Plant Circular RNA Database

Detail information of Os01g0566900_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os01g0566900_circ_g.3
					
						ID in PlantcircBase
						osa_circ_002254
					
						Alias
						Os_ciR5838
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr1: 21700702-21702809  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Os01g0566900						
					
						Parent gene annotation
						
							Similar to 3'-5' exonuclease domain-containing protein-like. (Os
01t0566900-01)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os01g0566900_circ_g.1 Os01g0566900_circ_g.2 						
					
						Support reads
						2
					
						Tissues
						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
						Os01t0566900-01:5

General Information
CircRNA Name	Os01g0566900_circ_g.3
ID in PlantcircBase	osa_circ_002254
Alias	Os_ciR5838
Organism	Oryza sativa
Position	chr1: 21700702-21702809 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	find_circ
Parent gene	Os01g0566900
Parent gene annotation	Similar to 3'-5' exonuclease domain-containing protein-like. (Os 01t0566900-01)
Parent gene strand	-
Alternative splicing	Os01g0566900_circ_g.1 Os01g0566900_circ_g.2
Support reads	2
Tissues	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	Os01t0566900-01:5

			
						 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  
						
							TGGTGACATATTCTGATTCAAGTGCTGGTTTGCAAGCTTCAATAAGTTCTTTCCCACCCTCAAT
AGCATCAACTAAGTAAACAGCGTCAGGAAATGCAATcagggacagttggaagaggtggccaatc
cgcatacttgttgtcatttatgcaaaagcacctgcagtatagctcactgcgaactgacagacgc
cataaaga

									
								

					

						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
						
							CAGGGACAGTTGGAAGAGGTGGCCAATCCGCATACTTGTTGTCATTTATGCAAAAGCACCTGCA
GTATAGCTCACTGCGAACTGACAGACGCCATAAAGATACTTTGCTTAACTTCTCCATCATTTTC
TCATGTATACTGAGAAGGAAGCGGACATCATCTGTGGCTGCTCGAATCATCATTTCAGATAAAG
GCCTATGCGTCCAAAAGTTAGGGTCCTGAAAACCGATGTAAGCACTTGTCAGTTGTCAAGAAAC
CAGGATATCAGCACAGTGAAGCATCGGATAGCCAAGCATTATCATAAAATAGAGAGTAACATAA
GATTTCAGATCTTCAGCACAATAACTTTCTGTCTAACAAAGTTCTACAATTCCCGTCACATATT
GCTAACCTGCCTTAGAAGGGTACGGACTTCTTCCTTTTCAGGATATGCCATTCCTACACAAAGC
AGTATCACACCATATGATCAATCAAACAGAACACAAGAAAATGTGCTGCGGTCCTTCATACACT
TTGTCAACATCTAGGTAGCTTAAAGAGCATAACAATTAATTGATAAAAATGTTTGACAGAAGCA
GCAAACTGCTGTGATGCAACCACAGTACATTTTGTAGTTTCAATGCACAACCTACCAAAAGGCT
TTCAACATATTTGCAAAGTATTAATTTAAAGAATTACAGAAGTAATAGAAAACTGTATAAGAGA
GAGGGAGCAATCATCCCAGGTGTTCTAATATTCATGGGTGAACTGATAGGTTGCAGCCTAAGGC
CTAATCATACACACATTAAATGAACATATAATAAGGCAGAATGTCCACGTTGAAACGATTCATG
ACTGAAATAACCATGTCATATAGAAGTTACGCTTGGACAAAACTTGCAGCAGCTTGGATATGTA
AGGCATATACATCAAAGTTAAAGCACTAGCAGTAACACTAAGCATAATGTGTTGCATTACATTA
ACTTATAGTTCAAAATAAGAACCTGGCACCAAAAGATCACAATCAAGTGGAACTTCATGAATAC
AAAAAAAAAAACTCTGAGGCAACACTTCCTTTTTTTTTTCTAAAGGAAAAAAAAAAGGGTGGTA
TGGCGACAATGCTTAAGAATATATAAATGTAAAACGTAGGAGCAGATAATATGTATAAGGAAAA
GAAAGAGCTTGCATGCCAGCACAAGGTAAACTACAACCAAGGGGAGCTTATATAAGTATACAGT
ATACTGTGAAAGAACAGATCAGAAGGAACAAAACATGCACAGCAGTTTCGTCTTTTCGATTCAA
AGGAACTCAATGGTTTAAACTAATTCAGTATAGTAAGTACCACAATATCGGGGATCAGCAAGGA
GGCTGACAAAAGATATGTACTCATCGTATCCTCTCTTTTTCCCTTCCTGCTCCTCTAACAGAGA
ATAAGCGATCTGCACAAGAGTGATAATTGAAGTCCCTCCAAATAGAAACTACCATACAAATAGC
TGCCAATTCGCATTACATATCTACAATGGCGAATGATAATGCAATTATTTCAGCTCTGTACAGG
GTTAATGGTCCTAAGCTCATGATAAATTGGTAATGGTTCAGTTTTGATGAATAGAATTAGAAAA
GCAGCAGATTATAATTTGCATGTGCACAACAGAAAAATTACCGAGATGCCTATAAATTTAGTCA
GTAAGCATGCCACTGTGGCGCATACCACATGCATATGAACATCATTAAGAAAGCAGCAGATAAT
AATTTACATGTAAACAACAGAGAAAGTACCGAGTTAACTATAAATTTAGTCAGTAAGCATGCCA
CTATAGTGCACACCACATGCATATGCTGATTACCTGTGTATCCATCACATTATGCAATTTTATG
CCAAACTGGAAATACAGAGCCTGCAATATCGTAACTCTCAACCATTAGTCAGGATCAATCTTCT
AGAACAGAAAAAAATAATAATGCACTACAATAACTTCAGAGTTGTGGGTTAGGCACCTCACTGT
CCCTTTTGCAGTCATGAATAACTTTGGTGACATATTCTGATTCAAGTGCTGGTTTGCAAGCTTC
AATAAGTTCTTTCCCACCCTCAATAGCATCAACTAAGTAAACAGCGTCAGGAAATGCAAT
						
