Plant Circular RNA Database

Detail information of Zm00001d020036_circ_g.4

			
						 General Information
					
						CircRNA Name
						Zm00001d020036_circ_g.4
					
						ID in PlantcircBase
						zma_circ_009309
					
						Alias
						zma_circ_0002768
					
						Organism
						
							Zea mays						
					
						Position
						
							chr7: 87390220-87391162  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Zm00001d020036						
					
						Parent gene annotation
						
							Embryonic flower 2; VEF family protein  
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d020036_circ_g.1 Zm00001d020036_circ_g.2 Zm00001d020036_circ_g.3 						
					
						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
						Zm00001d020036_T003:4
Zm00001d020036_T012:3
Zm00001d020036_T002:4
Zm00001d020036_T011:2
Zm00001d020036_T009:3
Zm00001d020036_T007:3
Zm00001d020036_T001:3
Zm00001d020036_T004:3
Zm00001d020036_T013:3
Zm00001d020036_T008:3
Zm00001d020036_T005:3
Zm00001d020036_T006:3

General Information
CircRNA Name	Zm00001d020036_circ_g.4
ID in PlantcircBase	zma_circ_009309
Alias	zma_circ_0002768
Organism	Zea mays
Position	chr7: 87390220-87391162 JBrowse»
Reference genome	AGPv4.38
Type	ue-circRNA
Identification method	find_circ
Parent gene	Zm00001d020036
Parent gene annotation	Embryonic flower 2; VEF family protein
Parent gene strand	+
Alternative splicing	Zm00001d020036_circ_g.1 Zm00001d020036_circ_g.2 Zm00001d020036_circ_g.3
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	Zm00001d020036_T003:4 Zm00001d020036_T012:3 Zm00001d020036_T002:4 Zm00001d020036_T011:2 Zm00001d020036_T009:3 Zm00001d020036_T007:3 Zm00001d020036_T001:3 Zm00001d020036_T004:3 Zm00001d020036_T013:3 Zm00001d020036_T008:3 Zm00001d020036_T005:3 Zm00001d020036_T006:3

			
						 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  
						
							TGTCCGCACAAGAGGCTGGTGCAAGAGATATGTCTTTGTCTCCATATAGTAGTTACTCATATAA
TGATGTCCCACCTTCGTCATTATCAGATATCATAAGtgcttgaagggaaatgctcctggggtaa
aataccaactaatttacttgcttcatctttggagagttgtgtcaatttaagtttgggacatatt
gtggagtt

						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: 322
Transcript exons: 87390220-87390356,87390469-87390528,87391038-87391162
TGCTTGAAGGGAAATGCTCCTGGGGTAAAATACCAACTAATTTACTTGCTTCATCTTTGGAGAG
TTGTGTCAATTTAAGTTTGGGACATATTGTGGAGTTGGCATCTAAAGTTACAATGAGACCAAGC
TTCTTAGAGCCAAAATTTCTGGAGCAAGACAGTTGCTTGACATTTTGCTCTCATAAGGTTGATG
CTGTGGGTTCATATAAACTACAACTATGCATGTCCGCACAAGAGGCTGGTGCAAGAGATATGTC
TTTGTCTCCATATAGTAGTTACTCATATAATGATGTCCCACCTTCGTCATTATCAGATATCATA
AG
						
						Genomic sequence
						
							TGCTTGAAGGGAAATGCTCCTGGGGTAAAATACCAACTAATTTACTTGCTTCATCTTTGGAGAG
TTGTGTCAATTTAAGTTTGGGACATATTGTGGAGTTGGCATCTAAAGTTACAATGAGACCAAGC
TTCTTAGAGGTATGTCAAATTGATCCCTGCCCCTGTAGTATTTAAGATTCACATCACTAAAACA
TCGATTGTAATGTTCAACTTGCTTGGGATCAAAGGCTCTGTTGTTTTATACATGCAGCCAAAAT
TTCTGGAGCAAGACAGTTGCTTGACATTTTGCTCTCATAAGGTTGATGCTGTGGTAAGGTCTCC
TCTATTTTTACATTCATGTTTAATATGATTTTGTCCAGGGATCTCCATGTTTCTCTTATTACTA
ATGCTACTAATACATTCTTTGAGTCCAAGATTAGTGTGGTTAACAGGTATGCATCACTTGCAAC
TGCCAGTCCATTGGATGACATGTCACTGCATCACAAGTTTATAAATTCAGCTTTGGGCATACAT
TGCCACCGAATGCGCTATATCCACTTTTCCATGGAATTGCTGGAAAATGACTTTAGCTTTCAAT
TTAAATGCCCCAAACTTTTGGCAAAAGTATTTCAATTTTTATGAGGGGTAATAAACTTGTGAAG
GGGGGAATCTACAAGCTTTTAGTTGTTGCTATTCTGCAGTATAAGAGCATCAGATCTATCGGGT
CCCACTTTGGAAACCTGTGTTGAGCACTTGAGTTGCTTCTTTCTTTTTGTGGTGCTGGTGGTTG
GAGGGGGAAGAGGGGTTGGCAGTCAAAATCATTAACCTTTATTCTTGCAGGGTTCATATAAACT
ACAACTATGCATGTCCGCACAAGAGGCTGGTGCAAGAGATATGTCTTTGTCTCCATATAGTAGT
TACTCATATAATGATGTCCCACCTTCGTCATTATCAGATATCATAAG

