Plant Circular RNA Database

Detail information of Os01g0111200_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os01g0111200_circ_g.3
					
						ID in PlantcircBase
						osa_circ_000122
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr1: 590087-591178  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os01g0111200						
					
						Parent gene annotation
						
							Like-Sm ribonucleoprotein (LSM)-related domain domain containing
 protein. (Os01t0111200-01)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os01g0111200_circ_g.1 Os01g0111200_circ_g.2 						
					
						Support reads
						2
					
						Tissues
						shoot
					
						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
						Os01t0111200-01:2

General Information
CircRNA Name	Os01g0111200_circ_g.3
ID in PlantcircBase	osa_circ_000122
Alias	NA
Organism	Oryza sativa
Position	chr1: 590087-591178 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	Os01g0111200
Parent gene annotation	Like-Sm ribonucleoprotein (LSM)-related domain domain containing protein. (Os01t0111200-01)
Parent gene strand	+
Alternative splicing	Os01g0111200_circ_g.1 Os01g0111200_circ_g.2
Support reads	2
Tissues	shoot
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	Os01t0111200-01:2

			
						 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  
						
							AACTAGGGTTGTAGAACCATTGCTACCTGATCCACCGTCACGTGCTCTTCCTGAAAATAATGAG
CCTATATTGCCATTGCCGAAACAAACACCTCAAAAGgatttgcaagttaagtcatcaccacctc
caccgccaccaccacaaccagctgccccgcacaatgatcctgccataatacaggtaccgcaatg
aaacaaaa

						Assembled circRNA sequence  
						
							NA
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
						
							NA						
					
						Genomic sequence
						
							GATTTGCAAGTTAAGTCATCACCACCTCCACCGCCACCACCACAACCAGCTGCCCCGCACAATG
ATCCTGCCATAATACAGGTACCGCAATGAAACAAAAACATTGAAAAATACTTCTTAGAGCCGCA
CAACTCATGCAATTCTGTTCTGCAGTCGCACTACTCTCAGCCAGCATCGGCTTCTTCAAGTTTG
CCTTCTGCTGGAAGTGCAGTATTGCCAGACCTCAGCTCCCAGGCAGCTCAATATGGGCTTCAGA
GGCCAAGTTTTCAGAGCAATATTCCTCTATATCAACCTGGGAGTGTTCCATGGGGATCCTCTGC
TCCACCTTCTGCTGGAAATGCATCAGGCCTTTCAGTTCCCCCAATGTATTGGCAGGGATATTAT
CCACCTGGTGGGCTTCCACCTCATTTGCAGCAACCTCCTTTGCTCCAGCCAGGATTATCAGTTC
CCCAGGGTCTCCAATATGCAGGATTGAATCCCACTCTATCGTCAGGGCCACAAAAACTGTCAGA
ACTGCAGCCCCCCTTGCTGCAACCACCTGGTACTACCCAAGGCCCTTCCTCAGGTATCCTGCCC
ACTACAACAGCACCTTCTTCTGCTAACTTACTATCTCCAGAAACTTCAAAGCCCCTTCTGCCGA
ACATGGGTCCTTTGTTTACTCCTCCAGTTCCATCTGTGGGCGCCACCCTTCCTTTAGCTAGCCT
GCCAACATCCATTGCTGAAAGTAGTGCAATGGCCCCACATAATTTTAGTTCGCTTGTGAGCAAT
AAGACTGCGGATATTCCAGGTTCAACATTGGCATACCAATCAGTGTCACAGGCAGTTTCTTCGA
CTGTTGCTTCATCTAGCTCAGCCCATATGGATATGCCCGTACCTTTGTTGGCATCATCAGGTCA
ACTACTGCAGAATGCTCCATCGATGCTTTCATCATCTCAGTCCATGCAGACACCTTTACAGATG
AGCAGCAAAGATTTCAAGGCAGTTGAATCAAAAACTAGGGTTGTAGAACCATTGCTACCTGATC
CACCGTCACGTGCTCTTCCTGAAAATAATGAGCCTATATTGCCATTGCCGAAACAAACACCTCA
AAAG

