Plant Circular RNA Database

Detail information of AT3G60130_circ_g.2

			
						 General Information
					
						CircRNA Name
						AT3G60130_circ_g.2
					
						ID in PlantcircBase
						ath_circ_028405
					
						Alias
						NA
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 22210558-22211784  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						PcircRNA_finder
					
						Parent gene
						
							AT3G60130						
					
						Parent gene annotation
						
							Beta-glucosidase 16
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT3G60130_circ_g.1 						
					
						Support reads
						1
					
						Tissues
						aerial
					
						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
						AT3G60130.3:5
AT3G60130.2:5
AT3G60130.1:6

General Information
CircRNA Name	AT3G60130_circ_g.2
ID in PlantcircBase	ath_circ_028405
Alias	NA
Organism	Arabidpsis thaliana
Position	chr3: 22210558-22211784 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	PcircRNA_finder
Parent gene	AT3G60130
Parent gene annotation	Beta-glucosidase 16
Parent gene strand	+
Alternative splicing	AT3G60130_circ_g.1
Support reads	1
Tissues	aerial
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	AT3G60130.3:5 AT3G60130.2:5 AT3G60130.1:6

			
						 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  
						
							TTGCTTAGGTGGCGATGCAGCCACGGAGCCTTACATCGTCGGCCATAACCTCCTCCTTGCTCAT
GGAGTTGCCGTAAAAGTATATAGAGAAAAGTACCAGtgtgaaggagctgcacatgaagatggta
gaggtccaagtatctgggactccttctctgaaaaattcccaggtttttttcctaattagaaacc
ccaaaagc

									
								

					

						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: 627
Transcript exons: 22210558-22210627,22210837-22210895,22210988-22211063,22
211153-22211230,22211360-22211447,22211529-22211784
TGTGAAGGAGCTGCACATGAAGATGGTAGAGGTCCAAGTATCTGGGACTCCTTCTCTGAAAAAT
TCCCAGAAAAGATAATGGATGGTAGTAATGGGTCCATTGCAGATGATTCTTACAATCTTTACAA
GGAAGATGTGAATTTGCTGCATCAAATTGGCTTCGATGCTTACCGATTTTCGATCTCATGGTCA
CGGATTTTGCCTCGTGGGACTCTAAAGGGAGGAATCAACCAGGCTGGAATTGAATATTATAACA
ACTTGATTAATCAACTTATATCTAAAGGAGTGAAGCCATTTGTCACACTCTTTCACTGGGACTT
ACCAGATGCACTCGAAAATGCTTACGGTGGCCTCCTTGGAGATGAATTTGTGAACGATTTCCGA
GACTATGCAGAACTTTGTTTCCAGAAGTTTGGAGATAGAGTGAAGCAGTGGACGACACTAAACG
AGCCATATACAATGGTACATGAAGGTTATATAACAGGTCAAAAGGCACCTGGAAGATGTTCCAA
TTTCTATAAACCTGATTGCTTAGGTGGCGATGCAGCCACGGAGCCTTACATCGTCGGCCATAAC
CTCCTCCTTGCTCATGGAGTTGCCGTAAAAGTATATAGAGAAAAGTACCAG
						
					

						Genomic sequence
						
							TGTGAAGGAGCTGCACATGAAGATGGTAGAGGTCCAAGTATCTGGGACTCCTTCTCTGAAAAAT
TCCCAGGTTTTTTTCCTAATTAGAAACCCCAAAAGCTTTAGATCTCTATAAAGATTTAAGCCTC
AAAATGTTGGAGTTTGGTTCATATATGTGAATCTGGTTTTGTCTTGTGTTCATAACAAAAATGG
GTTGATGATGATGAACCTTCTTGATACTTCTTTCTTTTTCTTGGTATTAAATTTAAAGATAAAT
ATTTTTGTCATTTTCATTTTCAGAAAAGATAATGGATGGTAGTAATGGGTCCATTGCAGATGAT
TCTTACAATCTTTACAAGGTCTTATTTGCTTTCTTCACCCAAAAAAGAAATAAAGTCAATTATA
CATCAAGCATTACATTTTGCTTCATGATTTTTTTTTGGAAAATCAGGAAGATGTGAATTTGCTG
CATCAAATTGGCTTCGATGCTTACCGATTTTCGATCTCATGGTCACGGATTTTGCCTCGTAAGA
TATCGATATTATCGGATTAGATCTTTGTAACTTGTAAGCGTTGTTATATATTCTTGATGTAACT
CTTCTCAATTGTTTATTAGGTGGGACTCTAAAGGGAGGAATCAACCAGGCTGGAATTGAATATT
ATAACAACTTGATTAATCAACTTATATCTAAAGGTAATGTTTCTCTGTTTCTCAGTCTATTTGA
TTTTAATGCACATAGAGGAAATCTTGGTGATGTTTAGGATATTGCCAAAACCCTTGTAATTTTT
TTTTTTTTTTCTTGTAATGTTGTAAATGTGTCAGGAGTGAAGCCATTTGTCACACTCTTTCACT
GGGACTTACCAGATGCACTCGAAAATGCTTACGGTGGCCTCCTTGGAGATGAATTTGTGTAAGT
TCATTCATAAGATCTCTATATGGTAAGATTACGACACTGCGAAGATTTGTTGTTGATATTTTGG
TAATGAAACAGGAACGATTTCCGAGACTATGCAGAACTTTGTTTCCAGAAGTTTGGAGATAGAG
TGAAGCAGTGGACGACACTAAACGAGCCATATACAATGGTACATGAAGGTTATATAACAGGTCA
AAAGGCACCTGGAAGATGTTCCAATTTCTATAAACCTGATTGCTTAGGTGGCGATGCAGCCACG
GAGCCTTACATCGTCGGCCATAACCTCCTCCTTGCTCATGGAGTTGCCGTAAAAGTATATAGAG
AAAAGTACCAG
						
