Plant Circular RNA Database

Detail information of AT2G02560_circ_g.7

			
						 General Information
					
						CircRNA Name
						AT2G02560_circ_g.7
					
						ID in PlantcircBase
						ath_circ_012578
					
						Alias
						2:692853-693067
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr2: 692853-693067  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT2G02560						
					
						Parent gene annotation
						
							Cullin-associated NEDD8-dissociated protein 1
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT2G02560_circ_g.1 AT2G02560_circ_g.2 AT2G02560_circ_g.3 AT2G02560_circ_g.4 AT2G02560_circ_g.5 AT2G02560_circ_g.6 AT2G02560_circ_g.8 AT2G02560_circ_g.9 						
					
						Support reads
						1/1
					
						Tissues
						root;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  
						
							GC-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
						AT2G02560.2:2
AT2G02560.1:2

General Information
CircRNA Name	AT2G02560_circ_g.7
ID in PlantcircBase	ath_circ_012578
Alias	2:692853-693067
Organism	Arabidpsis thaliana
Position	chr2: 692853-693067 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT2G02560
Parent gene annotation	Cullin-associated NEDD8-dissociated protein 1
Parent gene strand	+
Alternative splicing	AT2G02560_circ_g.1 AT2G02560_circ_g.2 AT2G02560_circ_g.3 AT2G02560_circ_g.4 AT2G02560_circ_g.5 AT2G02560_circ_g.6 AT2G02560_circ_g.8 AT2G02560_circ_g.9
Support reads	1/1
Tissues	root;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	GC-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	AT2G02560.2:2 AT2G02560.1:2

			
						 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  
						
							AGGTACTGTTGTTACAGATGGATGTATTCAACACATTCATTGATCTGTTGCGGCAAACGGGAAA
TGTTACAAAAGGTCAAACTGACACCGATGAATCAAGgcctgcccgaaactaattgatagattta
aggaaagggaggaaaatgtgaaggtatgtaatttaatccattaatgctctattcttgctttgca
atatggtt

						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: 134
Transcript exons: 692853-692903,692985-693067
GCCTGCCCGAAACTAATTGATAGATTTAAGGAAAGGGAGGAAAATGTGAAGATGGATGTATTCA
ACACATTCATTGATCTGTTGCGGCAAACGGGAAATGTTACAAAAGGTCAAACTGACACCGATGA
ATCAAG
						
						Genomic sequence
						
							GCCTGCCCGAAACTAATTGATAGATTTAAGGAAAGGGAGGAAAATGTGAAGGTATGTAATTTAA
TCCATTAATGCTCTATTCTTGCTTTGCAATATGGTTATTGATCTAAGACTGAGGTACTGTTGTT
ACAGATGGATGTATTCAACACATTCATTGATCTGTTGCGGCAAACGGGAAATGTTACAAAAGGT
CAAACTGACACCGATGAATCAAG

Sequences
Splice junction sequence	AGGTACTGTTGTTACAGATGGATGTATTCAACACATTCATTGATCTGTTGCGGCAAACGGGAAA TGTTACAAAAGGTCAAACTGACACCGATGAATCAAGgcctgcccgaaactaattgatagattta aggaaagggaggaaaatgtgaaggtatgtaatttaatccattaatgctctattcttgctttgca atatggtt
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: 134 Transcript exons: 692853-692903,692985-693067 GCCTGCCCGAAACTAATTGATAGATTTAAGGAAAGGGAGGAAAATGTGAAGATGGATGTATTCA ACACATTCATTGATCTGTTGCGGCAAACGGGAAATGTTACAAAAGGTCAAACTGACACCGATGA ATCAAG
Genomic sequence	GCCTGCCCGAAACTAATTGATAGATTTAAGGAAAGGGAGGAAAATGTGAAGGTATGTAATTTAA TCCATTAATGCTCTATTCTTGCTTTGCAATATGGTTATTGATCTAAGACTGAGGTACTGTTGTT ACAGATGGATGTATTCAACACATTCATTGATCTGTTGCGGCAAACGGGAAATGTTACAAAAGGT CAAACTGACACCGATGAATCAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.233907426

Conservation Information
Conserved circRNAs	NA
PMCS	0.233907426

			
						 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 AT2G02560_circ_g.7

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