Plant Circular RNA Database

Detail information of Os01g0513900_circ_g.4

			
						 General Information
					
						CircRNA Name
						Os01g0513900_circ_g.4
					
						ID in PlantcircBase
						osa_circ_001927
					
						Alias
						Os_ciR1299
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr1: 18152219-18152777  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer, find_circ
					
						Parent gene
						
							Os01g0513900						
					
						Parent gene annotation
						
							Similar to Kinesin heavy chain (Fragment). (Os01t0513900-01)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os01g0513900_circ_g.1 Os01g0513900_circ_g.2 Os01g0513900_circ_g.3 Os01g0513900_circ_g.5 Os01g0513900_circ_g.6 Os01g0513900_circ_g.7 Os01g0513900_circ_g.8 Os01g0513900_circ_g.9 Os01g0513900_circ_g.10 Os01g0513900_circ_g.11 Os01g0513900_circ_g.12 Os01g0513900_circ_g.13 Os01g0513900_circ_g.14 Os01g0513900_circ_g.15 Os01g0513900_circ_g.16 Os01g0513900_circ_g.17 Os01g0513900_circ_g.18 						
					
						Support reads
						18/2
					
						Tissues
						root/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  
						
							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
						Os01t0513900-01:2

General Information
CircRNA Name	Os01g0513900_circ_g.4
ID in PlantcircBase	osa_circ_001927
Alias	Os_ciR1299
Organism	Oryza sativa
Position	chr1: 18152219-18152777 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ue-circRNA
Identification method	CIRCexplorer, find_circ
Parent gene	Os01g0513900
Parent gene annotation	Similar to Kinesin heavy chain (Fragment). (Os01t0513900-01)
Parent gene strand	+
Alternative splicing	Os01g0513900_circ_g.1 Os01g0513900_circ_g.2 Os01g0513900_circ_g.3 Os01g0513900_circ_g.5 Os01g0513900_circ_g.6 Os01g0513900_circ_g.7 Os01g0513900_circ_g.8 Os01g0513900_circ_g.9 Os01g0513900_circ_g.10 Os01g0513900_circ_g.11 Os01g0513900_circ_g.12 Os01g0513900_circ_g.13 Os01g0513900_circ_g.14 Os01g0513900_circ_g.15 Os01g0513900_circ_g.16 Os01g0513900_circ_g.17 Os01g0513900_circ_g.18
Support reads	18/2
Tissues	root/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	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	Os01t0513900-01:2

			
						 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  
						
							ACCCTTCCAGACAAGGTGTTTGGACCAGCTTCCCAGACAGAAGTGGTGTATGAAGAGGGAGCTA
AGGATGTTGCTATGTCTGCATTGACAGGCATTAATGcttcgtgagaaggctgggttcttgctgt
tttccccagacttcaaggaatctgcaatttactagcgaaaatgggtgtatcaagacctccaagc
acccctgc

									
								

					

