNVDQVNGRNGPNMDSA AQSKSEELHDGNLELTEGISSNNVALVKDNVVLNKDPTLVLHEKLPVESSFGDADLNGKVMAHE LLQGGLPSKIELENKESSTVEDGDVFSFQAGRQNIDFQMEYRRG(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	responsive to drought stress

			
						 Other Information
					
						References
						Ma et al., 2021b;Zhang et al., 2019

circRNA

Detail information of Zm00001d001978_circ_g.3

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