Plant Circular RNA Database

Detail information of AT1G48410_circ_g.9

			
						 General Information
					
						CircRNA Name
						AT1G48410_circ_g.9
					
						ID in PlantcircBase
						ath_circ_006301
					
						Alias
						1:17888939-17890411
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 17888939-17890411  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT1G48410						
					
						Parent gene annotation
						
							ICU9
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT1G48410_circ_g.8 AT1G48410_circ_g.10 AT1G48410_circ_g.11 						
					
						Support reads
						1/1
					
						Tissues
						seedling;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
						AT1G48410.3:6
AT1G48410.1:6
AT1G48410.2:6

General Information
CircRNA Name	AT1G48410_circ_g.9
ID in PlantcircBase	ath_circ_006301
Alias	1:17888939-17890411
Organism	Arabidpsis thaliana
Position	chr1: 17888939-17890411 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT1G48410
Parent gene annotation	ICU9
Parent gene strand	-
Alternative splicing	AT1G48410_circ_g.8 AT1G48410_circ_g.10 AT1G48410_circ_g.11
Support reads	1/1
Tissues	seedling;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	AT1G48410.3:6 AT1G48410.1:6 AT1G48410.2:6

			
						 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  
						
							TCAGCATCAGATAAAGGTCGAGAAGAAATATCCCGGTTAAGCAAATCACAGACAAACTGAATCA
CAGGGTTTGCCTCTATGAAGGCTGTCGATGACATATcttattcatcatgttccattgaccaact
tgtggcagacaagtcccttcccttccagactcgtggtacttaagctgcagaacattaaaatcag
attggaac

									
								

					

						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: 653
Transcript exons: 17888939-17889010,17889109-17889216,17889685-17889801,17
889873-17890011,17890102-17890208,17890302-17890411
CTTATTCATCATGTTCCATTGACCAACTTGTGGCAGACAAGTCCCTTCCCTTCCAGACTCGTGG
TACTTAAGCCATGGAGGAGGCAGTATACGAGCCTCAACAGAAGCCAGAGAAGTACTTATTTTGA
TGCCAAACTCTTGAGCATAATTATCTTTAGCATAATCATTGAGTTGCACCGTCTGTAAGATATC
TTTTTCTCGATCTATCGGGCGCTGACAGGTAACCTTCAGCAAAGCAGTGATCTGTCTCTCATTC
AATCTTTTGGAATACCGCTGGCCTTCAACAATCTTGCATACCTCCATTGGTAAGTAATTAGGCC
TATTAGAATTCCCAACTTGCAAGCATGGTAGTTGAGTGTGCTGAATGCGAAAACCATATGTTTC
GTGGAAGTATTCTACAACAGATTTCTGAGTATTTCTTTCATCTACTGGGAATGTCAATTCCCGA
GTGGCCACAGCAGTCAAACCGGAAATGCGGTACTTCCGGCGCATGTTTCCTCGATGAGTCACTT
CAACTTTGACACCTCTAAGAGCCTTTTTTATCTTAACACGATCAGCATCAGATAAAGGTCGAGA
AGAAATATCCCGGTTAAGCAAATCACAGACAAACTGAATCACAGGGTTTGCCTCTATGAAGGCT
GTCGATGACATAT
						
					

