Plant Circular RNA Database

Detail information of Os05g0109600_circ_g.2

			
						 General Information
					
						CircRNA Name
						Os05g0109600_circ_g.2
					
						ID in PlantcircBase
						osa_circ_026221
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr5: 518834-519250  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os05g0109600						
					
						Parent gene annotation
						
							RNA binding protein PufA. (Os05t0109600-01)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os05g0109600_circ_g.1 Os05g0109600_circ_g.3 						
					
						Support reads
						1
					
						Tissues
						shoot, root
					
						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
						Os05t0109600-01:2

General Information
CircRNA Name	Os05g0109600_circ_g.2
ID in PlantcircBase	osa_circ_026221
Alias	NA
Organism	Oryza sativa
Position	chr5: 518834-519250 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	Os05g0109600
Parent gene annotation	RNA binding protein PufA. (Os05t0109600-01)
Parent gene strand	-
Alternative splicing	Os05g0109600_circ_g.1 Os05g0109600_circ_g.3
Support reads	1
Tissues	shoot, root
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	Os05t0109600-01:2

			
						 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  
						
							TTACATGGTTCCCATTTTGATCACGTACACAGCGCATGACGTGTCCATCCAGCTCAGCAACCAT
TTTAGTCTGCTGATCTAAACCAACAACCTCTATAGCctgaacaacgtagttgccgtattgatct
tgagccagcaagcaaacggactggagaatctcatccatcattatttgctgtgttgtaggatcat
cacaatgc

						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: 324
Transcript exons: 518834-518944,519038-519250
CTGAACAACGTAGTTGCCGTATTGATCTTGAGCCAGCAAGCAAACGGACTGGAGAATCTCATCC
ATCATTATTTGCTGTGTTGTAGGATCATCACAATGCTCCAGCACCCTCTGTATAACCCGACAAC
CATATGGATGAGTGGATAACATCACAACTTGACCATAGAATGTTGAGACAATGAACTGGATAGC
ATGTTGAGGGATGCATTCTATGCATTTCTGTATTACATGGTTCCCATTTTGATCACGTACACAG
CGCATGACGTGTCCATCCAGCTCAGCAACCATTTTAGTCTGCTGATCTAAACCAACAACCTCTA
TAGC
						
						Genomic sequence
						
							CTGAACAACGTAGTTGCCGTATTGATCTTGAGCCAGCAAGCAAACGGACTGGAGAATCTCATCC
ATCATTATTTGCTGTGTTGTAGGATCATCACAATGCTCCAGCACCCTCTGGGAGTTTCACATGA
AGGATGACAAGTGAGTTTGCATATTAACATCTGTAAACCTCAACATAAACTGATTACACGCATA
TTATATGCATACCTGTATAACCCGACAACCATATGGATGAGTGGATAACATCACAACTTGACCA
TAGAATGTTGAGACAATGAACTGGATAGCATGTTGAGGGATGCATTCTATGCATTTCTGTATTA
CATGGTTCCCATTTTGATCACGTACACAGCGCATGACGTGTCCATCCAGCTCAGCAACCATTTT
AGTCTGCTGATCTAAACCAACAACCTCTATAGC

