Plant Circular RNA Database

Detail information of BGIOSGA000730_circ_g.3

			
						 General Information
					
						CircRNA Name
						BGIOSGA000730_circ_g.3
					
						ID in PlantcircBase
						osi_circ_002439
					
						Alias
						1:35974890|35975589
					
						Organism
						
							Oryza sativa ssp. indica						
					
						Position
						
							chr1: 35974890-35975589  JBrowse»						
					
						Reference genome
						
							Oryza_indica.ASM465v1.42						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							BGIOSGA000730						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						-
					
						Alternative splicing
						
							BGIOSGA000730_circ_g.1 BGIOSGA000730_circ_g.2 BGIOSGA000730_circ_g.4 BGIOSGA000730_circ_g.5 						
					
						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  
						
							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
						BGIOSGA000730-TA:3

General Information
CircRNA Name	BGIOSGA000730_circ_g.3
ID in PlantcircBase	osi_circ_002439
Alias	1:35974890\|35975589
Organism	Oryza sativa ssp. indica
Position	chr1: 35974890-35975589 JBrowse»
Reference genome	Oryza_indica.ASM465v1.42
Type	e-circRNA
Identification method	find_circ
Parent gene	BGIOSGA000730
Parent gene annotation	NA
Parent gene strand	-
Alternative splicing	BGIOSGA000730_circ_g.1 BGIOSGA000730_circ_g.2 BGIOSGA000730_circ_g.4 BGIOSGA000730_circ_g.5
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	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	BGIOSGA000730-TA:3

			
						 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  
						
							AGAAGGAAGGATCGATCCAAACCCGCAAATAGTCAAGGCCGCCACGGCGAGGATCCCACCGAGA
GGAGGCCGTCCAATCCTTCACCACGCCACGAAACACctcctgaatgtcctctttcaaaacttcc
agtgagcatctctctttgttctcagtgttcagaattgatacctgcttacaacagaactcattcc
cgggtaaa

						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
						
							CTCCTGAATGTCCTCTTTCAAAACTTCCAGTGAGCATCTCTCTTTGTTCTCAGTGTTCAGAATT
GATACCTGCTTACAACAGAACTCATTCCCGGGTAAACAAAAAGTGTGCACTATTAAATTGTAAC
TGTTGTGAAGAAAGGTGATCTCACTTGTGCTAAATAGACTTGGTCACAACTCTCTAAGCTGCTC
GAGCAACCCTCCTCTGAAGAAGCGGGCTCCTTGAGGATTTCTTGAGCTTTGGGTGAGTCACTGG
AGGCATTCGGACACCTCAGGTAAGATTTGCACGAGTTCATGAATTTGGAGAATGGAACAAGCAC
CTGGAATCGAGGAGCAAGATAAGCAGCGTTAGCGCCTCGCGCAAAATGGTGAAAGTTACAACTC
CCAAGCAGATTCAGAGTAAAAAAACCCGCCCTCTCATGGCTTCTAAGATCCCCATAGAACACAT
GCCCTGTGCTCGACATCATAGCTTCCACATCAACATCAGGTCCAACCTTTTCCTGAAGTAAGTA
CTTTATCGGAGATTGCACAACGCAAAGTAGAATGGTACGGAAACAAGATATCTTTCCCACTGTC
TCCTCATGTGAGCTAGATAGAGATAGAAGGAAGGATCGATCCAAACCCGCAAATAGTCAAGGCC
GCCACGGCGAGGATCCCACCGAGAGGAGGCCGTCCAATCCTTCACCACGCCACGAAACAC

Sequences
Splice junction sequence	AGAAGGAAGGATCGATCCAAACCCGCAAATAGTCAAGGCCGCCACGGCGAGGATCCCACCGAGA GGAGGCCGTCCAATCCTTCACCACGCCACGAAACACctcctgaatgtcctctttcaaaacttcc agtgagcatctctctttgttctcagtgttcagaattgatacctgcttacaacagaactcattcc cgggtaaa
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	CTCCTGAATGTCCTCTTTCAAAACTTCCAGTGAGCATCTCTCTTTGTTCTCAGTGTTCAGAATT GATACCTGCTTACAACAGAACTCATTCCCGGGTAAACAAAAAGTGTGCACTATTAAATTGTAAC TGTTGTGAAGAAAGGTGATCTCACTTGTGCTAAATAGACTTGGTCACAACTCTCTAAGCTGCTC GAGCAACCCTCCTCTGAAGAAGCGGGCTCCTTGAGGATTTCTTGAGCTTTGGGTGAGTCACTGG AGGCATTCGGACACCTCAGGTAAGATTTGCACGAGTTCATGAATTTGGAGAATGGAACAAGCAC CTGGAATCGAGGAGCAAGATAAGCAGCGTTAGCGCCTCGCGCAAAATGGTGAAAGTTACAACTC CCAAGCAGATTCAGAGTAAAAAAACCCGCCCTCTCATGGCTTCTAAGATCCCCATAGAACACAT GCCCTGTGCTCGACATCATAGCTTCCACATCAACATCAGGTCCAACCTTTTCCTGAAGTAAGTA CTTTATCGGAGATTGCACAACGCAAAGTAGAATGGTACGGAAACAAGATATCTTTCCCACTGTC TCCTCATGTGAGCTAGATAGAGATAGAAGGAAGGATCGATCCAAACCCGCAAATAGTCAAGGCC GCCACGGCGAGGATCCCACCGAGAGGAGGCCGTCCAATCCTTCACCACGCCACGAAACAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS

