Plant Circular RNA Database

Detail information of AT3G20720_circ_g.9

			
						 General Information
					
						CircRNA Name
						AT3G20720_circ_g.9
					
						ID in PlantcircBase
						ath_circ_023012
					
						Alias
						3:7245394-7246355
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 7245394-7246355  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT3G20720						
					
						Parent gene annotation
						
							Amino-terminal region of chorein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT3G20720_circ_g.8 						
					
						Support reads
						1/1
					
						Tissues
						leaf;flower
					
						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
						AT3G20720.2:3
AT3G20720.1:3

General Information
CircRNA Name	AT3G20720_circ_g.9
ID in PlantcircBase	ath_circ_023012
Alias	3:7245394-7246355
Organism	Arabidpsis thaliana
Position	chr3: 7245394-7246355 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT3G20720
Parent gene annotation	Amino-terminal region of chorein
Parent gene strand	+
Alternative splicing	AT3G20720_circ_g.8
Support reads	1/1
Tissues	leaf;flower
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	AT3G20720.2:3 AT3G20720.1:3

			
						 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  
						
							GAAATTGACGCAATGGGAAGGATAGTCGCAGGGGTTTTACGTGTACTGAAGCTTGAAGAATCTA
TTGGCCAGGCGACTCTTAATCAATTAAGCAACCTTGatggaactccaggaaactggaatggcga
tggtttcccacatttgggaaggccagatgacattgatgtctctgttgagttaagagattggttg
tttgcttt

									
								

					

						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: 654
Transcript exons: 7245394-7245677,7245897-7246109,7246199-7246355
ATGGAACTCCAGGAAACTGGAATGGCGATGGTTTCCCACATTTGGGAAGGCCAGATGACATTGA
TGTCTCTGTTGAGTTAAGAGATTGGTTGTTTGCTTTGGAGGGCAGAGAAGGTGTTGGCACAAGA
ATTTTGAATAATGAAGATATTGGAAGAGAAGAGAGGTGTTGGCACACAAATTTCCGTACTTTCC
GAGTAATAGCCAAGAGTACACCAAAGAACGTGGATTCAAATGGGACAGAAAACCAGTGTGATGC
TCACAAGTATCCTGTGGACTCAATTATTGTCAGTGTCGAAGGTCTACAGACAGTGAAGCCTCAA
ATGCAGAAAGGGACCGATTCTTGTAATGGTTTGTCTACAAATGGAGTTCACGAAAACGGTCAAA
TGCATGGAGGGGTGAACATTGAAGCTAATATTGTGGCATCTGAAGACAAATCTGTTCATGATGA
CTTATTGAACTGGGTGGCAGAAAGTCTGAAATTCTCTGTTAAGCAACCTGTTGAGGCAGTTGTA
ACAAAGGATGAGCTGCAACATTTGACTTTCTTGTGCAAATCTGAAATTGACGCAATGGGAAGGA
TAGTCGCAGGGGTTTTACGTGTACTGAAGCTTGAAGAATCTATTGGCCAGGCGACTCTTAATCA
ATTAAGCAACCTTG
						
					

						Genomic sequence
						
							ATGGAACTCCAGGAAACTGGAATGGCGATGGTTTCCCACATTTGGGAAGGCCAGATGACATTGA
TGTCTCTGTTGAGTTAAGAGATTGGTTGTTTGCTTTGGAGGGCAGAGAAGGTGTTGGCACAAGA
ATTTTGAATAATGAAGATATTGGAAGAGAAGAGAGGTGTTGGCACACAAATTTCCGTACTTTCC
GAGTAATAGCCAAGAGTACACCAAAGAACGTGGATTCAAATGGGACAGAAAACCAGTGTGATGC
TCACAAGTATCCTGTGGACTCAATTATTGTAAGTATCTGTACTCCTTTCCACTGCTCAATTTCT
TTCCCTGAACTTTCTGAGGTTAATGATAACCACTTCACTTTAAGGAGAGTTTGGTGGTGATCTT
AGAAAAACCCTATGTAATTCTTCAAGCAGCCTTTATCTTTCTGGTGTCTTACGAATGCCATAAG
GATCGTGGACCATTTTGTGGTACTAAGCCTTTAAAATTTTATCCGGGAAATATAGGTCAGTGTC
GAAGGTCTACAGACAGTGAAGCCTCAAATGCAGAAAGGGACCGATTCTTGTAATGGTTTGTCTA
CAAATGGAGTTCACGAAAACGGTCAAATGCATGGAGGGGTGAACATTGAAGCTAATATTGTGGC
ATCTGAAGACAAATCTGTTCATGATGACTTATTGAACTGGGTGGCAGAAAGTCTGAAATTCTCT
GTTAAGCAACCTGTAAGTCAAGCAGAGCTCATTGCTCTTTGCTTCTTCCTTTTTAGTAAAGTAG
TTTTTGTAATAAAGGTCTTTTGTTCTTTGTGCTGCAGGTTGAGGCAGTTGTAACAAAGGATGAG
CTGCAACATTTGACTTTCTTGTGCAAATCTGAAATTGACGCAATGGGAAGGATAGTCGCAGGGG
TTTTACGTGTACTGAAGCTTGAAGAATCTATTGGCCAGGCGACTCTTAATCAATTAAGCAACCT
TG
						
