Plant Circular RNA Database

Detail information of AT1G80040_circ_g.2

			
						 General Information
					
						CircRNA Name
						AT1G80040_circ_g.2
					
						ID in PlantcircBase
						ath_circ_011213
					
						Alias
						At_ciR1641
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 30109693-30110621  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						find_circ, CIRI-full
					
						Parent gene
						
							AT1G80040						
					
						Parent gene annotation
						
							F18B13.13 protein
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT1G80040_circ_g.1 AT1G80040_circ_g.3 						
					
						Support reads
						6
					
						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
						AT1G80040.2:2
AT1G80040.3:3
AT1G80040.4:2
AT1G80040.1:2

General Information
CircRNA Name	AT1G80040_circ_g.2
ID in PlantcircBase	ath_circ_011213
Alias	At_ciR1641
Organism	Arabidpsis thaliana
Position	chr1: 30109693-30110621 JBrowse»
Reference genome	TAIR10.38
Type	u-circRNA
Identification method	find_circ, CIRI-full
Parent gene	AT1G80040
Parent gene annotation	F18B13.13 protein
Parent gene strand	-
Alternative splicing	AT1G80040_circ_g.1 AT1G80040_circ_g.3
Support reads	6
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	AT1G80040.2:2 AT1G80040.3:3 AT1G80040.4:2 AT1G80040.1:2

			
						 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  
						
							ATTCTTCAGCTTTCTTCTCCTCAGAAGATGCGAAAGAGTATAAGCTCTTCATAGCAGCATTAAA
ATCACTTCCATTATCTTCTAGTGCCTTGACGAGAACctccagatttctaagcttttcctgatac
tgaggaaccagttgcttcaaaagtcctagctgatggttcgcatcctccaatgccttctgccgct
catgctgg

						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: 489
Transcript exons: 30109693-30109866,30110307-30110621
CTCCAGATTTCTAAGCTTTTCCTGATACTGAGGAACCAGTTGCTTCAAAAGTCCTAGCTGATGG
TTCGCATCCTCCAATGCCTTCTGCCGCTCATGCTGGATAGCAACAGCACGTTTGAGGACTGTGT
TGTCCTTCACCAAGGTCTCCACCTGTTGCTGCACTGCCACTTTCTCCTCTTGGAATTTGTTTCC
AGCTTCTTCACGAGCACGTGCACTTAACATCTTCTCTAAGGCCTCAAGGACTCTTGCTGCACGT
ACTTTTGCATCATCTGTACCAGACGATTGTAACACTTCCCTGACTAACAATTCAACCCAGTCAT
CACCACTGGTCGGGGGGTTTCCACCACAAACGGCATCAGTTTCCTGAGTAGCAGCACCTCCTGC
GGCCAATTCTTCAGCTTTCTTCTCCTCAGAAGATGCGAAAGAGTATAAGCTCTTCATAGCAGCA
TTAAAATCACTTCCATTATCTTCTAGTGCCTTGACGAGAAC
						
