Plant Circular RNA Database

Detail information of AT2G02960_circ_g.1

			
						 General Information
					
						CircRNA Name
						AT2G02960_circ_g.1
					
						ID in PlantcircBase
						ath_circ_012622
					
						Alias
						2:862308-863995
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr2: 862308-863995  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT2G02960						
					
						Parent gene annotation
						
							RING/FYVE/PHD zinc finger superfamily protein
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT2G02960_circ_g.2 AT2G02960_circ_g.3 AT2G02960_circ_g.4 						
					
						Support reads
						1/1
					
						Tissues
						root;flower
					
						Exon boundary  
						
							No-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
						AT2G02960.3:7
AT2G02960.6:7
AT2G02960.2:7
AT2G02960.5:6
AT2G02960.1:7
AT2G02960.4:7

General Information
CircRNA Name	AT2G02960_circ_g.1
ID in PlantcircBase	ath_circ_012622
Alias	2:862308-863995
Organism	Arabidpsis thaliana
Position	chr2: 862308-863995 JBrowse»
Reference genome	TAIR10.38
Type	u-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT2G02960
Parent gene annotation	RING/FYVE/PHD zinc finger superfamily protein
Parent gene strand	-
Alternative splicing	AT2G02960_circ_g.2 AT2G02960_circ_g.3 AT2G02960_circ_g.4
Support reads	1/1
Tissues	root;flower
Exon boundary	No-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	AT2G02960.3:7 AT2G02960.6:7 AT2G02960.2:7 AT2G02960.5:6 AT2G02960.1:7 AT2G02960.4:7

			
						 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  
						
							CATCATCAGAAATATCTAACGCCTTATCATTAACCACCGGCGACTCTGATCTCATCTCCTCAAC
CTCCGCATTAACCGGAGACATATGACTGCCATATGActtgtaatggctccatgcttgtgacatt
agatcagaattcagacaggatcgtcatgctgttgttgtgtagatgtagtcgcatgagccacggc
ggatgatg

									
								

					

						Assembled circRNA sequence  
						
							NA
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
						
							NA						
					

						Genomic sequence
						
							CTTGTAATGGCTCCATGCTTGTGACATTAGATCAGAATTCAGACAGGATCGTCATGCTGTTGTT
GTGTAGATGTAGTCGCATGAGCCACGGCGGATGATGATATTCCCGGTGATACCGTGAAGTGAAC
TGTTCTAGGCTGCCCTGACTGAAGCACCAACGCAAACTGTGTAGCCAAAGCTGCAGCTTCCTGT
TCAATCGGGTTACATTAAGTCGATACCAGTGACTCAGTTTGATTCATAAAACAGTAAGAAAAAA
AAAAGACTGTCCGGAAAAATCCTTGCATGAGTTCTTATACTACTAACCTGTCTCTGTCTTCGGC
GCTGTAGAATACTGATGGCCCAAGCCATGATATAGCATGGAAGAAGAAATCCAGCAGCTCGGAG
CAGGACAAGCTAAAATAAGAATCAGACAATTTTGTGGTTTGGTGTTACAACTTAAATGCAACTG
AGACAAAAAATAAAAGAAAAAGAAAAAAGGAAGAAGCTTCAATGAGCTTACAGATAGTATCGAA
GATGGGTCGTCTTCTTCGCCATCAGTATCATCTGTTATGGTCAGTGCGTGTCGTAAGAGAAGAA
GAGCCATTAACTGTGAAAAAGAAAAGTGTGTTTTGCGGTTATCACAAGCGAGGGATTGTGTTGA
GACTTAAAATAGAAATCTGTCAAGAAGCTTTAAGGCTTACTATTAGAGCAGCTGAGCGACAGAA
TGCGGCCCCGCTTGCACTTGAAGCTGTATATTCCACATATTCAGACTCTAAATACCGACGTTCA
GCTTCAGCAATTGCAAGGAGACGAGGATCATGCACATCCAAACCTGAGATTGTCCATCCTCCAC
TGCAACGCACATGCCAAAGTCAGAAACATAATAATAACCAACCTCAGATAAAATTCTGAGCAGC
AGAAACATGAAATTAACCATACCCAATGTCAATAGTTGTTTCTTCAGGCTGAAGTGGAGGTGGT
GGAGCGGTATATCCAGGTTGATAAGGCTAGCAAGAGAAGTTAAAGACCATCAGATATTGATAAA
CCCAATCAGAGTCACATAGAGAATTCTACTAAGTTGGTGATACAGATGCATGAACGTTGCTCAG
CATTCAGATATACTTAATGTGAGCATCATTTATCCATATTCATACCAAATCATGACTTGAAAGT
GACAATTGGTGTATTAAAAGGTGGAATGCACGATCTTAAATCATTCATCATGTGTGATCTATCA
TCGAATATATGCATAGTCATATTGCCACATCGATTCAAGTCTATAATCCTAAAGATTACAACAA
AAAAGGTAACATACCTGGTGACAAATCTCGCATATAATGTTTCCCTTTTCATTGCACCAACGCT
GAACACATTTTCTATGAGCATACTGGTCAAAAACATAACAAAAAATTCGTCAACAGTCAATTAT
TCTAGAACAAAGCCATTGCTCAATATAGACCAAATGGTTTAAGAATTAGATGATGATGAAAACT
AACCTTTAGGCTGCCACTGCAAGCACAAGGGCTCTCAAGATTCTCAACAGGAGACTCATCAGAA
CAAATACGACATTCACCAGAAACAATAAGCGGTTCATTCTCATCATCATGATCATCATCAGAAA
TATCTAACGCCTTATCATTAACCACCGGCGACTCTGATCTCATCTCCTCAACCTCCGCATTAAC
CGGAGACATATGACTGCCATATGA
						