Conservation Information
Conserved circRNAs	NA
PMCS

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							35975358-35974892(-)
35974928-35975524(-)
35975256-35974919(+)
						
						Potential amino acid sequence
						
							MMSSTGHVFYGDLRSHERAGFFTLNLLGSCNFHHFARGANAAYLAPRFQVLVPFSKFMNSCKSY
LRCPNASSDSPKAQEILKEPASSEEGCSSSLESCDQVYLAQVSILNTENKERCSLEVLKEDIQE
VFRGVVKDWTASSRWDPRRGGLDYLREKVGPDVDVEAMMSSTGHVFYGDLRSHERAGFFTLNLL
GSCNFHHFARGANAAYLAPRFQVLVPFSKFMNSCKSYLRCPNASSDSPKAQEILKEPASSEEGC
SSSLESCDQVYLAQVSILNTENKERCSLEVLKEDIQEVFRGVVKDWTASSRWDPRRGGLDYLRE
KVGPDVDVEAMMSSTGHVFYGDLRSHERAGFFTLNLLGSCNFHHFARGANAAYLAPRFQVLVPF
SKFMNSCKSYLRCPNASSDSPKAQEILKEPASSEEGCSSSLESCDQVYLAQVSILNTENKERCS
LEVLKEDIQEVFRGVVKDWTASSRWDPRRGGLDYLREKVGPDVDVEAMMSSTGHVFYGDLRSHE
RAGFFTLNLLGSCNFHHFARGANAAYLAPRFQVLVPFSKFMNSCKSYLRCPNASSDSPKAQEIL
KEPASSEEGCSSSLESCDQVYLAQVSILNTENKERCSLEVLKEDIQE(-)
MLTGSFERGHSGGVSWRGEGLDGLLSVGSSPWRP*(-)
MVKVTTPKQIQSKKTRPLMASKIPIEHMPCARHHSFHINIRSNLFPQIVKAATARIPPRGGRPI
LHHATKHLLNVLFQNFQ*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	35975358-35974892(-) 35974928-35975524(-) 35975256-35974919(+)
Potential amino acid sequence	MMSSTGHVFYGDLRSHERAGFFTLNLLGSCNFHHFARGANAAYLAPRFQVLVPFSKFMNSCKSY LRCPNASSDSPKAQEILKEPASSEEGCSSSLESCDQVYLAQVSILNTENKERCSLEVLKEDIQE VFRGVVKDWTASSRWDPRRGGLDYLREKVGPDVDVEAMMSSTGHVFYGDLRSHERAGFFTLNLL GSCNFHHFARGANAAYLAPRFQVLVPFSKFMNSCKSYLRCPNASSDSPKAQEILKEPASSEEGC SSSLESCDQVYLAQVSILNTENKERCSLEVLKEDIQEVFRGVVKDWTASSRWDPRRGGLDYLRE KVGPDVDVEAMMSSTGHVFYGDLRSHERAGFFTLNLLGSCNFHHFARGANAAYLAPRFQVLVPF SKFMNSCKSYLRCPNASSDSPKAQEILKEPASSEEGCSSSLESCDQVYLAQVSILNTENKERCS LEVLKEDIQEVFRGVVKDWTASSRWDPRRGGLDYLREKVGPDVDVEAMMSSTGHVFYGDLRSHE RAGFFTLNLLGSCNFHHFARGANAAYLAPRFQVLVPFSKFMNSCKSYLRCPNASSDSPKAQEIL KEPASSEEGCSSSLESCDQVYLAQVSILNTENKERCSLEVLKEDIQE(-) MLTGSFERGHSGGVSWRGEGLDGLLSVGSSPWRP(-) MVKVTTPKQIQSKKTRPLMASKIPIEHMPCARHHSFHINIRSNLFPQIVKAATARIPPRGGRPI LHHATKHLLNVLFQNFQ(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Huang et al., 2021

circRNA

Detail information of BGIOSGA000730_circ_g.3

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