Plant Circular RNA Database

Detail information of Os01g0180800_circ_g.15

			
						 General Information
					
						CircRNA Name
						Os01g0180800_circ_g.15
					
						ID in PlantcircBase
						osa_circ_000546
					
						Alias
						Os01circ03901
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr1: 4258097-4258243  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ei-circRNA							
									
						Identification method
						SMALT, Segemehl
					
						Parent gene
						
							Os01g0180850						
					
						Parent gene annotation
						
							Hypothetical protein. (Os01t0180850-00)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os01g0180800_circ_g.13 Os01g0180800_circ_g.14 						
					
						Support reads
						2
					
						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
						Os01t0180800-01:1
Os01t0180800-03:1
Os01t0180850-00:1
Os01t0180800-01:1
Os01t0180800-03:1

General Information
CircRNA Name	Os01g0180800_circ_g.15
ID in PlantcircBase	osa_circ_000546
Alias	Os01circ03901
Organism	Oryza sativa
Position	chr1: 4258097-4258243 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ei-circRNA
Identification method	SMALT, Segemehl
Parent gene	Os01g0180850
Parent gene annotation	Hypothetical protein. (Os01t0180850-00)
Parent gene strand	-
Alternative splicing	Os01g0180800_circ_g.13 Os01g0180800_circ_g.14
Support reads	2
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	Os01t0180800-01:1 Os01t0180800-03:1 Os01t0180850-00:1 Os01t0180800-01:1 Os01t0180800-03:1

			
						 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  
						
							GGATTGGTTGTACGAAGATGGTGAGGATGAGACCAAAGGAGTGTATGTTGCTAAGCTTGAAGAA
CTTAAAAAGctgtatgacaagtacaatgattttgtgactgctgaagacaaggaagcattcattg
ctaagcttcaagaggttga

						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: 147
Transcript exons: 4258097-4258243
CTGTATGACAAGTACAATGATTTTGTGACTGCTGAAGACAAGGAAGCATTCATTGCTAAGCTTC
AAGAGGTTGAGGATTGGTTGTACGAAGATGGTGAGGATGAGACCAAAGGAGTGTATGTTGCTAA
GCTTGAAGAACTTAAAAAG
						
						Genomic sequence
						
							CTGTATGACAAGTACAATGATTTTGTGACTGCTGAAGACAAGGAAGCATTCATTGCTAAGCTTC
AAGAGGTTGAGGATTGGTTGTACGAAGATGGTGAGGATGAGACCAAAGGAGTGTATGTTGCTAA
GCTTGAAGAACTTAAAAAG

Sequences
Splice junction sequence	GGATTGGTTGTACGAAGATGGTGAGGATGAGACCAAAGGAGTGTATGTTGCTAAGCTTGAAGAA CTTAAAAAGctgtatgacaagtacaatgattttgtgactgctgaagacaaggaagcattcattg ctaagcttcaagaggttga
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: 147 Transcript exons: 4258097-4258243 CTGTATGACAAGTACAATGATTTTGTGACTGCTGAAGACAAGGAAGCATTCATTGCTAAGCTTC AAGAGGTTGAGGATTGGTTGTACGAAGATGGTGAGGATGAGACCAAAGGAGTGTATGTTGCTAA GCTTGAAGAACTTAAAAAG
Genomic sequence	CTGTATGACAAGTACAATGATTTTGTGACTGCTGAAGACAAGGAAGCATTCATTGCTAAGCTTC AAGAGGTTGAGGATTGGTTGTACGAAGATGGTGAGGATGAGACCAAAGGAGTGTATGTTGCTAA GCTTGAAGAACTTAAAAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_011264 						
					
						PMCS
						0.346620295

Conservation Information
Conserved circRNAs	osi_circ_011264
PMCS	0.346620295

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							4258189-4258121(+)
4258151-4258161(-)
						
						Potential amino acid sequence
						
							MVRMRPKECMLLSLKNLKSCMTSTMIL*(+)
MNASLSSAVTKSLYLSYSFLSSSSLATYTPLVSSSPSSYNQSSTS*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	4258189-4258121(+) 4258151-4258161(-)
Potential amino acid sequence	MVRMRPKECMLLSLKNLKSCMTSTMIL(+) MNASLSSAVTKSLYLSYSFLSSSSLATYTPLVSSSPSSYNQSSTS(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Lu et al., 2015

circRNA

Detail information of Os01g0180800_circ_g.15

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