Plant Circular RNA Database

Detail information of AT2G02080_circ_g.1

			
						 General Information
					
						CircRNA Name
						AT2G02080_circ_g.1
					
						ID in PlantcircBase
						ath_circ_012535
					
						Alias
						At_ciR3814
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr2: 520264-521205  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						circRNA_finder, find_circ
					
						Parent gene
						
							AT2G02080						
					
						Parent gene annotation
						
							Protein indeterminate-domain 4, chloroplastic
							
						Parent gene strand
						-
					
						Alternative splicing
						
							NA						
					
						Support reads
						2/2
					
						Tissues
						leaf/whole_plant
					
						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  
						
							CT-AC							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
						AT2G02080.2:2
AT2G02080.6:2
AT2G02080.3:2
AT2G02080.5:2
AT2G02080.1:2
AT2G02080.4:2

General Information
CircRNA Name	AT2G02080_circ_g.1
ID in PlantcircBase	ath_circ_012535
Alias	At_ciR3814
Organism	Arabidpsis thaliana
Position	chr2: 520264-521205 JBrowse»
Reference genome	TAIR10.38
Type	ue-circRNA
Identification method	circRNA_finder, find_circ
Parent gene	AT2G02080
Parent gene annotation	Protein indeterminate-domain 4, chloroplastic
Parent gene strand	-
Alternative splicing	NA
Support reads	2/2
Tissues	leaf/whole_plant
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	CT-AC 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	AT2G02080.2:2 AT2G02080.6:2 AT2G02080.3:2 AT2G02080.5:2 AT2G02080.1:2 AT2G02080.4:2

			
						 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  
						
							AAGAAAGGCTGAGCAGAGGATGATGATGAAGGAATAACGCTTGTGTTATATGATGATGACGACA
TCTTTAGATCTTCTTCTTTGCGTGGAAGAGAATAATctagagaagatggtaccacagtcacatc
gatactctttagtaccacaagtcttagagtgagctttccaatctgattgaacagcgtaacgctt
agaacatt

									
								

					

						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: 622
Transcript exons: 520264-520660,520981-521205
CTAGAGAAGATGGTACCACAGTCACATCGATACTCTTTAGTACCACAAGTCTTAGAGTGAGCTT
TCCAATCTGATTGAACAGCGTAACGCTTAGAACATTTCTCACATTTCCACTTCTTTTCGCCATG
TTTACGGTAATAATGCTTCTTGATTCCGGTGAGGTCTCCGAGAGCACGTGACGGGTCATGGTGA
ACGCACGTTGGCTCCGGACAAAGATACACTTTCCTCTTCACTTCTTTGGTTGATTTTTGTTTCA
GCTTCCATGGGAGATTGTGTCCTCTTCGGTGAAGCTGTAGATTTTGTTCTCTTTGAAACCCTTT
GTTACATACATCGCATATGAATCTGTTTGTAGCCATTAGTGTCTTTGGAGATAATGCTACCACT
TCCGCATCAGGATTTGGGTTTCCGGGTTGGTTTCTTCGTTTCTTGGGTGGTGGAGCTGAGGAGT
TAGGTTGTTGAATCATTGACATAAAAGTATCTTTCCGGTTAAAGTCGTTATCTCCGGTGCCGGA
GCTGGTGATGAAGAAAGGCTGAGCAGAGGATGATGATGAAGGAATAACGCTTGTGTTATATGAT
GATGACGACATCTTTAGATCTTCTTCTTTGCGTGGAAGAGAATAAT
Transcript length: 626
Transcript exons: 520264-520660,520977-521205
CTAGAGAAGATGGTACCACAGTCACATCGATACTCTTTAGTACCACAAGTCTTAGAGTGAGCTT
TCCAATCTGATTGAACAGCGTAACGCTTAGAACATTTCTCACATTTCCACTTCTTTTCGCCATG
TTTACGGTAATAATGCTTCTTGATTCCGGTGAGGTCTCCGAGAGCACGTGACGGGTCATGGTGA
ACGCACGTTGGCTCCGGACAAAGATACACTTTCCTCTTCACTTCTTTGGTTGATTTTTGTTTCA
GCTTCCATGGGAGATTGTGTCCTCTTCGGTGAAGCTGTAGATTTTGTTCTCTTTGAAACCCTTT
GTTACATACATCGCATATGAATCTGTTTGTAGCCATTAGTGTCTTTGGAGATAATGCTACCACT
TCCGCATCAGGATTTGCTTGGGTTTCCGGGTTGGTTTCTTCGTTTCTTGGGTGGTGGAGCTGAG
GAGTTAGGTTGTTGAATCATTGACATAAAAGTATCTTTCCGGTTAAAGTCGTTATCTCCGGTGC
CGGAGCTGGTGATGAAGAAAGGCTGAGCAGAGGATGATGATGAAGGAATAACGCTTGTGTTATA
TGATGATGACGACATCTTTAGATCTTCTTCTTTGCGTGGAAGAGAATAAT
						