					

			
		

Sequences
Splice junction sequence	TGGTGACATATTCTGATTCAAGTGCTGGTTTGCAAGCTTCAATAAGTTCTTTCCCACCCTCAAT AGCATCAACTAAGTAAACAGCGTCAGGAAATGCAATcagggacagttggaagaggtggccaatc cgcatacttgttgtcatttatgcaaaagcacctgcagtatagctcactgcgaactgacagacgc cataaaga
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	CAGGGACAGTTGGAAGAGGTGGCCAATCCGCATACTTGTTGTCATTTATGCAAAAGCACCTGCA GTATAGCTCACTGCGAACTGACAGACGCCATAAAGATACTTTGCTTAACTTCTCCATCATTTTC TCATGTATACTGAGAAGGAAGCGGACATCATCTGTGGCTGCTCGAATCATCATTTCAGATAAAG GCCTATGCGTCCAAAAGTTAGGGTCCTGAAAACCGATGTAAGCACTTGTCAGTTGTCAAGAAAC CAGGATATCAGCACAGTGAAGCATCGGATAGCCAAGCATTATCATAAAATAGAGAGTAACATAA GATTTCAGATCTTCAGCACAATAACTTTCTGTCTAACAAAGTTCTACAATTCCCGTCACATATT GCTAACCTGCCTTAGAAGGGTACGGACTTCTTCCTTTTCAGGATATGCCATTCCTACACAAAGC AGTATCACACCATATGATCAATCAAACAGAACACAAGAAAATGTGCTGCGGTCCTTCATACACT TTGTCAACATCTAGGTAGCTTAAAGAGCATAACAATTAATTGATAAAAATGTTTGACAGAAGCA GCAAACTGCTGTGATGCAACCACAGTACATTTTGTAGTTTCAATGCACAACCTACCAAAAGGCT TTCAACATATTTGCAAAGTATTAATTTAAAGAATTACAGAAGTAATAGAAAACTGTATAAGAGA GAGGGAGCAATCATCCCAGGTGTTCTAATATTCATGGGTGAACTGATAGGTTGCAGCCTAAGGC CTAATCATACACACATTAAATGAACATATAATAAGGCAGAATGTCCACGTTGAAACGATTCATG ACTGAAATAACCATGTCATATAGAAGTTACGCTTGGACAAAACTTGCAGCAGCTTGGATATGTA AGGCATATACATCAAAGTTAAAGCACTAGCAGTAACACTAAGCATAATGTGTTGCATTACATTA ACTTATAGTTCAAAATAAGAACCTGGCACCAAAAGATCACAATCAAGTGGAACTTCATGAATAC AAAAAAAAAAACTCTGAGGCAACACTTCCTTTTTTTTTTCTAAAGGAAAAAAAAAAGGGTGGTA TGGCGACAATGCTTAAGAATATATAAATGTAAAACGTAGGAGCAGATAATATGTATAAGGAAAA GAAAGAGCTTGCATGCCAGCACAAGGTAAACTACAACCAAGGGGAGCTTATATAAGTATACAGT ATACTGTGAAAGAACAGATCAGAAGGAACAAAACATGCACAGCAGTTTCGTCTTTTCGATTCAA AGGAACTCAATGGTTTAAACTAATTCAGTATAGTAAGTACCACAATATCGGGGATCAGCAAGGA GGCTGACAAAAGATATGTACTCATCGTATCCTCTCTTTTTCCCTTCCTGCTCCTCTAACAGAGA ATAAGCGATCTGCACAAGAGTGATAATTGAAGTCCCTCCAAATAGAAACTACCATACAAATAGC TGCCAATTCGCATTACATATCTACAATGGCGAATGATAATGCAATTATTTCAGCTCTGTACAGG GTTAATGGTCCTAAGCTCATGATAAATTGGTAATGGTTCAGTTTTGATGAATAGAATTAGAAAA GCAGCAGATTATAATTTGCATGTGCACAACAGAAAAATTACCGAGATGCCTATAAATTTAGTCA GTAAGCATGCCACTGTGGCGCATACCACATGCATATGAACATCATTAAGAAAGCAGCAGATAAT AATTTACATGTAAACAACAGAGAAAGTACCGAGTTAACTATAAATTTAGTCAGTAAGCATGCCA CTATAGTGCACACCACATGCATATGCTGATTACCTGTGTATCCATCACATTATGCAATTTTATG CCAAACTGGAAATACAGAGCCTGCAATATCGTAACTCTCAACCATTAGTCAGGATCAATCTTCT AGAACAGAAAAAAATAATAATGCACTACAATAACTTCAGAGTTGTGGGTTAGGCACCTCACTGT CCCTTTTGCAGTCATGAATAACTTTGGTGACATATTCTGATTCAAGTGCTGGTTTGCAAGCTTC AATAAGTTCTTTCCCACCCTCAATAGCATCAACTAAGTAAACAGCGTCAGGAAATGCAAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_010146 						
					
