Plant Circular RNA Database

Detail information of AT1G54270_circ_g.2

			
						 General Information
					
						CircRNA Name
						AT1G54270_circ_g.2
					
						ID in PlantcircBase
						ath_circ_007302
					
						Alias
						1:20260494-20262045
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 20260494-20262045  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT1G54270						
					
						Parent gene annotation
						
							eIF4A-2
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT1G54270_circ_g.1 AT1G54270_circ_g.3 AT1G54270_circ_g.4 AT1G54270_circ_g.5 						
					
						Support reads
						3/1
					
						Tissues
						seedling;leaf
					
						Exon boundary  
						
							Yes-No							"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
						AT1G54270.1:4
AT1G54270.2:4

General Information
CircRNA Name	AT1G54270_circ_g.2
ID in PlantcircBase	ath_circ_007302
Alias	1:20260494-20262045
Organism	Arabidpsis thaliana
Position	chr1: 20260494-20262045 JBrowse»
Reference genome	TAIR10.38
Type	u-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT1G54270
Parent gene annotation	eIF4A-2
Parent gene strand	+
Alternative splicing	AT1G54270_circ_g.1 AT1G54270_circ_g.3 AT1G54270_circ_g.4 AT1G54270_circ_g.5
Support reads	3/1
Tissues	seedling;leaf
Exon boundary	Yes-No "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	AT1G54270.1:4 AT1G54270.2:4

			
						 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  
						
							GCTGTTTGATATTCAGAAATTCTACAATGTGGTTGTTGAGGAGCTTCCCTCAAACGTGGCTGAT
TTGCTGTGAAGAAGAAGAAGAAGAAGAAGAAGAAAGtatggcaggatccgcaccggaaggaaca
caatttgatacgcgtcagtttgaccagaggctgaatgaagtgtaagtcctaagatctttagttt
cattactc

									
								

					

						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
						
							TATGGCAGGATCCGCACCGGAAGGAACACAATTTGATACGCGTCAGTTTGACCAGAGGCTGAAT
GAAGTGTAAGTCCTAAGATCTTTAGTTTCATTACTCGTTTTTGATGAGATTTTTTTTGTATTTG
CTAATCTTATTGTTTGTTTGGGTGCAGTCTCGATGGACAGGATGAGTTCTTCACCTCATATGAT
GAGGTCCATGAGAGCTTTGATGCCATGGGTTTGCAAGAGAATCTTCTTAGGGGTATCTATGCTT
ACGGTAAGTGAAGAAGGTTTAAAGAAACAACCTTTTGTTTGTTATGTTGGGATTCCTATTAACT
TTATCGTATGTGCTCTTTCCTGTGATTGATTGGTTGATTTTTTTCTAGGTTTCGAAAAGCCTTC
TGCTATTCAGCAAAGAGGAATTGTACCCTTTTGCAAGGGTCTTGATGTGATCCAGCAGGCACAG
TCTGGTACTGGAAAAACCGCCACTTTCTGCTCTGGTGTCTTGCAGCAGCTTGACTATGCCCTTC
TCCAGTGCCAGGCTCTCGTTTTGGCTCCCACCAGAGAGCTTGCTCAGCAGATTGAGAAGGTCAT
GCGTGCCCTTGGTGACTACCAAGGTGTCAAGGTTCATGCCTGTGTTGGTGGAACCAGTGTCCGT
GAGGATCAGCGCATTCTCCAGGCTGGTGTTCATGTTGTCGTTGGAACTCCCGGTCGTGTTTTTG
ACATGCTTAGAAGACAATCTCTCCGCCCTGACTGCATCAAGATGTTTGTCCTTGATGAAGCTGA
TGAAATGCTCTCCCGTGGTTTCAAGGATCAGGTTTGTTATCTTCTTCAAAGTTTGAATCTACCC
TCTGTGGTTATCTCTGATATTGACTTGGTTTTGTGTTGTTTTCTGGTGAATTTGCAGATCTATG
ACATATTCCAGCTTCTCCCACCAAAGATTCAGGTTGGAGTGTTCTCTGCGACAATGCCTCCGGA
AGCTTTGGAGATCACAAGAAAATTCATGAGCAAACCAGTGAGAATCTTGGTGAAACGTGATGAG
CTCACACTTGAAGGTATCAAGCAATTCTACGTGAACGTGGAGAAAGAAGACTGGAAGCTTGAGA
CTCTCTGCGATCTCTACGAGACTCTAGCCATCACTCAGAGTGTCATCTTTGTCAACACTCGTCG
CAAGGTCGACTGGCTCACAGACAAAATGAGAAGCCGTGACCACACAGTCTCAGCAACTCATGGA
GACATGGACCAAAACACCAGAGACATCATCATGAGAGAGTTCAGGTCTGGCTCGTCTCGTGTTC
TAATCACAACCGATCTCTTGGCTCGTGGTATCGATGTGCAGCAAGTCTCTCTAGTCATAAACTT
TGACCTCCCAACTCAGCCAGAGAATTACCTTCACCGTATCGGAAGAAGTGGAAGGTTCGGGAGA
AAGGGTGTGGCGATTAACTTTGTGACTCTTGATGATCAGAGAATGCTGTTTGATATTCAGAAAT
TCTACAATGTGGTTGTTGAGGAGCTTCCCTCAAACGTGGCTGATTTGCTGTGAAGAAGAAGAAG
AAGAAGAAGAAGAAAG
						