					

			
		

Sequences
Splice junction sequence	TTGCTTAGGTGGCGATGCAGCCACGGAGCCTTACATCGTCGGCCATAACCTCCTCCTTGCTCAT GGAGTTGCCGTAAAAGTATATAGAGAAAAGTACCAGtgtgaaggagctgcacatgaagatggta gaggtccaagtatctgggactccttctctgaaaaattcccaggtttttttcctaattagaaacc ccaaaagc
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: 627 Transcript exons: 22210558-22210627,22210837-22210895,22210988-22211063,22 211153-22211230,22211360-22211447,22211529-22211784 TGTGAAGGAGCTGCACATGAAGATGGTAGAGGTCCAAGTATCTGGGACTCCTTCTCTGAAAAAT TCCCAGAAAAGATAATGGATGGTAGTAATGGGTCCATTGCAGATGATTCTTACAATCTTTACAA GGAAGATGTGAATTTGCTGCATCAAATTGGCTTCGATGCTTACCGATTTTCGATCTCATGGTCA CGGATTTTGCCTCGTGGGACTCTAAAGGGAGGAATCAACCAGGCTGGAATTGAATATTATAACA ACTTGATTAATCAACTTATATCTAAAGGAGTGAAGCCATTTGTCACACTCTTTCACTGGGACTT ACCAGATGCACTCGAAAATGCTTACGGTGGCCTCCTTGGAGATGAATTTGTGAACGATTTCCGA GACTATGCAGAACTTTGTTTCCAGAAGTTTGGAGATAGAGTGAAGCAGTGGACGACACTAAACG AGCCATATACAATGGTACATGAAGGTTATATAACAGGTCAAAAGGCACCTGGAAGATGTTCCAA TTTCTATAAACCTGATTGCTTAGGTGGCGATGCAGCCACGGAGCCTTACATCGTCGGCCATAAC CTCCTCCTTGCTCATGGAGTTGCCGTAAAAGTATATAGAGAAAAGTACCAG
Genomic sequence	TGTGAAGGAGCTGCACATGAAGATGGTAGAGGTCCAAGTATCTGGGACTCCTTCTCTGAAAAAT TCCCAGGTTTTTTTCCTAATTAGAAACCCCAAAAGCTTTAGATCTCTATAAAGATTTAAGCCTC AAAATGTTGGAGTTTGGTTCATATATGTGAATCTGGTTTTGTCTTGTGTTCATAACAAAAATGG GTTGATGATGATGAACCTTCTTGATACTTCTTTCTTTTTCTTGGTATTAAATTTAAAGATAAAT ATTTTTGTCATTTTCATTTTCAGAAAAGATAATGGATGGTAGTAATGGGTCCATTGCAGATGAT TCTTACAATCTTTACAAGGTCTTATTTGCTTTCTTCACCCAAAAAAGAAATAAAGTCAATTATA CATCAAGCATTACATTTTGCTTCATGATTTTTTTTTGGAAAATCAGGAAGATGTGAATTTGCTG CATCAAATTGGCTTCGATGCTTACCGATTTTCGATCTCATGGTCACGGATTTTGCCTCGTAAGA TATCGATATTATCGGATTAGATCTTTGTAACTTGTAAGCGTTGTTATATATTCTTGATGTAACT CTTCTCAATTGTTTATTAGGTGGGACTCTAAAGGGAGGAATCAACCAGGCTGGAATTGAATATT ATAACAACTTGATTAATCAACTTATATCTAAAGGTAATGTTTCTCTGTTTCTCAGTCTATTTGA TTTTAATGCACATAGAGGAAATCTTGGTGATGTTTAGGATATTGCCAAAACCCTTGTAATTTTT TTTTTTTTTTCTTGTAATGTTGTAAATGTGTCAGGAGTGAAGCCATTTGTCACACTCTTTCACT GGGACTTACCAGATGCACTCGAAAATGCTTACGGTGGCCTCCTTGGAGATGAATTTGTGTAAGT TCATTCATAAGATCTCTATATGGTAAGATTACGACACTGCGAAGATTTGTTGTTGATATTTTGG TAATGAAACAGGAACGATTTCCGAGACTATGCAGAACTTTGTTTCCAGAAGTTTGGAGATAGAG TGAAGCAGTGGACGACACTAAACGAGCCATATACAATGGTACATGAAGGTTATATAACAGGTCA AAAGGCACCTGGAAGATGTTCCAATTTCTATAAACCTGATTGCTTAGGTGGCGATGCAGCCACG GAGCCTTACATCGTCGGCCATAACCTCCTCCTTGCTCATGGAGTTGCCGTAAAAGTATATAGAG AAAAGTACCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.261792207

