Plant Circular RNA Database

Detail information of Os10g0542200_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os10g0542200_circ_g.3
					
						ID in PlantcircBase
						osa_circ_007862
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr10: 21170196-21171457  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os10g0542200						
					
						Parent gene annotation
						
							Ubiquilin domain containing protein. (Os10t0542200-01);Hypotheti
cal conserved gene. (Os10t0542200-03)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os10g0542200_circ_g.2 Os10g0542200_circ_g.4 Os10g0542200_circ_g.5 Os10g0542200_circ_g.6 Os10g0542200_circ_g.7 						
					
						Support reads
						1
					
						Tissues
						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  
						
							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
						Os10t0542266-00:2
Os10t0542200-03:4
Os10t0542200-01:4
Os10t0542266-00:2

General Information
CircRNA Name	Os10g0542200_circ_g.3
ID in PlantcircBase	osa_circ_007862
Alias	NA
Organism	Oryza sativa
Position	chr10: 21170196-21171457 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	Os10g0542200
Parent gene annotation	Ubiquilin domain containing protein. (Os10t0542200-01);Hypotheti cal conserved gene. (Os10t0542200-03)
Parent gene strand	-
Alternative splicing	Os10g0542200_circ_g.2 Os10g0542200_circ_g.4 Os10g0542200_circ_g.5 Os10g0542200_circ_g.6 Os10g0542200_circ_g.7
Support reads	1
Tissues	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	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	Os10t0542266-00:2 Os10t0542200-03:4 Os10t0542200-01:4 Os10t0542266-00:2

			
						 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  
						
							GGGATGTAAGCTGGCGAATAAATTCTGGATTTTGGAACATTTCCCTCAACTGAGTGTTTGATTC
CATGAGGTTGCGTGTATTTGGGTTGAAGTTAAGCAAcattggatgtattgggtacacctatgcc
acctccagcaccaagcccactaagcatgcccatcaaggtgtcgaggctaacatttccccgcatg
cctgcatt

									
								

					

						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: 295
Transcript exons: 21170196-21170288,21171080-21171108,21171213-21171271,21
171344-21171457
CATTGGATGTATTGGGTACACCTATGCCACCTCCAGCACCAAGCCCACTAAGCATGCCCATCAA
GGTGTCGAGGCTAACATTTCCCCGCATGCCTGTCGCATTGCCTCCTTGGCTACCATCCTGCCTA
GGTTGATTTTGACCAAGCTGTGATAATAATGTCTGCTGGAACGAGAGTAATTGCTGCATAGTTT
CTGGGGATGTAAGCTGGCGAATAAATTCTGGATTTTGGAACATTTCCCTCAACTGAGTGTTTGA
TTCCATGAGGTTGCGTGTATTTGGGTTGAAGTTAAGCAA
						
					

						Genomic sequence
						
							CATTGGATGTATTGGGTACACCTATGCCACCTCCAGCACCAAGCCCACTAAGCATGCCCATCAA
GGTGTCGAGGCTAACATTTCCCCGCATGCCTGCATTTTATTTCATTGGCATTTGCCACATTACT
TAACAAAAAGGTGAAAAAAAATGCATTTGTAAGAATTTAATTATCAAATGCTCAGTACTCGAAT
TACCACTACACATCTAACATTGCTCCACAATTTAGAAGGCAGTACAGTTGACTACACAAACAAC
TCGTATAATCTCTTCCATACCAATATAGCACAGTCAAGCAGCTAAAGAGCTCAGACACGTTCAA
CACATAACAGATTACTTAAATGGAACTATGGTTGTGACTAAAGGTGTAGGGAGCTCTCATCCAT
TCTCCAATAATCAAATCCACAAGCAGCATTCAGTCATAGGCAACCCATTTCCATTTCTAAGTAA
GGAAAAAAAATCATACATGTGTCACGCATCACCCCAAAGACCTTGTTTTGCGATCCCCAAAACG
AGGCCTGGTCGCACGGTCGCACCATATCGATCATTGATATTTCTTTTTTTCCAATATTTCAAGG
AAACTCAAATTTAGAAATTCCAATGTTATGCACCACAATAAGGTAGTGTCAAGAATCAACCACT
AGTAATAATCATCATAATGTGTTTATATAATGTAATGGCCTTATGGAAGAACGGAAATCTTGAA
GAACTAATACAGGTCAACCAAGCAGTGAAAGAAAGGCAACTATTGGTGCTAGAACGAACCACCA
CTAAAAGATAACTCAGTACGCACTAAAACTTATGTAAAACCTGACATACTAATCCATCTTAAAA
CAAGAAAAGATATTAGATGGTGCATATTAAAAAAACAATCAAGAGAAAATACCTGTCGCATTGC
CTCCTTGGCTACCATCCCTGAATCAAGAAAATCAAAAGATAATTAACAAACACATAATGAAAGA
AATACAGTATAAATGAGCTAGATGCAATTCAGGTACTGTTGAACAAGAGTTACTCACTGCCTAG
GTTGATTTTGACCAAGCTGTGATAATAATGTCTGCTGGAACGAGAGTAATTGCTGCCAAAAAAG
GGAAAGTTAATCTAGATAGAGATGGAGCTAGCCACATACATAAAACGTAACATATGTTACCTGC
ATAGTTTCTGGGGATGTAAGCTGGCGAATAAATTCTGGATTTTGGAACATTTCCCTCAACTGAG
TGTTTGATTCCATGAGGTTGCGTGTATTTGGGTTGAAGTTAAGCAA
						
