Plant Circular RNA Database

Detail information of AT3G60190_circ_g.2

			
						 General Information
					
						CircRNA Name
						AT3G60190_circ_g.2
					
						ID in PlantcircBase
						ath_circ_028409
					
						Alias
						3:22245192-22247032
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 22245192-22247032  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT3G60190						
					
						Parent gene annotation
						
							Dynamin-related protein 1E
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT3G60190_circ_g.1 AT3G60190_circ_g.3 AT3G60190_circ_g.4 AT3G60190_circ_g.5 						
					
						Support reads
						2
					
						Tissues
						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  
						
							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
						AT3G60190.1:9

General Information
CircRNA Name	AT3G60190_circ_g.2
ID in PlantcircBase	ath_circ_028409
Alias	3:22245192-22247032
Organism	Arabidpsis thaliana
Position	chr3: 22245192-22247032 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT3G60190
Parent gene annotation	Dynamin-related protein 1E
Parent gene strand	-
Alternative splicing	AT3G60190_circ_g.1 AT3G60190_circ_g.3 AT3G60190_circ_g.4 AT3G60190_circ_g.5
Support reads	2
Tissues	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	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	AT3G60190.1:9

			
						 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  
						
							TTTGGAGAGTAGATACTGAGGTGAATAGGAACTGGAGATATCTGTTTGTTTTTCCCTGTGATTC
TATCAGTCTCATCCTGAATCTCCCTGCGAACCAAAGagcatccacagaagcttcagctggacct
ctaaagtaacccagtgccccttcgattagacggcgataaccctgttctggtgcaatcaagtgag
gttgataa

									
								

					

						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: 983
Transcript exons: 22245192-22245417,22245499-22245569,22245659-22245778,22
245871-22246065,22246256-22246320,22246413-22246503,2224
6642-22246703,22246795-22246845,22246931-22247032
AGCATCCACAGAAGCTTCAGCTGGACCTCTAAAGTAACCCAGTGCCCCTTCGATTAGACGGCGA
TAACCCTGTTCTGGTGCAATCAAGTGAGGTTGATAACCATCTGCCTCGGACACGATTTTCTTCA
CGCTTTGTAGAGAAAGATGGCGATCAAAAGGAAGCTTTTTAAGTGCAGCTGGAAGTTGGTTGTC
AAAGACTCCATAGATACGGTCACCTCCAGGACGCCCGCCATCAAGATGTTCCTTGAATATCTTA
TCGAATGCACGGCACATCTCCAATATAGTGTATAGTTGAGCCCCAGCATCAACTGCGACAGGCC
GACCCATTCGGTCTAACTCTCTTTCAAGTTCTTCAATGCTTTTGTTTATTAAGGATAGTATACT
TGGAATACGGGTCCTGATAACAGACTCCAAGTGCTTAGAGAGCAGCTTTGCCAGATATTCTGAA
CCCATTTTGCTGGCTAAGTGACCATAGTCAGGACTGGTATCAAAATATTCTCGTTCCTTGCGTC
TTGCAAGCATCATATCGACATTCTTATTAATATCTGCTTGTGAACGGTTCACTATCCCAACCCA
AGGATGTTGCAGCCTGTAAGATCTTCCTTCAAGAACTTCTAACGCATTAGTTCCTTTGTCCATC
AAGTCTAACTTGGTAAGAACACCAAATGTCCTCTCACCTGTTGGATCGACATCTTTTGCGAGCT
TAATTGCATCTGATGTGGCAATGTCTTGGTTGGCAGGAGATATAGCCAATATGATACAATTGGG
CTTATCAACATATGTGCGAACCATGGATTCGATATCCTCAGCAATGGTTTCCGGCTGTCCCTCA
ACAGCCACTTTAGTTAAACCGGGCAAATCAATGAGTGTCAAATTCACAACATTTGGAGAGTAGA
TACTGAGGTGAATAGGAACTGGAGATATCTGTTTGTTTTTCCCTGTGATTCTATCAGTCTCATC
CTGAATCTCCCTGCGAACCAAAG
						
					

