Plant Circular RNA Database

Detail information of AT1G58060_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT1G58060_circ_g.3
					
						ID in PlantcircBase
						ath_circ_007873
					
						Alias
						1:21494957-21496305
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 21494957-21496305  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT1G58060						
					
						Parent gene annotation
						
							DExH-box ATP-dependent RNA helicase DExH7, chloroplastic
							
						Parent gene strand
						-
					
						Alternative splicing
						
							1_circ_ag.8 1_circ_ag.9 1_circ_ag.10 AT1G58060_circ_g.1 AT1G58060_circ_g.2 AT1G58060_circ_g.4 AT1G58060_circ_g.5 AT1G58060_circ_g.6 AT1G58060_circ_g.7 AT1G58060_circ_g.8 AT1G58060_circ_g.9 						
					
						Support reads
						2/1
					
						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  
						
							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
						AT1G58060.1:4

General Information
CircRNA Name	AT1G58060_circ_g.3
ID in PlantcircBase	ath_circ_007873
Alias	1:21494957-21496305
Organism	Arabidpsis thaliana
Position	chr1: 21494957-21496305 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT1G58060
Parent gene annotation	DExH-box ATP-dependent RNA helicase DExH7, chloroplastic
Parent gene strand	-
Alternative splicing	1_circ_ag.8 1_circ_ag.9 1_circ_ag.10 AT1G58060_circ_g.1 AT1G58060_circ_g.2 AT1G58060_circ_g.4 AT1G58060_circ_g.5 AT1G58060_circ_g.6 AT1G58060_circ_g.7 AT1G58060_circ_g.8 AT1G58060_circ_g.9
Support reads	2/1
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	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	AT1G58060.1:4

			
						 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  
						
							TTATTTGCTTGCAAGAGCTTATTGATAGAATGAAGGACTTACAGCGAGTTTCCTCAGTAGAATG
CCAGTAGTACAAAACAGCAGCCTAGTCTTGTCACTCcttgtctttaatagatgtatcagatctt
agcgcagcaggagaatctggagcaagaaggtagttaatactctcataaatctcctccaggaagt
gggtagtg

									
								

					

						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: 394
Transcript exons: 21494957-21495140,21495224-21495309,21495767-21495832,21
496248-21496305
CTTGTCTTTAATAGATGTATCAGATCTTAGCGCAGCAGGAGAATCTGGAGCAAGAAGGTAGTTA
ATACTCTCATAAATCTCCTCCAGGAAGTGGGTAGTGACTGGATGTGTTCGTCCTTGAGCAGTGA
TCACAGGACAATGACCAAAATATCTTGAGAATAGATCAGCGTCAACAGTAGCAGACATAAGGAT
AACTTTCAGTTTACGTGATGTATTATCGCATGATTGCTTCTCAATCAGGCTCTTCAAAATAATT
AGAAGAAAATCACCCAAAAGAGACCGCTCATGCACTTCATCAACTATAATATGTGTAACATCGT
TCAAGGTTCTATCCCCAGCGAGTTTCCTCAGTAGAATGCCAGTAGTACAAAACAGCAGCCTAGT
CTTGTCACTC
						
					

						Genomic sequence
						
							CTTGTCTTTAATAGATGTATCAGATCTTAGCGCAGCAGGAGAATCTGGAGCAAGAAGGTAGTTA
ATACTCTCATAAATCTCCTCCAGGAAGTGGGTAGTGACTGGATGTGTTCGTCCTTGAGCAGTGA
TCACAGGACAATGACCAAAATATCTTGAGAATAGATCAGCGTCAACAGTAGCAGACCTGAACGG
GATCAGAAGCATATATTAATATGATTTTTAATTACTATATGCATCTGCCTTAAAAAAAAACCCA
TGAATACGTACATAAGGATAACTTTCAGTTTACGTGATGTATTATCGCATGATTGCTTCTCAAT
CAGGCTCTTCAAAATAATTAGAAGAAAATCACCCTGAAATGGGAAGAAGAAAAGTAGTTCTTAC
CCACAAGTTGATTTAAAACAAAAAAGATTGAAAGGTAGTCTCCTGTCAGATTGTTCGACGCTTG
AATGTGAAATAATCTAGTATTCTTTATGGAGAGAGGAGATTGAGATACTAAAAATGCTTCACAG
CAAAATGATTATTCTAAGTAGAGTCAAAAGAAGCCAGAAGAGGAGAAATATGGTGAAAAAGGTA
TAGACTACCAAGGATGCAAGCTTCTGGTCTTCACCGTTGTAAAAGTTTAAATACACAGTGGAGT
GTCACTCTAAGAGCACATTTTAAAATTGAATGCTAAAATCCCAGTTTTTATTGCTAACAGGTTC
TTGTATTCATTAGATGATGTTGTGTAGATTCTTAAGCAAAACCCTTTACTGTGTATCTATTTTT
CTTAGCAATGATGAAATTTATGGCTTACTAATGAAGACTCACCAAAAGAGACCGCTCATGCACT
TCATCAACTATAATATGTGTAACATCGTTCAAGGTTCTATCCCCCTGCAACGAGCAAACAGAAA
ACAACAATAAGAGAGAATGCTGATTATGTAATCATTATGCTATAGAAAAATAGCATTACAGTGT
CTCAACAACTGGAATTGCCAATTCTTCATATTTGTTTCGCAGAAAAAAAAACCCGCTGATACTA
CTAATAATGAGCCAACTACGTCAACTATTGGACTTCTAATGTCCCCCTTACTTAGCAGAGACTC
TATCTACATAATACTTTCTGCAAAATCGTGTTCTCTAGAAACCATAATTTCAGTAATGCAGCTA
TGATATTTCAATTTTGTCCACATCACCAGAATGTTTGTGCAGCATAACAATGTTCCTCTTTCTC
AGTACCATACAACACTATAACACGTAAGAAGAATTATTTGCTTGCAAGAGCTTATTGATAGAAT
GAAGGACTTACAGCGAGTTTCCTCAGTAGAATGCCAGTAGTACAAAACAGCAGCCTAGTCTTGT
CACTC
						
