Plant Circular RNA Database

Detail information of BGIOSGA025213_circ_g.2

			
						 General Information
					
						CircRNA Name
						BGIOSGA025213_circ_g.2
					
						ID in PlantcircBase
						osi_circ_007041
					
						Alias
						7:3495887|3501569
					
						Organism
						
							Oryza sativa ssp. indica						
					
						Position
						
							chr7: 3495887-3501569  JBrowse»						
					
						Reference genome
						
							Oryza_indica.ASM465v1.42						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							BGIOSGA025213						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						+
					
						Alternative splicing
						
							BGIOSGA025213_circ_g.3 BGIOSGA025213_circ_g.4 						
					
						Support reads
						NA
					
						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  
						
							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
						BGIOSGA025213-TA:7

General Information
CircRNA Name	BGIOSGA025213_circ_g.2
ID in PlantcircBase	osi_circ_007041
Alias	7:3495887\|3501569
Organism	Oryza sativa ssp. indica
Position	chr7: 3495887-3501569 JBrowse»
Reference genome	Oryza_indica.ASM465v1.42
Type	e-circRNA
Identification method	find_circ
Parent gene	BGIOSGA025213
Parent gene annotation	NA
Parent gene strand	+
Alternative splicing	BGIOSGA025213_circ_g.3 BGIOSGA025213_circ_g.4
Support reads	NA
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	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	BGIOSGA025213-TA:7

			
						 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  
						
							AGAGATCGGTTCATTCCACTTGGATGTACCAATTGATAGTATAGTATCTGCATTGCTTTCTTTG
TTTGAAAGATTGACTGGGAAACGCCCACGGTACAAGatgggagtgcttgaaggacattttgtct
ggcggctatacggatggcatcttgtgcagcataggaatgccggttattttcaagagtgtacggt
acaactgc

						Assembled circRNA sequence  
						
							NA
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
						
							NA						
					
						Genomic sequence
						
							TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

Sequences
Splice junction sequence	AGAGATCGGTTCATTCCACTTGGATGTACCAATTGATAGTATAGTATCTGCATTGCTTTCTTTG TTTGAAAGATTGACTGGGAAACGCCCACGGTACAAGatgggagtgcttgaaggacattttgtct ggcggctatacggatggcatcttgtgcagcataggaatgccggttattttcaagagtgtacggt acaactgc
Assembled circRNA sequence	NA 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	NA
Genomic sequence	TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS

Conservation Information
Conserved circRNAs	NA
PMCS

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							3495909-3501482(-)
3495952-3496021(+)
						
						Potential amino acid sequence
						
							MSFKHSHLVPWAFPSQSFKQRKQCRYYTINWYIQVE*(-)
MPVIFKSVRYNCQVFCLNSKIVMIRPKISLANDGNYREFRWFSAWTFKDALVDFQLPLDISEVT
SQDTVPFGYGFIQFLDVSLASETCEELFTANAPRIDLALNGVEVFVNASGSHHQLRKLSLRIDS
MRNATLACGGVYMYANQQGCDGGRLYYDGCCCIAVNGDVVAQGSQFSLKDVEVLDALVDLDAVS
SYRASVSSFREQASHRTKVPFVKVPYKLCKPFQSGMVPTGPVEVMYHRPEEEIAFGPSCWLWDY
LRRSRASGFLLPLSGGADSSSVAAIVGCMCQLVVKDIENGDEQVKADAMRIGQYKDGEFPKDSR
ELAKRLFYTVYMGTENSSEGTRSRAKMLAEEIGSFHLDVPIDSIVSALLSLFERLTGKRPRYKM
GVLEGHFVWRLYGWHLVQHRNAGYFQECTVQLPGVLLKQQDSHD*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	3495909-3501482(-) 3495952-3496021(+)
Potential amino acid sequence	MSFKHSHLVPWAFPSQSFKQRKQCRYYTINWYIQVE(-) MPVIFKSVRYNCQVFCLNSKIVMIRPKISLANDGNYREFRWFSAWTFKDALVDFQLPLDISEVT SQDTVPFGYGFIQFLDVSLASETCEELFTANAPRIDLALNGVEVFVNASGSHHQLRKLSLRIDS MRNATLACGGVYMYANQQGCDGGRLYYDGCCCIAVNGDVVAQGSQFSLKDVEVLDALVDLDAVS SYRASVSSFREQASHRTKVPFVKVPYKLCKPFQSGMVPTGPVEVMYHRPEEEIAFGPSCWLWDY LRRSRASGFLLPLSGGADSSSVAAIVGCMCQLVVKDIENGDEQVKADAMRIGQYKDGEFPKDSR ELAKRLFYTVYMGTENSSEGTRSRAKMLAEEIGSFHLDVPIDSIVSALLSLFERLTGKRPRYKM GVLEGHFVWRLYGWHLVQHRNAGYFQECTVQLPGVLLKQQDSHD(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Huang et al., 2021

circRNA

Detail information of BGIOSGA025213_circ_g.2

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