						Genomic sequence
						
							AGCATCCACAGAAGCTTCAGCTGGACCTCTAAAGTAACCCAGTGCCCCTTCGATTAGACGGCGA
TAACCCTGTTCTGGTGCAATCAAGTGAGGTTGATAACCATCTGCCTCGGACACGATTTTCTTCA
CGCTTTGTAGAGAAAGATGGCGATCAAAAGGAAGCTTTTTAAGTGCAGCTGGAAGTTGGTTGTC
AAAGACTCCATAGATACGGTCACCTCCAGGACGCCTAAAATGTAAAAAGAGGTTAACCAAAAAT
CAACAACCTAAGCAAAAAAAATTCCACAGGAAGATTAGCAAAGATGTTTACCCGCCATCAAGAT
GTTCCTTGAATATCTTATCGAATGCACGGCACATCTCCAATATAGTGTATAGTTGAGCCTGAGA
ATGAGACCAACAGATTTAGCACATATCAAAAAACGTAAAACTTTATGGAAGAGAAATAGTTTCA
CATAATTGTACTCTCTCACCCCAGCATCAACTGCGACAGGCCGACCCATTCGGTCTAACTCTCT
TTCAAGTTCTTCAATGCTTTTGTTTATTAAGGATAGTATACTTGGAATACGGGTCCTGATAACA
GACTCCAAGTGCTGCATAAAAAAACAAAGACCATAAATCAAATGAATAACAATGAATAAACAAT
CCGATAAAGTCTCAAGTATTTCAGCCTTTGATTGAATACCTTAGAGAGCAGCTTTGCCAGATAT
TCTGAACCCATTTTGCTGGCTAAGTGACCATAGTCAGGACTGGTATCAAAATATTCTCGTTCCT
TGCGTCTTGCAAGCATCATATCGACATTCTTATTAATATCTGCTTGTGAACGGTTCACTATCCC
AACCCAAGGATGTTGCAGCCTGTAAGATCTTCCTTCAAGAACCTTATTAAGGCAAGCAGTTCTG
AATGTTAGATCAAAATTTCTAACTAAAAAAAGTAAGAACTGGAAAGCACGCTGTAGATTTAGTT
ACTTTTATCATCCCTAGATTGGTTTGCCAATCATAATACCAGTCATGTATAATCATTAAAGTGG
ACCATGACACATGAACCAAAAGAGACGAAGAGGTGCTTACTTCTAACGCATTAGTTCCTTTGTC
CATCAAGTCTAACTTGGTAAGAACACCAAATGTCCTCTCACCTGAGACGATCAAAAACTTATTT
CATCATCTAAAGACAGTACTTCCTGCCATATATATATATCAATCATAGGTAACAAAATAGTAAA
CGAACCTGTTGGATCGACATCTTTTGCGAGCTTAATTGCATCTGATGTGGCAATGTCTTGGTTG
GCAGGAGATATAGCCAATATGATACAATTGGGCTGCAAACAAACAGAAATTAAGCTATTGGTAC
TACTAAAAAAGTTAACCATCTGCAACTAGAACTTGAGCATATAGTTTAAAAGTCGTATAAGGTT
TTTGCATTTTTAAAAAAAAATGAAAGATCTAGCAATTCTCACCTTATCAACATATGTGCGAACC
ATGGATTCGATATCCTCAGCAATGGTTTCCGGCTGTCCCTCTGGAAATCAGAGGCAGTATCAAT
AACTACATATACGGTCATCAAATAATAAAGAAATGGAAACCCAAAGAAGAGGTCAAAAGAAACA
TACCAACAGCCACTTTAGTTAAACCGGGCAAATCAATGAGTGTCAAATTCACAACTGTTTCCAT
AAAAAAGAGCAAACATCAATGTTAAATCAACAAACAAGAATGTTACAGGAATCAGACTGAGATT
ATTAAAGATACCATTTGGAGAGTAGATACTGAGGTGAATAGGAACTGGAGATATCTGTTTGTTT
TTCCCTGTGATTCTATCAGTCTCATCCTGAATCTCCCTGCGAACCAAAG
						
					

			
		