					

			
		

Sequences
Splice junction sequence	TTATTTGCTTGCAAGAGCTTATTGATAGAATGAAGGACTTACAGCGAGTTTCCTCAGTAGAATG CCAGTAGTACAAAACAGCAGCCTAGTCTTGTCACTCcttgtctttaatagatgtatcagatctt agcgcagcaggagaatctggagcaagaaggtagttaatactctcataaatctcctccaggaagt gggtagtg
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: 394 Transcript exons: 21494957-21495140,21495224-21495309,21495767-21495832,21 496248-21496305 CTTGTCTTTAATAGATGTATCAGATCTTAGCGCAGCAGGAGAATCTGGAGCAAGAAGGTAGTTA ATACTCTCATAAATCTCCTCCAGGAAGTGGGTAGTGACTGGATGTGTTCGTCCTTGAGCAGTGA TCACAGGACAATGACCAAAATATCTTGAGAATAGATCAGCGTCAACAGTAGCAGACATAAGGAT AACTTTCAGTTTACGTGATGTATTATCGCATGATTGCTTCTCAATCAGGCTCTTCAAAATAATT AGAAGAAAATCACCCAAAAGAGACCGCTCATGCACTTCATCAACTATAATATGTGTAACATCGT TCAAGGTTCTATCCCCAGCGAGTTTCCTCAGTAGAATGCCAGTAGTACAAAACAGCAGCCTAGT CTTGTCACTC
Genomic sequence	CTTGTCTTTAATAGATGTATCAGATCTTAGCGCAGCAGGAGAATCTGGAGCAAGAAGGTAGTTA ATACTCTCATAAATCTCCTCCAGGAAGTGGGTAGTGACTGGATGTGTTCGTCCTTGAGCAGTGA TCACAGGACAATGACCAAAATATCTTGAGAATAGATCAGCGTCAACAGTAGCAGACCTGAACGG GATCAGAAGCATATATTAATATGATTTTTAATTACTATATGCATCTGCCTTAAAAAAAAACCCA TGAATACGTACATAAGGATAACTTTCAGTTTACGTGATGTATTATCGCATGATTGCTTCTCAAT CAGGCTCTTCAAAATAATTAGAAGAAAATCACCCTGAAATGGGAAGAAGAAAAGTAGTTCTTAC CCACAAGTTGATTTAAAACAAAAAAGATTGAAAGGTAGTCTCCTGTCAGATTGTTCGACGCTTG AATGTGAAATAATCTAGTATTCTTTATGGAGAGAGGAGATTGAGATACTAAAAATGCTTCACAG CAAAATGATTATTCTAAGTAGAGTCAAAAGAAGCCAGAAGAGGAGAAATATGGTGAAAAAGGTA TAGACTACCAAGGATGCAAGCTTCTGGTCTTCACCGTTGTAAAAGTTTAAATACACAGTGGAGT GTCACTCTAAGAGCACATTTTAAAATTGAATGCTAAAATCCCAGTTTTTATTGCTAACAGGTTC TTGTATTCATTAGATGATGTTGTGTAGATTCTTAAGCAAAACCCTTTACTGTGTATCTATTTTT CTTAGCAATGATGAAATTTATGGCTTACTAATGAAGACTCACCAAAAGAGACCGCTCATGCACT TCATCAACTATAATATGTGTAACATCGTTCAAGGTTCTATCCCCCTGCAACGAGCAAACAGAAA ACAACAATAAGAGAGAATGCTGATTATGTAATCATTATGCTATAGAAAAATAGCATTACAGTGT CTCAACAACTGGAATTGCCAATTCTTCATATTTGTTTCGCAGAAAAAAAAACCCGCTGATACTA CTAATAATGAGCCAACTACGTCAACTATTGGACTTCTAATGTCCCCCTTACTTAGCAGAGACTC TATCTACATAATACTTTCTGCAAAATCGTGTTCTCTAGAAACCATAATTTCAGTAATGCAGCTA TGATATTTCAATTTTGTCCACATCACCAGAATGTTTGTGCAGCATAACAATGTTCCTCTTTCTC AGTACCATACAACACTATAACACGTAAGAAGAATTATTTGCTTGCAAGAGCTTATTGATAGAAT GAAGGACTTACAGCGAGTTTCCTCAGTAGAATGCCAGTAGTACAAAACAGCAGCCTAGTCTTGT CACTC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.192315759

Conservation Information
Conserved circRNAs	NA
PMCS	0.192315759

			
						 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 AT1G58060_circ_g.3

Address

Any questions?

Supported by