Plant Circular RNA Database

Detail information of Os07g0475900_circ_g.4

			
						 General Information
					
						CircRNA Name
						Os07g0475900_circ_g.4
					
						ID in PlantcircBase
						osa_circ_033758
					
						Alias
						Os_ciR10918
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr7: 17202094-17202201  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, find_circ
					
						Parent gene
						
							Os07g0475900						
					
						Parent gene annotation
						
							Similar to kinase family protein. (Os07t0475900-01)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os07g0475900_circ_g.5 						
					
						Support reads
						2/1
					
						Tissues
						root/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
						Os07t0475900-01:1

General Information
CircRNA Name	Os07g0475900_circ_g.4
ID in PlantcircBase	osa_circ_033758
Alias	Os_ciR10918
Organism	Oryza sativa
Position	chr7: 17202094-17202201 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, find_circ
Parent gene	Os07g0475900
Parent gene annotation	Similar to kinase family protein. (Os07t0475900-01)
Parent gene strand	-
Alternative splicing	Os07g0475900_circ_g.5
Support reads	2/1
Tissues	root/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	Os07t0475900-01:1

			
						 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  
						
							TCAGGCTTGAGTACTTTGATTGCTACATCTTGACTACAGTATGTCCCATGGTATttcattatat
atacttcctgtgcaaactcacgcagcatatcaacgctgacccgc

						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: 108
Transcript exons: 17202094-17202201
TTCATTATATATACTTCCTGTGCAAACTCACGCAGCATATCAACGCTGACCCGCTCAGGCTTGA
GTACTTTGATTGCTACATCTTGACTACAGTATGTCCCATGGTAT
						
						Genomic sequence
						
							TTCATTATATATACTTCCTGTGCAAACTCACGCAGCATATCAACGCTGACCCGCTCAGGCTTGA
GTACTTTGATTGCTACATCTTGACTACAGTATGTCCCATGGTAT

Sequences
Splice junction sequence	TCAGGCTTGAGTACTTTGATTGCTACATCTTGACTACAGTATGTCCCATGGTATttcattatat atacttcctgtgcaaactcacgcagcatatcaacgctgacccgc
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: 108 Transcript exons: 17202094-17202201 TTCATTATATATACTTCCTGTGCAAACTCACGCAGCATATCAACGCTGACCCGCTCAGGCTTGA GTACTTTGATTGCTACATCTTGACTACAGTATGTCCCATGGTAT
Genomic sequence	TTCATTATATATACTTCCTGTGCAAACTCACGCAGCATATCAACGCTGACCCGCTCAGGCTTGA GTACTTTGATTGCTACATCTTGACTACAGTATGTCCCATGGTAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.297777469

Conservation Information
Conserved circRNAs	NA
PMCS	0.297777469

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							17202189-17202139(+)
17202196-17202198(+)
17202133-17202096(-)
						
						Potential amino acid sequence
						
							MSHGISLYILPVQTHAAYQR*(+)
MVFHYIYFLCKLTQHINADPLRLEYFDCYILTTVCPMVFHYIYFLCKLTQHINADPLRLEYFDC
YILTTVCPMVFHYIYFLCKLTQHINADPLRLEYFDCYILTTVCPMV(+)
MLREFAQEVYIMKYHGTYCSQDVAIKVLKPERVSVDMLREFAQEVYIMKYHGTYCSQDVAIKVL
KPERVSVDMLREFAQEVYIMKYHGTYCSQDVAIKVLKPERVSVDMLREFAQEVYIM(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	17202189-17202139(+) 17202196-17202198(+) 17202133-17202096(-)
Potential amino acid sequence	MSHGISLYILPVQTHAAYQR*(+) MVFHYIYFLCKLTQHINADPLRLEYFDCYILTTVCPMVFHYIYFLCKLTQHINADPLRLEYFDC YILTTVCPMVFHYIYFLCKLTQHINADPLRLEYFDCYILTTVCPMV(+) MLREFAQEVYIMKYHGTYCSQDVAIKVLKPERVSVDMLREFAQEVYIMKYHGTYCSQDVAIKVL KPERVSVDMLREFAQEVYIMKYHGTYCSQDVAIKVLKPERVSVDMLREFAQEVYIM(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ye et al., 2015;Chu et al., 2017

circRNA

Detail information of Os07g0475900_circ_g.4

Address

Any questions?

Supported by