Plant Circular RNA Database

Detail information of Os10g0477000_circ_g.9

			
						 General Information
					
						CircRNA Name
						Os10g0477000_circ_g.9
					
						ID in PlantcircBase
						osa_circ_007122
					
						Alias
						Os10circ05855/Os_ciR3607
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr10: 17786344-17787455  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, CIRI, PcircRNA_finder, SMALT, Segemehl, find_circ
					
						Parent gene
						
							Os10g0477000						
					
						Parent gene annotation
						
							Armadillo-like helical domain containing protein. (Os10t0477000-
01)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os10g0477000_circ_g.6 Os10g0477000_circ_g.7 Os10g0477000_circ_g.8 Os10g0477000_circ_g.10 Os10g0477000_circ_g.11 						
					
						Support reads
						2/2/8
					
						Tissues
						leaf/root/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  
						
							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
						Os10t0477000-01:3

General Information
CircRNA Name	Os10g0477000_circ_g.9
ID in PlantcircBase	osa_circ_007122
Alias	Os10circ05855/Os_ciR3607
Organism	Oryza sativa
Position	chr10: 17786344-17787455 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, CIRI, PcircRNA_finder, SMALT, Segemehl, find_circ
Parent gene	Os10g0477000
Parent gene annotation	Armadillo-like helical domain containing protein. (Os10t0477000- 01)
Parent gene strand	+
Alternative splicing	Os10g0477000_circ_g.6 Os10g0477000_circ_g.7 Os10g0477000_circ_g.8 Os10g0477000_circ_g.10 Os10g0477000_circ_g.11
Support reads	2/2/8
Tissues	leaf/root/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	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	Os10t0477000-01:3

			
						 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  
						
							TATCTTTTGCTTTGATTTCTGTTGCCAGACACTTACATGCCAGAAGCTACTTGCTACAGTTGTT
CGACGGAAGCACACATGTACTTATGTTGTTCAGTTGgtccataataaatttttctcgacagtgt
ctagatccaggaatcagggcaaggtacttcagtccgcgactcatggaggtacagtttttgctgt
tatgattt

									
								

					

						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: 385
Transcript exons: 17786344-17786419,17786751-17786987,17787384-17787455
GTCCATAATAAATTTTTCTCGACAGTGTCTAGATCCAGGAATCAGGGCAAGGTACTTCAGTCCG
CGACTCATGGAGGCTGTGATTTGGTTCTTGGCCAGATGGGTCGCAACCTATTTAGTACCACTTG
ATGTGAGTAGGGGGCAAGTAAACAGAGCAGAAATTGACAGTGTGGATAAACACATGCTCCAACA
TTCTAGAAAAATGCTAAACAGTTTTGCTTGGGAGAATAACCAAGGAGAGCGTGTTCTTGATTTT
GTTGTTCTTATTTCAATGGTAGCACTTACTACATATCAGGGAGAAATTGAGCTGCAGACACTTA
CATGCCAGAAGCTACTTGCTACAGTTGTTCGACGGAAGCACACATGTACTTATGTTGTTCAGTT
G
						
					