					

						Genomic sequence
						
							CTAGAGAAGATGGTACCACAGTCACATCGATACTCTTTAGTACCACAAGTCTTAGAGTGAGCTT
TCCAATCTGATTGAACAGCGTAACGCTTAGAACATTTCTCACATTTCCACTTCTTTTCGCCATG
TTTACGGTAATAATGCTTCTTGATTCCGGTGAGGTCTCCGAGAGCACGTGACGGGTCATGGTGA
ACGCACGTTGGCTCCGGACAAAGATACACTTTCCTCTTCACTTCTTTGGTTGATTTTTGTTTCA
GCTTCCATGGGAGATTGTGTCCTCTTCGGTGAAGCTGTAGATTTTGTTCTCTTTGAAACCCTTT
GTTACATACATCGCATATGAATCTGTTTGTAGCCATTAGTGTCTTTGGAGATAATGCTACCACT
TCCGCATCAGGATCTGTTTCATATAATTAAAGAATTTAATCATTTAAATTAAGTCACCAATTAG
ACCCAAAATGTCAATCTATGTAGACTATATCGAAAAAAATGATACACACACATGTAAACATAAA
TCAAATGACATATACACGTATAAACATATAAGATATACTGGCCTGTCAATATATATGAAATCTT
GATACTAGCTAGATATACAAAACAAAATAGAACAAATGATTAGGGTTCTTTTTCTTCTTGGTAT
TATCTTAAAGCTTATATATAGTGATTCTTATAGAAAGGTGATAAATATATAGAGATTTATATGT
AAGAGATACTTGCTTGGGTTTCCGGGTTGGTTTCTTCGTTTCTTGGGTGGTGGAGCTGAGGAGT
TAGGTTGTTGAATCATTGACATAAAAGTATCTTTCCGGTTAAAGTCGTTATCTCCGGTGCCGGA
GCTGGTGATGAAGAAAGGCTGAGCAGAGGATGATGATGAAGGAATAACGCTTGTGTTATATGAT
GATGACGACATCTTTAGATCTTCTTCTTTGCGTGGAAGAGAATAAT
						
					

			
		

