Plant Circular RNA Database

Detail information of AT2G42700_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT2G42700_circ_g.3
					
						ID in PlantcircBase
						ath_circ_018003
					
						Alias
						2:17778726-17779968
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr2: 17778726-17779968  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT2G42700						
					
						Parent gene annotation
						
							Sec1-like protein (InterPro:IPR001619)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT2G42700_circ_g.1 AT2G42700_circ_g.2 AT2G42700_circ_g.4 						
					
						Support reads
						1
					
						Tissues
						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
						AT2G42700.1:3
AT2G42700.2:3
AT2G42700.3:3

General Information
CircRNA Name	AT2G42700_circ_g.3
ID in PlantcircBase	ath_circ_018003
Alias	2:17778726-17779968
Organism	Arabidpsis thaliana
Position	chr2: 17778726-17779968 JBrowse»
Reference genome	TAIR10.38
Type	ue-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT2G42700
Parent gene annotation	Sec1-like protein (InterPro:IPR001619)
Parent gene strand	+
Alternative splicing	AT2G42700_circ_g.1 AT2G42700_circ_g.2 AT2G42700_circ_g.4
Support reads	1
Tissues	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	AT2G42700.1:3 AT2G42700.2:3 AT2G42700.3:3

			
						 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  
						
							TGGTTTGCCTCCCATAAGTACTGGATCTATGTCTGACACTGATGATGTTCCTCCTGGTGCAACT
CTTACCGCACATTTTCTTTACCAGCTGGCCCTTAAGatagaagaggatgtaaaagatgcgattg
tgtatatcgatgctggctgcacagaaagttttcaatttgtaggagctttccctttgttcttgga
actaggtg

									
								

					

						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: 738
Transcript exons: 17778726-17778869,17779083-17779232,17779525-17779968
ATAGAAGAGGATGTAAAAGATGCGATTGTGTATATCGATGCTGGCTGCACAGAAAGTTTTCAAT
TTGTAGGAGCTTTCCCTTTGTTCTTGGAACTAGGTGCTCGAGCTGTCTGCAGTCTTGAAAACAT
GACTTCCTTAGATGCGGTGGCTGATTGGAATTCAAAGTCTGATTGTGCCAAGAGAATTGTGATT
ATGACATCTCGACTTCTCAATGATGCTCATCGGTATATGCTACGGTGTCTAAGCACCCATGAAG
GTGTTCAGCGCTGCACCGTATTCACATCTATTTCAGAGGGGTCTCACTCAGCTATCCCTGATTC
ACCTCTAGGTCCAGACGCGTATCGAGAGTATGAAACCTTACTTGTTCAGGATTACAATGAACAT
ACTAAGAAAAGCGACAAAATATCTAAAGACAAAGGGGTTTCTAAGTTCTCTTCTGCACTTGAAT
CCCTTACTATGGAGCCTATTGAAAGCGAAAATGTAGATATTTCATCAGGTGGTGCACAAGGTTT
GGTTGTCTCAGTTCACCACTTCCCCTTGATTATTTGTCCTTTCACTCCTCGAGCGTTTGTCTTA
CCTTCCCAAGGATCAGTCGCAGAAGCGTCCTTGTCCCGTCAACATGAGGATTCTCTTAGTTTTG
GTTTGCCTCCCATAAGTACTGGATCTATGTCTGACACTGATGATGTTCCTCCTGGTGCAACTCT
TACCGCACATTTTCTTTACCAGCTGGCCCTTAAG
						
					

						Genomic sequence
						
							ATAGAAGAGGATGTAAAAGATGCGATTGTGTATATCGATGCTGGCTGCACAGAAAGTTTTCAAT
TTGTAGGAGCTTTCCCTTTGTTCTTGGAACTAGGTGCTCGAGCTGTCTGCAGTCTTGAAAACAT
GACTTCCTTAGATGCGGTAAGCTTGTTACCGTTTCTTTTTTTCCTGCACAATGTTGGCTAAGGA
ATATCCTATCAATCAACGGTTAGTGTTGGTAATTGAGGATCTAGATAAAGAACAGGAAGATTGT
TATCCTCATACTTTTGGTATGAAGGGGATCTTTTTACCTAGAAAGTGAGAAATCTTCTGATTTA
ATTTATATGATGTGACTTTTGATGCCTTGTGCTCTAGGTGGCTGATTGGAATTCAAAGTCTGAT
TGTGCCAAGAGAATTGTGATTATGACATCTCGACTTCTCAATGATGCTCATCGGTATATGCTAC
GGTGTCTAAGCACCCATGAAGGTGTTCAGCGCTGCACCGTATTCACATCTATTTCAGAGGTGCT
CTTCTTTAACGTTATCCTTGGTCTCATTCTTTATTTAATCTCTTTTTTTTCTCTGGATATATAT
ATTGGCTTTTTTATTTTCTAGAACAATCACAAGCTATTTGACTTATCAACACTAGTGATCGTTA
TATAATCAAATTCAAAGTGATTGTAATGTATTCTCTAACTTAATTTAGCAGTTCTGCTTCTCTA
TGCCTTCTTCAAAATAATTTTCCATCTATAAGAGACTCTTCAGAATATTTGTTTCTTTTCTTGC
GTCATTGAATATTAATCTGAACGTTGTACAGGGGTCTCACTCAGCTATCCCTGATTCACCTCTA
GGTCCAGACGCGTATCGAGAGTATGAAACCTTACTTGTTCAGGATTACAATGAACATACTAAGA
AAAGCGACAAAATATCTAAAGACAAAGGGGTTTCTAAGTTCTCTTCTGCACTTGAATCCCTTAC
TATGGAGCCTATTGAAAGCGAAAATGTAGATATTTCATCAGGTGGTGCACAAGGTTTGGTTGTC
TCAGTTCACCACTTCCCCTTGATTATTTGTCCTTTCACTCCTCGAGCGTTTGTCTTACCTTCCC
AAGGATCAGTCGCAGAAGCGTCCTTGTCCCGTCAACATGAGGATTCTCTTAGTTTTGGTTTGCC
TCCCATAAGTACTGGATCTATGTCTGACACTGATGATGTTCCTCCTGGTGCAACTCTTACCGCA
CATTTTCTTTACCAGCTGGCCCTTAAG
						
