Plant Circular RNA Database

Detail information of Os08g0109000_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os08g0109000_circ_g.3
					
						ID in PlantcircBase
						osa_circ_035574
					
						Alias
						Os_ciR2464
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr8: 447565-449208  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, find_circ
					
						Parent gene
						
							Os08g0109000						
					
						Parent gene annotation
						
							ENTH/VHS domain containing protein. (Os08t0109000-01)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os08g0109000_circ_g.4 						
					
						Support reads
						4/1
					
						Tissues
						root/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  
						
							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
						Os08t0109000-01:4

General Information
CircRNA Name	Os08g0109000_circ_g.3
ID in PlantcircBase	osa_circ_035574
Alias	Os_ciR2464
Organism	Oryza sativa
Position	chr8: 447565-449208 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, find_circ
Parent gene	Os08g0109000
Parent gene annotation	ENTH/VHS domain containing protein. (Os08t0109000-01)
Parent gene strand	+
Alternative splicing	Os08g0109000_circ_g.4
Support reads	4/1
Tissues	root/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	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	Os08t0109000-01:4

			
						 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  
						
							TTGTACGGCATGATGCGTTGCTTTCAGTTCAGCCAACTACAACAGTAGCTTCTACTCTCAAGGA
GGAAGAGGAAGAAGATGCCGAAAGCCTTTACCGGAGtctgctggcgttcagttttcgaatcgcc
caaatgttgttgttacacaagcacaagctccagtcccggtcccagaaccaacaatcgaaccaaa
taataaca

									
								

					

						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: 482
Transcript exons: 447565-447728,448584-448659,448849-448934,449053-449208
TCTGCTGGCGTTCAGTTTTCGAATCGCCCAAATGTTGTTGTTACACAAGCACAAGCTCCAGTCC
CGGTCCCAGAACCAACAATCGAACCAAATAATAACAGTTTATCTAGGAGATTGGACGAAGGACA
GAAGGAAGTGCATGCGCAGCCTGTTTCCGAGTCAAGTATAATTCGGAAAGCTTCTAGTGTCATG
GAAGTTCTAAAGGACGTGCTTGATTCGATGGATCCTAGACACCCTGAGGGAGCAACTGATGAGT
TTGTGTTGGATCTTGTGGAGCAATGCACATTTCAAAAACAGCGAATAATGCATCTAGTTATGAC
ATCAAGGGATGAAGTGGTGGTATCACAAGCAATAGAACTGAACGAAGAGCTTCACAAGGTCCTT
GTACGGCATGATGCGTTGCTTTCAGTTCAGCCAACTACAACAGTAGCTTCTACTCTCAAGGAGG
AAGAGGAAGAAGATGCCGAAAGCCTTTACCGGAG
						
					

