Plant Circular RNA Database

Detail information of Zm00001d034018_circ_g.2

			
						 General Information
					
						CircRNA Name
						Zm00001d034018_circ_g.2
					
						ID in PlantcircBase
						zma_circ_006930
					
						Alias
						zma_circ_0000550
					
						Organism
						
							Zea mays						
					
						Position
						
							chr1: 281260284-281267167  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Zm00001d034018						
					
						Parent gene annotation
						
							Tousled-like kinase 1  
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d034018_circ_g.1 Zm00001d034018_circ_g.3 Zm00001d034018_circ_g.4 Zm00001d034018_circ_g.5 						
					
						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  
						
							CT-AC							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
						Zm00001d034018_T010:8
Zm00001d034018_T025:8
Zm00001d034018_T007:9
Zm00001d034018_T044:8
Zm00001d034018_T019:8
Zm00001d034018_T009:9
Zm00001d034018_T018:3
Zm00001d034018_T016:9
Zm00001d034018_T033:9
Zm00001d034018_T008:9
Zm00001d034018_T012:7
Zm00001d034018_T027:6
Zm00001d034018_T028:9
Zm00001d034018_T032:6
Zm00001d034018_T026:9
Zm00001d034018_T022:9
Zm00001d034018_T003:9
Zm00001d034018_T023:8
Zm00001d034018_T002:9
Zm00001d034018_T005:10
Zm00001d034018_T046:9
Zm00001d034018_T006:9
Zm00001d034018_T030:8
Zm00001d034018_T024:8
Zm00001d034018_T036:8
Zm00001d034018_T045:8
Zm00001d034018_T004:10
Zm00001d034018_T043:9
Zm00001d034018_T041:10
Zm00001d034018_T014:7
Zm00001d034018_T015:9
Zm00001d034018_T034:9
Zm00001d034018_T035:9
Zm00001d034018_T029:7
Zm00001d034018_T042:8
Zm00001d034018_T001:9
Zm00001d034018_T013:9
Zm00001d034018_T031:8
Zm00001d034018_T017:7
Zm00001d034018_T039:8
Zm00001d034018_T038:7
Zm00001d034018_T021:8
Zm00001d034018_T020:7
Zm00001d034018_T037:8
Zm00001d034018_T040:10

General Information
CircRNA Name	Zm00001d034018_circ_g.2
ID in PlantcircBase	zma_circ_006930
Alias	zma_circ_0000550
Organism	Zea mays
Position	chr1: 281260284-281267167 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	find_circ
Parent gene	Zm00001d034018
Parent gene annotation	Tousled-like kinase 1
Parent gene strand	-
Alternative splicing	Zm00001d034018_circ_g.1 Zm00001d034018_circ_g.3 Zm00001d034018_circ_g.4 Zm00001d034018_circ_g.5
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	CT-AC 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	Zm00001d034018_T010:8 Zm00001d034018_T025:8 Zm00001d034018_T007:9 Zm00001d034018_T044:8 Zm00001d034018_T019:8 Zm00001d034018_T009:9 Zm00001d034018_T018:3 Zm00001d034018_T016:9 Zm00001d034018_T033:9 Zm00001d034018_T008:9 Zm00001d034018_T012:7 Zm00001d034018_T027:6 Zm00001d034018_T028:9 Zm00001d034018_T032:6 Zm00001d034018_T026:9 Zm00001d034018_T022:9 Zm00001d034018_T003:9 Zm00001d034018_T023:8 Zm00001d034018_T002:9 Zm00001d034018_T005:10 Zm00001d034018_T046:9 Zm00001d034018_T006:9 Zm00001d034018_T030:8 Zm00001d034018_T024:8 Zm00001d034018_T036:8 Zm00001d034018_T045:8 Zm00001d034018_T004:10 Zm00001d034018_T043:9 Zm00001d034018_T041:10 Zm00001d034018_T014:7 Zm00001d034018_T015:9 Zm00001d034018_T034:9 Zm00001d034018_T035:9 Zm00001d034018_T029:7 Zm00001d034018_T042:8 Zm00001d034018_T001:9 Zm00001d034018_T013:9 Zm00001d034018_T031:8 Zm00001d034018_T017:7 Zm00001d034018_T039:8 Zm00001d034018_T038:7 Zm00001d034018_T021:8 Zm00001d034018_T020:7 Zm00001d034018_T037:8 Zm00001d034018_T040:10

