Plant Circular RNA Database

Detail information of AT4G19610_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT4G19610_circ_g.3
					
						ID in PlantcircBase
						ath_circ_031726
					
						Alias
						4:10678778-10680235
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr4: 10678778-10680235  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT4G19610						
					
						Parent gene annotation
						
							Nucleotide/nucleic acid binding protein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT4G19610_circ_g.2 AT4G19610_circ_g.4 AT4G19610_circ_g.5 						
					
						Support reads
						1/1
					
						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  
						
							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
						AT4G19610.1:6

General Information
CircRNA Name	AT4G19610_circ_g.3
ID in PlantcircBase	ath_circ_031726
Alias	4:10678778-10680235
Organism	Arabidpsis thaliana
Position	chr4: 10678778-10680235 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT4G19610
Parent gene annotation	Nucleotide/nucleic acid binding protein
Parent gene strand	+
Alternative splicing	AT4G19610_circ_g.2 AT4G19610_circ_g.4 AT4G19610_circ_g.5
Support reads	1/1
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	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	AT4G19610.1:6

			
						 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  
						
							TCTTCCTGACACCAATGAAGAGAGAAGTGACATTGAAGAAAATGGCGTGAGAAGAGTCAACTTG
GAGCAGCAGGTTGAAATCGATCCAGATGTAACTGAGagaagaagagcttatggaacattttagc
acattcggtaagatatcagaagtccatcttgttcttgacaaggagacaaaaaggtccaggggaa
ttgcctac

									
								

					

						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: 883
Transcript exons: 10678778-10678909,10679045-10679134,10679233-10679350,10
679442-10679765,10679853-10679917,10680082-10680235
AGAAGAAGAGCTTATGGAACATTTTAGCACATTCGGTAAGATATCAGAAGTCCATCTTGTTCTT
GACAAGGAGACAAAAAGGTCCAGGGGAATTGCCTACATCCTTTACCTGATTCCGGAATGTGCGG
CAAGGGCAATGGAGGAATTAGATAACTCAAGTTTTCAGGGCCGGTTGTTGCATATTTTGCCAGC
TAAGCACCGTGAAACATCTGATAAACAAGTGAATGACACTTCTAACCTGCCAAAAACATTCAAG
CAGAAGAGAGAGGAACAAAGAAAGGCATCTGAAGCTGGTGGAGATACAAAGGCTTGGAATAGTT
TATTCATGCGACCCGATACTATTCTAGAAAACATAGTCAGGGTGTATGGTGTAAGCAAGAGTGA
GTTACTTGACCGTGAAGCTGAAGATCCTGCTGTACGCCTTGCTTTGGGAGAAACAAAAGTGATT
GCGGAGACCAAAGAAGCCCTTGCGAAAGCTGGAGTAAATGTTACTTCTTTGGAAAAATTTGCTA
CAAGGAATGGTGATGAGAAAAACCGAAGCAAACATATCCTCTTAGTAAAGAATTTGCCATTTGC
TTCCACTGAAAAGGAACTGGCTCAAATGTTTGGAAAATTTGGAAGTCTAGACAAAATTATCCTC
CCTCCGACGAAGACGATGGCCTTGGCTGTGTTTCTGGAGCCGGCTGAGGCACGCGCAGCTCTTA
AGGGAATGGCATACAAGCGTTACAAAGATGCTCCCTTGTATCTGGAGTGGGCTCCTGGAAATAT
TCTTGAGCCAAAAAATCTTCCTGACACCAATGAAGAGAGAAGTGACATTGAAGAAAATGGCGTG
AGAAGAGTCAACTTGGAGCAGCAGGTTGAAATCGATCCAGATGTAACTGAG
						
					