						Genomic sequence
						
							GTCCATAATAAATTTTTCTCGACAGTGTCTAGATCCAGGAATCAGGGCAAGGTACTTCAGTCCG
CGACTCATGGAGGTACAGTTTTTGCTGTTATGATTTATCTGTCAACTTTGTTGTCTTTACTTTG
GAAATTTCTTTCTTTTCTTGTTTGATTGTTGAGCAGAATCCTACCAGTATTCTGACATGCAGGG
ATCTTTGGATTGGGTAGTTCCCTCCGCTAAGGTCTCAAGGCCTTGAGGATTTATTTTTTCTTTT
CATATTGACTTCATTGTCACTTTAGGGGATATTTTCTTGATTATTATACCATGGACACTGAATT
ATTCCCCTTACTCTTTTATCATTGTATTCTTTGGAGTCTTCTTTTATACTTTTCTGGCTTCCAT
AATTTCTTTGTATCTCCTGGCAGGCTGTGATTTGGTTCTTGGCCAGATGGGTCGCAACCTATTT
AGTACCACTTGATGTGAGTAGGGGGCAAGTAAACAGAGCAGAAATTGACAGTGTGGATAAACAC
ATGCTCCAACATTCTAGAAAAATGCTAAACAGTTTTGCTTGGGAGAATAACCAAGGAGAGCGTG
TTCTTGATTTTGTTGTTCTTATTTCAATGGTAGCACTTACTACATATCAGGGAGAAATTGAGCT
GCAGGTAACTTTTGCTTGCACTGGTCATTCTGTAATTCTGCAAAAAATATGTTGTGCACACTGC
GTATGTGTTTTGCAGTGACTAGTGTTTAGCAATAGCCATTCTGTGCAAAAATAAGTTACTTTCT
CTAGTAAAAATTTTAGAGTTCTTTTTATTATTATCACCTTTGACCTTTAGTTGTTATCACCAAG
ATGCCCTTAAAGAAAATGAAAACTTTGATACATAAGTACATGACGAATACTTTCTTGGTAAAAT
ATCTGAGATTTGACCACACTCTTCCTGCAGTAACAATATTTTTTTATTGAAGGGAGTTTATTGG
TGTACGCATGCCAGAAGTATCTCTCTGCCTGTCCATTCAGGAGTCTATGTCTTATCTTTTGCTT
TGATTTCTGTTGCCAGACACTTACATGCCAGAAGCTACTTGCTACAGTTGTTCGACGGAAGCAC
ACATGTACTTATGTTGTTCAGTTG
						
					

			
		

Sequences
Splice junction sequence	TATCTTTTGCTTTGATTTCTGTTGCCAGACACTTACATGCCAGAAGCTACTTGCTACAGTTGTT CGACGGAAGCACACATGTACTTATGTTGTTCAGTTGgtccataataaatttttctcgacagtgt ctagatccaggaatcagggcaaggtacttcagtccgcgactcatggaggtacagtttttgctgt tatgattt
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: 385 Transcript exons: 17786344-17786419,17786751-17786987,17787384-17787455 GTCCATAATAAATTTTTCTCGACAGTGTCTAGATCCAGGAATCAGGGCAAGGTACTTCAGTCCG CGACTCATGGAGGCTGTGATTTGGTTCTTGGCCAGATGGGTCGCAACCTATTTAGTACCACTTG ATGTGAGTAGGGGGCAAGTAAACAGAGCAGAAATTGACAGTGTGGATAAACACATGCTCCAACA TTCTAGAAAAATGCTAAACAGTTTTGCTTGGGAGAATAACCAAGGAGAGCGTGTTCTTGATTTT GTTGTTCTTATTTCAATGGTAGCACTTACTACATATCAGGGAGAAATTGAGCTGCAGACACTTA CATGCCAGAAGCTACTTGCTACAGTTGTTCGACGGAAGCACACATGTACTTATGTTGTTCAGTT G
Genomic sequence	GTCCATAATAAATTTTTCTCGACAGTGTCTAGATCCAGGAATCAGGGCAAGGTACTTCAGTCCG CGACTCATGGAGGTACAGTTTTTGCTGTTATGATTTATCTGTCAACTTTGTTGTCTTTACTTTG GAAATTTCTTTCTTTTCTTGTTTGATTGTTGAGCAGAATCCTACCAGTATTCTGACATGCAGGG ATCTTTGGATTGGGTAGTTCCCTCCGCTAAGGTCTCAAGGCCTTGAGGATTTATTTTTTCTTTT CATATTGACTTCATTGTCACTTTAGGGGATATTTTCTTGATTATTATACCATGGACACTGAATT ATTCCCCTTACTCTTTTATCATTGTATTCTTTGGAGTCTTCTTTTATACTTTTCTGGCTTCCAT AATTTCTTTGTATCTCCTGGCAGGCTGTGATTTGGTTCTTGGCCAGATGGGTCGCAACCTATTT AGTACCACTTGATGTGAGTAGGGGGCAAGTAAACAGAGCAGAAATTGACAGTGTGGATAAACAC ATGCTCCAACATTCTAGAAAAATGCTAAACAGTTTTGCTTGGGAGAATAACCAAGGAGAGCGTG TTCTTGATTTTGTTGTTCTTATTTCAATGGTAGCACTTACTACATATCAGGGAGAAATTGAGCT GCAGGTAACTTTTGCTTGCACTGGTCATTCTGTAATTCTGCAAAAAATATGTTGTGCACACTGC GTATGTGTTTTGCAGTGACTAGTGTTTAGCAATAGCCATTCTGTGCAAAAATAAGTTACTTTCT CTAGTAAAAATTTTAGAGTTCTTTTTATTATTATCACCTTTGACCTTTAGTTGTTATCACCAAG ATGCCCTTAAAGAAAATGAAAACTTTGATACATAAGTACATGACGAATACTTTCTTGGTAAAAT ATCTGAGATTTGACCACACTCTTCCTGCAGTAACAATATTTTTTTATTGAAGGGAGTTTATTGG TGTACGCATGCCAGAAGTATCTCTCTGCCTGTCCATTCAGGAGTCTATGTCTTATCTTTTGCTT TGATTTCTGTTGCCAGACACTTACATGCCAGAAGCTACTTGCTACAGTTGTTCGACGGAAGCAC ACATGTACTTATGTTGTTCAGTTG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_008514 						
					
