Plant Circular RNA Database

Detail information of Os04g0507000_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os04g0507000_circ_g.3
					
						ID in PlantcircBase
						osa_circ_024509
					
						Alias
						Os_ciR9450
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr4: 25335577-25337687  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, PcircRNA_finder, find_circ
					
						Parent gene
						
							Os04g0507000						
					
						Parent gene annotation
						
							Similar to DNA mismatch repair protein. (Os04t0507000-01)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							NA						
					
						Support reads
						2/3
					
						Tissues
						root/shoot, 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  
						
							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
						Os04t0507000-01:5

General Information
CircRNA Name	Os04g0507000_circ_g.3
ID in PlantcircBase	osa_circ_024509
Alias	Os_ciR9450
Organism	Oryza sativa
Position	chr4: 25335577-25337687 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, PcircRNA_finder, find_circ
Parent gene	Os04g0507000
Parent gene annotation	Similar to DNA mismatch repair protein. (Os04t0507000-01)
Parent gene strand	-
Alternative splicing	NA
Support reads	2/3
Tissues	root/shoot, 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	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	Os04t0507000-01:5

			
						 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  
						
							TTCATTACAGAGATCTCCTTGTTTGTTCATCTTCCTAGACACAATGGAAATGCTTCGTGAGACT
TTCCTTGGTTTAGACCAGGACCTCCTGTTAAATAGCcacagagtaaccacatcgagtcaaatca
tccaatgtctgccgcaaattctgtaaggaaatgtgctctgatgtcatagaatattatcaacata
atgtaaaa

									
								

					

						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: 475
Transcript exons: 25335577-25335624,25336245-25336364,25336794-25336869,25
337348-25337445,25337555-25337687
CACAGAGTAACCACATCGAGTCAAATCATCCAATGTCTGCCGCAAATTCATGACTGGACATCCA
GCTTTTGGAATACTATCAGAACGCAAGCCTCCAAAAGGATTTAAGCCTGCATGCTCCACAAGGA
TACATGCATCAAACCCAACAGCCTCGTAGAAATCTCCCACTCTGCAAAGTAGAACTTCACGAGG
AAACTTCGATTTGAATTGCAACATTTCCGTGTTCAGGCTTCCATCCTTCAAGCTTCCATTTCTT
AAAGTTGGATCCAATCCTAAAATATTTGAATACACAAGTCTCTGAGTCAATTGCATTGATGATG
GTTTCCTGCACCTCTCCATTTTCTCTTTCCACCACAGAATATGTGGCAGCATGCCTTCATTACA
GAGATCTCCTTGTTTGTTCATCTTCCTAGACACAATGGAAATGCTTCGTGAGACTTTCCTTGGT
TTAGACCAGGACCTCCTGTTAAATAGC
						
					