						Genomic sequence
						
							CTCCAGATTTCTAAGCTTTTCCTGATACTGAGGAACCAGTTGCTTCAAAAGTCCTAGCTGATGG
TTCGCATCCTCCAATGCCTTCTGCCGCTCATGCTGGATAGCAACAGCACGTTTGAGGACTGTGT
TGTCCTTCACCAAGGTCTCCACCTGTTGCTGCACTGCCACTTTCTCCTGTAAAATCATATGAGA
TTGTTATTTTGAGACAAGATATGCCAAAAATACTAAGAAGAGATTGTTACTAAGAACAAAATTA
CTATGATAACTTTATTTCCCCCATTGAAAAACAAACCCTCTTCAGATATCATAGTTAATGCAGA
ACAAATGGACGATGATTGTCCTTTCACAGTTGATTCCTCATTGCCATTATACATAATTGTGTTT
AGATCCAACAAACTTGTAATCAGTGACGAGCGTATGCACCTACATAAGAAGTAACTAATGGTTC
AACCTATGTCCTACAGCAACTGAAACTGTCTTCCATGCCCAGAGCTCAAAGAACAAATATGATT
ATCACTATTCATGGTCTGATAGCCAGTATGTATGCACAAGGTGCATATGTAAGGGTATATTTTG
AAAGAAACACATTAAGAAAGATGCAATGCTTTATTTACCTCTTGGAATTTGTTTCCAGCTTCTT
CACGAGCACGTGCACTTAACATCTTCTCTAAGGCCTCAAGGACTCTTGCTGCACGTACTTTTGC
ATCATCTGTACCAGACGATTGTAACACTTCCCTGACTAACAATTCAACCCAGTCATCACCACTG
GTCGGGGGGTTTCCACCACAAACGGCATCAGTTTCCTGAGTAGCAGCACCTCCTGCGGCCAATT
CTTCAGCTTTCTTCTCCTCAGAAGATGCGAAAGAGTATAAGCTCTTCATAGCAGCATTAAAATC
ACTTCCATTATCTTCTAGTGCCTTGACGAGAAC

Sequences
Splice junction sequence	ATTCTTCAGCTTTCTTCTCCTCAGAAGATGCGAAAGAGTATAAGCTCTTCATAGCAGCATTAAA ATCACTTCCATTATCTTCTAGTGCCTTGACGAGAACctccagatttctaagcttttcctgatac tgaggaaccagttgcttcaaaagtcctagctgatggttcgcatcctccaatgccttctgccgct catgctgg
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: 489 Transcript exons: 30109693-30109866,30110307-30110621 CTCCAGATTTCTAAGCTTTTCCTGATACTGAGGAACCAGTTGCTTCAAAAGTCCTAGCTGATGG TTCGCATCCTCCAATGCCTTCTGCCGCTCATGCTGGATAGCAACAGCACGTTTGAGGACTGTGT TGTCCTTCACCAAGGTCTCCACCTGTTGCTGCACTGCCACTTTCTCCTCTTGGAATTTGTTTCC AGCTTCTTCACGAGCACGTGCACTTAACATCTTCTCTAAGGCCTCAAGGACTCTTGCTGCACGT ACTTTTGCATCATCTGTACCAGACGATTGTAACACTTCCCTGACTAACAATTCAACCCAGTCAT CACCACTGGTCGGGGGGTTTCCACCACAAACGGCATCAGTTTCCTGAGTAGCAGCACCTCCTGC GGCCAATTCTTCAGCTTTCTTCTCCTCAGAAGATGCGAAAGAGTATAAGCTCTTCATAGCAGCA TTAAAATCACTTCCATTATCTTCTAGTGCCTTGACGAGAAC
Genomic sequence	CTCCAGATTTCTAAGCTTTTCCTGATACTGAGGAACCAGTTGCTTCAAAAGTCCTAGCTGATGG TTCGCATCCTCCAATGCCTTCTGCCGCTCATGCTGGATAGCAACAGCACGTTTGAGGACTGTGT TGTCCTTCACCAAGGTCTCCACCTGTTGCTGCACTGCCACTTTCTCCTGTAAAATCATATGAGA TTGTTATTTTGAGACAAGATATGCCAAAAATACTAAGAAGAGATTGTTACTAAGAACAAAATTA CTATGATAACTTTATTTCCCCCATTGAAAAACAAACCCTCTTCAGATATCATAGTTAATGCAGA ACAAATGGACGATGATTGTCCTTTCACAGTTGATTCCTCATTGCCATTATACATAATTGTGTTT AGATCCAACAAACTTGTAATCAGTGACGAGCGTATGCACCTACATAAGAAGTAACTAATGGTTC AACCTATGTCCTACAGCAACTGAAACTGTCTTCCATGCCCAGAGCTCAAAGAACAAATATGATT ATCACTATTCATGGTCTGATAGCCAGTATGTATGCACAAGGTGCATATGTAAGGGTATATTTTG AAAGAAACACATTAAGAAAGATGCAATGCTTTATTTACCTCTTGGAATTTGTTTCCAGCTTCTT CACGAGCACGTGCACTTAACATCTTCTCTAAGGCCTCAAGGACTCTTGCTGCACGTACTTTTGC ATCATCTGTACCAGACGATTGTAACACTTCCCTGACTAACAATTCAACCCAGTCATCACCACTG GTCGGGGGGTTTCCACCACAAACGGCATCAGTTTCCTGAGTAGCAGCACCTCCTGCGGCCAATT CTTCAGCTTTCTTCTCCTCAGAAGATGCGAAAGAGTATAAGCTCTTCATAGCAGCATTAAAATC ACTTCCATTATCTTCTAGTGCCTTGACGAGAAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.288967857