						PMCS
						0.246255043

Conservation Information
Conserved circRNAs	osi_circ_008514
PMCS	0.246255043

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							17787393-17786348(+)
17786415-17786800(+)
17787443-17786800(+)
17786417-17787404(-)
						
						Potential amino acid sequence
						
							MPEATCYSCSTEAHMYLCCSVGP*(+)
MEAVIWFLARWVATYLVPLDVSRGQVNRAEIDSVDKHMLQHSRKMLNSFAWENNQGERVLDFVV
LISMVALTTYQGEIELQTLTCQKLLATVVRRKHTCTYVVQLVHNKFFSTVSRSRNQGKVLQSAT
HGGCDLVLGQMGRNLFSTT*(+)
MLFSWSIINFSRQCLDPGIRARYFSPRLMEAVIWFLARWVATYLVPLDVSRGQVNRAEIDSVDK
HMLQHSRKMLNSFAWENNQGERVLDFVVLISMVALTTYQGEIELQTLTCQKLLATVVRRKHTCT
YVVQLVHNKFFSTVSRSRNQGKVLQSATHGGCDLVLGQMGRNLFSTT*(+)
MSRGLKYLALIPGSRHCREKFIMDQLNNISTCVLPSNNCSK*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	17787393-17786348(+) 17786415-17786800(+) 17787443-17786800(+) 17786417-17787404(-)
Potential amino acid sequence	MPEATCYSCSTEAHMYLCCSVGP(+) MEAVIWFLARWVATYLVPLDVSRGQVNRAEIDSVDKHMLQHSRKMLNSFAWENNQGERVLDFVV LISMVALTTYQGEIELQTLTCQKLLATVVRRKHTCTYVVQLVHNKFFSTVSRSRNQGKVLQSAT HGGCDLVLGQMGRNLFSTT(+) MLFSWSIINFSRQCLDPGIRARYFSPRLMEAVIWFLARWVATYLVPLDVSRGQVNRAEIDSVDK HMLQHSRKMLNSFAWENNQGERVLDFVVLISMVALTTYQGEIELQTLTCQKLLATVVRRKHTCT YVVQLVHNKFFSTVSRSRNQGKVLQSATHGGCDLVLGQMGRNLFSTT(+) MSRGLKYLALIPGSRHCREKFIMDQLNNISTCVLPSNNCSK(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

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

circRNA

Detail information of Os10g0477000_circ_g.9

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