Sequences
Splice junction sequence	TGTCCGCACAAGAGGCTGGTGCAAGAGATATGTCTTTGTCTCCATATAGTAGTTACTCATATAA TGATGTCCCACCTTCGTCATTATCAGATATCATAAGtgcttgaagggaaatgctcctggggtaa aataccaactaatttacttgcttcatctttggagagttgtgtcaatttaagtttgggacatatt gtggagtt
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: 322 Transcript exons: 87390220-87390356,87390469-87390528,87391038-87391162 TGCTTGAAGGGAAATGCTCCTGGGGTAAAATACCAACTAATTTACTTGCTTCATCTTTGGAGAG TTGTGTCAATTTAAGTTTGGGACATATTGTGGAGTTGGCATCTAAAGTTACAATGAGACCAAGC TTCTTAGAGCCAAAATTTCTGGAGCAAGACAGTTGCTTGACATTTTGCTCTCATAAGGTTGATG CTGTGGGTTCATATAAACTACAACTATGCATGTCCGCACAAGAGGCTGGTGCAAGAGATATGTC TTTGTCTCCATATAGTAGTTACTCATATAATGATGTCCCACCTTCGTCATTATCAGATATCATA AG
Genomic sequence	TGCTTGAAGGGAAATGCTCCTGGGGTAAAATACCAACTAATTTACTTGCTTCATCTTTGGAGAG TTGTGTCAATTTAAGTTTGGGACATATTGTGGAGTTGGCATCTAAAGTTACAATGAGACCAAGC TTCTTAGAGGTATGTCAAATTGATCCCTGCCCCTGTAGTATTTAAGATTCACATCACTAAAACA TCGATTGTAATGTTCAACTTGCTTGGGATCAAAGGCTCTGTTGTTTTATACATGCAGCCAAAAT TTCTGGAGCAAGACAGTTGCTTGACATTTTGCTCTCATAAGGTTGATGCTGTGGTAAGGTCTCC TCTATTTTTACATTCATGTTTAATATGATTTTGTCCAGGGATCTCCATGTTTCTCTTATTACTA ATGCTACTAATACATTCTTTGAGTCCAAGATTAGTGTGGTTAACAGGTATGCATCACTTGCAAC TGCCAGTCCATTGGATGACATGTCACTGCATCACAAGTTTATAAATTCAGCTTTGGGCATACAT TGCCACCGAATGCGCTATATCCACTTTTCCATGGAATTGCTGGAAAATGACTTTAGCTTTCAAT TTAAATGCCCCAAACTTTTGGCAAAAGTATTTCAATTTTTATGAGGGGTAATAAACTTGTGAAG GGGGGAATCTACAAGCTTTTAGTTGTTGCTATTCTGCAGTATAAGAGCATCAGATCTATCGGGT CCCACTTTGGAAACCTGTGTTGAGCACTTGAGTTGCTTCTTTCTTTTTGTGGTGCTGGTGGTTG GAGGGGGAAGAGGGGTTGGCAGTCAAAATCATTAACCTTTATTCTTGCAGGGTTCATATAAACT ACAACTATGCATGTCCGCACAAGAGGCTGGTGCAAGAGATATGTCTTTGTCTCCATATAGTAGT TACTCATATAATGATGTCCCACCTTCGTCATTATCAGATATCATAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.154523815

Conservation Information
Conserved circRNAs	NA
PMCS	0.154523815

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							87390337-87390223(+)
						
						Potential amino acid sequence
						
							MRPSFLEPKFLEQDSCLTFCSHKVDAVVRYASLATASPLDDMSLHHKFINSALGIHCHRMRYIH
FSMELLENDFSFQFKCPKLLAKGSYKLQLCMSAQEAGARDMSLSPYSSYSYNDVPPSSLSDIIS
A*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	87390337-87390223(+)
Potential amino acid sequence	MRPSFLEPKFLEQDSCLTFCSHKVDAVVRYASLATASPLDDMSLHHKFINSALGIHCHRMRYIH FSMELLENDFSFQFKCPKLLAKGSYKLQLCMSAQEAGARDMSLSPYSSYSYNDVPPSSLSDIIS A*(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b

circRNA

Detail information of Zm00001d020036_circ_g.4

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