						Genomic sequence
						
							TCTGCTGGCGTTCAGTTTTCGAATCGCCCAAATGTTGTTGTTACACAAGCACAAGCTCCAGTCC
CGGTCCCAGAACCAACAATCGAACCAAATAATAACAGTTTATCTAGGAGATTGGACGAAGGACA
GAAGGAAGTGCATGCGCAGCCTGTTTCCGAGTCAAGGTATTTTCTGGTTTCTACTTTAATTATG
ATATCATGTTGTATGTATATGAAGCTTGCACTTTTGTTGTTCCAATCTCACAGTACTTACAATA
CTTGATCAAAATTTCCATGTTTTAGCAATTGAAATCGATTTTTCCTAGAGTAAGTTCTTTTCTA
CTGAATAGTGAAACTGATAGTTGCATTAAAATACTTTCATCAAATGTTCCATGGCCAGAGAAAA
TTGTTCCTAGAACATCCAGCATAATTATTCAACTCTTTACTCACAGCTGATGATGAACTGACAG
CTGCGGCCCATGACTTGTTCTAATCGTCTCAATGTCATTTGAGCAACAATGCCACAAGTTTACT
GTGTACAAACATTGATGCTTTTGACATAACACTGTGGGTAATCAAATGGTATACTCTGGTTTTA
ATATGTAAGACTCACATGTTGGTTTCTAGAATTGATGCGGCATTTTAGATTGAAATGTGTGCGT
TTATAGCACTTATTAATTGCTATTATTTTTTTCTGTGTGCATCTTTGGTTGCTATGAACTATCC
TTGTTGATGTACCATGGTAGGAGCAAATAGCATGGTGCTGATAGAAGAAATCGATGGTTCTCAA
ATGGAATATCCAGGATCTAAACACTTCTTTCTGCATGATAGTATTCCACATTTAGTAAATTAGT
AGCATGCCTTATCCATAGGGTGTTATGTCTAGCATATATGCATTTTCTGTTGTTTATTAACACT
ATTAGAGAATATAATAGTTTGATGGTGTCACGATTGTGATGATTATTACCTCTTTGTGTTAACC
ATTCAACTGCCTTTTGGCTTTTCAATCGTTTTTACAGTGTACTTTGGTTTATATTGCAGTATAA
TTCGGAAAGCTTCTAGTGTCATGGAAGTTCTAAAGGACGTGCTTGATTCGATGGATCCTAGACA
CCCTGAGGTATAGATATGGTGGATTGTATCCTCATTTGCGTGATCAATAGTTTCTTTTTCATTT
CTTGATTGTTGTTTATAGATTTACCTTTTTGCTTTCGTATGCCTCCTCCGGGGAAAATAACTTA
AGAGGCAATTTATTTTTCTCAAGCACCGTGAACTCTTACATGGTTATATCTGCAACTGTATTTT
GTAGGGAGCAACTGATGAGTTTGTGTTGGATCTTGTGGAGCAATGCACATTTCAAAAACAGCGA
ATAATGCATCTAGTTATGACATCAAGGTAAGTGTCCACTGTTTGGTGCTCTTCAATATCTTTTG
ACATTGCTCCTTCAGTCCGTGATATGTTTATAAGCAGCTATTTTTACATTGACATATGAGTTGC
TATCCTTTGTTGCTAGGGATGAAGTGGTGGTATCACAAGCAATAGAACTGAACGAAGAGCTTCA
CAAGGTCCTTGTACGGCATGATGCGTTGCTTTCAGTTCAGCCAACTACAACAGTAGCTTCTACT
CTCAAGGAGGAAGAGGAAGAAGATGCCGAAAGCCTTTACCGGAG
						
					

			
		