Conservation Information
Conserved circRNAs	NA
PMCS	0.261792207

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							22210845-22211781(+)
						
						Potential amino acid sequence
						
							MDGSNGSIADDSYNLYKEDVNLLHQIGFDAYRFSISWSRILPRGTLKGGINQAGIEYYNNLINQ
LISKGVKPFVTLFHWDLPDALENAYGGLLGDEFVNDFRDYAELCFQKFGDRVKQWTTLNEPYTM
VHEGYITGQKAPGRCSNFYKPDCLGGDAATEPYIVGHNLLLAHGVAVKVYREKYQCEGAAHEDG
RGPSIWDSFSEKFPEKIMDGSNGSIADDSYNLYKEDVNLLHQIGFDAYRFSISWSRILPRGTLK
GGINQAGIEYYNNLINQLISKGVKPFVTLFHWDLPDALENAYGGLLGDEFVNDFRDYAELCFQK
FGDRVKQWTTLNEPYTMVHEGYITGQKAPGRCSNFYKPDCLGGDAATEPYIVGHNLLLAHGVAV
KVYREKYQCEGAAHEDGRGPSIWDSFSEKFPEKIMDGSNGSIADDSYNLYKEDVNLLHQIGFDA
YRFSISWSRILPRGTLKGGINQAGIEYYNNLINQLISKGVKPFVTLFHWDLPDALENAYGGLLG
DEFVNDFRDYAELCFQKFGDRVKQWTTLNEPYTMVHEGYITGQKAPGRCSNFYKPDCLGGDAAT
EPYIVGHNLLLAHGVAVKVYREKYQCEGAAHEDGRGPSIWDSFSEKFPEKIMDGSNGSIADDSY
NLYKEDVNLLHQIGFDAYRFSISWSRILPRGTLKGGINQAGIEYYNNLINQLISKGVKPFVTLF
HWDLPDALENAYGGLLGDEFVNDFRDYAELCFQKFGDRVKQWTTLNEPYTMVHEGYITGQKAPG
RCSNFYKPDCLGGDAATEPYIVGHNLLLAHGVAVKVYREKYQ(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	22210845-22211781(+)
Potential amino acid sequence	MDGSNGSIADDSYNLYKEDVNLLHQIGFDAYRFSISWSRILPRGTLKGGINQAGIEYYNNLINQ LISKGVKPFVTLFHWDLPDALENAYGGLLGDEFVNDFRDYAELCFQKFGDRVKQWTTLNEPYTM VHEGYITGQKAPGRCSNFYKPDCLGGDAATEPYIVGHNLLLAHGVAVKVYREKYQCEGAAHEDG RGPSIWDSFSEKFPEKIMDGSNGSIADDSYNLYKEDVNLLHQIGFDAYRFSISWSRILPRGTLK GGINQAGIEYYNNLINQLISKGVKPFVTLFHWDLPDALENAYGGLLGDEFVNDFRDYAELCFQK FGDRVKQWTTLNEPYTMVHEGYITGQKAPGRCSNFYKPDCLGGDAATEPYIVGHNLLLAHGVAV KVYREKYQCEGAAHEDGRGPSIWDSFSEKFPEKIMDGSNGSIADDSYNLYKEDVNLLHQIGFDA YRFSISWSRILPRGTLKGGINQAGIEYYNNLINQLISKGVKPFVTLFHWDLPDALENAYGGLLG DEFVNDFRDYAELCFQKFGDRVKQWTTLNEPYTMVHEGYITGQKAPGRCSNFYKPDCLGGDAAT EPYIVGHNLLLAHGVAVKVYREKYQCEGAAHEDGRGPSIWDSFSEKFPEKIMDGSNGSIADDSY NLYKEDVNLLHQIGFDAYRFSISWSRILPRGTLKGGINQAGIEYYNNLINQLISKGVKPFVTLF HWDLPDALENAYGGLLGDEFVNDFRDYAELCFQKFGDRVKQWTTLNEPYTMVHEGYITGQKAPG RCSNFYKPDCLGGDAATEPYIVGHNLLLAHGVAVKVYREKYQ(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of AT3G60130_circ_g.2

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