Plant Circular RNA Database

Detail information of Os05g0574550_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os05g0574550_circ_g.3
					
						ID in PlantcircBase
						osa_circ_029057
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr5: 28623377-28623701  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, PcircRNA_finder
					
						Parent gene
						
							Os05g0574500						
					
						Parent gene annotation
						
							Similar to GTP-binding nuclear protein Ran1B (Fragment). (Os05t0
574500-01)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os05g0574550_circ_g.1 Os05g0574550_circ_g.2 Os05g0574550_circ_g.4 Os05g0574550_circ_g.5 Os05g0574550_circ_g.6 						
					
						Support reads
						30
					
						Tissues
						shoot, root, seed
					
						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
						Os05t0574550-00:2
Os05t0574550-00:2
Os05t0574500-01:2

General Information
CircRNA Name	Os05g0574550_circ_g.3
ID in PlantcircBase	osa_circ_029057
Alias	NA
Organism	Oryza sativa
Position	chr5: 28623377-28623701 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, PcircRNA_finder
Parent gene	Os05g0574500
Parent gene annotation	Similar to GTP-binding nuclear protein Ran1B (Fragment). (Os05t0 574500-01)
Parent gene strand	-
Alternative splicing	Os05g0574550_circ_g.1 Os05g0574550_circ_g.2 Os05g0574550_circ_g.4 Os05g0574550_circ_g.5 Os05g0574550_circ_g.6
Support reads	30
Tissues	shoot, root, seed
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	Os05t0574550-00:2 Os05t0574550-00:2 Os05t0574500-01:2

			
						 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  
						
							CCACCAAACTTCTCTTGTCCAGCAGTGTCCCAGCAGTAGAAGCGGATCTTACCACAGTTGGTGG
TAAAATCTAGAGGGTGAACTTCGACACCAATGGTTGctgcacaagtccctatgccatgttggaa
cattcttgtaagtcagccttgaagtgacatcaaacataattatcgcacattgaccatggatact
gcacaaca

						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: 208
Transcript exons: 28623377-28623466,28623584-28623701
CTGCACAAGTCCCTATGCCATGTTGGAACATTCTTGTAAGTCAGCCTTGAAGTGACATCAAACA
TAATTATCGCACATTGACCATGGATATAGTATCCATCCCTAAGTCCACCAAACTTCTCTTGTCC
AGCAGTGTCCCAGCAGTAGAAGCGGATCTTACCACAGTTGGTGGTAAAATCTAGAGGGTGAACT
TCGACACCAATGGTTG
						
						Genomic sequence
						
							CTGCACAAGTCCCTATGCCATGTTGGAACATTCTTGTAAGTCAGCCTTGAAGTGACATCAAACA
TAATTATCGCACATTGACCATGGATACTGCACAACAGAAGTTAAGGACAGAACAATCAGGCAAG
CACAAGGAGACATCCATATGCATGGAAAAATATTAAGGGAAGCTATGATAATTGGCTTAAGCAC
TTCTCTAGCACTTACTAGTATCCATCCCTAAGTCCACCAAACTTCTCTTGTCCAGCAGTGTCCC
AGCAGTAGAAGCGGATCTTACCACAGTTGGTGGTAAAATCTAGAGGGTGAACTTCGACACCAAT
GGTTG

Sequences
Splice junction sequence	CCACCAAACTTCTCTTGTCCAGCAGTGTCCCAGCAGTAGAAGCGGATCTTACCACAGTTGGTGG TAAAATCTAGAGGGTGAACTTCGACACCAATGGTTGctgcacaagtccctatgccatgttggaa cattcttgtaagtcagccttgaagtgacatcaaacataattatcgcacattgaccatggatact gcacaaca
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: 208 Transcript exons: 28623377-28623466,28623584-28623701 CTGCACAAGTCCCTATGCCATGTTGGAACATTCTTGTAAGTCAGCCTTGAAGTGACATCAAACA TAATTATCGCACATTGACCATGGATATAGTATCCATCCCTAAGTCCACCAAACTTCTCTTGTCC AGCAGTGTCCCAGCAGTAGAAGCGGATCTTACCACAGTTGGTGGTAAAATCTAGAGGGTGAACT TCGACACCAATGGTTG
Genomic sequence	CTGCACAAGTCCCTATGCCATGTTGGAACATTCTTGTAAGTCAGCCTTGAAGTGACATCAAACA TAATTATCGCACATTGACCATGGATACTGCACAACAGAAGTTAAGGACAGAACAATCAGGCAAG CACAAGGAGACATCCATATGCATGGAAAAATATTAAGGGAAGCTATGATAATTGGCTTAAGCAC TTCTCTAGCACTTACTAGTATCCATCCCTAAGTCCACCAAACTTCTCTTGTCCAGCAGTGTCCC AGCAGTAGAAGCGGATCTTACCACAGTTGGTGGTAAAATCTAGAGGGTGAACTTCGACACCAAT GGTTG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.355283282

Conservation Information
Conserved circRNAs	NA
PMCS	0.355283282

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							28623409-28623652(-)
28623443-28623652(-)
						
						Potential amino acid sequence
						
							MFQHGIGTCAATIGVEVHPLDFTTNCGKIRFYCWDTAGQEKFGGLRDGYYIHGQCAIIMFDVTS
RLTYKNVPTWHRDLCSNHWCRSSPSRFYHQLW*(-)
MFDVTSRLTYKNVPTWHRDLCSNHWCRSSPSRFYHQLW*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	28623409-28623652(-) 28623443-28623652(-)
Potential amino acid sequence	MFQHGIGTCAATIGVEVHPLDFTTNCGKIRFYCWDTAGQEKFGGLRDGYYIHGQCAIIMFDVTS RLTYKNVPTWHRDLCSNHWCRSSPSRFYHQLW(-) MFDVTSRLTYKNVPTWHRDLCSNHWCRSSPSRFYHQLW(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os05g0574550_circ_g.3

Address

Any questions?

Supported by