						Genomic sequence
						
							CTTATTCATCATGTTCCATTGACCAACTTGTGGCAGACAAGTCCCTTCCCTTCCAGACTCGTGG
TACTTAAGCTGCAGAACATTAAAATCAGATTGGAACCCTAATTTGAGTCATTAAGATACAGAGA
AAAAGTGTAATAGCAAAGAGACAATGGGAACGATTACTATACCCATGGAGGAGGCAGTATACGA
GCCTCAACAGAAGCCAGAGAAGTACTTATTTTGATGCCAAACTCTTGAGCATAATTATCTTTAG
CATAATCATTGAGTTGCACCGTCTAGAAATCAGAAAATATTGTATAATGTTAGCAATAAACAAT
TGAGTTTTCAACAACAGCAGCCAGAAGACACACGCGCTGCTAAATTAAGAGCACAACTCTGAAG
ATGGTAATCTGCCTCACTATTTATGAAGTAAAGGCATCATCTCAAGGTAAATCACTCTCTTCAA
GCAAACATATGCATCCAAGTAAAGAAGAAACAGGTTTTTAAGCCATTCATTCCATAACATCCTT
TCAGCCACAAGTTTATATGATTAAAAACAAGTTAGATATGAATTGAGAAAATCACTTACTTCAA
GTAAACACATGCAACCAAGTAAGAATAAACAGATTTTACAATGATCTATTCCACAATGAGGCTT
TATCACCAGCATACATTATTTAAAACGACTATCAAGATAGGCGGACAAAAAGATACTCTTGATT
CAAGTGAAGGAAAACAAAGTTATCGAAAATAAAGAAACATACCTGTAAGATATCTTTTTCTCGA
TCTATCGGGCGCTGACAGGTAACCTTCAGCAAAGCAGTGATCTGTCTCTCATTCAATCTTTTGG
AATACCGCTGGCCTTCAACAATCTTGCATACCTGTGCAGCAACACATTAGAATCGGAAGTACTG
GTGAGCTAATAAAACCTGATGACGTATTTCAAAGTTACCTCCATTGGTAAGTAATTAGGCCTAT
TAGAATTCCCAACTTGCAAGCATGGTAGTTGAGTGTGCTGAATGCGAAAACCATATGTTTCGTG
GAAGTATTCTACAACAGATTTCTGAGTATTTCTTTCATCTACTGGGAATCTGAAAAGGATAAAA
ACAGAGAGTAAAAATTAATTTCATCAAGTTCAACATTCGCGAAATAAGAGTAGTAAATCTAAAA
CAAATACGCACGTCAATTCCCGAGTGGCCACAGCAGTCAAACCGGAAATGCGGTACTTCCGGCG
CATGTTTCCTCGATGAGTCACTTCAACTTTGACACCTCTAAGAGCCTTTTTTATCTGTTGACAG
AAGAAGATTCCAAGTCACTAAGCAAAGAAGAGTAGATTAATACAACATTTCACTTACTACAGAA
AATGACAATTGATTCATACCTTAACACGATCAGCATCAGATAAAGGTCGAGAAGAAATATCCCG
GTTAAGCAAATCACAGACAAACTGAATCACAGGGTTTGCCTCTATGAAGGCTGTCGATGACATA
T
						
					

			
		

