Plant Circular RNA Database

Detail information of AT1G09910_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT1G09910_circ_g.3
					
						ID in PlantcircBase
						ath_circ_001766
					
						Alias
						1:3221328-3223649
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 3221328-3223649  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT1G09910						
					
						Parent gene annotation
						
							Rhamnogalacturonate lyase family protein
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT1G09910_circ_g.2 AT1G09910_circ_g.4 AT1G09910_circ_g.5 						
					
						Support reads
						1/2
					
						Tissues
						root;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
						AT1G09910.1:9
AT1G09910.3:9
AT1G09910.2:9

General Information
CircRNA Name	AT1G09910_circ_g.3
ID in PlantcircBase	ath_circ_001766
Alias	1:3221328-3223649
Organism	Arabidpsis thaliana
Position	chr1: 3221328-3223649 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT1G09910
Parent gene annotation	Rhamnogalacturonate lyase family protein
Parent gene strand	-
Alternative splicing	AT1G09910_circ_g.2 AT1G09910_circ_g.4 AT1G09910_circ_g.5
Support reads	1/2
Tissues	root;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	AT1G09910.1:9 AT1G09910.3:9 AT1G09910.2:9

			
						 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  
						
							GAACTTCGAGCACATTGTCAATACCGTTATACTCTATCCCAGTGATAATTCCACCTGGCTTTGA
CAGTGTAACTTGGAGGATCCCATTGTCCATCACAACcttgcattcaatttgccaagaaccagaa
tcaccaggcggagccaaaccaacataagcacctcttgctgaaatcaaatcattgtttatgaacc
tatacaaa

									
								

					