					

			
		

Sequences
Splice junction sequence	CATCATCAGAAATATCTAACGCCTTATCATTAACCACCGGCGACTCTGATCTCATCTCCTCAAC CTCCGCATTAACCGGAGACATATGACTGCCATATGActtgtaatggctccatgcttgtgacatt agatcagaattcagacaggatcgtcatgctgttgttgtgtagatgtagtcgcatgagccacggc ggatgatg
Assembled circRNA sequence	NA 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	NA
Genomic sequence	CTTGTAATGGCTCCATGCTTGTGACATTAGATCAGAATTCAGACAGGATCGTCATGCTGTTGTT GTGTAGATGTAGTCGCATGAGCCACGGCGGATGATGATATTCCCGGTGATACCGTGAAGTGAAC TGTTCTAGGCTGCCCTGACTGAAGCACCAACGCAAACTGTGTAGCCAAAGCTGCAGCTTCCTGT TCAATCGGGTTACATTAAGTCGATACCAGTGACTCAGTTTGATTCATAAAACAGTAAGAAAAAA AAAAGACTGTCCGGAAAAATCCTTGCATGAGTTCTTATACTACTAACCTGTCTCTGTCTTCGGC GCTGTAGAATACTGATGGCCCAAGCCATGATATAGCATGGAAGAAGAAATCCAGCAGCTCGGAG CAGGACAAGCTAAAATAAGAATCAGACAATTTTGTGGTTTGGTGTTACAACTTAAATGCAACTG AGACAAAAAATAAAAGAAAAAGAAAAAAGGAAGAAGCTTCAATGAGCTTACAGATAGTATCGAA GATGGGTCGTCTTCTTCGCCATCAGTATCATCTGTTATGGTCAGTGCGTGTCGTAAGAGAAGAA GAGCCATTAACTGTGAAAAAGAAAAGTGTGTTTTGCGGTTATCACAAGCGAGGGATTGTGTTGA GACTTAAAATAGAAATCTGTCAAGAAGCTTTAAGGCTTACTATTAGAGCAGCTGAGCGACAGAA TGCGGCCCCGCTTGCACTTGAAGCTGTATATTCCACATATTCAGACTCTAAATACCGACGTTCA GCTTCAGCAATTGCAAGGAGACGAGGATCATGCACATCCAAACCTGAGATTGTCCATCCTCCAC TGCAACGCACATGCCAAAGTCAGAAACATAATAATAACCAACCTCAGATAAAATTCTGAGCAGC AGAAACATGAAATTAACCATACCCAATGTCAATAGTTGTTTCTTCAGGCTGAAGTGGAGGTGGT GGAGCGGTATATCCAGGTTGATAAGGCTAGCAAGAGAAGTTAAAGACCATCAGATATTGATAAA CCCAATCAGAGTCACATAGAGAATTCTACTAAGTTGGTGATACAGATGCATGAACGTTGCTCAG CATTCAGATATACTTAATGTGAGCATCATTTATCCATATTCATACCAAATCATGACTTGAAAGT GACAATTGGTGTATTAAAAGGTGGAATGCACGATCTTAAATCATTCATCATGTGTGATCTATCA TCGAATATATGCATAGTCATATTGCCACATCGATTCAAGTCTATAATCCTAAAGATTACAACAA AAAAGGTAACATACCTGGTGACAAATCTCGCATATAATGTTTCCCTTTTCATTGCACCAACGCT GAACACATTTTCTATGAGCATACTGGTCAAAAACATAACAAAAAATTCGTCAACAGTCAATTAT TCTAGAACAAAGCCATTGCTCAATATAGACCAAATGGTTTAAGAATTAGATGATGATGAAAACT AACCTTTAGGCTGCCACTGCAAGCACAAGGGCTCTCAAGATTCTCAACAGGAGACTCATCAGAA CAAATACGACATTCACCAGAAACAATAAGCGGTTCATTCTCATCATCATGATCATCATCAGAAA TATCTAACGCCTTATCATTAACCACCGGCGACTCTGATCTCATCTCCTCAACCTCCGCATTAAC CGGAGACATATGACTGCCATATGA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.265517092

Conservation Information
Conserved circRNAs	NA
PMCS	0.265517092

			
						 Functional Information
					
						Coding potential
						NA
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							ath-miR5658 						
					
						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	ath-miR5658
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Philips et al., 2020

circRNA

Detail information of AT2G02960_circ_g.1

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