Sequences
Splice junction sequence	TTACATGGTTCCCATTTTGATCACGTACACAGCGCATGACGTGTCCATCCAGCTCAGCAACCAT TTTAGTCTGCTGATCTAAACCAACAACCTCTATAGCctgaacaacgtagttgccgtattgatct tgagccagcaagcaaacggactggagaatctcatccatcattatttgctgtgttgtaggatcat cacaatgc
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: 324 Transcript exons: 518834-518944,519038-519250 CTGAACAACGTAGTTGCCGTATTGATCTTGAGCCAGCAAGCAAACGGACTGGAGAATCTCATCC ATCATTATTTGCTGTGTTGTAGGATCATCACAATGCTCCAGCACCCTCTGTATAACCCGACAAC CATATGGATGAGTGGATAACATCACAACTTGACCATAGAATGTTGAGACAATGAACTGGATAGC ATGTTGAGGGATGCATTCTATGCATTTCTGTATTACATGGTTCCCATTTTGATCACGTACACAG CGCATGACGTGTCCATCCAGCTCAGCAACCATTTTAGTCTGCTGATCTAAACCAACAACCTCTA TAGC
Genomic sequence	CTGAACAACGTAGTTGCCGTATTGATCTTGAGCCAGCAAGCAAACGGACTGGAGAATCTCATCC ATCATTATTTGCTGTGTTGTAGGATCATCACAATGCTCCAGCACCCTCTGGGAGTTTCACATGA AGGATGACAAGTGAGTTTGCATATTAACATCTGTAAACCTCAACATAAACTGATTACACGCATA TTATATGCATACCTGTATAACCCGACAACCATATGGATGAGTGGATAACATCACAACTTGACCA TAGAATGTTGAGACAATGAACTGGATAGCATGTTGAGGGATGCATTCTATGCATTTCTGTATTA CATGGTTCCCATTTTGATCACGTACACAGCGCATGACGTGTCCATCCAGCTCAGCAACCATTTT AGTCTGCTGATCTAAACCAACAACCTCTATAGC

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_015968 						
					
						PMCS
						0.799755638

Conservation Information
Conserved circRNAs	osi_circ_015968
PMCS	0.799755638

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							519216-518836(-)
518897-519246(-)
						
						Potential amino acid sequence
						
							MVAELDGHVMRCVRDQNGNHVIQKCIECIPQHAIQFIVSTFYGQVVMLSTHPYGCRVIQRVLEH
CDDPTTQQIMMDEILQSVCLLAQDQYGNYVVQAIEVVGLDQQTKMVAELDGHVMRCVRDQNGNH
VIQKCIECIPQHAIQFIVSTFYGQVVMLSTHPYGCRVIQRVLEHCDDPTTQQIMMDEILQSVCL
LAQDQYGNYVVQAIEVVGLDQQTKMVAELDGHVMRCVRDQNGNHVIQKCIECIPQHAIQFIVST
FYGQVVMLSTHPYGCRVIQRVLEHCDDPTTQQIMMDEILQSVCLLAQDQYGNYVVQAIEVVGLD
QQTKMVAELDGHVMRCVRDQNGNHVIQKCIECIPQHAIQFIVSTFYGQVVMLSTHPYGCRVIQR
VLEHCDDPTTQQIMMDEILQSVCLLAQDQYGNYVVQ(-)
MRFSSPFACWLKINTATTLFRL*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	519216-518836(-) 518897-519246(-)
Potential amino acid sequence	MVAELDGHVMRCVRDQNGNHVIQKCIECIPQHAIQFIVSTFYGQVVMLSTHPYGCRVIQRVLEH CDDPTTQQIMMDEILQSVCLLAQDQYGNYVVQAIEVVGLDQQTKMVAELDGHVMRCVRDQNGNH VIQKCIECIPQHAIQFIVSTFYGQVVMLSTHPYGCRVIQRVLEHCDDPTTQQIMMDEILQSVCL LAQDQYGNYVVQAIEVVGLDQQTKMVAELDGHVMRCVRDQNGNHVIQKCIECIPQHAIQFIVST FYGQVVMLSTHPYGCRVIQRVLEHCDDPTTQQIMMDEILQSVCLLAQDQYGNYVVQAIEVVGLD QQTKMVAELDGHVMRCVRDQNGNHVIQKCIECIPQHAIQFIVSTFYGQVVMLSTHPYGCRVIQR VLEHCDDPTTQQIMMDEILQSVCLLAQDQYGNYVVQ(-) MRFSSPFACWLKINTATTLFRL*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os05g0109600_circ_g.2

Address

Any questions?

Supported by