						PMCS
						0.12144122

Conservation Information
Conserved circRNAs	osi_circ_010146
PMCS	0.12144122

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							21702804-21702110(+)
21702540-21702798(-)
21700748-21702798(-)
						
						Potential amino acid sequence
						
							MQSGTVGRGGQSAYLLSFMQKHLQYSSLRTDRRHKDTLLNFSIIFSCILRRKRTSSVAARIIIS
DKGLCVQKLGSCLRRVRTSSFSGYAIPQYRGSARRLTKDMYSSYPLFFPSCSSNRE*(+)
MDTQIAYSLLEEQEGKKRGYDEYISFVSLLADPRYCGMAYPEKEEVRTLLRQDPNFWTHRPLSE
MMIRAATDDVRFLLSIHEKMMEKLSKVSLWRLSVRSELYCRCFCINDNKYADWPPLPTVPDCIS
*(-)
MTTSMRIGHLFQLSLIAFPDAVYLVDAIEGGKELIEACKPALESEYVTKVIHDCKRDSEALYFQ
FGIKLHNVMDTQIAYSLLEEQEGKKRGYDEYISFVSLLADPRYCGMAYPEKEEVRTLLRQDPNF
WTHRPLSEMMIRAATDDVRFLLSIHEKMMEKLSKVSLWRLSVRSELYCRCFCINDNKYADWPPL
PTVPDCIS*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	21702804-21702110(+) 21702540-21702798(-) 21700748-21702798(-)
Potential amino acid sequence	MQSGTVGRGGQSAYLLSFMQKHLQYSSLRTDRRHKDTLLNFSIIFSCILRRKRTSSVAARIIIS DKGLCVQKLGSCLRRVRTSSFSGYAIPQYRGSARRLTKDMYSSYPLFFPSCSSNRE(+) MDTQIAYSLLEEQEGKKRGYDEYISFVSLLADPRYCGMAYPEKEEVRTLLRQDPNFWTHRPLSE MMIRAATDDVRFLLSIHEKMMEKLSKVSLWRLSVRSELYCRCFCINDNKYADWPPLPTVPDCIS (-) MTTSMRIGHLFQLSLIAFPDAVYLVDAIEGGKELIEACKPALESEYVTKVIHDCKRDSEALYFQ FGIKLHNVMDTQIAYSLLEEQEGKKRGYDEYISFVSLLADPRYCGMAYPEKEEVRTLLRQDPNF WTHRPLSEMMIRAATDDVRFLLSIHEKMMEKLSKVSLWRLSVRSELYCRCFCINDNKYADWPPL PTVPDCIS*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ye et al., 2015

circRNA

Detail information of Os01g0566900_circ_g.3

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