						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
						
							CTTGCATTCAATTTGCCAAGAACCAGAATCACCAGGCGGAGCCAAACCAACATAAGCACCTCTT
GCTGAAATCAAATCATTGTTTATGAACCTATACAAAAATTCAACATGTTAATATACACTAAGAA
ATATTACAGAAGCAATATAAAATAAAGGAAGATGCAGGAAAAAGAAAAAAAAATTAGAATGTAA
AAAACACAAATACCTGTCACGGATAAGTAATCTACCACGGGCTGTGCCACGTTCTTCAGACTTT
GGATAGTCGTCAGATGCCACAAAGCTATAAGGCCACCTTTCAACCTCAGCCATCATCTGCAGAT
TACCTCATACAAGTGAGCCCTTACAGTACCACAAATCTTTTTCTGTATTCAGCAAGTCCAATAG
CGATTTGCTTCACTCGTACCTTTATCTTAGCATCGTCCCATAAGCAAAGTGGATCATCTCCATT
GGCTGTGGAATTTAGGTAAATGAAAACAGGGCCATAGACTTTCTTCCAAGGCTCACCGTGTTCA
AAACGAGGCATCATGGTTTTTCCAGCATAATGAGTACTGTGAAACACCTGAAATAACCATTACG
GAAATTAACACTTCTAAGTATTATACTGAAACATTCACCACATATGTCACAGGGACACTTACTG
CAAGAGTGGTTGGGCCAACATGTGAAGTCAGGTTTTGTTTGAGTGGTCCGCCTGAGCGGAACTC
ATTACTGGGCGTAATTTGCCAAAATCCTACTGGTGGATCGAAGGATATCCATCCATGTACTCTC
AGATCCTTATTCTCACACGAATATTGGTATTTATCATCTACCTGTCAGAGAAGAAAAATGATTT
AGTTATCTGTGAAACAGTATTTACCGGATTCATTATTTGAAGTTGTAATACATCACAAAACGAG
CATAAGTTCATAATATACGCATTCATGTATCAGTAAATGGGAGAATAAACAGCTCAACAACGCA
TGAGAAAGAACAAAATGTTGTAATTTCTAAACGATGGAAAAAATATGGAACTCATACTTCGCCT
TGTAGGCGTGGATCACAAGGAGCAGTGAGCAGAGAAGCTTCCTGGTAATCTAGAGTTTGGCATC
TTCCTTTGCATAGATCATCTGGAAAAGGCATTATCCTTTTTCTGTCATCTGCCACAGCCATGTA
ATGGAATCTGTAAAAAAAGAATCGCAACAGGAAAATATATGAGTATCAAACAACTACACACTTT
TGTGTTTACGAACAATTAAACCCAATAAATAGATATCTGACATATTGCACAATTCTTTTGCTTG
GAATCTATGGTACTCTTCACATGGACAGGCAATCACTAACATTTCTAACTTTCTTCTCTTAAGG
AGATTAGACATTACATAAGATAGAGAATGGGGATAATATTACTTGTCTTTTCTGAGCTTGAAGG
CAATTCTAGTTTCTCCAAGTTCAAAGCCAGGCCAATCCTTAAGATGTTCATAAATGCCGTATGA
GTACACTCCAGAAGAGCCACGGAGCATTATAAACCTGAAAGAAAGAGCAACTAGTCAATGTCTT
TCTCTACTTTTGTTTCTCGCCAAAGGAAATATATTATGTAAGATAGACCTTTTATCGATATTCA
AGGGAATGTACTTGCCCTCAAGGGATGGATCCCATGTTCTTAGAAATGAGATCTCAACCTGTTC
TTCGGTCTCGACTATGACCCTGAAAGTCACTCCACTGATGCTGCATATATGATATCAAACAATC
CAACGATTAGTACACATCATATACCATCCAACAATTAGTACCGATTATATAACATCATATACAC
AAGAGAAAAAAAGAGAAAAGCATTAAAAGAGAGGATTCTGATGCAGCAGTGACAGCTGACAACT
TCAGTTAAGCAGAGGAAACTTGTTTTGAGTATACATCAACTTAACTCCACCAATATCGAAAAAT
CCCACTAACAGATGTTGCAATCAATAGCACGATGAAGACCTATAGAATAACATTCCTGAGCTCC
TAATCCTAGTGAATGTTAAGGTAAATGCATAGAGTGCATACACATCAAATATTCCCTTGCCTCC
AGGTTCATTCCAGTGCAGGTCCCAGTACCTATACATTCATTTATATTATCGATTAACTTGGCTT
CTCACAGAATTTGAAGGAAAAAAAGACTTTTGTTCTCCTCTGAAGAAAGCAGTATAACTAAAAT
CATATATTAAAACATGATTCATACCCTCTGTTAGTCTCCTTGTTACGAACTTCGAGCACATTGT
CAATACCGTTATACTCTATCCCAGTGATAATTCCACCTGGCTTTGACAGTGTAACTTGGAGGAT
CCCATTGTCCATCACAAC
						
					

			
		

