Plant Circular RNA Database

Detail information of AT1G15570_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT1G15570_circ_g.3
					
						ID in PlantcircBase
						ath_circ_002758
					
						Alias
						1:5362960-5364252
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 5362960-5364252  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT1G15570						
					
						Parent gene annotation
						
							CYCA2
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT1G15570_circ_g.1 AT1G15570_circ_g.2 AT1G15570_circ_g.4 AT1G15570_circ_g.5 AT1G15570_circ_g.6 AT1G15570_circ_g.7 AT1G15570_circ_g.8 						
					
						Support reads
						2
					
						Tissues
						leaf
					
						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
						AT1G15570.1:5

General Information
CircRNA Name	AT1G15570_circ_g.3
ID in PlantcircBase	ath_circ_002758
Alias	1:5362960-5364252
Organism	Arabidpsis thaliana
Position	chr1: 5362960-5364252 JBrowse»
Reference genome	TAIR10.38
Type	ue-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT1G15570
Parent gene annotation	CYCA2
Parent gene strand	+
Alternative splicing	AT1G15570_circ_g.1 AT1G15570_circ_g.2 AT1G15570_circ_g.4 AT1G15570_circ_g.5 AT1G15570_circ_g.6 AT1G15570_circ_g.7 AT1G15570_circ_g.8
Support reads	2
Tissues	leaf
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	AT1G15570.1:5

			
						 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  
						
							TCTACCTCACAGTGTATCTCATAGACTGGTTCCTCCATGGAAACTACGTGCAAAGACAGCAACT
TCAACTGCTCGGCATCACTTGCATGCTAATTGCCTCatcagaggaagatgatgcaatcctaaga
ctctaagacttcttcaaggctgtgttttatcgtgggatttttaaacatggggaaggaaaatgct
gtgtctcg

									
								

					

						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: 901
Transcript exons: 5362960-5363249,5363361-5363607,5363704-5363840,5363938-
5364030,5364119-5364252
ATCAGAGGAAGATGATGCAATCCTAAGACTCTAAGACTTCTTCAAGGCTGTGTTTTATCGTGGG
ATTTTTAAACATGGGGAAGGAAAATGCTGTGTCTCGGCCATTCACTCGTTCCCTTGCCTCTGCT
TTGCGCGCTTCAGAAGTGACTTCTACTACACAGAATCAACAGAGAGTAAACACAAAAAGACCAG
CCTTGGAGGATACAAGAGCCACTGGACCCAACAAGAGGAAGAAGCGAGCGGTTCTAGGGGAGAT
CACAAATGTTAACTCCAATACAGCTATACTTGAGGCCAAAAACAGCAAGCAGATAAAGAAAGGA
CGCGGTCATGGATTGGCGAGTACATCCCAGTTGGCAACTTCTGTTACTTCAGAAGTCACAGATC
TTCAGTCCAGGACCGATGCAAAAGTTGAAGTTGCATCAAATACAGCAGGAAACCTTTCTGTTTC
TAAAGGCACAGATAACACAGCTGATAACTGTATTGAGATATGGAATTCTAGATTGCCTCCAAGA
CCTCTTGGGAGATCAGCTTCTACAGCTGAGAAAAGTGCTGTTATTGGTAGTTCAACTGTACCGG
ATATCCCAAAATTTGTAGACATCGATTCAGATGACAAGGATCCTTTACTGTGCTGCCTCTATGC
CCCTGAAATCCACTACAATTTGCGTGTTTCAGAGCTTAAACGCAGACCACTTCCGGACTTTATG
GAGAGAATACAGAAGGATGTCACCCAGTCCATGCGGGGAATTCTGGTTGATTGGCTTGTGGAGG
TCTCTGAAGAATACACACTTGCATCTGACACTCTCTACCTCACAGTGTATCTCATAGACTGGTT
CCTCCATGGAAACTACGTGCAAAGACAGCAACTTCAACTGCTCGGCATCACTTGCATGCTAATT
GCCTC
						
					