Sequences
Splice junction sequence	AAGAAAGGCTGAGCAGAGGATGATGATGAAGGAATAACGCTTGTGTTATATGATGATGACGACA TCTTTAGATCTTCTTCTTTGCGTGGAAGAGAATAATctagagaagatggtaccacagtcacatc gatactctttagtaccacaagtcttagagtgagctttccaatctgattgaacagcgtaacgctt agaacatt
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: 622 Transcript exons: 520264-520660,520981-521205 CTAGAGAAGATGGTACCACAGTCACATCGATACTCTTTAGTACCACAAGTCTTAGAGTGAGCTT TCCAATCTGATTGAACAGCGTAACGCTTAGAACATTTCTCACATTTCCACTTCTTTTCGCCATG TTTACGGTAATAATGCTTCTTGATTCCGGTGAGGTCTCCGAGAGCACGTGACGGGTCATGGTGA ACGCACGTTGGCTCCGGACAAAGATACACTTTCCTCTTCACTTCTTTGGTTGATTTTTGTTTCA GCTTCCATGGGAGATTGTGTCCTCTTCGGTGAAGCTGTAGATTTTGTTCTCTTTGAAACCCTTT GTTACATACATCGCATATGAATCTGTTTGTAGCCATTAGTGTCTTTGGAGATAATGCTACCACT TCCGCATCAGGATTTGGGTTTCCGGGTTGGTTTCTTCGTTTCTTGGGTGGTGGAGCTGAGGAGT TAGGTTGTTGAATCATTGACATAAAAGTATCTTTCCGGTTAAAGTCGTTATCTCCGGTGCCGGA GCTGGTGATGAAGAAAGGCTGAGCAGAGGATGATGATGAAGGAATAACGCTTGTGTTATATGAT GATGACGACATCTTTAGATCTTCTTCTTTGCGTGGAAGAGAATAAT Transcript length: 626 Transcript exons: 520264-520660,520977-521205 CTAGAGAAGATGGTACCACAGTCACATCGATACTCTTTAGTACCACAAGTCTTAGAGTGAGCTT TCCAATCTGATTGAACAGCGTAACGCTTAGAACATTTCTCACATTTCCACTTCTTTTCGCCATG TTTACGGTAATAATGCTTCTTGATTCCGGTGAGGTCTCCGAGAGCACGTGACGGGTCATGGTGA ACGCACGTTGGCTCCGGACAAAGATACACTTTCCTCTTCACTTCTTTGGTTGATTTTTGTTTCA GCTTCCATGGGAGATTGTGTCCTCTTCGGTGAAGCTGTAGATTTTGTTCTCTTTGAAACCCTTT GTTACATACATCGCATATGAATCTGTTTGTAGCCATTAGTGTCTTTGGAGATAATGCTACCACT TCCGCATCAGGATTTGCTTGGGTTTCCGGGTTGGTTTCTTCGTTTCTTGGGTGGTGGAGCTGAG GAGTTAGGTTGTTGAATCATTGACATAAAAGTATCTTTCCGGTTAAAGTCGTTATCTCCGGTGC CGGAGCTGGTGATGAAGAAAGGCTGAGCAGAGGATGATGATGAAGGAATAACGCTTGTGTTATA TGATGATGACGACATCTTTAGATCTTCTTCTTTGCGTGGAAGAGAATAAT
Genomic sequence	CTAGAGAAGATGGTACCACAGTCACATCGATACTCTTTAGTACCACAAGTCTTAGAGTGAGCTT TCCAATCTGATTGAACAGCGTAACGCTTAGAACATTTCTCACATTTCCACTTCTTTTCGCCATG TTTACGGTAATAATGCTTCTTGATTCCGGTGAGGTCTCCGAGAGCACGTGACGGGTCATGGTGA ACGCACGTTGGCTCCGGACAAAGATACACTTTCCTCTTCACTTCTTTGGTTGATTTTTGTTTCA GCTTCCATGGGAGATTGTGTCCTCTTCGGTGAAGCTGTAGATTTTGTTCTCTTTGAAACCCTTT GTTACATACATCGCATATGAATCTGTTTGTAGCCATTAGTGTCTTTGGAGATAATGCTACCACT TCCGCATCAGGATCTGTTTCATATAATTAAAGAATTTAATCATTTAAATTAAGTCACCAATTAG ACCCAAAATGTCAATCTATGTAGACTATATCGAAAAAAATGATACACACACATGTAAACATAAA TCAAATGACATATACACGTATAAACATATAAGATATACTGGCCTGTCAATATATATGAAATCTT GATACTAGCTAGATATACAAAACAAAATAGAACAAATGATTAGGGTTCTTTTTCTTCTTGGTAT TATCTTAAAGCTTATATATAGTGATTCTTATAGAAAGGTGATAAATATATAGAGATTTATATGT AAGAGATACTTGCTTGGGTTTCCGGGTTGGTTTCTTCGTTTCTTGGGTGGTGGAGCTGAGGAGT TAGGTTGTTGAATCATTGACATAAAAGTATCTTTCCGGTTAAAGTCGTTATCTCCGGTGCCGGA GCTGGTGATGAAGAAAGGCTGAGCAGAGGATGATGATGAAGGAATAACGCTTGTGTTATATGAT GATGACGACATCTTTAGATCTTCTTCTTTGCGTGGAAGAGAATAAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.529210439

Conservation Information
Conserved circRNAs	NA
PMCS	0.529210439

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

			
						 Other Information
					
						References
						Ye et al., 2015;Chu et al., 2017

circRNA

Detail information of AT2G02080_circ_g.1

Address

Any questions?

Supported by