Sequences
Splice junction sequence	TTTGGAGAGTAGATACTGAGGTGAATAGGAACTGGAGATATCTGTTTGTTTTTCCCTGTGATTC TATCAGTCTCATCCTGAATCTCCCTGCGAACCAAAGagcatccacagaagcttcagctggacct ctaaagtaacccagtgccccttcgattagacggcgataaccctgttctggtgcaatcaagtgag gttgataa
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: 983 Transcript exons: 22245192-22245417,22245499-22245569,22245659-22245778,22 245871-22246065,22246256-22246320,22246413-22246503,2224 6642-22246703,22246795-22246845,22246931-22247032 AGCATCCACAGAAGCTTCAGCTGGACCTCTAAAGTAACCCAGTGCCCCTTCGATTAGACGGCGA TAACCCTGTTCTGGTGCAATCAAGTGAGGTTGATAACCATCTGCCTCGGACACGATTTTCTTCA CGCTTTGTAGAGAAAGATGGCGATCAAAAGGAAGCTTTTTAAGTGCAGCTGGAAGTTGGTTGTC AAAGACTCCATAGATACGGTCACCTCCAGGACGCCCGCCATCAAGATGTTCCTTGAATATCTTA TCGAATGCACGGCACATCTCCAATATAGTGTATAGTTGAGCCCCAGCATCAACTGCGACAGGCC GACCCATTCGGTCTAACTCTCTTTCAAGTTCTTCAATGCTTTTGTTTATTAAGGATAGTATACT TGGAATACGGGTCCTGATAACAGACTCCAAGTGCTTAGAGAGCAGCTTTGCCAGATATTCTGAA CCCATTTTGCTGGCTAAGTGACCATAGTCAGGACTGGTATCAAAATATTCTCGTTCCTTGCGTC TTGCAAGCATCATATCGACATTCTTATTAATATCTGCTTGTGAACGGTTCACTATCCCAACCCA AGGATGTTGCAGCCTGTAAGATCTTCCTTCAAGAACTTCTAACGCATTAGTTCCTTTGTCCATC AAGTCTAACTTGGTAAGAACACCAAATGTCCTCTCACCTGTTGGATCGACATCTTTTGCGAGCT TAATTGCATCTGATGTGGCAATGTCTTGGTTGGCAGGAGATATAGCCAATATGATACAATTGGG CTTATCAACATATGTGCGAACCATGGATTCGATATCCTCAGCAATGGTTTCCGGCTGTCCCTCA ACAGCCACTTTAGTTAAACCGGGCAAATCAATGAGTGTCAAATTCACAACATTTGGAGAGTAGA TACTGAGGTGAATAGGAACTGGAGATATCTGTTTGTTTTTCCCTGTGATTCTATCAGTCTCATC CTGAATCTCCCTGCGAACCAAAG
Genomic sequence	AGCATCCACAGAAGCTTCAGCTGGACCTCTAAAGTAACCCAGTGCCCCTTCGATTAGACGGCGA TAACCCTGTTCTGGTGCAATCAAGTGAGGTTGATAACCATCTGCCTCGGACACGATTTTCTTCA CGCTTTGTAGAGAAAGATGGCGATCAAAAGGAAGCTTTTTAAGTGCAGCTGGAAGTTGGTTGTC AAAGACTCCATAGATACGGTCACCTCCAGGACGCCTAAAATGTAAAAAGAGGTTAACCAAAAAT CAACAACCTAAGCAAAAAAAATTCCACAGGAAGATTAGCAAAGATGTTTACCCGCCATCAAGAT GTTCCTTGAATATCTTATCGAATGCACGGCACATCTCCAATATAGTGTATAGTTGAGCCTGAGA ATGAGACCAACAGATTTAGCACATATCAAAAAACGTAAAACTTTATGGAAGAGAAATAGTTTCA CATAATTGTACTCTCTCACCCCAGCATCAACTGCGACAGGCCGACCCATTCGGTCTAACTCTCT TTCAAGTTCTTCAATGCTTTTGTTTATTAAGGATAGTATACTTGGAATACGGGTCCTGATAACA GACTCCAAGTGCTGCATAAAAAAACAAAGACCATAAATCAAATGAATAACAATGAATAAACAAT CCGATAAAGTCTCAAGTATTTCAGCCTTTGATTGAATACCTTAGAGAGCAGCTTTGCCAGATAT TCTGAACCCATTTTGCTGGCTAAGTGACCATAGTCAGGACTGGTATCAAAATATTCTCGTTCCT TGCGTCTTGCAAGCATCATATCGACATTCTTATTAATATCTGCTTGTGAACGGTTCACTATCCC AACCCAAGGATGTTGCAGCCTGTAAGATCTTCCTTCAAGAACCTTATTAAGGCAAGCAGTTCTG AATGTTAGATCAAAATTTCTAACTAAAAAAAGTAAGAACTGGAAAGCACGCTGTAGATTTAGTT ACTTTTATCATCCCTAGATTGGTTTGCCAATCATAATACCAGTCATGTATAATCATTAAAGTGG ACCATGACACATGAACCAAAAGAGACGAAGAGGTGCTTACTTCTAACGCATTAGTTCCTTTGTC CATCAAGTCTAACTTGGTAAGAACACCAAATGTCCTCTCACCTGAGACGATCAAAAACTTATTT CATCATCTAAAGACAGTACTTCCTGCCATATATATATATCAATCATAGGTAACAAAATAGTAAA CGAACCTGTTGGATCGACATCTTTTGCGAGCTTAATTGCATCTGATGTGGCAATGTCTTGGTTG GCAGGAGATATAGCCAATATGATACAATTGGGCTGCAAACAAACAGAAATTAAGCTATTGGTAC TACTAAAAAAGTTAACCATCTGCAACTAGAACTTGAGCATATAGTTTAAAAGTCGTATAAGGTT TTTGCATTTTTAAAAAAAAATGAAAGATCTAGCAATTCTCACCTTATCAACATATGTGCGAACC ATGGATTCGATATCCTCAGCAATGGTTTCCGGCTGTCCCTCTGGAAATCAGAGGCAGTATCAAT AACTACATATACGGTCATCAAATAATAAAGAAATGGAAACCCAAAGAAGAGGTCAAAAGAAACA TACCAACAGCCACTTTAGTTAAACCGGGCAAATCAATGAGTGTCAAATTCACAACTGTTTCCAT AAAAAAGAGCAAACATCAATGTTAAATCAACAAACAAGAATGTTACAGGAATCAGACTGAGATT ATTAAAGATACCATTTGGAGAGTAGATACTGAGGTGAATAGGAACTGGAGATATCTGTTTGTTT TTCCCTGTGATTCTATCAGTCTCATCCTGAATCTCCCTGCGAACCAAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.236256472

Conservation Information
Conserved circRNAs	NA
PMCS	0.236256472

			
						 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 AT3G60190_circ_g.2

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