			
						 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  
						
							ACCTATCACTAAGTTCATGGTAATTTGTTGCTTCTTGATGCGATTTAGAAAGGTCTTCCTCCAA
AAATGCAACTTTGCCACGTAATGTTGACAATTCGTCcaataggttccagctccctgagaagtga
gctccatcccctgagacccaacatcattctccactatcttgctgaggccaaagtcggtaacttt
tgcaacac

									
								

					

						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: 1154
Transcript exons: 281260284-281260548,281261331-281261541,281262073-281262
252,281262328-281262425,281262786-281262852,281264443-28
1264509,281264759-281264871,281266932-281266976,28126706
0-281267167
CAATAGGTTCCAGCTCCCTGAGAAGTGAGCTCCATCCCCTGAGACCCAACATCATTCTCCACTA
TCTTGCTGAGGCCAAAGTCGGTAACTTTTGCAACACCAACCTCATCAAAGAGAACATTGCCCGG
CTTTAGATCATAGTGAATGATCTTTTGGCCCCTCTTGTTTAGATAAACCAGGCCCTGAAATATT
TGAACAATTATGATCCTTCCTTCTTTTTCTGGAAGAATTGGTGTAGCTTTAAGGACTGCATCAA
GATCCTTGCCACTGCAATATTCTAGGACAGTGCAGAATGTATTGTGATCAATCTCAAATATATC
CCATAGCCTGACAATGTTTGGATGAACCAAAGTTTTGTGAATGTTATATTCACGAATCGCATGC
CGTATGTAGCTCTGTTTTTTCTCCTCACTCCATTGAGCATTCAATCCATGAAGCTTGCATGCCA
CATATTTGTACTCCACCAAATCAAAAGCCCTGTAAACCTCACTAAACCCTCCCTTTCCAAGAAG
ATTTAAGAGAGCATAACGATGGTGAAGAATTTGGAAGTTGTTAAAGCGTGAGCCATCTTCATCT
CTGAGACGCTTCATCTCTCGTATAAGCCTCCCCTTTTCCAACTCATACCGATCTCTCTCTCTCA
TATACTGTTCTTCCTCCCGTTTTATACTCATTAACCGAGATTTACATATTTCATCTTGTAAGAG
GATGTCCTCCTCAGACATGCCAGTCTCAGCATCACTGCCATCACCCTTGTCAGATTGTCTTTTC
TTAAGTGATTTACGATGCCTTTCAATAGTCTCCTTAGTTTCCAGCAAAGATTTCAGGTGAGCAT
TAAGATCTTTTATTGCCTGACCGTCTTCCCAAGTTTCAGATATGATAGTCCCAGCTCTCATAAC
AGCAACATTTCCAAGTCTGAAAGATTCCTGCCTTATTCTCATTCTCGCTTCTTGCCTCTCTGCT
TTTGACACAGCTATCAGCAGATCGGACAGGATTTTCATTTGCTTTAATCTCATTTGTTGGTCAT
GATCTTTGAGATCCTTCAATTCCTTTGCTAACCTATCACTAAGTTCATGGTAATTTGTTGCTTC
TTGATGCGATTTAGAAAGGTCTTCCTCCAAAAATGCAACTTTGCCACGTAATGTTGACAATTCG
TC
						
					

						Genomic sequence
						
							TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.						
					

			
		