						Genomic sequence
						
							AGAAGAAGAGCTTATGGAACATTTTAGCACATTCGGTAAGATATCAGAAGTCCATCTTGTTCTT
GACAAGGAGACAAAAAGGTCCAGGGGAATTGCCTACATCCTTTACCTGATTCCGGAATGTGCGG
CAAGGTATTATTTATGTCAAAAAGTAGTTTTATTACTGCTGGTAACCCCTTGAGGTCTAAGTGC
ATGCTTTTCAAGAAGTAGCCTTGTGTTGAGCTCTAGCTGTTAGTTCAGGTTTTAAAACATTTGA
TGGTGATGCAGGGCAATGGAGGAATTAGATAACTCAAGTTTTCAGGGCCGGTTGTTGCATATTT
TGCCAGCTAAGCACCGTGAAACATCTGATAAACAAGTGTCAGTGGCCTACCCTTTCTAAGTTTT
GGTCTTCCAACTTGTAAATTTTTTTTGGACTAGCTTTTCTGTTAGTTGTTTAACATGGCCTTTT
TCAACAGGAATGACACTTCTAACCTGCCAAAAACATTCAAGCAGAAGAGAGAGGAACAAAGAAA
GGCATCTGAAGCTGGTGGAGATACAAAGGCTTGGAATAGTTTATTCATGCGACCCGATACTGTA
CGTTTTTCCTGTTTAAAGAATGCATCCTTTAGTGTTTTTTAAATATAGCTTGCTTCATGTTTTT
TTTCTTTTCCTTTTTGTGTTGTAGATTCTAGAAAACATAGTCAGGGTGTATGGTGTAAGCAAGA
GTGAGTTACTTGACCGTGAAGCTGAAGATCCTGCTGTACGCCTTGCTTTGGGAGAAACAAAAGT
GATTGCGGAGACCAAAGAAGCCCTTGCGAAAGCTGGAGTAAATGTTACTTCTTTGGAAAAATTT
GCTACAAGGAATGGTGATGAGAAAAACCGAAGCAAACATATCCTCTTAGTAAAGAATTTGCCAT
TTGCTTCCACTGAAAAGGAACTGGCTCAAATGTTTGGAAAATTTGGAAGTCTAGACAAAATTAT
CCTCCCTCCGACGAAGACGATGGCCTTGGTACTTTTCTTTCCATGTGTCCTACGTCAGTATATT
GGACGAATAGTTAATTGCTCTCTAACCTGCCCTTAATTACATGACCTGCAGGCTGTGTTTCTGG
AGCCGGCTGAGGCACGCGCAGCTCTTAAGGGAATGGCATACAAGCGTTACAAGTAAGCTTTAAA
ATTAACTTTAATGTTTACTAAATCAGGAGGGGAAGAACAACTTCTGTATTAATGTCTAAAATCC
GTTTGTCTTTCCCTAAAGTGCTTCTTGGAGATAAATGACCATGCTAGTTAAAACTAAACTACTT
CATCACATTTTCCTATTATCACAGAGATGCTCCCTTGTATCTGGAGTGGGCTCCTGGAAATATT
CTTGAGCCAAAAAATCTTCCTGACACCAATGAAGAGAGAAGTGACATTGAAGAAAATGGCGTGA
GAAGAGTCAACTTGGAGCAGCAGGTTGAAATCGATCCAGATGTAACTGAG
						
					

			
		