						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: 212
Transcript exons: 18152219-18152347,18152695-18152777
CTTCGTGAGAAGGCTGGGTTCTTGCTGTTTTCCCCAGACTTCAAGGAATCTGCAATTTACTAGC
GAAAATGGGTGTATCAAGACCTCCAAGCACCCCTGCATCAAAGATTGAGCGCACACCGATGTCG
AGTTTGGACCAGCTTCCCAGACAGAAGTGGTGTATGAAGAGGGAGCTAAGGATGTTGCTATGTC
TGCATTGACAGGCATTAATG
Transcript length: 232
Transcript exons: 18152219-18152392,18152720-18152777
CTTCGTGAGAAGGCTGGGTTCTTGCTGTTTTCCCCAGACTTCAAGGAATCTGCAATTTACTAGC
GAAAATGGGTGTATCAAGACCTCCAAGCACCCCTGCATCAAAGATTGAGCGCACACCGATGTCG
ACCCCAACCCCTGGTGGCAGCACTAGGGTCAAGGAGGAGAAGATTTGTGGTGTATGAAGAGGGA
GCTAAGGATGTTGCTATGTCTGCATTGACAGGCATTAATG
Transcript length: 252
Transcript exons: 18152219-18152401,18152709-18152777
CTTCGTGAGAAGGCTGGGTTCTTGCTGTTTTCCCCAGACTTCAAGGAATCTGCAATTTACTAGC
GAAAATGGGTGTATCAAGACCTCCAAGCACCCCTGCATCAAAGATTGAGCGCACACCGATGTCG
ACCCCAACCCCTGGTGGCAGCACTAGGGTCAAGGAGGAGAAGATTTTTGTCACAGCCCAGACAG
AAGTGGTGTATGAAGAGGGAGCTAAGGATGTTGCTATGTCTGCATTGACAGGCATTAATG
Transcript length: 405
Transcript exons: 18152219-18152533,18152688-18152777
CTTCGTGAGAAGGCTGGGTTCTTGCTGTTTTCCCCAGACTTCAAGGAATCTGCAATTTACTAGC
GAAAATGGGTGTATCAAGACCTCCAAGCACCCCTGCATCAAAGATTGAGCGCACACCGATGTCG
ACCCCAACCCCTGGTGGCAGCACTAGGGTCAAGGAGGAGAAGATTTTTGTCACAGTGAGGGTGC
GACCATTGAGCAAGAAAGAACTGGCCTTGAAGGATCAGGTGGCATGGGAGTGCGATGATAACCA
GACAATTTTGTACAAGGGCCCCCCACAGGATCGGGCTGCACCCACCTCTTACACTTTCGACAAG
GTGTTTGGACCAGCTTCCCAGACAGAAGTGGTGTATGAAGAGGGAGCTAAGGATGTTGCTATGT
CTGCATTGACAGGCATTAATG
						
					

						Genomic sequence
						
							CTTCGTGAGAAGGCTGGGTTCTTGCTGTTTTCCCCAGACTTCAAGGAATCTGCAATTTACTAGC
GAAAATGGGTGTATCAAGACCTCCAAGCACCCCTGCATCAAAGATTGAGCGCACACCGATGTCG
ACCCCAACCCCTGGTGGCAGCACTAGGGTCAAGGAGGAGAAGATTTTTGTCACAGTGAGGGTGC
GACCATTGAGCAAGAAAGAACTGGCCTTGAAGGATCAGGTGGCATGGGAGTGCGATGATAACCA
GACAATTTTGTACAAGGGCCCCCCACAGGATCGGGCTGCACCCACCTCTTACACTTTCGGTAGG
CTTTTCAGTGATCTATTCATGACTGCATATCTCAAGCAATTATGTTTGTAGTGACACTCTTGAT
CAATGACTTCATATCTCAATCCTATAAGTTTGAAGTTACCTCAGTAGCTAAATTGACTAATTTA
AATTCCATCTTACCCTTCCAGACAAGGTGTTTGGACCAGCTTCCCAGACAGAAGTGGTGTATGA
AGAGGGAGCTAAGGATGTTGCTATGTCTGCATTGACAGGCATTAATG
						
					

			
		