Sequences
Splice junction sequence	AACTAGGGTTGTAGAACCATTGCTACCTGATCCACCGTCACGTGCTCTTCCTGAAAATAATGAG CCTATATTGCCATTGCCGAAACAAACACCTCAAAAGgatttgcaagttaagtcatcaccacctc caccgccaccaccacaaccagctgccccgcacaatgatcctgccataatacaggtaccgcaatg aaacaaaa
Assembled circRNA sequence	NA 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	NA
Genomic sequence	GATTTGCAAGTTAAGTCATCACCACCTCCACCGCCACCACCACAACCAGCTGCCCCGCACAATG ATCCTGCCATAATACAGGTACCGCAATGAAACAAAAACATTGAAAAATACTTCTTAGAGCCGCA CAACTCATGCAATTCTGTTCTGCAGTCGCACTACTCTCAGCCAGCATCGGCTTCTTCAAGTTTG CCTTCTGCTGGAAGTGCAGTATTGCCAGACCTCAGCTCCCAGGCAGCTCAATATGGGCTTCAGA GGCCAAGTTTTCAGAGCAATATTCCTCTATATCAACCTGGGAGTGTTCCATGGGGATCCTCTGC TCCACCTTCTGCTGGAAATGCATCAGGCCTTTCAGTTCCCCCAATGTATTGGCAGGGATATTAT CCACCTGGTGGGCTTCCACCTCATTTGCAGCAACCTCCTTTGCTCCAGCCAGGATTATCAGTTC CCCAGGGTCTCCAATATGCAGGATTGAATCCCACTCTATCGTCAGGGCCACAAAAACTGTCAGA ACTGCAGCCCCCCTTGCTGCAACCACCTGGTACTACCCAAGGCCCTTCCTCAGGTATCCTGCCC ACTACAACAGCACCTTCTTCTGCTAACTTACTATCTCCAGAAACTTCAAAGCCCCTTCTGCCGA ACATGGGTCCTTTGTTTACTCCTCCAGTTCCATCTGTGGGCGCCACCCTTCCTTTAGCTAGCCT GCCAACATCCATTGCTGAAAGTAGTGCAATGGCCCCACATAATTTTAGTTCGCTTGTGAGCAAT AAGACTGCGGATATTCCAGGTTCAACATTGGCATACCAATCAGTGTCACAGGCAGTTTCTTCGA CTGTTGCTTCATCTAGCTCAGCCCATATGGATATGCCCGTACCTTTGTTGGCATCATCAGGTCA ACTACTGCAGAATGCTCCATCGATGCTTTCATCATCTCAGTCCATGCAGACACCTTTACAGATG AGCAGCAAAGATTTCAAGGCAGTTGAATCAAAAACTAGGGTTGTAGAACCATTGCTACCTGATC CACCGTCACGTGCTCTTCCTGAAAATAATGAGCCTATATTGCCATTGCCGAAACAAACACCTCA AAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.231922703

Conservation Information
Conserved circRNAs	NA
PMCS	0.231922703

			
				
						 Functional Information
					

				
						Coding potential
						Y
					

						Potential coding position
						
							590451-591175(+)
591139-590159(+)
590162-591174(-)
						
					

						Potential amino acid sequence
						
							MYWQGYYPPGGLPPHLQQPPLLQPGLSVPQGLQYAGLNPTLSSGPQKLSELQPPLLQPPGTTQG
PSSGILPTTTAPSSANLLSPETSKPLLPNMGPLFTPPVPSVGATLPLASLPTSIAESSAMAPHN
FSSLVSNKTADIPGSTLAYQSVSQAVSSTVASSSSAHMDMPVPLLASSGQLLQNAPSMLSSSQS
MQTPLQMSSKDFKAVESKTRVVEPLLPDPPSRALPENNEPILPLPKQTPQKDLQVKSSPPPPPP
PQPAAPHNDPAIIQSHYSQPASASSSLPSAGSAVLPDLSSQAAQYGLQRPSFQSNIPLYQPGSV
PWGSSAPPSAGNASGLSVPPMYWQGYYPPGGLPPHLQQPPLLQPGLSVPQGLQYAGLNPTLSSG
PQKLSELQPPLLQPPGTTQGPSSGILPTTTAPSSANLLSPETSKPLLPNMGPLFTPPVPSVGAT
LPLASLPTSIAESSAMAPHNFSSLVSNKTADIPGSTLAYQSVSQAVSSTVASSSSAHMDMPVPL
LASSGQLLQNAPSMLSSSQSMQTPLQMSSKDFKAVESKTRVVEPLLPDPPSRALPENNEPILPL
PKQTPQKDLQVKSSPPPPPPPQPAAPHNDPAIIQSHYSQPASASSSLPSAGSAVLPDLSSQAAQ
YGLQRPSFQSNIPLYQPGSVPWGSSAPPSAGNASGLSVPPMYWQGYYPPGGLPPHLQQPPLLQP
GLSVPQGLQYAGLNPTLSSGPQKLSELQPPLLQPPGTTQGPSSGILPTTTAPSSANLLSPETSK
PLLPNMGPLFTPPVPSVGATLPLASLPTSIAESSAMAPHNFSSLVSNKTADIPGSTLAYQSVSQ
AVSSTVASSSSAHMDMPVPLLASSGQLLQNAPSMLSSSQSMQTPLQMSSKDFKAVESKTRVVEP
LLPDPPSRALPENNEPILPLPKQTPQKDLQVKSSPPPPPPPQPAAPHNDPAIIQSHYSQPASAS
SSLPSAGSAVLPDLSSQAAQYGLQRPSFQSNIPLYQPGSVPWGSSAPPSAGNASGLSVPPMYWQ
GYYPPGGLPPHLQQPPLLQPGLSVPQGLQYAGLNPTLSSGPQKLSELQPPLLQPPGTTQGPSSG
ILPTTTAPSSANLLSPETSKPLLPNMGPLFTPPVPSVGATLPLASLPTSIAESSAMAPHNFSSL
VSNKTADIPGSTLAYQSVSQAVSSTVASSSSAHMDMPVPLLASSGQLLQNAPSMLSSSQSMQTP
LQMSSKDFKAVESKTRVVEPLLPDPPSRALPENNEPILPLPKQTPQK(+)
MSLYCHCRNKHLKRICKLSHHHLHRHHHNQLPRTMILP*(+)
MAGSLCGAAGCGGGGGGGDDLTCKSF*(-)
						
