Plant Circular RNA Database

Detail information of AT3G02470_circ_g.4

			
						 General Information
					
						CircRNA Name
						AT3G02470_circ_g.4
					
						ID in PlantcircBase
						ath_circ_019300
					
						Alias
						3:509305-509952
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 509305-509952  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT3G02470						
					
						Parent gene annotation
						
							S-adenosylmethionine decarboxylase proenzyme 1
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT3G02470_circ_g.1 AT3G02470_circ_g.2 AT3G02470_circ_g.3 AT3G02470_circ_g.5 AT3G02470_circ_g.6 						
					
						Support reads
						1/1/2/1
					
						Tissues
						seedling;leaf;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
						AT3G02470.1:2
AT3G02470.3:2
AT3G02470.4:2

General Information
CircRNA Name	AT3G02470_circ_g.4
ID in PlantcircBase	ath_circ_019300
Alias	3:509305-509952
Organism	Arabidpsis thaliana
Position	chr3: 509305-509952 JBrowse»
Reference genome	TAIR10.38
Type	u-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT3G02470
Parent gene annotation	S-adenosylmethionine decarboxylase proenzyme 1
Parent gene strand	+
Alternative splicing	AT3G02470_circ_g.1 AT3G02470_circ_g.2 AT3G02470_circ_g.3 AT3G02470_circ_g.5 AT3G02470_circ_g.6
Support reads	1/1/2/1
Tissues	seedling;leaf;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	AT3G02470.1:2 AT3G02470.3:2 AT3G02470.4:2

			
						 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  
						
							TAGTAGTTCCTTATTTTACGAAGCTCCCCTCGGTTACAGCATTGAAGACGTTCGTCCAAACGGT
GGAATCAAGAAATTCAAATCTTCTGTCTACTCAAACgtttgagggtttcgtttgatatctggag
aaaggggtttctggaaacaaggagttcataattcgcgatcttgatctatcgatcttcatttata
tatgtaag

						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: 251
Transcript exons: 509305-509399,509797-509952
GTTTGAGGGTTTCGTTTGATATCTGGAGAAAGGGGTTTCTGGAAACAAGGAGTTCATAATTCGC
GATCTTGATCTATCGATCTTCATTTATATATAAAAGCGTGAATGAGATTATGATGGAGTCGAAA
GGTGGTAAAAAGAAGTCCAGCAGTAGTAGTTCCTTATTTTACGAAGCTCCCCTCGGTTACAGCA
TTGAAGACGTTCGTCCAAACGGTGGAATCAAGAAATTCAAATCTTCTGTCTACTCAAAC
						
						Genomic sequence
						
							GTTTGAGGGTTTCGTTTGATATCTGGAGAAAGGGGTTTCTGGAAACAAGGAGTTCATAATTCGC
GATCTTGATCTATCGATCTTCATTTATATATGTAAGTATCTCTCACGATTGACGTCGTTCTTCG
ATTGATTCATTAGCCTAGCTAGGTTAGATAGACATCGTTCTTATCGTCCTAGGTTTTGGTATAA
GAGATTGATATTCGCATGCATGGTTAGGTTGACTTATACCTGAAACCAACGACTTGGTTTCGAT
TTTTGTTTTGTTACATGTATGATTGCCTATTGTCTTAGGCTTTGTTTTTAGTTATGGATCTGCT
ATAATAATTGGTTTCTACTCATCATTCGAGATATACAATTGAAAATTGAATGGTTCTTATGGTT
TATAGATTCGTATTGTCCTGATAAACATTGTTGTGTGATCTTTTGAATACCTGGTATTTTTATT
TTTCATCTGATCTTTTTCCTTTGGATTTGTTTTGTCTAATACAGAAAAGCGTGAATGAGATTAT
GATGGAGTCGAAAGGTGGTAAAAAGAAGTCCAGCAGTAGTAGTTCCTTATTTTACGAAGCTCCC
CTCGGTTACAGCATTGAAGACGTTCGTCCAAACGGTGGAATCAAGAAATTCAAATCTTCTGTCT
ACTCAAAC

Sequences
Splice junction sequence	TAGTAGTTCCTTATTTTACGAAGCTCCCCTCGGTTACAGCATTGAAGACGTTCGTCCAAACGGT GGAATCAAGAAATTCAAATCTTCTGTCTACTCAAACgtttgagggtttcgtttgatatctggag aaaggggtttctggaaacaaggagttcataattcgcgatcttgatctatcgatcttcatttata tatgtaag
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: 251 Transcript exons: 509305-509399,509797-509952 GTTTGAGGGTTTCGTTTGATATCTGGAGAAAGGGGTTTCTGGAAACAAGGAGTTCATAATTCGC GATCTTGATCTATCGATCTTCATTTATATATAAAAGCGTGAATGAGATTATGATGGAGTCGAAA GGTGGTAAAAAGAAGTCCAGCAGTAGTAGTTCCTTATTTTACGAAGCTCCCCTCGGTTACAGCA TTGAAGACGTTCGTCCAAACGGTGGAATCAAGAAATTCAAATCTTCTGTCTACTCAAAC
Genomic sequence	GTTTGAGGGTTTCGTTTGATATCTGGAGAAAGGGGTTTCTGGAAACAAGGAGTTCATAATTCGC GATCTTGATCTATCGATCTTCATTTATATATGTAAGTATCTCTCACGATTGACGTCGTTCTTCG ATTGATTCATTAGCCTAGCTAGGTTAGATAGACATCGTTCTTATCGTCCTAGGTTTTGGTATAA GAGATTGATATTCGCATGCATGGTTAGGTTGACTTATACCTGAAACCAACGACTTGGTTTCGAT TTTTGTTTTGTTACATGTATGATTGCCTATTGTCTTAGGCTTTGTTTTTAGTTATGGATCTGCT ATAATAATTGGTTTCTACTCATCATTCGAGATATACAATTGAAAATTGAATGGTTCTTATGGTT TATAGATTCGTATTGTCCTGATAAACATTGTTGTGTGATCTTTTGAATACCTGGTATTTTTATT TTTCATCTGATCTTTTTCCTTTGGATTTGTTTTGTCTAATACAGAAAAGCGTGAATGAGATTAT GATGGAGTCGAAAGGTGGTAAAAAGAAGTCCAGCAGTAGTAGTTCCTTATTTTACGAAGCTCCC CTCGGTTACAGCATTGAAGACGTTCGTCCAAACGGTGGAATCAAGAAATTCAAATCTTCTGTCT ACTCAAAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.311280108

Conservation Information
Conserved circRNAs	NA
PMCS	0.311280108

			
						 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 AT3G02470_circ_g.4

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