						Genomic sequence
						
							ATCAGAGGAAGATGATGCAATCCTAAGACTCTAAGACTTCTTCAAGGCTGTGTTTTATCGTGGG
ATTTTTAAACATGGGGAAGGAAAATGCTGTGTCTCGGCCATTCACTCGTTCCCTTGCCTCTGCT
TTGCGCGCTTCAGAAGTGACTTCTACTACACAGAATCAACAGAGAGTAAACACAAAAAGACCAG
CCTTGGAGGATACAAGAGCCACTGGACCCAACAAGAGGAAGAAGCGAGCGGTTCTAGGGGAGAT
CACAAATGTTAACTCCAATACAGCTATACTTGAGGTTGTTAAAACTATATTATGTTTCTTTATA
GTGTTTGGTTTCCTGTGAATTTTTGTAAAGATCTTGTGAAGTAAAACATGCATCACTGAAACAT
GGGTTTTGCCATTTCAGGCCAAAAACAGCAAGCAGATAAAGAAAGGACGCGGTCATGGATTGGC
GAGTACATCCCAGTTGGCAACTTCTGTTACTTCAGAAGTCACAGATCTTCAGTCCAGGACCGAT
GCAAAAGTTGAAGTTGCATCAAATACAGCAGGAAACCTTTCTGTTTCTAAAGGCACAGATAACA
CAGCTGATAACTGTATTGAGATATGGAATTCTAGATTGCCTCCAAGACCTCTTGGGAGATCAGC
TTCTACAGGTGATCCATTTAACACAAGTTTTCATATGATTAGTTCCTATTGTATAAAGGAGTGG
TCTTTAATGACTTATAAATCTTTTTTGCAAATGGTTACAGCTGAGAAAAGTGCTGTTATTGGTA
GTTCAACTGTACCGGATATCCCAAAATTTGTAGACATCGATTCAGATGACAAGGATCCTTTACT
GTGCTGCCTCTATGCCCCTGAAATCCACTACAATTTGCGTGTTTCAGAGGTAATTCCTAGGCTT
TGATAGTCTCTAAAGAAACTTGGTGAGCCAAAGGACTGAAAGTTTTATTGCTTGTGCTTCTGTG
TCACTTCTCTTCTGGCAGCTTAAACGCAGACCACTTCCGGACTTTATGGAGAGAATACAGAAGG
ATGTCACCCAGTCCATGCGGGGAATTCTGGTTGATTGGCTTGTGGAGGTTAGTGTTTAGTTCTA
CTTTTGATGCTAACTTTTGAAGCTACTATGACCTTTTCCGGGTTCTCACAAAAGTCTGATTTCA
ATCACAGGTCTCTGAAGAATACACACTTGCATCTGACACTCTCTACCTCACAGTGTATCTCATA
GACTGGTTCCTCCATGGAAACTACGTGCAAAGACAGCAACTTCAACTGCTCGGCATCACTTGCA
TGCTAATTGCCTC
						
					

			
		