Sequences
Splice junction sequence	GAACTTCGAGCACATTGTCAATACCGTTATACTCTATCCCAGTGATAATTCCACCTGGCTTTGA CAGTGTAACTTGGAGGATCCCATTGTCCATCACAACcttgcattcaatttgccaagaaccagaa tcaccaggcggagccaaaccaacataagcacctcttgctgaaatcaaatcattgtttatgaacc tatacaaa
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	CTTGCATTCAATTTGCCAAGAACCAGAATCACCAGGCGGAGCCAAACCAACATAAGCACCTCTT GCTGAAATCAAATCATTGTTTATGAACCTATACAAAAATTCAACATGTTAATATACACTAAGAA ATATTACAGAAGCAATATAAAATAAAGGAAGATGCAGGAAAAAGAAAAAAAAATTAGAATGTAA AAAACACAAATACCTGTCACGGATAAGTAATCTACCACGGGCTGTGCCACGTTCTTCAGACTTT GGATAGTCGTCAGATGCCACAAAGCTATAAGGCCACCTTTCAACCTCAGCCATCATCTGCAGAT TACCTCATACAAGTGAGCCCTTACAGTACCACAAATCTTTTTCTGTATTCAGCAAGTCCAATAG CGATTTGCTTCACTCGTACCTTTATCTTAGCATCGTCCCATAAGCAAAGTGGATCATCTCCATT GGCTGTGGAATTTAGGTAAATGAAAACAGGGCCATAGACTTTCTTCCAAGGCTCACCGTGTTCA AAACGAGGCATCATGGTTTTTCCAGCATAATGAGTACTGTGAAACACCTGAAATAACCATTACG GAAATTAACACTTCTAAGTATTATACTGAAACATTCACCACATATGTCACAGGGACACTTACTG CAAGAGTGGTTGGGCCAACATGTGAAGTCAGGTTTTGTTTGAGTGGTCCGCCTGAGCGGAACTC ATTACTGGGCGTAATTTGCCAAAATCCTACTGGTGGATCGAAGGATATCCATCCATGTACTCTC AGATCCTTATTCTCACACGAATATTGGTATTTATCATCTACCTGTCAGAGAAGAAAAATGATTT AGTTATCTGTGAAACAGTATTTACCGGATTCATTATTTGAAGTTGTAATACATCACAAAACGAG CATAAGTTCATAATATACGCATTCATGTATCAGTAAATGGGAGAATAAACAGCTCAACAACGCA TGAGAAAGAACAAAATGTTGTAATTTCTAAACGATGGAAAAAATATGGAACTCATACTTCGCCT TGTAGGCGTGGATCACAAGGAGCAGTGAGCAGAGAAGCTTCCTGGTAATCTAGAGTTTGGCATC TTCCTTTGCATAGATCATCTGGAAAAGGCATTATCCTTTTTCTGTCATCTGCCACAGCCATGTA ATGGAATCTGTAAAAAAAGAATCGCAACAGGAAAATATATGAGTATCAAACAACTACACACTTT TGTGTTTACGAACAATTAAACCCAATAAATAGATATCTGACATATTGCACAATTCTTTTGCTTG GAATCTATGGTACTCTTCACATGGACAGGCAATCACTAACATTTCTAACTTTCTTCTCTTAAGG AGATTAGACATTACATAAGATAGAGAATGGGGATAATATTACTTGTCTTTTCTGAGCTTGAAGG CAATTCTAGTTTCTCCAAGTTCAAAGCCAGGCCAATCCTTAAGATGTTCATAAATGCCGTATGA GTACACTCCAGAAGAGCCACGGAGCATTATAAACCTGAAAGAAAGAGCAACTAGTCAATGTCTT TCTCTACTTTTGTTTCTCGCCAAAGGAAATATATTATGTAAGATAGACCTTTTATCGATATTCA AGGGAATGTACTTGCCCTCAAGGGATGGATCCCATGTTCTTAGAAATGAGATCTCAACCTGTTC TTCGGTCTCGACTATGACCCTGAAAGTCACTCCACTGATGCTGCATATATGATATCAAACAATC CAACGATTAGTACACATCATATACCATCCAACAATTAGTACCGATTATATAACATCATATACAC AAGAGAAAAAAAGAGAAAAGCATTAAAAGAGAGGATTCTGATGCAGCAGTGACAGCTGACAACT TCAGTTAAGCAGAGGAAACTTGTTTTGAGTATACATCAACTTAACTCCACCAATATCGAAAAAT CCCACTAACAGATGTTGCAATCAATAGCACGATGAAGACCTATAGAATAACATTCCTGAGCTCC TAATCCTAGTGAATGTTAAGGTAAATGCATAGAGTGCATACACATCAAATATTCCCTTGCCTCC AGGTTCATTCCAGTGCAGGTCCCAGTACCTATACATTCATTTATATTATCGATTAACTTGGCTT CTCACAGAATTTGAAGGAAAAAAAGACTTTTGTTCTCCTCTGAAGAAAGCAGTATAACTAAAAT CATATATTAAAACATGATTCATACCCTCTGTTAGTCTCCTTGTTACGAACTTCGAGCACATTGT CAATACCGTTATACTCTATCCCAGTGATAATTCCACCTGGCTTTGACAGTGTAACTTGGAGGAT CCCATTGTCCATCACAAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.126660002

Conservation Information
Conserved circRNAs	NA
PMCS	0.126660002

			
						 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 AT1G09910_circ_g.3

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