					

						Sponge-miRNAs
						
							NA						
					

						circRNA-miRNA-mRNA network
						 VISUALIZATION
					

						Potential function description
						NA
					

			
		

Functional Information
Coding potential	Y
Potential coding position	590451-591175(+) 591139-590159(+) 590162-591174(-)
Potential amino acid sequence	MYWQGYYPPGGLPPHLQQPPLLQPGLSVPQGLQYAGLNPTLSSGPQKLSELQPPLLQPPGTTQG PSSGILPTTTAPSSANLLSPETSKPLLPNMGPLFTPPVPSVGATLPLASLPTSIAESSAMAPHN FSSLVSNKTADIPGSTLAYQSVSQAVSSTVASSSSAHMDMPVPLLASSGQLLQNAPSMLSSSQS MQTPLQMSSKDFKAVESKTRVVEPLLPDPPSRALPENNEPILPLPKQTPQKDLQVKSSPPPPPP PQPAAPHNDPAIIQSHYSQPASASSSLPSAGSAVLPDLSSQAAQYGLQRPSFQSNIPLYQPGSV PWGSSAPPSAGNASGLSVPPMYWQGYYPPGGLPPHLQQPPLLQPGLSVPQGLQYAGLNPTLSSG PQKLSELQPPLLQPPGTTQGPSSGILPTTTAPSSANLLSPETSKPLLPNMGPLFTPPVPSVGAT LPLASLPTSIAESSAMAPHNFSSLVSNKTADIPGSTLAYQSVSQAVSSTVASSSSAHMDMPVPL LASSGQLLQNAPSMLSSSQSMQTPLQMSSKDFKAVESKTRVVEPLLPDPPSRALPENNEPILPL PKQTPQKDLQVKSSPPPPPPPQPAAPHNDPAIIQSHYSQPASASSSLPSAGSAVLPDLSSQAAQ YGLQRPSFQSNIPLYQPGSVPWGSSAPPSAGNASGLSVPPMYWQGYYPPGGLPPHLQQPPLLQP GLSVPQGLQYAGLNPTLSSGPQKLSELQPPLLQPPGTTQGPSSGILPTTTAPSSANLLSPETSK PLLPNMGPLFTPPVPSVGATLPLASLPTSIAESSAMAPHNFSSLVSNKTADIPGSTLAYQSVSQ AVSSTVASSSSAHMDMPVPLLASSGQLLQNAPSMLSSSQSMQTPLQMSSKDFKAVESKTRVVEP LLPDPPSRALPENNEPILPLPKQTPQKDLQVKSSPPPPPPPQPAAPHNDPAIIQSHYSQPASAS SSLPSAGSAVLPDLSSQAAQYGLQRPSFQSNIPLYQPGSVPWGSSAPPSAGNASGLSVPPMYWQ GYYPPGGLPPHLQQPPLLQPGLSVPQGLQYAGLNPTLSSGPQKLSELQPPLLQPPGTTQGPSSG ILPTTTAPSSANLLSPETSKPLLPNMGPLFTPPVPSVGATLPLASLPTSIAESSAMAPHNFSSL VSNKTADIPGSTLAYQSVSQAVSSTVASSSSAHMDMPVPLLASSGQLLQNAPSMLSSSQSMQTP LQMSSKDFKAVESKTRVVEPLLPDPPSRALPENNEPILPLPKQTPQK(+) MSLYCHCRNKHLKRICKLSHHHLHRHHHNQLPRTMILP(+) MAGSLCGAAGCGGGGGGGDDLTCKSF(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os01g0111200_circ_g.3

Address

Any questions?

Supported by