Sequences
Splice junction sequence	TCTACCTCACAGTGTATCTCATAGACTGGTTCCTCCATGGAAACTACGTGCAAAGACAGCAACT TCAACTGCTCGGCATCACTTGCATGCTAATTGCCTCatcagaggaagatgatgcaatcctaaga ctctaagacttcttcaaggctgtgttttatcgtgggatttttaaacatggggaaggaaaatgct gtgtctcg
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: 901 Transcript exons: 5362960-5363249,5363361-5363607,5363704-5363840,5363938- 5364030,5364119-5364252 ATCAGAGGAAGATGATGCAATCCTAAGACTCTAAGACTTCTTCAAGGCTGTGTTTTATCGTGGG ATTTTTAAACATGGGGAAGGAAAATGCTGTGTCTCGGCCATTCACTCGTTCCCTTGCCTCTGCT TTGCGCGCTTCAGAAGTGACTTCTACTACACAGAATCAACAGAGAGTAAACACAAAAAGACCAG CCTTGGAGGATACAAGAGCCACTGGACCCAACAAGAGGAAGAAGCGAGCGGTTCTAGGGGAGAT CACAAATGTTAACTCCAATACAGCTATACTTGAGGCCAAAAACAGCAAGCAGATAAAGAAAGGA CGCGGTCATGGATTGGCGAGTACATCCCAGTTGGCAACTTCTGTTACTTCAGAAGTCACAGATC TTCAGTCCAGGACCGATGCAAAAGTTGAAGTTGCATCAAATACAGCAGGAAACCTTTCTGTTTC TAAAGGCACAGATAACACAGCTGATAACTGTATTGAGATATGGAATTCTAGATTGCCTCCAAGA CCTCTTGGGAGATCAGCTTCTACAGCTGAGAAAAGTGCTGTTATTGGTAGTTCAACTGTACCGG ATATCCCAAAATTTGTAGACATCGATTCAGATGACAAGGATCCTTTACTGTGCTGCCTCTATGC CCCTGAAATCCACTACAATTTGCGTGTTTCAGAGCTTAAACGCAGACCACTTCCGGACTTTATG GAGAGAATACAGAAGGATGTCACCCAGTCCATGCGGGGAATTCTGGTTGATTGGCTTGTGGAGG TCTCTGAAGAATACACACTTGCATCTGACACTCTCTACCTCACAGTGTATCTCATAGACTGGTT CCTCCATGGAAACTACGTGCAAAGACAGCAACTTCAACTGCTCGGCATCACTTGCATGCTAATT GCCTC
Genomic sequence	ATCAGAGGAAGATGATGCAATCCTAAGACTCTAAGACTTCTTCAAGGCTGTGTTTTATCGTGGG ATTTTTAAACATGGGGAAGGAAAATGCTGTGTCTCGGCCATTCACTCGTTCCCTTGCCTCTGCT TTGCGCGCTTCAGAAGTGACTTCTACTACACAGAATCAACAGAGAGTAAACACAAAAAGACCAG CCTTGGAGGATACAAGAGCCACTGGACCCAACAAGAGGAAGAAGCGAGCGGTTCTAGGGGAGAT CACAAATGTTAACTCCAATACAGCTATACTTGAGGTTGTTAAAACTATATTATGTTTCTTTATA GTGTTTGGTTTCCTGTGAATTTTTGTAAAGATCTTGTGAAGTAAAACATGCATCACTGAAACAT GGGTTTTGCCATTTCAGGCCAAAAACAGCAAGCAGATAAAGAAAGGACGCGGTCATGGATTGGC GAGTACATCCCAGTTGGCAACTTCTGTTACTTCAGAAGTCACAGATCTTCAGTCCAGGACCGAT GCAAAAGTTGAAGTTGCATCAAATACAGCAGGAAACCTTTCTGTTTCTAAAGGCACAGATAACA CAGCTGATAACTGTATTGAGATATGGAATTCTAGATTGCCTCCAAGACCTCTTGGGAGATCAGC TTCTACAGGTGATCCATTTAACACAAGTTTTCATATGATTAGTTCCTATTGTATAAAGGAGTGG TCTTTAATGACTTATAAATCTTTTTTGCAAATGGTTACAGCTGAGAAAAGTGCTGTTATTGGTA GTTCAACTGTACCGGATATCCCAAAATTTGTAGACATCGATTCAGATGACAAGGATCCTTTACT GTGCTGCCTCTATGCCCCTGAAATCCACTACAATTTGCGTGTTTCAGAGGTAATTCCTAGGCTT TGATAGTCTCTAAAGAAACTTGGTGAGCCAAAGGACTGAAAGTTTTATTGCTTGTGCTTCTGTG TCACTTCTCTTCTGGCAGCTTAAACGCAGACCACTTCCGGACTTTATGGAGAGAATACAGAAGG ATGTCACCCAGTCCATGCGGGGAATTCTGGTTGATTGGCTTGTGGAGGTTAGTGTTTAGTTCTA CTTTTGATGCTAACTTTTGAAGCTACTATGACCTTTTCCGGGTTCTCACAAAAGTCTGATTTCA ATCACAGGTCTCTGAAGAATACACACTTGCATCTGACACTCTCTACCTCACAGTGTATCTCATA GACTGGTTCCTCCATGGAAACTACGTGCAAAGACAGCAACTTCAACTGCTCGGCATCACTTGCA TGCTAATTGCCTC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.222561002

Conservation Information
Conserved circRNAs	NA
PMCS	0.222561002

			
						 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 AT1G15570_circ_g.3

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