Plant Circular RNA Database

Detail information of AT1G55250_circ_g.4

			
						 General Information
					
						CircRNA Name
						AT1G55250_circ_g.4
					
						ID in PlantcircBase
						ath_circ_007468
					
						Alias
						1:20607968-20608198
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 20607968-20608198  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT1G55250						
					
						Parent gene annotation
						
							E3 ubiquitin-protein ligase BRE1-like 2
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT1G55250_circ_g.1 AT1G55250_circ_g.2 AT1G55250_circ_g.3 						
					
						Support reads
						3
					
						Tissues
						seedling
					
						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
						AT1G55250.1:1
AT1G55250.5:1
AT1G55250.3:1

General Information
CircRNA Name	AT1G55250_circ_g.4
ID in PlantcircBase	ath_circ_007468
Alias	1:20607968-20608198
Organism	Arabidpsis thaliana
Position	chr1: 20607968-20608198 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT1G55250
Parent gene annotation	E3 ubiquitin-protein ligase BRE1-like 2
Parent gene strand	+
Alternative splicing	AT1G55250_circ_g.1 AT1G55250_circ_g.2 AT1G55250_circ_g.3
Support reads	3
Tissues	seedling
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	AT1G55250.1:1 AT1G55250.5:1 AT1G55250.3:1

			
						 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  
						
							ACAATGGAGTTGATGGGACTCTTTGAGAACACCATTGATACACAGAAGACGAAAGCTGAAAGCA
TTTCACAAAGTTTACATGCTGTAAAATCGACAGAAGgttcagttccaccatgcgctgctgatga
aacgtttctatgtagacttctgcaagtagattccttagatactagtaagagtgatgaggtagta
agaaaggt

						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: 231
Transcript exons: 20607968-20608198
GTTCAGTTCCACCATGCGCTGCTGATGAAACGTTTCTATGTAGACTTCTGCAAGTAGATTCCTT
AGATACTAGTAAGAGTGATGAGGTAGTAAGAAAGGTTGAAGAAGCTCTTGCTTTGCGTCATTCC
TCTACAATGGAGTTGATGGGACTCTTTGAGAACACCATTGATACACAGAAGACGAAAGCTGAAA
GCATTTCACAAAGTTTACATGCTGTAAAATCGACAGAAG
Transcript length: 231
Transcript exons: 20607968-20608198
GTTCAGTTCCACCATGCGCTGCTGATGAAACGTTTCTATGTAGACTTCTGCAAGTAGATTCCTT
AGATACTAGTAAGAGTGATGAGGTAGTAAGAAAGGTTGAAGAAGCTCTTGCTTTGCGTCATTCC
TCTACAATGGAGTTGATGGGACTCTTTTAGAACACCATTGATACACAGAAGACGAAAGCTGAAA
GCATTTCACAAAGTTTACATGCTGTAAAATCGACAGAAG
						
						Genomic sequence
						
							GTTCAGTTCCACCATGCGCTGCTGATGAAACGTTTCTATGTAGACTTCTGCAAGTAGATTCCTT
AGATACTAGTAAGAGTGATGAGGTAGTAAGAAAGGTTGAAGAAGCTCTTGCTTTGCGTCATTCC
TCTACAATGGAGTTGATGGGACTCTTTGAGAACACCATTGATACACAGAAGACGAAAGCTGAAA
GCATTTCACAAAGTTTACATGCTGTAAAATCGACAGAAG

Sequences
Splice junction sequence	ACAATGGAGTTGATGGGACTCTTTGAGAACACCATTGATACACAGAAGACGAAAGCTGAAAGCA TTTCACAAAGTTTACATGCTGTAAAATCGACAGAAGgttcagttccaccatgcgctgctgatga aacgtttctatgtagacttctgcaagtagattccttagatactagtaagagtgatgaggtagta agaaaggt
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: 231 Transcript exons: 20607968-20608198 GTTCAGTTCCACCATGCGCTGCTGATGAAACGTTTCTATGTAGACTTCTGCAAGTAGATTCCTT AGATACTAGTAAGAGTGATGAGGTAGTAAGAAAGGTTGAAGAAGCTCTTGCTTTGCGTCATTCC TCTACAATGGAGTTGATGGGACTCTTTGAGAACACCATTGATACACAGAAGACGAAAGCTGAAA GCATTTCACAAAGTTTACATGCTGTAAAATCGACAGAAG Transcript length: 231 Transcript exons: 20607968-20608198 GTTCAGTTCCACCATGCGCTGCTGATGAAACGTTTCTATGTAGACTTCTGCAAGTAGATTCCTT AGATACTAGTAAGAGTGATGAGGTAGTAAGAAAGGTTGAAGAAGCTCTTGCTTTGCGTCATTCC TCTACAATGGAGTTGATGGGACTCTTTTAGAACACCATTGATACACAGAAGACGAAAGCTGAAA GCATTTCACAAAGTTTACATGCTGTAAAATCGACAGAAG
Genomic sequence	GTTCAGTTCCACCATGCGCTGCTGATGAAACGTTTCTATGTAGACTTCTGCAAGTAGATTCCTT AGATACTAGTAAGAGTGATGAGGTAGTAAGAAAGGTTGAAGAAGCTCTTGCTTTGCGTCATTCC TCTACAATGGAGTTGATGGGACTCTTTGAGAACACCATTGATACACAGAAGACGAAAGCTGAAA GCATTTCACAAAGTTTACATGCTGTAAAATCGACAGAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.445419613

Conservation Information
Conserved circRNAs	NA
PMCS	0.445419613

			
						 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 AT1G55250_circ_g.4

Address

Any questions?

Supported by