					

			
		

Sequences
Splice junction sequence	GGGATGTAAGCTGGCGAATAAATTCTGGATTTTGGAACATTTCCCTCAACTGAGTGTTTGATTC CATGAGGTTGCGTGTATTTGGGTTGAAGTTAAGCAAcattggatgtattgggtacacctatgcc acctccagcaccaagcccactaagcatgcccatcaaggtgtcgaggctaacatttccccgcatg cctgcatt
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: 295 Transcript exons: 21170196-21170288,21171080-21171108,21171213-21171271,21 171344-21171457 CATTGGATGTATTGGGTACACCTATGCCACCTCCAGCACCAAGCCCACTAAGCATGCCCATCAA GGTGTCGAGGCTAACATTTCCCCGCATGCCTGTCGCATTGCCTCCTTGGCTACCATCCTGCCTA GGTTGATTTTGACCAAGCTGTGATAATAATGTCTGCTGGAACGAGAGTAATTGCTGCATAGTTT CTGGGGATGTAAGCTGGCGAATAAATTCTGGATTTTGGAACATTTCCCTCAACTGAGTGTTTGA TTCCATGAGGTTGCGTGTATTTGGGTTGAAGTTAAGCAA
Genomic sequence	CATTGGATGTATTGGGTACACCTATGCCACCTCCAGCACCAAGCCCACTAAGCATGCCCATCAA GGTGTCGAGGCTAACATTTCCCCGCATGCCTGCATTTTATTTCATTGGCATTTGCCACATTACT TAACAAAAAGGTGAAAAAAAATGCATTTGTAAGAATTTAATTATCAAATGCTCAGTACTCGAAT TACCACTACACATCTAACATTGCTCCACAATTTAGAAGGCAGTACAGTTGACTACACAAACAAC TCGTATAATCTCTTCCATACCAATATAGCACAGTCAAGCAGCTAAAGAGCTCAGACACGTTCAA CACATAACAGATTACTTAAATGGAACTATGGTTGTGACTAAAGGTGTAGGGAGCTCTCATCCAT TCTCCAATAATCAAATCCACAAGCAGCATTCAGTCATAGGCAACCCATTTCCATTTCTAAGTAA GGAAAAAAAATCATACATGTGTCACGCATCACCCCAAAGACCTTGTTTTGCGATCCCCAAAACG AGGCCTGGTCGCACGGTCGCACCATATCGATCATTGATATTTCTTTTTTTCCAATATTTCAAGG AAACTCAAATTTAGAAATTCCAATGTTATGCACCACAATAAGGTAGTGTCAAGAATCAACCACT AGTAATAATCATCATAATGTGTTTATATAATGTAATGGCCTTATGGAAGAACGGAAATCTTGAA GAACTAATACAGGTCAACCAAGCAGTGAAAGAAAGGCAACTATTGGTGCTAGAACGAACCACCA CTAAAAGATAACTCAGTACGCACTAAAACTTATGTAAAACCTGACATACTAATCCATCTTAAAA CAAGAAAAGATATTAGATGGTGCATATTAAAAAAACAATCAAGAGAAAATACCTGTCGCATTGC CTCCTTGGCTACCATCCCTGAATCAAGAAAATCAAAAGATAATTAACAAACACATAATGAAAGA AATACAGTATAAATGAGCTAGATGCAATTCAGGTACTGTTGAACAAGAGTTACTCACTGCCTAG GTTGATTTTGACCAAGCTGTGATAATAATGTCTGCTGGAACGAGAGTAATTGCTGCCAAAAAAG GGAAAGTTAATCTAGATAGAGATGGAGCTAGCCACATACATAAAACGTAACATATGTTACCTGC ATAGTTTCTGGGGATGTAAGCTGGCGAATAAATTCTGGATTTTGGAACATTTCCCTCAACTGAG TGTTTGATTCCATGAGGTTGCGTGTATTTGGGTTGAAGTTAAGCAA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.216385347

Conservation Information
Conserved circRNAs	NA
PMCS	0.216385347

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							21171424-21171238(+)
21171426-21171452(-)
21170200-21171452(-)
						
						Potential amino acid sequence
						
							MRLRVFGLKLSNIGCIGYTYATSSTKPTKHAHQGVEANISPHACRIASLATILPRLILTKL*(+
)
MESNTQLREMFQNPEFIRQLTSPETMQQLLSFQQTLLSQLGQNQPRQDGSQGGNATGMRGNVSL
DTLMGMLSGLGAGGGIGVPNTSNVA*(-)
MLLNFNPNTRNLMESNTQLREMFQNPEFIRQLTSPETMQQLLSFQQTLLSQLGQNQPRQDGSQG
GNATGMRGNVSLDTLMGMLSGLGAGGGIGVPNTSNVA*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	21171424-21171238(+) 21171426-21171452(-) 21170200-21171452(-)
Potential amino acid sequence	MRLRVFGLKLSNIGCIGYTYATSSTKPTKHAHQGVEANISPHACRIASLATILPRLILTKL(+ ) MESNTQLREMFQNPEFIRQLTSPETMQQLLSFQQTLLSQLGQNQPRQDGSQGGNATGMRGNVSL DTLMGMLSGLGAGGGIGVPNTSNVA(-) MLLNFNPNTRNLMESNTQLREMFQNPEFIRQLTSPETMQQLLSFQQTLLSQLGQNQPRQDGSQG GNATGMRGNVSLDTLMGMLSGLGAGGGIGVPNTSNVA*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os10g0542200_circ_g.3

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