Conservation Information
Conserved circRNAs	NA
PMCS	0.288967857

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							30110574-30109695(-)
						
						Potential amino acid sequence
						
							MKSLYSFASSEEKKAEELAAGGAATQETDAVCGGNPPTSGDDWVELLVREVLQSSGTDDAKVRA
ARVLEALEKMLSARAREEAGNKFQEEKVAVQQQVETLVKDNTVLKRAVAIQHERQKALEDANHQ
LGLLKQLVPQYQEKLRNLEVLVKALEDNGSDFNAAMKSLYSFASSEEKKAEELAAGGAATQETD
AVCGGNPPTSGDDWVELLVREVLQSSGTDDAKVRAARVLEALEKMLSARAREEAGNKFQEEKVA
VQQQVETLVKDNTVLKRAVAIQHERQKALEDANHQLGLLKQLVPQYQEKLRNLEVLVKALEDNG
SDFNAAMKSLYSFASSEEKKAEELAAGGAATQETDAVCGGNPPTSGDDWVELLVREVLQSSGTD
DAKVRAARVLEALEKMLSARAREEAGNKFQEEKVAVQQQVETLVKDNTVLKRAVAIQHERQKAL
EDANHQLGLLKQLVPQYQEKLRNLEVLVKALEDNGSDFNAAMKSLYSFASSEEKKAEELAAGGA
ATQETDAVCGGNPPTSGDDWVELLVREVLQSSGTDDAKVRAARVLEALEKMLSARAREEAGNKF
QEEKVAVQQQVETLVKDNTVLKRAVAIQHERQKALEDANHQLGLLKQLVPQYQEKLRNLE(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	30110574-30109695(-)
Potential amino acid sequence	MKSLYSFASSEEKKAEELAAGGAATQETDAVCGGNPPTSGDDWVELLVREVLQSSGTDDAKVRA ARVLEALEKMLSARAREEAGNKFQEEKVAVQQQVETLVKDNTVLKRAVAIQHERQKALEDANHQ LGLLKQLVPQYQEKLRNLEVLVKALEDNGSDFNAAMKSLYSFASSEEKKAEELAAGGAATQETD AVCGGNPPTSGDDWVELLVREVLQSSGTDDAKVRAARVLEALEKMLSARAREEAGNKFQEEKVA VQQQVETLVKDNTVLKRAVAIQHERQKALEDANHQLGLLKQLVPQYQEKLRNLEVLVKALEDNG SDFNAAMKSLYSFASSEEKKAEELAAGGAATQETDAVCGGNPPTSGDDWVELLVREVLQSSGTD DAKVRAARVLEALEKMLSARAREEAGNKFQEEKVAVQQQVETLVKDNTVLKRAVAIQHERQKAL EDANHQLGLLKQLVPQYQEKLRNLEVLVKALEDNGSDFNAAMKSLYSFASSEEKKAEELAAGGA ATQETDAVCGGNPPTSGDDWVELLVREVLQSSGTDDAKVRAARVLEALEKMLSARAREEAGNKF QEEKVAVQQQVETLVKDNTVLKRAVAIQHERQKALEDANHQLGLLKQLVPQYQEKLRNLE(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ye et al., 2015

circRNA

Detail information of AT1G80040_circ_g.2

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