Plant Circular RNA Database

Detail information of AT1G59890_circ_g.11

			
						 General Information
					
						CircRNA Name
						AT1G59890_circ_g.11
					
						ID in PlantcircBase
						ath_circ_008092
					
						Alias
						1:22050039-22050402
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 22050039-22050402  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT1G59890						
					
						Parent gene annotation
						
							SIN3-like 5
							
						Parent gene strand
						+
					
						Alternative splicing
						
							NA						
					
						Support reads
						1/1
					
						Tissues
						seedling;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
						AT1G59890.2:2
AT1G59890.3:2
AT1G59890.4:2
AT1G59890.1:2

General Information
CircRNA Name	AT1G59890_circ_g.11
ID in PlantcircBase	ath_circ_008092
Alias	1:22050039-22050402
Organism	Arabidpsis thaliana
Position	chr1: 22050039-22050402 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT1G59890
Parent gene annotation	SIN3-like 5
Parent gene strand	+
Alternative splicing	NA
Support reads	1/1
Tissues	seedling;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	AT1G59890.2:2 AT1G59890.3:2 AT1G59890.4:2 AT1G59890.1:2

			
						 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  
						
							AAGTGGTCCGGGTGAAGAATCTCTAGGGATGTCACGTGCCTTGGAAGGATTGAACATTATCAAT
GAGGTTGAATGTAAGATAGCTTGCAGTTCTTTCAAGtcatctgcccaaacccgtctcggaattc
aacttatgaacagctggaatgatcagcctgaagttacagctgtaacagtggaaccaggttttgc
taattatc

						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: 276
Transcript exons: 22050039-22050199,22050288-22050402
TCATCTGCCCAAACCCGTCTCGGAATTCAACTTATGAACAGCTGGAATGATCAGCCTGAAGTTA
CAGCTGTAACAGTGGAACCAGGTTTTGCTAATTATCTGCAGAATGACTTTCTTTCGTTTGTCAG
TGATGAAGAGAAACCCGGACTATTTCTGAAAAGGAACAAGGCAAAATTAAGTGGTCCGGGTGAA
GAATCTCTAGGGATGTCACGTGCCTTGGAAGGATTGAACATTATCAATGAGGTTGAATGTAAGA
TAGCTTGCAGTTCTTTCAAG
						
						Genomic sequence
						
							TCATCTGCCCAAACCCGTCTCGGAATTCAACTTATGAACAGCTGGAATGATCAGCCTGAAGTTA
CAGCTGTAACAGTGGAACCAGGTTTTGCTAATTATCTGCAGAATGACTTTCTTTCGTTTGTCAG
TGATGAAGAGAAACCCGGACTATTTCTGAAAAGGTGAATGAAGCAATGATTAGAGCATAACCTT
TTTTCGTCTTCAGTTGTGGTAGTACAGTTAGTAATCACCTTAGCATACTCTTTTCAGGAACAAG
GCAAAATTAAGTGGTCCGGGTGAAGAATCTCTAGGGATGTCACGTGCCTTGGAAGGATTGAACA
TTATCAATGAGGTTGAATGTAAGATAGCTTGCAGTTCTTTCAAG

Sequences
Splice junction sequence	AAGTGGTCCGGGTGAAGAATCTCTAGGGATGTCACGTGCCTTGGAAGGATTGAACATTATCAAT GAGGTTGAATGTAAGATAGCTTGCAGTTCTTTCAAGtcatctgcccaaacccgtctcggaattc aacttatgaacagctggaatgatcagcctgaagttacagctgtaacagtggaaccaggttttgc taattatc
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: 276 Transcript exons: 22050039-22050199,22050288-22050402 TCATCTGCCCAAACCCGTCTCGGAATTCAACTTATGAACAGCTGGAATGATCAGCCTGAAGTTA CAGCTGTAACAGTGGAACCAGGTTTTGCTAATTATCTGCAGAATGACTTTCTTTCGTTTGTCAG TGATGAAGAGAAACCCGGACTATTTCTGAAAAGGAACAAGGCAAAATTAAGTGGTCCGGGTGAA GAATCTCTAGGGATGTCACGTGCCTTGGAAGGATTGAACATTATCAATGAGGTTGAATGTAAGA TAGCTTGCAGTTCTTTCAAG
Genomic sequence	TCATCTGCCCAAACCCGTCTCGGAATTCAACTTATGAACAGCTGGAATGATCAGCCTGAAGTTA CAGCTGTAACAGTGGAACCAGGTTTTGCTAATTATCTGCAGAATGACTTTCTTTCGTTTGTCAG TGATGAAGAGAAACCCGGACTATTTCTGAAAAGGTGAATGAAGCAATGATTAGAGCATAACCTT TTTTCGTCTTCAGTTGTGGTAGTACAGTTAGTAATCACCTTAGCATACTCTTTTCAGGAACAAG GCAAAATTAAGTGGTCCGGGTGAAGAATCTCTAGGGATGTCACGTGCCTTGGAAGGATTGAACA TTATCAATGAGGTTGAATGTAAGATAGCTTGCAGTTCTTTCAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.231976885

Conservation Information
Conserved circRNAs	NA
PMCS	0.231976885

			
						 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 AT1G59890_circ_g.11

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