						Genomic sequence
						
							CACAGAGTAACCACATCGAGTCAAATCATCCAATGTCTGCCGCAAATTCTGTAAGGAAATGTGC
TCTGATGTCATAGAATATTATCAACATAATGTAAAAAGATGTGCATTATTAGTTATAAAGTATA
AACCATATTAAATCAATGTTTGCCACAAGTTCTGAATGCTCTTTTCATACTATTGCCAACAGAA
CAATAAGATATGAAGCATGCTAACTTCAATTCCTAGCATGTCTCCTAGTTCAAACCATATTGGT
GAATAAAGCTTGAACTATATTGATGGATCATGAGCATACGAAATGCTAGACAGGTGTGATGTAA
GTAACTAACAAAATAAATAAGTCTTCCATATCCACAATGTGTAATTGCAAAAAAAAGGCAGGCA
ACTTACAAAATGTTATTGTGGTTAGACTGAAACTTATATGTAGATAAAAGGCAGCAGTAAGTGC
CGCACAGTATGGTACTGATACGCTGACTCTTCAAAAGCATAACAAAGGAACGCAACAAGATCTG
TTTCACAGAAGAAGTTCAAGCTCCTCGTTCTCCACTTTTTCAAAAAACAAATTACATAATGATG
CAAAAATTTGATAATTAACTAGGCAGATCACTATGATAGTTCTTAAAGCAATCCTAATTTCAGA
GCATCAGCATAGTTATGTAACAGTTTACCATGACTGGACATCCAGCTTTTGGAATACTATCAGA
ACGCAAGCCTCCAAAAGGATTTAAGCCTGCATGCTCCACAAGGATACATGCATCAAACCCAACA
GCCTCGTAGAAATCTCCCACCTGAATGGAGAAAGGTTATTCCGTTATAGGTCTATGTATTTGGA
TTTTTTTTCCAGCTTGAATGTAAGAGGAAAACCAGAAGAACGCTGGAGAGATACATTAATTCTG
AGTATTATATTTAGCAAAATGCTGAAAGCGAATCCAGATTGACAGATGGAAATGGGTATGGAGG
GGTATGTAGTGAAACAAAAAGTAAATTGTTTTGGAAACAAGGACAGCAGTGCACGTAAGTTATG
GCATAGTAAAGATTTCCCAGAGGCACATAAAACACACCATCACATGTCATAGATGTTCAGAAAG
AAACATCTATGACATTATAGGTTTTGATAACTAAAAATTCCCAGCTAAGAAATTCTTGGCATTT
CTCCAGATTTTCGCAAAAAAGACGATCAAGCATGTGAACAAAATAAAAGAATAGAATAGCATTA
CTCTGCAAAGTAGAACTTCACGAGGAAACTTCGATTTGAATTGCAACATTTCCGTGTTCAGGCT
TCCATCCTTCAAGCTGCAAAGATTCATATCAACATTTGTGTTAATGAAAAGAAAGTAAATACCA
AGAAATGTGCCTGATTTGACCAACACAAAAATGGCTCAAGCAAGAAATATTTAATAAAATGAAA
GAAAAATAACCATGGAAGAAAGGAATTGATTATATATGATACAAAATTACAATAAACTTTCTCC
AAACTAGTCAGATTGCTCTGGTAGAAATTCTTTTTCAAGACATACATGAAGCCGTGATTGCCAT
AAAATTCTCCAATGATTAAGCAAAGAATAGGAACATACAAATTGTAAGATTAATAGAACTAAGC
AAACAAATGGAGTAATGAACACATACATATTTCACTTTAGAATATGAAAAACTGAAGTAATTCA
CAGTAACTTAAAAATAGTACAACGTCATGCTAGCCTTCTATTTCTTAAAGAAAATGTGAAAGAA
ATGATCATTGCATAATTATATTAAGCATGAGCATCTGATTCACCTTCCATTTCTTAAAGTTGGA
TCCAATCCTAAAATATTTGAATACACAAGTCTCTGAGTCAATTGCATTGATGATGGTTTCCTGC
ACCTCTCCATTTTCTGAGAACATTAAACAGAATAACAGCAATAACAAAGCTGAAGCATTAGTGA
TTCCCTGTCAATACATTGGAGAGAAAAAAAATACATATATGCCAACTTTTGCAAGCACCTCTTT
CCACCACAGAATATGTGGCAGCATGCCTTCATTACAGAGATCTCCTTGTTTGTTCATCTTCCTA
GACACAATGGAAATGCTTCGTGAGACTTTCCTTGGTTTAGACCAGGACCTCCTGTTAAATAGC
						
					

			
		