					

			
		

Sequences
Splice junction sequence	GAAATTGACGCAATGGGAAGGATAGTCGCAGGGGTTTTACGTGTACTGAAGCTTGAAGAATCTA TTGGCCAGGCGACTCTTAATCAATTAAGCAACCTTGatggaactccaggaaactggaatggcga tggtttcccacatttgggaaggccagatgacattgatgtctctgttgagttaagagattggttg tttgcttt
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: 654 Transcript exons: 7245394-7245677,7245897-7246109,7246199-7246355 ATGGAACTCCAGGAAACTGGAATGGCGATGGTTTCCCACATTTGGGAAGGCCAGATGACATTGA TGTCTCTGTTGAGTTAAGAGATTGGTTGTTTGCTTTGGAGGGCAGAGAAGGTGTTGGCACAAGA ATTTTGAATAATGAAGATATTGGAAGAGAAGAGAGGTGTTGGCACACAAATTTCCGTACTTTCC GAGTAATAGCCAAGAGTACACCAAAGAACGTGGATTCAAATGGGACAGAAAACCAGTGTGATGC TCACAAGTATCCTGTGGACTCAATTATTGTCAGTGTCGAAGGTCTACAGACAGTGAAGCCTCAA ATGCAGAAAGGGACCGATTCTTGTAATGGTTTGTCTACAAATGGAGTTCACGAAAACGGTCAAA TGCATGGAGGGGTGAACATTGAAGCTAATATTGTGGCATCTGAAGACAAATCTGTTCATGATGA CTTATTGAACTGGGTGGCAGAAAGTCTGAAATTCTCTGTTAAGCAACCTGTTGAGGCAGTTGTA ACAAAGGATGAGCTGCAACATTTGACTTTCTTGTGCAAATCTGAAATTGACGCAATGGGAAGGA TAGTCGCAGGGGTTTTACGTGTACTGAAGCTTGAAGAATCTATTGGCCAGGCGACTCTTAATCA ATTAAGCAACCTTG
Genomic sequence	ATGGAACTCCAGGAAACTGGAATGGCGATGGTTTCCCACATTTGGGAAGGCCAGATGACATTGA TGTCTCTGTTGAGTTAAGAGATTGGTTGTTTGCTTTGGAGGGCAGAGAAGGTGTTGGCACAAGA ATTTTGAATAATGAAGATATTGGAAGAGAAGAGAGGTGTTGGCACACAAATTTCCGTACTTTCC GAGTAATAGCCAAGAGTACACCAAAGAACGTGGATTCAAATGGGACAGAAAACCAGTGTGATGC TCACAAGTATCCTGTGGACTCAATTATTGTAAGTATCTGTACTCCTTTCCACTGCTCAATTTCT TTCCCTGAACTTTCTGAGGTTAATGATAACCACTTCACTTTAAGGAGAGTTTGGTGGTGATCTT AGAAAAACCCTATGTAATTCTTCAAGCAGCCTTTATCTTTCTGGTGTCTTACGAATGCCATAAG GATCGTGGACCATTTTGTGGTACTAAGCCTTTAAAATTTTATCCGGGAAATATAGGTCAGTGTC GAAGGTCTACAGACAGTGAAGCCTCAAATGCAGAAAGGGACCGATTCTTGTAATGGTTTGTCTA CAAATGGAGTTCACGAAAACGGTCAAATGCATGGAGGGGTGAACATTGAAGCTAATATTGTGGC ATCTGAAGACAAATCTGTTCATGATGACTTATTGAACTGGGTGGCAGAAAGTCTGAAATTCTCT GTTAAGCAACCTGTAAGTCAAGCAGAGCTCATTGCTCTTTGCTTCTTCCTTTTTAGTAAAGTAG TTTTTGTAATAAAGGTCTTTTGTTCTTTGTGCTGCAGGTTGAGGCAGTTGTAACAAAGGATGAG CTGCAACATTTGACTTTCTTGTGCAAATCTGAAATTGACGCAATGGGAAGGATAGTCGCAGGGG TTTTACGTGTACTGAAGCTTGAAGAATCTATTGGCCAGGCGACTCTTAATCAATTAAGCAACCT TG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.193110144

Conservation Information
Conserved circRNAs	NA
PMCS	0.193110144

			
						 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 AT3G20720_circ_g.9

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