Sequences
Splice junction sequence	TCTTCCTGACACCAATGAAGAGAGAAGTGACATTGAAGAAAATGGCGTGAGAAGAGTCAACTTG GAGCAGCAGGTTGAAATCGATCCAGATGTAACTGAGagaagaagagcttatggaacattttagc acattcggtaagatatcagaagtccatcttgttcttgacaaggagacaaaaaggtccaggggaa ttgcctac
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: 883 Transcript exons: 10678778-10678909,10679045-10679134,10679233-10679350,10 679442-10679765,10679853-10679917,10680082-10680235 AGAAGAAGAGCTTATGGAACATTTTAGCACATTCGGTAAGATATCAGAAGTCCATCTTGTTCTT GACAAGGAGACAAAAAGGTCCAGGGGAATTGCCTACATCCTTTACCTGATTCCGGAATGTGCGG CAAGGGCAATGGAGGAATTAGATAACTCAAGTTTTCAGGGCCGGTTGTTGCATATTTTGCCAGC TAAGCACCGTGAAACATCTGATAAACAAGTGAATGACACTTCTAACCTGCCAAAAACATTCAAG CAGAAGAGAGAGGAACAAAGAAAGGCATCTGAAGCTGGTGGAGATACAAAGGCTTGGAATAGTT TATTCATGCGACCCGATACTATTCTAGAAAACATAGTCAGGGTGTATGGTGTAAGCAAGAGTGA GTTACTTGACCGTGAAGCTGAAGATCCTGCTGTACGCCTTGCTTTGGGAGAAACAAAAGTGATT GCGGAGACCAAAGAAGCCCTTGCGAAAGCTGGAGTAAATGTTACTTCTTTGGAAAAATTTGCTA CAAGGAATGGTGATGAGAAAAACCGAAGCAAACATATCCTCTTAGTAAAGAATTTGCCATTTGC TTCCACTGAAAAGGAACTGGCTCAAATGTTTGGAAAATTTGGAAGTCTAGACAAAATTATCCTC CCTCCGACGAAGACGATGGCCTTGGCTGTGTTTCTGGAGCCGGCTGAGGCACGCGCAGCTCTTA AGGGAATGGCATACAAGCGTTACAAAGATGCTCCCTTGTATCTGGAGTGGGCTCCTGGAAATAT TCTTGAGCCAAAAAATCTTCCTGACACCAATGAAGAGAGAAGTGACATTGAAGAAAATGGCGTG AGAAGAGTCAACTTGGAGCAGCAGGTTGAAATCGATCCAGATGTAACTGAG
Genomic sequence	AGAAGAAGAGCTTATGGAACATTTTAGCACATTCGGTAAGATATCAGAAGTCCATCTTGTTCTT GACAAGGAGACAAAAAGGTCCAGGGGAATTGCCTACATCCTTTACCTGATTCCGGAATGTGCGG CAAGGTATTATTTATGTCAAAAAGTAGTTTTATTACTGCTGGTAACCCCTTGAGGTCTAAGTGC ATGCTTTTCAAGAAGTAGCCTTGTGTTGAGCTCTAGCTGTTAGTTCAGGTTTTAAAACATTTGA TGGTGATGCAGGGCAATGGAGGAATTAGATAACTCAAGTTTTCAGGGCCGGTTGTTGCATATTT TGCCAGCTAAGCACCGTGAAACATCTGATAAACAAGTGTCAGTGGCCTACCCTTTCTAAGTTTT GGTCTTCCAACTTGTAAATTTTTTTTGGACTAGCTTTTCTGTTAGTTGTTTAACATGGCCTTTT TCAACAGGAATGACACTTCTAACCTGCCAAAAACATTCAAGCAGAAGAGAGAGGAACAAAGAAA GGCATCTGAAGCTGGTGGAGATACAAAGGCTTGGAATAGTTTATTCATGCGACCCGATACTGTA CGTTTTTCCTGTTTAAAGAATGCATCCTTTAGTGTTTTTTAAATATAGCTTGCTTCATGTTTTT TTTCTTTTCCTTTTTGTGTTGTAGATTCTAGAAAACATAGTCAGGGTGTATGGTGTAAGCAAGA GTGAGTTACTTGACCGTGAAGCTGAAGATCCTGCTGTACGCCTTGCTTTGGGAGAAACAAAAGT GATTGCGGAGACCAAAGAAGCCCTTGCGAAAGCTGGAGTAAATGTTACTTCTTTGGAAAAATTT GCTACAAGGAATGGTGATGAGAAAAACCGAAGCAAACATATCCTCTTAGTAAAGAATTTGCCAT TTGCTTCCACTGAAAAGGAACTGGCTCAAATGTTTGGAAAATTTGGAAGTCTAGACAAAATTAT CCTCCCTCCGACGAAGACGATGGCCTTGGTACTTTTCTTTCCATGTGTCCTACGTCAGTATATT GGACGAATAGTTAATTGCTCTCTAACCTGCCCTTAATTACATGACCTGCAGGCTGTGTTTCTGG AGCCGGCTGAGGCACGCGCAGCTCTTAAGGGAATGGCATACAAGCGTTACAAGTAAGCTTTAAA ATTAACTTTAATGTTTACTAAATCAGGAGGGGAAGAACAACTTCTGTATTAATGTCTAAAATCC GTTTGTCTTTCCCTAAAGTGCTTCTTGGAGATAAATGACCATGCTAGTTAAAACTAAACTACTT CATCACATTTTCCTATTATCACAGAGATGCTCCCTTGTATCTGGAGTGGGCTCCTGGAAATATT CTTGAGCCAAAAAATCTTCCTGACACCAATGAAGAGAGAAGTGACATTGAAGAAAATGGCGTGA GAAGAGTCAACTTGGAGCAGCAGGTTGAAATCGATCCAGATGTAACTGAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.210478327

Conservation Information
Conserved circRNAs	NA
PMCS	0.210478327

			
						 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 AT4G19610_circ_g.3

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