Sequences
Splice junction sequence	ACCCTTCCAGACAAGGTGTTTGGACCAGCTTCCCAGACAGAAGTGGTGTATGAAGAGGGAGCTA AGGATGTTGCTATGTCTGCATTGACAGGCATTAATGcttcgtgagaaggctgggttcttgctgt tttccccagacttcaaggaatctgcaatttactagcgaaaatgggtgtatcaagacctccaagc acccctgc
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: 212 Transcript exons: 18152219-18152347,18152695-18152777 CTTCGTGAGAAGGCTGGGTTCTTGCTGTTTTCCCCAGACTTCAAGGAATCTGCAATTTACTAGC GAAAATGGGTGTATCAAGACCTCCAAGCACCCCTGCATCAAAGATTGAGCGCACACCGATGTCG AGTTTGGACCAGCTTCCCAGACAGAAGTGGTGTATGAAGAGGGAGCTAAGGATGTTGCTATGTC TGCATTGACAGGCATTAATG Transcript length: 232 Transcript exons: 18152219-18152392,18152720-18152777 CTTCGTGAGAAGGCTGGGTTCTTGCTGTTTTCCCCAGACTTCAAGGAATCTGCAATTTACTAGC GAAAATGGGTGTATCAAGACCTCCAAGCACCCCTGCATCAAAGATTGAGCGCACACCGATGTCG ACCCCAACCCCTGGTGGCAGCACTAGGGTCAAGGAGGAGAAGATTTGTGGTGTATGAAGAGGGA GCTAAGGATGTTGCTATGTCTGCATTGACAGGCATTAATG Transcript length: 252 Transcript exons: 18152219-18152401,18152709-18152777 CTTCGTGAGAAGGCTGGGTTCTTGCTGTTTTCCCCAGACTTCAAGGAATCTGCAATTTACTAGC GAAAATGGGTGTATCAAGACCTCCAAGCACCCCTGCATCAAAGATTGAGCGCACACCGATGTCG ACCCCAACCCCTGGTGGCAGCACTAGGGTCAAGGAGGAGAAGATTTTTGTCACAGCCCAGACAG AAGTGGTGTATGAAGAGGGAGCTAAGGATGTTGCTATGTCTGCATTGACAGGCATTAATG Transcript length: 405 Transcript exons: 18152219-18152533,18152688-18152777 CTTCGTGAGAAGGCTGGGTTCTTGCTGTTTTCCCCAGACTTCAAGGAATCTGCAATTTACTAGC GAAAATGGGTGTATCAAGACCTCCAAGCACCCCTGCATCAAAGATTGAGCGCACACCGATGTCG ACCCCAACCCCTGGTGGCAGCACTAGGGTCAAGGAGGAGAAGATTTTTGTCACAGTGAGGGTGC GACCATTGAGCAAGAAAGAACTGGCCTTGAAGGATCAGGTGGCATGGGAGTGCGATGATAACCA GACAATTTTGTACAAGGGCCCCCCACAGGATCGGGCTGCACCCACCTCTTACACTTTCGACAAG GTGTTTGGACCAGCTTCCCAGACAGAAGTGGTGTATGAAGAGGGAGCTAAGGATGTTGCTATGT CTGCATTGACAGGCATTAATG
Genomic sequence	CTTCGTGAGAAGGCTGGGTTCTTGCTGTTTTCCCCAGACTTCAAGGAATCTGCAATTTACTAGC GAAAATGGGTGTATCAAGACCTCCAAGCACCCCTGCATCAAAGATTGAGCGCACACCGATGTCG ACCCCAACCCCTGGTGGCAGCACTAGGGTCAAGGAGGAGAAGATTTTTGTCACAGTGAGGGTGC GACCATTGAGCAAGAAAGAACTGGCCTTGAAGGATCAGGTGGCATGGGAGTGCGATGATAACCA GACAATTTTGTACAAGGGCCCCCCACAGGATCGGGCTGCACCCACCTCTTACACTTTCGGTAGG CTTTTCAGTGATCTATTCATGACTGCATATCTCAAGCAATTATGTTTGTAGTGACACTCTTGAT CAATGACTTCATATCTCAATCCTATAAGTTTGAAGTTACCTCAGTAGCTAAATTGACTAATTTA AATTCCATCTTACCCTTCCAGACAAGGTGTTTGGACCAGCTTCCCAGACAGAAGTGGTGTATGA AGAGGGAGCTAAGGATGTTGCTATGTCTGCATTGACAGGCATTAATG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_009638 						
					
						PMCS
						0.554198413

Conservation Information
Conserved circRNAs	osi_circ_009638
PMCS	0.554198413

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							18152776-18152278(+)
18152288-18152223(+)
18152322-18152774(-)
						
						Potential amino acid sequence
						
							MLREKAGFLLFSPDFKESAIY*(+)
MGVSRPPSTPASKIERTPMSTPTPGGSTRVKEEKIFVTVRVRPLSKKELALKDQVAWECDDNQT
ILYKGPPQDRAAPTSYTFDKVFGPASQTEVVYEEGAKDVAMSALTGINAS*(+)
MQGCLEVLIHPFSLVNCRFLEVWGKQQEPSLLTKH*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	18152776-18152278(+) 18152288-18152223(+) 18152322-18152774(-)
Potential amino acid sequence	MLREKAGFLLFSPDFKESAIY(+) MGVSRPPSTPASKIERTPMSTPTPGGSTRVKEEKIFVTVRVRPLSKKELALKDQVAWECDDNQT ILYKGPPQDRAAPTSYTFDKVFGPASQTEVVYEEGAKDVAMSALTGINAS(+) MQGCLEVLIHPFSLVNCRFLEVWGKQQEPSLLTKH*(-)
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 Os01g0513900_circ_g.4

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