					

			
		

Sequences
Splice junction sequence	GCTGTTTGATATTCAGAAATTCTACAATGTGGTTGTTGAGGAGCTTCCCTCAAACGTGGCTGAT TTGCTGTGAAGAAGAAGAAGAAGAAGAAGAAGAAAGtatggcaggatccgcaccggaaggaaca caatttgatacgcgtcagtttgaccagaggctgaatgaagtgtaagtcctaagatctttagttt cattactc
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	TATGGCAGGATCCGCACCGGAAGGAACACAATTTGATACGCGTCAGTTTGACCAGAGGCTGAAT GAAGTGTAAGTCCTAAGATCTTTAGTTTCATTACTCGTTTTTGATGAGATTTTTTTTGTATTTG CTAATCTTATTGTTTGTTTGGGTGCAGTCTCGATGGACAGGATGAGTTCTTCACCTCATATGAT GAGGTCCATGAGAGCTTTGATGCCATGGGTTTGCAAGAGAATCTTCTTAGGGGTATCTATGCTT ACGGTAAGTGAAGAAGGTTTAAAGAAACAACCTTTTGTTTGTTATGTTGGGATTCCTATTAACT TTATCGTATGTGCTCTTTCCTGTGATTGATTGGTTGATTTTTTTCTAGGTTTCGAAAAGCCTTC TGCTATTCAGCAAAGAGGAATTGTACCCTTTTGCAAGGGTCTTGATGTGATCCAGCAGGCACAG TCTGGTACTGGAAAAACCGCCACTTTCTGCTCTGGTGTCTTGCAGCAGCTTGACTATGCCCTTC TCCAGTGCCAGGCTCTCGTTTTGGCTCCCACCAGAGAGCTTGCTCAGCAGATTGAGAAGGTCAT GCGTGCCCTTGGTGACTACCAAGGTGTCAAGGTTCATGCCTGTGTTGGTGGAACCAGTGTCCGT GAGGATCAGCGCATTCTCCAGGCTGGTGTTCATGTTGTCGTTGGAACTCCCGGTCGTGTTTTTG ACATGCTTAGAAGACAATCTCTCCGCCCTGACTGCATCAAGATGTTTGTCCTTGATGAAGCTGA TGAAATGCTCTCCCGTGGTTTCAAGGATCAGGTTTGTTATCTTCTTCAAAGTTTGAATCTACCC TCTGTGGTTATCTCTGATATTGACTTGGTTTTGTGTTGTTTTCTGGTGAATTTGCAGATCTATG ACATATTCCAGCTTCTCCCACCAAAGATTCAGGTTGGAGTGTTCTCTGCGACAATGCCTCCGGA AGCTTTGGAGATCACAAGAAAATTCATGAGCAAACCAGTGAGAATCTTGGTGAAACGTGATGAG CTCACACTTGAAGGTATCAAGCAATTCTACGTGAACGTGGAGAAAGAAGACTGGAAGCTTGAGA CTCTCTGCGATCTCTACGAGACTCTAGCCATCACTCAGAGTGTCATCTTTGTCAACACTCGTCG CAAGGTCGACTGGCTCACAGACAAAATGAGAAGCCGTGACCACACAGTCTCAGCAACTCATGGA GACATGGACCAAAACACCAGAGACATCATCATGAGAGAGTTCAGGTCTGGCTCGTCTCGTGTTC TAATCACAACCGATCTCTTGGCTCGTGGTATCGATGTGCAGCAAGTCTCTCTAGTCATAAACTT TGACCTCCCAACTCAGCCAGAGAATTACCTTCACCGTATCGGAAGAAGTGGAAGGTTCGGGAGA AAGGGTGTGGCGATTAACTTTGTGACTCTTGATGATCAGAGAATGCTGTTTGATATTCAGAAAT TCTACAATGTGGTTGTTGAGGAGCTTCCCTCAAACGTGGCTGATTTGCTGTGAAGAAGAAGAAG AAGAAGAAGAAGAAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.558540856

Conservation Information
Conserved circRNAs	NA
PMCS	0.558540856

			
						 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 AT1G54270_circ_g.2

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