Sequences
Splice junction sequence	TTGTACGGCATGATGCGTTGCTTTCAGTTCAGCCAACTACAACAGTAGCTTCTACTCTCAAGGA GGAAGAGGAAGAAGATGCCGAAAGCCTTTACCGGAGtctgctggcgttcagttttcgaatcgcc caaatgttgttgttacacaagcacaagctccagtcccggtcccagaaccaacaatcgaaccaaa taataaca
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: 482 Transcript exons: 447565-447728,448584-448659,448849-448934,449053-449208 TCTGCTGGCGTTCAGTTTTCGAATCGCCCAAATGTTGTTGTTACACAAGCACAAGCTCCAGTCC CGGTCCCAGAACCAACAATCGAACCAAATAATAACAGTTTATCTAGGAGATTGGACGAAGGACA GAAGGAAGTGCATGCGCAGCCTGTTTCCGAGTCAAGTATAATTCGGAAAGCTTCTAGTGTCATG GAAGTTCTAAAGGACGTGCTTGATTCGATGGATCCTAGACACCCTGAGGGAGCAACTGATGAGT TTGTGTTGGATCTTGTGGAGCAATGCACATTTCAAAAACAGCGAATAATGCATCTAGTTATGAC ATCAAGGGATGAAGTGGTGGTATCACAAGCAATAGAACTGAACGAAGAGCTTCACAAGGTCCTT GTACGGCATGATGCGTTGCTTTCAGTTCAGCCAACTACAACAGTAGCTTCTACTCTCAAGGAGG AAGAGGAAGAAGATGCCGAAAGCCTTTACCGGAG
Genomic sequence	TCTGCTGGCGTTCAGTTTTCGAATCGCCCAAATGTTGTTGTTACACAAGCACAAGCTCCAGTCC CGGTCCCAGAACCAACAATCGAACCAAATAATAACAGTTTATCTAGGAGATTGGACGAAGGACA GAAGGAAGTGCATGCGCAGCCTGTTTCCGAGTCAAGGTATTTTCTGGTTTCTACTTTAATTATG ATATCATGTTGTATGTATATGAAGCTTGCACTTTTGTTGTTCCAATCTCACAGTACTTACAATA CTTGATCAAAATTTCCATGTTTTAGCAATTGAAATCGATTTTTCCTAGAGTAAGTTCTTTTCTA CTGAATAGTGAAACTGATAGTTGCATTAAAATACTTTCATCAAATGTTCCATGGCCAGAGAAAA TTGTTCCTAGAACATCCAGCATAATTATTCAACTCTTTACTCACAGCTGATGATGAACTGACAG CTGCGGCCCATGACTTGTTCTAATCGTCTCAATGTCATTTGAGCAACAATGCCACAAGTTTACT GTGTACAAACATTGATGCTTTTGACATAACACTGTGGGTAATCAAATGGTATACTCTGGTTTTA ATATGTAAGACTCACATGTTGGTTTCTAGAATTGATGCGGCATTTTAGATTGAAATGTGTGCGT TTATAGCACTTATTAATTGCTATTATTTTTTTCTGTGTGCATCTTTGGTTGCTATGAACTATCC TTGTTGATGTACCATGGTAGGAGCAAATAGCATGGTGCTGATAGAAGAAATCGATGGTTCTCAA ATGGAATATCCAGGATCTAAACACTTCTTTCTGCATGATAGTATTCCACATTTAGTAAATTAGT AGCATGCCTTATCCATAGGGTGTTATGTCTAGCATATATGCATTTTCTGTTGTTTATTAACACT ATTAGAGAATATAATAGTTTGATGGTGTCACGATTGTGATGATTATTACCTCTTTGTGTTAACC ATTCAACTGCCTTTTGGCTTTTCAATCGTTTTTACAGTGTACTTTGGTTTATATTGCAGTATAA TTCGGAAAGCTTCTAGTGTCATGGAAGTTCTAAAGGACGTGCTTGATTCGATGGATCCTAGACA CCCTGAGGTATAGATATGGTGGATTGTATCCTCATTTGCGTGATCAATAGTTTCTTTTTCATTT CTTGATTGTTGTTTATAGATTTACCTTTTTGCTTTCGTATGCCTCCTCCGGGGAAAATAACTTA AGAGGCAATTTATTTTTCTCAAGCACCGTGAACTCTTACATGGTTATATCTGCAACTGTATTTT GTAGGGAGCAACTGATGAGTTTGTGTTGGATCTTGTGGAGCAATGCACATTTCAAAAACAGCGA ATAATGCATCTAGTTATGACATCAAGGTAAGTGTCCACTGTTTGGTGCTCTTCAATATCTTTTG ACATTGCTCCTTCAGTCCGTGATATGTTTATAAGCAGCTATTTTTACATTGACATATGAGTTGC TATCCTTTGTTGCTAGGGATGAAGTGGTGGTATCACAAGCAATAGAACTGAACGAAGAGCTTCA CAAGGTCCTTGTACGGCATGATGCGTTGCTTTCAGTTCAGCCAACTACAACAGTAGCTTCTACT CTCAAGGAGGAAGAGGAAGAAGATGCCGAAAGCCTTTACCGGAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_018272 						
					
						PMCS
						0.226784033

Conservation Information
Conserved circRNAs	osi_circ_018272
PMCS	0.226784033

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							448610-448585(+)
449188-447656(+)
						
						Potential amino acid sequence
						
							MEVLKDVLDSMDPRHPEGATDEFVLDLVEQCTFQKQRIMHLVMTSRDEVVVSQAIELNEELHKV
LVRHDALLSVQPTTTVASTLKEEEEEDAESLYRSLLAFSFRIAQMLLLHKHKLQSRSQNQQSNQ
IITVYLGDWTKDRRKCMRSLFPSQV*(+)
MPKAFTGVCWRSVFESPKCCCYTSTSSSPGPRTNNRTK*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	448610-448585(+) 449188-447656(+)
Potential amino acid sequence	MEVLKDVLDSMDPRHPEGATDEFVLDLVEQCTFQKQRIMHLVMTSRDEVVVSQAIELNEELHKV LVRHDALLSVQPTTTVASTLKEEEEEDAESLYRSLLAFSFRIAQMLLLHKHKLQSRSQNQQSNQ IITVYLGDWTKDRRKCMRSLFPSQV(+) MPKAFTGVCWRSVFESPKCCCYTSTSSSPGPRTNNRTK(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

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

circRNA

Detail information of Os08g0109000_circ_g.3

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