Sequences
Splice junction sequence	TCAGCATCAGATAAAGGTCGAGAAGAAATATCCCGGTTAAGCAAATCACAGACAAACTGAATCA CAGGGTTTGCCTCTATGAAGGCTGTCGATGACATATcttattcatcatgttccattgaccaact tgtggcagacaagtcccttcccttccagactcgtggtacttaagctgcagaacattaaaatcag attggaac
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: 653 Transcript exons: 17888939-17889010,17889109-17889216,17889685-17889801,17 889873-17890011,17890102-17890208,17890302-17890411 CTTATTCATCATGTTCCATTGACCAACTTGTGGCAGACAAGTCCCTTCCCTTCCAGACTCGTGG TACTTAAGCCATGGAGGAGGCAGTATACGAGCCTCAACAGAAGCCAGAGAAGTACTTATTTTGA TGCCAAACTCTTGAGCATAATTATCTTTAGCATAATCATTGAGTTGCACCGTCTGTAAGATATC TTTTTCTCGATCTATCGGGCGCTGACAGGTAACCTTCAGCAAAGCAGTGATCTGTCTCTCATTC AATCTTTTGGAATACCGCTGGCCTTCAACAATCTTGCATACCTCCATTGGTAAGTAATTAGGCC TATTAGAATTCCCAACTTGCAAGCATGGTAGTTGAGTGTGCTGAATGCGAAAACCATATGTTTC GTGGAAGTATTCTACAACAGATTTCTGAGTATTTCTTTCATCTACTGGGAATGTCAATTCCCGA GTGGCCACAGCAGTCAAACCGGAAATGCGGTACTTCCGGCGCATGTTTCCTCGATGAGTCACTT CAACTTTGACACCTCTAAGAGCCTTTTTTATCTTAACACGATCAGCATCAGATAAAGGTCGAGA AGAAATATCCCGGTTAAGCAAATCACAGACAAACTGAATCACAGGGTTTGCCTCTATGAAGGCT GTCGATGACATAT
Genomic sequence	CTTATTCATCATGTTCCATTGACCAACTTGTGGCAGACAAGTCCCTTCCCTTCCAGACTCGTGG TACTTAAGCTGCAGAACATTAAAATCAGATTGGAACCCTAATTTGAGTCATTAAGATACAGAGA AAAAGTGTAATAGCAAAGAGACAATGGGAACGATTACTATACCCATGGAGGAGGCAGTATACGA GCCTCAACAGAAGCCAGAGAAGTACTTATTTTGATGCCAAACTCTTGAGCATAATTATCTTTAG CATAATCATTGAGTTGCACCGTCTAGAAATCAGAAAATATTGTATAATGTTAGCAATAAACAAT TGAGTTTTCAACAACAGCAGCCAGAAGACACACGCGCTGCTAAATTAAGAGCACAACTCTGAAG ATGGTAATCTGCCTCACTATTTATGAAGTAAAGGCATCATCTCAAGGTAAATCACTCTCTTCAA GCAAACATATGCATCCAAGTAAAGAAGAAACAGGTTTTTAAGCCATTCATTCCATAACATCCTT TCAGCCACAAGTTTATATGATTAAAAACAAGTTAGATATGAATTGAGAAAATCACTTACTTCAA GTAAACACATGCAACCAAGTAAGAATAAACAGATTTTACAATGATCTATTCCACAATGAGGCTT TATCACCAGCATACATTATTTAAAACGACTATCAAGATAGGCGGACAAAAAGATACTCTTGATT CAAGTGAAGGAAAACAAAGTTATCGAAAATAAAGAAACATACCTGTAAGATATCTTTTTCTCGA TCTATCGGGCGCTGACAGGTAACCTTCAGCAAAGCAGTGATCTGTCTCTCATTCAATCTTTTGG AATACCGCTGGCCTTCAACAATCTTGCATACCTGTGCAGCAACACATTAGAATCGGAAGTACTG GTGAGCTAATAAAACCTGATGACGTATTTCAAAGTTACCTCCATTGGTAAGTAATTAGGCCTAT TAGAATTCCCAACTTGCAAGCATGGTAGTTGAGTGTGCTGAATGCGAAAACCATATGTTTCGTG GAAGTATTCTACAACAGATTTCTGAGTATTTCTTTCATCTACTGGGAATCTGAAAAGGATAAAA ACAGAGAGTAAAAATTAATTTCATCAAGTTCAACATTCGCGAAATAAGAGTAGTAAATCTAAAA CAAATACGCACGTCAATTCCCGAGTGGCCACAGCAGTCAAACCGGAAATGCGGTACTTCCGGCG CATGTTTCCTCGATGAGTCACTTCAACTTTGACACCTCTAAGAGCCTTTTTTATCTGTTGACAG AAGAAGATTCCAAGTCACTAAGCAAAGAAGAGTAGATTAATACAACATTTCACTTACTACAGAA AATGACAATTGATTCATACCTTAACACGATCAGCATCAGATAAAGGTCGAGAAGAAATATCCCG GTTAAGCAAATCACAGACAAACTGAATCACAGGGTTTGCCTCTATGAAGGCTGTCGATGACATA T

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.204234968

Conservation Information
Conserved circRNAs	NA
PMCS	0.204234968

			
						 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 AT1G48410_circ_g.9

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