					

			
		

Sequences
Splice junction sequence	TGGTTTGCCTCCCATAAGTACTGGATCTATGTCTGACACTGATGATGTTCCTCCTGGTGCAACT CTTACCGCACATTTTCTTTACCAGCTGGCCCTTAAGatagaagaggatgtaaaagatgcgattg tgtatatcgatgctggctgcacagaaagttttcaatttgtaggagctttccctttgttcttgga actaggtg
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: 738 Transcript exons: 17778726-17778869,17779083-17779232,17779525-17779968 ATAGAAGAGGATGTAAAAGATGCGATTGTGTATATCGATGCTGGCTGCACAGAAAGTTTTCAAT TTGTAGGAGCTTTCCCTTTGTTCTTGGAACTAGGTGCTCGAGCTGTCTGCAGTCTTGAAAACAT GACTTCCTTAGATGCGGTGGCTGATTGGAATTCAAAGTCTGATTGTGCCAAGAGAATTGTGATT ATGACATCTCGACTTCTCAATGATGCTCATCGGTATATGCTACGGTGTCTAAGCACCCATGAAG GTGTTCAGCGCTGCACCGTATTCACATCTATTTCAGAGGGGTCTCACTCAGCTATCCCTGATTC ACCTCTAGGTCCAGACGCGTATCGAGAGTATGAAACCTTACTTGTTCAGGATTACAATGAACAT ACTAAGAAAAGCGACAAAATATCTAAAGACAAAGGGGTTTCTAAGTTCTCTTCTGCACTTGAAT CCCTTACTATGGAGCCTATTGAAAGCGAAAATGTAGATATTTCATCAGGTGGTGCACAAGGTTT GGTTGTCTCAGTTCACCACTTCCCCTTGATTATTTGTCCTTTCACTCCTCGAGCGTTTGTCTTA CCTTCCCAAGGATCAGTCGCAGAAGCGTCCTTGTCCCGTCAACATGAGGATTCTCTTAGTTTTG GTTTGCCTCCCATAAGTACTGGATCTATGTCTGACACTGATGATGTTCCTCCTGGTGCAACTCT TACCGCACATTTTCTTTACCAGCTGGCCCTTAAG
Genomic sequence	ATAGAAGAGGATGTAAAAGATGCGATTGTGTATATCGATGCTGGCTGCACAGAAAGTTTTCAAT TTGTAGGAGCTTTCCCTTTGTTCTTGGAACTAGGTGCTCGAGCTGTCTGCAGTCTTGAAAACAT GACTTCCTTAGATGCGGTAAGCTTGTTACCGTTTCTTTTTTTCCTGCACAATGTTGGCTAAGGA ATATCCTATCAATCAACGGTTAGTGTTGGTAATTGAGGATCTAGATAAAGAACAGGAAGATTGT TATCCTCATACTTTTGGTATGAAGGGGATCTTTTTACCTAGAAAGTGAGAAATCTTCTGATTTA ATTTATATGATGTGACTTTTGATGCCTTGTGCTCTAGGTGGCTGATTGGAATTCAAAGTCTGAT TGTGCCAAGAGAATTGTGATTATGACATCTCGACTTCTCAATGATGCTCATCGGTATATGCTAC GGTGTCTAAGCACCCATGAAGGTGTTCAGCGCTGCACCGTATTCACATCTATTTCAGAGGTGCT CTTCTTTAACGTTATCCTTGGTCTCATTCTTTATTTAATCTCTTTTTTTTCTCTGGATATATAT ATTGGCTTTTTTATTTTCTAGAACAATCACAAGCTATTTGACTTATCAACACTAGTGATCGTTA TATAATCAAATTCAAAGTGATTGTAATGTATTCTCTAACTTAATTTAGCAGTTCTGCTTCTCTA TGCCTTCTTCAAAATAATTTTCCATCTATAAGAGACTCTTCAGAATATTTGTTTCTTTTCTTGC GTCATTGAATATTAATCTGAACGTTGTACAGGGGTCTCACTCAGCTATCCCTGATTCACCTCTA GGTCCAGACGCGTATCGAGAGTATGAAACCTTACTTGTTCAGGATTACAATGAACATACTAAGA AAAGCGACAAAATATCTAAAGACAAAGGGGTTTCTAAGTTCTCTTCTGCACTTGAATCCCTTAC TATGGAGCCTATTGAAAGCGAAAATGTAGATATTTCATCAGGTGGTGCACAAGGTTTGGTTGTC TCAGTTCACCACTTCCCCTTGATTATTTGTCCTTTCACTCCTCGAGCGTTTGTCTTACCTTCCC AAGGATCAGTCGCAGAAGCGTCCTTGTCCCGTCAACATGAGGATTCTCTTAGTTTTGGTTTGCC TCCCATAAGTACTGGATCTATGTCTGACACTGATGATGTTCCTCCTGGTGCAACTCTTACCGCA CATTTTCTTTACCAGCTGGCCCTTAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.239977832

Conservation Information
Conserved circRNAs	NA
PMCS	0.239977832

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

			
						 Other Information
					
						References
						Philips et al., 2020

circRNA

Detail information of AT2G42700_circ_g.3

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