Plant Circular RNA Database

Detail information of AT3G06880_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT3G06880_circ_g.3
					
						ID in PlantcircBase
						ath_circ_020184
					
						Alias
						3:2171498-2172660
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 2171498-2172660  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT3G06880						
					
						Parent gene annotation
						
							Transducin/WD40 repeat-like superfamily protein
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT3G06880_circ_g.4 						
					
						Support reads
						2
					
						Tissues
						seedling
					
						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
						AT3G06880.5:5
AT3G06880.1:5
AT3G06880.4:5
AT3G06880.3:5
AT3G06880.2:5

General Information
CircRNA Name	AT3G06880_circ_g.3
ID in PlantcircBase	ath_circ_020184
Alias	3:2171498-2172660
Organism	Arabidpsis thaliana
Position	chr3: 2171498-2172660 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT3G06880
Parent gene annotation	Transducin/WD40 repeat-like superfamily protein
Parent gene strand	-
Alternative splicing	AT3G06880_circ_g.4
Support reads	2
Tissues	seedling
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	AT3G06880.5:5 AT3G06880.1:5 AT3G06880.4:5 AT3G06880.3:5 AT3G06880.2:5

			
						 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  
						
							TTTTACTCTTTAGCCCTTCTTGTAAACCACAAAACGTGGCTTTGCCTGTATCAATAATTCTTCT
AGCTATCTTACAACACCATCCATCTATTCCTGTATCcttcatcttgtgcccttttgttataaca
aagatcatatttccgaatgcttccagtttccttattgaatcttttgtttttatgacttcagcac
attccagt

									
								

					

						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: 795
Transcript exons: 2171498-2171620,2171709-2171840,2171926-2172051,2172151-
2172269,2172366-2172660
CTTCATCTTGTGCCCTTTTGTTATAACAAAGATCATATTTCCGAATGCTTCCAGTTTCCTTATT
GAATCTTTTGTTTTTATGACTTCAGCACATTCCAGTTTTCCTTTAACTATCTGCCATACCCTGA
TAGTTTTATCTGCTGATCCACTTAAGACACACTCTCCTGTTTCAGAGAGTGAAAAGCATGTTAC
TGTGCTTTTGTGCTCCTTGATGTCCCATAAAAGCGTAGCTATTTTCTTATTCACATTCCACACC
CTGATTGAACCATCTGAGAATCCACTAAAGAGCAAGCCTTTATGGTAGATGAGTGCTGTTACAG
CTCCACTGCCAGATTGATGCATCTCTACGGTTTGTGTATGAACACAAGATATGCGTTGGTCAGA
TTTGCTGAATAGATAATATGTTGCTTTATGCAGTTCGTCTGCCATCCAAGTCACATGTGAAAGA
CGTCTCAAAGACTCTCTAACTCCTTCCGAGAAATTGACTAGTTTGTGGATTCCTTTGCCAGAGC
TAAAATTATAGATGCATATACAAGCAAGAAGTCTTTCTTCAAGCTCCAAACCAGGGTGGAGAAA
TTGTGCTACCTCATCAAGTAAAACTTCACATGCTGAGTATTTTAAACTATTTGGACCTTTTGAA
ATCTCTATACTGAGCCATGCAATGGCTATAAGACATGCTTTTGAAACACTCTTGTTTTTACTCT
TTAGCCCTTCTTGTAAACCACAAAACGTGGCTTTGCCTGTATCAATAATTCTTCTAGCTATCTT
ACAACACCATCCATCTATTCCTGTATC
						
					

						Genomic sequence
						
							CTTCATCTTGTGCCCTTTTGTTATAACAAAGATCATATTTCCGAATGCTTCCAGTTTCCTTATT
GAATCTTTTGTTTTTATGACTTCAGCACATTCCAGTTTTCCTTTAACTATCTGCCATACCTATA
TAAAAGAAGGTCAAACATAGATACAGTTTTGTCCTGATCCTAGTGATCTGTCCGGGAAACAAAG
AGTTGAATCATTATCATACCCTGATAGTTTTATCTGCTGATCCACTTAAGACACACTCTCCTGT
TTCAGAGAGTGAAAAGCATGTTACTGTGCTTTTGTGCTCCTTGATGTCCCATAAAAGCGTAGCT
ATTTTCTTATTCACATTCCACACCTGATACATTGTTTTGCATTCTCAAGGTAAGATTCTGTGAA
ACATTTGTCTTCCTAGTCATTTTTATGAAAAGTATGATACATACCCTGATTGAACCATCTGAGA
ATCCACTAAAGAGCAAGCCTTTATGGTAGATGAGTGCTGTTACAGCTCCACTGCCAGATTGATG
CATCTCTACGGTTTGTGTATGAACACAAGATATGCGTTGGTCCTATCAATATTTGTGTATGATT
CTGTTATACATGGTTGGTTTAAGTTGTGAAAATGGTAGAGATTGTACTAATTTGGTTGCAGGTG
AAGAAAAACTTACAGATTTGCTGAATAGATAATATGTTGCTTTATGCAGTTCGTCTGCCATCCA
AGTCACATGTGAAAGACGTCTCAAAGACTCTCTAACTCCTTCCGAGAAATTGACTAGTTTGTGG
ATTCCTGTGTGAAAACTACACTTTAGTATAAAACTTAAGAGTCACATACTTTAGTTTGGTATGA
ACCATTAATTCACTACATGAAAGTTAGGAAATTCACCTTTGCCAGAGCTAAAATTATAGATGCA
TATACAAGCAAGAAGTCTTTCTTCAAGCTCCAAACCAGGGTGGAGAAATTGTGCTACCTCATCA
AGTAAAACTTCACATGCTGAGTATTTTAAACTATTTGGACCTTTTGAAATCTCTATACTGAGCC
ATGCAATGGCTATAAGACATGCTTTTGAAACACTCTTGTTTTTACTCTTTAGCCCTTCTTGTAA
ACCACAAAACGTGGCTTTGCCTGTATCAATAATTCTTCTAGCTATCTTACAACACCATCCATCT
ATTCCTGTATC
						
