Plant Circular RNA Database

Detail information of Os05g0241150_circ_g.2

			
						 General Information
					
						CircRNA Name
						Os05g0241150_circ_g.2
					
						ID in PlantcircBase
						osa_circ_027137
					
						Alias
						Os_ciR3088, 
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr5: 8602909-8603328  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ui-circRNA							
									
						Identification method
						CIRCexplorer, find_circ, CIRI-long
					
						Parent gene
						
							Os05g0241150						
					
						Parent gene annotation
						
							Hypothetical protein. (Os05t0241150-00)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os05g0241150_circ_g.1 						
					
						Support reads
						4/1
					
						Tissues
						root/shoot, root, 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
						Os05t0241200-01:3
Os05t0241200-02:2
Os05t0241200-01:3
Os05t0241150-00:2
Os05t0241200-02:2

General Information
CircRNA Name	Os05g0241150_circ_g.2
ID in PlantcircBase	osa_circ_027137
Alias	Os_ciR3088,
Organism	Oryza sativa
Position	chr5: 8602909-8603328 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ui-circRNA
Identification method	CIRCexplorer, find_circ, CIRI-long
Parent gene	Os05g0241150
Parent gene annotation	Hypothetical protein. (Os05t0241150-00)
Parent gene strand	-
Alternative splicing	Os05g0241150_circ_g.1
Support reads	4/1
Tissues	root/shoot, root, 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	Os05t0241200-01:3 Os05t0241200-02:2 Os05t0241200-01:3 Os05t0241150-00:2 Os05t0241200-02:2

			
						 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  
						
							ACCTCTTTCTTGTTAATATAGTTTTGTGTCGGTGAGCCATCTTTTGGTAGGAGTCTTGTACTGC
CTTGTCGGCTGGAGTTTTGGTCTCCCAAAGCGCGCGggaagcaaagcctgtgggatttgcagag
agataccctgctcttgtcaccggtttctttttcttcatgtggtatgcttactcacctgagcgca
ctttagaa

						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: 214
Transcript exons: 8602909-8602977,8603090-8603155,8603250-8603328
GGAAGCAAAGCCTGTGGGATTTGCAGAGAGATACCCTGCTCTTGTCACCGGTTTCTTTTTCTTC
ATGTGGTATTTTCTGAACGTGATATTTAACATCCTTAACAAGAAGATCTTCGACTACTTCCCCT
ATCCATATTTTGTGTCGGTGAGCCATCTTTTGGTAGGAGTCTTGTACTGCCTTGTCGGCTGGAG
TTTTGGTCTCCCAAAGCGCGCG
						
						Genomic sequence
						
							GGAAGCAAAGCCTGTGGGATTTGCAGAGAGATACCCTGCTCTTGTCACCGGTTTCTTTTTCTTC
ATGTGGTATGCTTACTCACCTGAGCGCACTTTAGAATTTACAATTGCAGGTGAGCGAACTGAGA
AGTTGCTGCCTAATGTGGTTTAGCTATTGCCAATTCACAATATGATTTTGTAGGTATTTTCTGA
ACGTGATATTTAACATCCTTAACAAGAAGATCTTCGACTACTTCCCCTATCCATAGTACGTTTG
CTTTATATGTGTGCCTCCTTTTCTTTTTCCTTTCATGTGACAACATGCATCTTCATGATCTAAA
ACCTCTTTCTTGTTAATATAGTTTTGTGTCGGTGAGCCATCTTTTGGTAGGAGTCTTGTACTGC
CTTGTCGGCTGGAGTTTTGGTCTCCCAAAGCGCGCG

Sequences
Splice junction sequence	ACCTCTTTCTTGTTAATATAGTTTTGTGTCGGTGAGCCATCTTTTGGTAGGAGTCTTGTACTGC CTTGTCGGCTGGAGTTTTGGTCTCCCAAAGCGCGCGggaagcaaagcctgtgggatttgcagag agataccctgctcttgtcaccggtttctttttcttcatgtggtatgcttactcacctgagcgca ctttagaa
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: 214 Transcript exons: 8602909-8602977,8603090-8603155,8603250-8603328 GGAAGCAAAGCCTGTGGGATTTGCAGAGAGATACCCTGCTCTTGTCACCGGTTTCTTTTTCTTC ATGTGGTATTTTCTGAACGTGATATTTAACATCCTTAACAAGAAGATCTTCGACTACTTCCCCT ATCCATATTTTGTGTCGGTGAGCCATCTTTTGGTAGGAGTCTTGTACTGCCTTGTCGGCTGGAG TTTTGGTCTCCCAAAGCGCGCG
Genomic sequence	GGAAGCAAAGCCTGTGGGATTTGCAGAGAGATACCCTGCTCTTGTCACCGGTTTCTTTTTCTTC ATGTGGTATGCTTACTCACCTGAGCGCACTTTAGAATTTACAATTGCAGGTGAGCGAACTGAGA AGTTGCTGCCTAATGTGGTTTAGCTATTGCCAATTCACAATATGATTTTGTAGGTATTTTCTGA ACGTGATATTTAACATCCTTAACAAGAAGATCTTCGACTACTTCCCCTATCCATAGTACGTTTG CTTTATATGTGTGCCTCCTTTTCTTTTTCCTTTCATGTGACAACATGCATCTTCATGATCTAAA ACCTCTTTCTTGTTAATATAGTTTTGTGTCGGTGAGCCATCTTTTGGTAGGAGTCTTGTACTGC CTTGTCGGCTGGAGTTTTGGTCTCCCAAAGCGCGCG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.351609048

Conservation Information
Conserved circRNAs	NA
PMCS	0.351609048

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							8602974-8603110(+)
8603270-8603121(-)
8603118-8603121(-)
						
						Potential amino acid sequence
						
							MWYFLNVIFNILNKKIFDYFPYPYFVSVSHLLVGVLYCLVGWSFGLPKRAGSKACGICREIPCS
CHRFLFLHVVFSERDI*(+)
MAHRHKIWIGEVVEDLLVKDVKYHVQKIPHEEKETGDKSRVSLCKSHRLCFPRALGDQNSSRQG
STRLLPKDGSPTQNMDRGSSRRSSC*(-)
MLNITFRKYHMKKKKPVTRAGYLSANPTGFASRALWETKTPADKAVQDSYQKMAHRHKIWIGEV
VEDLLVKDVKYHVQKIPHEEKETGDKSRVSLCKSHRLCFPRALGDQNSSRQGSTRLLPKDGSPT
QNMDRGSSRRSSC*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	8602974-8603110(+) 8603270-8603121(-) 8603118-8603121(-)
Potential amino acid sequence	MWYFLNVIFNILNKKIFDYFPYPYFVSVSHLLVGVLYCLVGWSFGLPKRAGSKACGICREIPCS CHRFLFLHVVFSERDI(+) MAHRHKIWIGEVVEDLLVKDVKYHVQKIPHEEKETGDKSRVSLCKSHRLCFPRALGDQNSSRQG STRLLPKDGSPTQNMDRGSSRRSSC(-) MLNITFRKYHMKKKKPVTRAGYLSANPTGFASRALWETKTPADKAVQDSYQKMAHRHKIWIGEV VEDLLVKDVKYHVQKIPHEEKETGDKSRVSLCKSHRLCFPRALGDQNSSRQGSTRLLPKDGSPT QNMDRGSSRRSSC*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

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

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Detail information of Os05g0241150_circ_g.2

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