Sequences
Splice junction sequence	ACCTATCACTAAGTTCATGGTAATTTGTTGCTTCTTGATGCGATTTAGAAAGGTCTTCCTCCAA AAATGCAACTTTGCCACGTAATGTTGACAATTCGTCcaataggttccagctccctgagaagtga gctccatcccctgagacccaacatcattctccactatcttgctgaggccaaagtcggtaacttt tgcaacac
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: 1154 Transcript exons: 281260284-281260548,281261331-281261541,281262073-281262 252,281262328-281262425,281262786-281262852,281264443-28 1264509,281264759-281264871,281266932-281266976,28126706 0-281267167 CAATAGGTTCCAGCTCCCTGAGAAGTGAGCTCCATCCCCTGAGACCCAACATCATTCTCCACTA TCTTGCTGAGGCCAAAGTCGGTAACTTTTGCAACACCAACCTCATCAAAGAGAACATTGCCCGG CTTTAGATCATAGTGAATGATCTTTTGGCCCCTCTTGTTTAGATAAACCAGGCCCTGAAATATT TGAACAATTATGATCCTTCCTTCTTTTTCTGGAAGAATTGGTGTAGCTTTAAGGACTGCATCAA GATCCTTGCCACTGCAATATTCTAGGACAGTGCAGAATGTATTGTGATCAATCTCAAATATATC CCATAGCCTGACAATGTTTGGATGAACCAAAGTTTTGTGAATGTTATATTCACGAATCGCATGC CGTATGTAGCTCTGTTTTTTCTCCTCACTCCATTGAGCATTCAATCCATGAAGCTTGCATGCCA CATATTTGTACTCCACCAAATCAAAAGCCCTGTAAACCTCACTAAACCCTCCCTTTCCAAGAAG ATTTAAGAGAGCATAACGATGGTGAAGAATTTGGAAGTTGTTAAAGCGTGAGCCATCTTCATCT CTGAGACGCTTCATCTCTCGTATAAGCCTCCCCTTTTCCAACTCATACCGATCTCTCTCTCTCA TATACTGTTCTTCCTCCCGTTTTATACTCATTAACCGAGATTTACATATTTCATCTTGTAAGAG GATGTCCTCCTCAGACATGCCAGTCTCAGCATCACTGCCATCACCCTTGTCAGATTGTCTTTTC TTAAGTGATTTACGATGCCTTTCAATAGTCTCCTTAGTTTCCAGCAAAGATTTCAGGTGAGCAT TAAGATCTTTTATTGCCTGACCGTCTTCCCAAGTTTCAGATATGATAGTCCCAGCTCTCATAAC AGCAACATTTCCAAGTCTGAAAGATTCCTGCCTTATTCTCATTCTCGCTTCTTGCCTCTCTGCT TTTGACACAGCTATCAGCAGATCGGACAGGATTTTCATTTGCTTTAATCTCATTTGTTGGTCAT GATCTTTGAGATCCTTCAATTCCTTTGCTAACCTATCACTAAGTTCATGGTAATTTGTTGCTTC TTGATGCGATTTAGAAAGGTCTTCCTCCAAAAATGCAACTTTGCCACGTAATGTTGACAATTCG TC
Genomic sequence	TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.054152122

Conservation Information
Conserved circRNAs	NA
PMCS	0.054152122

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							281267135-281260414(+)
281266945-281267067(-)
281260340-281267114(-)
						
						Potential amino acid sequence
						
							MQLCHVMLTIRPIGSSSLRSELHPLRPNIILHYLAEAKVGNFCNTNLIKENIARL*(+)
MRLKQMKILSDLLIAVSKAERQEARMRIRQESFRLGNVAVMRAGTIISETWEDGQAIKDLNAHL
KSLLETKETIERHRKSLKKRQSDKGDGSDAETGMSEEDILLQDEICKSRLMSIKREEEQYMRER
DRYELEKGRLIREMKRLRDEDGSRFNNFQILHHRYALLNLLGKGGFSEVYRAFDLVEYKYVACK
LHGLNAQWSEEKKQSYIRHAIREYNIHKTLVHPNIVRLWDIFEIDHNTFCTVLEYCSGKDLDAV
LKATPILPEKEGRIIIVQIFQGLVYLNKRGQKIIHYDLKPGNVLFDEVGVAKVTDFGLSKIVEN
DVGSQGMELTSQGAGTYWTNCQHYVAKLHFWRKTFLNRIKKQQITMNLVIG*(-)
MMLGLRGWSSLLRELEPIGRIVNITWQSCIFGGRPF*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	281267135-281260414(+) 281266945-281267067(-) 281260340-281267114(-)
Potential amino acid sequence	MQLCHVMLTIRPIGSSSLRSELHPLRPNIILHYLAEAKVGNFCNTNLIKENIARL(+) MRLKQMKILSDLLIAVSKAERQEARMRIRQESFRLGNVAVMRAGTIISETWEDGQAIKDLNAHL KSLLETKETIERHRKSLKKRQSDKGDGSDAETGMSEEDILLQDEICKSRLMSIKREEEQYMRER DRYELEKGRLIREMKRLRDEDGSRFNNFQILHHRYALLNLLGKGGFSEVYRAFDLVEYKYVACK LHGLNAQWSEEKKQSYIRHAIREYNIHKTLVHPNIVRLWDIFEIDHNTFCTVLEYCSGKDLDAV LKATPILPEKEGRIIIVQIFQGLVYLNKRGQKIIHYDLKPGNVLFDEVGVAKVTDFGLSKIVEN DVGSQGMELTSQGAGTYWTNCQHYVAKLHFWRKTFLNRIKKQQITMNLVIG(-) MMLGLRGWSSLLRELEPIGRIVNITWQSCIFGGRPF*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b

circRNA

Detail information of Zm00001d034018_circ_g.2

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