					

			
		

Sequences
Splice junction sequence	TTTTACTCTTTAGCCCTTCTTGTAAACCACAAAACGTGGCTTTGCCTGTATCAATAATTCTTCT AGCTATCTTACAACACCATCCATCTATTCCTGTATCcttcatcttgtgcccttttgttataaca aagatcatatttccgaatgcttccagtttccttattgaatcttttgtttttatgacttcagcac attccagt
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: 795 Transcript exons: 2171498-2171620,2171709-2171840,2171926-2172051,2172151- 2172269,2172366-2172660 CTTCATCTTGTGCCCTTTTGTTATAACAAAGATCATATTTCCGAATGCTTCCAGTTTCCTTATT GAATCTTTTGTTTTTATGACTTCAGCACATTCCAGTTTTCCTTTAACTATCTGCCATACCCTGA TAGTTTTATCTGCTGATCCACTTAAGACACACTCTCCTGTTTCAGAGAGTGAAAAGCATGTTAC TGTGCTTTTGTGCTCCTTGATGTCCCATAAAAGCGTAGCTATTTTCTTATTCACATTCCACACC CTGATTGAACCATCTGAGAATCCACTAAAGAGCAAGCCTTTATGGTAGATGAGTGCTGTTACAG CTCCACTGCCAGATTGATGCATCTCTACGGTTTGTGTATGAACACAAGATATGCGTTGGTCAGA TTTGCTGAATAGATAATATGTTGCTTTATGCAGTTCGTCTGCCATCCAAGTCACATGTGAAAGA CGTCTCAAAGACTCTCTAACTCCTTCCGAGAAATTGACTAGTTTGTGGATTCCTTTGCCAGAGC TAAAATTATAGATGCATATACAAGCAAGAAGTCTTTCTTCAAGCTCCAAACCAGGGTGGAGAAA TTGTGCTACCTCATCAAGTAAAACTTCACATGCTGAGTATTTTAAACTATTTGGACCTTTTGAA ATCTCTATACTGAGCCATGCAATGGCTATAAGACATGCTTTTGAAACACTCTTGTTTTTACTCT TTAGCCCTTCTTGTAAACCACAAAACGTGGCTTTGCCTGTATCAATAATTCTTCTAGCTATCTT ACAACACCATCCATCTATTCCTGTATC
Genomic sequence	CTTCATCTTGTGCCCTTTTGTTATAACAAAGATCATATTTCCGAATGCTTCCAGTTTCCTTATT GAATCTTTTGTTTTTATGACTTCAGCACATTCCAGTTTTCCTTTAACTATCTGCCATACCTATA TAAAAGAAGGTCAAACATAGATACAGTTTTGTCCTGATCCTAGTGATCTGTCCGGGAAACAAAG AGTTGAATCATTATCATACCCTGATAGTTTTATCTGCTGATCCACTTAAGACACACTCTCCTGT TTCAGAGAGTGAAAAGCATGTTACTGTGCTTTTGTGCTCCTTGATGTCCCATAAAAGCGTAGCT ATTTTCTTATTCACATTCCACACCTGATACATTGTTTTGCATTCTCAAGGTAAGATTCTGTGAA ACATTTGTCTTCCTAGTCATTTTTATGAAAAGTATGATACATACCCTGATTGAACCATCTGAGA ATCCACTAAAGAGCAAGCCTTTATGGTAGATGAGTGCTGTTACAGCTCCACTGCCAGATTGATG CATCTCTACGGTTTGTGTATGAACACAAGATATGCGTTGGTCCTATCAATATTTGTGTATGATT CTGTTATACATGGTTGGTTTAAGTTGTGAAAATGGTAGAGATTGTACTAATTTGGTTGCAGGTG AAGAAAAACTTACAGATTTGCTGAATAGATAATATGTTGCTTTATGCAGTTCGTCTGCCATCCA AGTCACATGTGAAAGACGTCTCAAAGACTCTCTAACTCCTTCCGAGAAATTGACTAGTTTGTGG ATTCCTGTGTGAAAACTACACTTTAGTATAAAACTTAAGAGTCACATACTTTAGTTTGGTATGA ACCATTAATTCACTACATGAAAGTTAGGAAATTCACCTTTGCCAGAGCTAAAATTATAGATGCA TATACAAGCAAGAAGTCTTTCTTCAAGCTCCAAACCAGGGTGGAGAAATTGTGCTACCTCATCA AGTAAAACTTCACATGCTGAGTATTTTAAACTATTTGGACCTTTTGAAATCTCTATACTGAGCC ATGCAATGGCTATAAGACATGCTTTTGAAACACTCTTGTTTTTACTCTTTAGCCCTTCTTGTAA ACCACAAAACGTGGCTTTGCCTGTATCAATAATTCTTCTAGCTATCTTACAACACCATCCATCT ATTCCTGTATC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.196151104

Conservation Information
Conserved circRNAs	NA
PMCS	0.196151104

			
						 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 AT3G06880_circ_g.3

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