Sequences
Splice junction sequence	TTCATTACAGAGATCTCCTTGTTTGTTCATCTTCCTAGACACAATGGAAATGCTTCGTGAGACT TTCCTTGGTTTAGACCAGGACCTCCTGTTAAATAGCcacagagtaaccacatcgagtcaaatca tccaatgtctgccgcaaattctgtaaggaaatgtgctctgatgtcatagaatattatcaacata atgtaaaa
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: 475 Transcript exons: 25335577-25335624,25336245-25336364,25336794-25336869,25 337348-25337445,25337555-25337687 CACAGAGTAACCACATCGAGTCAAATCATCCAATGTCTGCCGCAAATTCATGACTGGACATCCA GCTTTTGGAATACTATCAGAACGCAAGCCTCCAAAAGGATTTAAGCCTGCATGCTCCACAAGGA TACATGCATCAAACCCAACAGCCTCGTAGAAATCTCCCACTCTGCAAAGTAGAACTTCACGAGG AAACTTCGATTTGAATTGCAACATTTCCGTGTTCAGGCTTCCATCCTTCAAGCTTCCATTTCTT AAAGTTGGATCCAATCCTAAAATATTTGAATACACAAGTCTCTGAGTCAATTGCATTGATGATG GTTTCCTGCACCTCTCCATTTTCTCTTTCCACCACAGAATATGTGGCAGCATGCCTTCATTACA GAGATCTCCTTGTTTGTTCATCTTCCTAGACACAATGGAAATGCTTCGTGAGACTTTCCTTGGT TTAGACCAGGACCTCCTGTTAAATAGC
Genomic sequence	CACAGAGTAACCACATCGAGTCAAATCATCCAATGTCTGCCGCAAATTCTGTAAGGAAATGTGC TCTGATGTCATAGAATATTATCAACATAATGTAAAAAGATGTGCATTATTAGTTATAAAGTATA AACCATATTAAATCAATGTTTGCCACAAGTTCTGAATGCTCTTTTCATACTATTGCCAACAGAA CAATAAGATATGAAGCATGCTAACTTCAATTCCTAGCATGTCTCCTAGTTCAAACCATATTGGT GAATAAAGCTTGAACTATATTGATGGATCATGAGCATACGAAATGCTAGACAGGTGTGATGTAA GTAACTAACAAAATAAATAAGTCTTCCATATCCACAATGTGTAATTGCAAAAAAAAGGCAGGCA ACTTACAAAATGTTATTGTGGTTAGACTGAAACTTATATGTAGATAAAAGGCAGCAGTAAGTGC CGCACAGTATGGTACTGATACGCTGACTCTTCAAAAGCATAACAAAGGAACGCAACAAGATCTG TTTCACAGAAGAAGTTCAAGCTCCTCGTTCTCCACTTTTTCAAAAAACAAATTACATAATGATG CAAAAATTTGATAATTAACTAGGCAGATCACTATGATAGTTCTTAAAGCAATCCTAATTTCAGA GCATCAGCATAGTTATGTAACAGTTTACCATGACTGGACATCCAGCTTTTGGAATACTATCAGA ACGCAAGCCTCCAAAAGGATTTAAGCCTGCATGCTCCACAAGGATACATGCATCAAACCCAACA GCCTCGTAGAAATCTCCCACCTGAATGGAGAAAGGTTATTCCGTTATAGGTCTATGTATTTGGA TTTTTTTTCCAGCTTGAATGTAAGAGGAAAACCAGAAGAACGCTGGAGAGATACATTAATTCTG AGTATTATATTTAGCAAAATGCTGAAAGCGAATCCAGATTGACAGATGGAAATGGGTATGGAGG GGTATGTAGTGAAACAAAAAGTAAATTGTTTTGGAAACAAGGACAGCAGTGCACGTAAGTTATG GCATAGTAAAGATTTCCCAGAGGCACATAAAACACACCATCACATGTCATAGATGTTCAGAAAG AAACATCTATGACATTATAGGTTTTGATAACTAAAAATTCCCAGCTAAGAAATTCTTGGCATTT CTCCAGATTTTCGCAAAAAAGACGATCAAGCATGTGAACAAAATAAAAGAATAGAATAGCATTA CTCTGCAAAGTAGAACTTCACGAGGAAACTTCGATTTGAATTGCAACATTTCCGTGTTCAGGCT TCCATCCTTCAAGCTGCAAAGATTCATATCAACATTTGTGTTAATGAAAAGAAAGTAAATACCA AGAAATGTGCCTGATTTGACCAACACAAAAATGGCTCAAGCAAGAAATATTTAATAAAATGAAA GAAAAATAACCATGGAAGAAAGGAATTGATTATATATGATACAAAATTACAATAAACTTTCTCC AAACTAGTCAGATTGCTCTGGTAGAAATTCTTTTTCAAGACATACATGAAGCCGTGATTGCCAT AAAATTCTCCAATGATTAAGCAAAGAATAGGAACATACAAATTGTAAGATTAATAGAACTAAGC AAACAAATGGAGTAATGAACACATACATATTTCACTTTAGAATATGAAAAACTGAAGTAATTCA CAGTAACTTAAAAATAGTACAACGTCATGCTAGCCTTCTATTTCTTAAAGAAAATGTGAAAGAA ATGATCATTGCATAATTATATTAAGCATGAGCATCTGATTCACCTTCCATTTCTTAAAGTTGGA TCCAATCCTAAAATATTTGAATACACAAGTCTCTGAGTCAATTGCATTGATGATGGTTTCCTGC ACCTCTCCATTTTCTGAGAACATTAAACAGAATAACAGCAATAACAAAGCTGAAGCATTAGTGA TTCCCTGTCAATACATTGGAGAGAAAAAAAATACATATATGCCAACTTTTGCAAGCACCTCTTT CCACCACAGAATATGTGGCAGCATGCCTTCATTACAGAGATCTCCTTGTTTGTTCATCTTCCTA GACACAATGGAAATGCTTCGTGAGACTTTCCTTGGTTTAGACCAGGACCTCCTGTTAAATAGC

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_014553 						
					
						PMCS
						0.221503924

Conservation Information
Conserved circRNAs	osi_circ_014553
PMCS	0.221503924

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							25337584-25336301(+)
25335594-25337616(-)
25337619-25337681(-)
						
						Potential amino acid sequence
						
							MPSLQRSPCLFIFLDTMEMLRETFLGLDQDLLLNSHRVTTSSQIIQCLPQIHDWTSSFWNTIRT
QASKRI*(+)
MWLLCGYLTGGPGLNQGKSHEAFPLCLGR*(-)
MNKQGDLCNEGMLPHILWWKEKMERCRKPSSMQLTQRLVYSNILGLDPTLRNGSLKDGSLNTEM
LQFKSKFPREVLLCRVGDFYEAVGFDACILVEHAGLNPFGGLRSDSIPKAGCPVMNLRQTLDDL
TRCGYSVAI*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	25337584-25336301(+) 25335594-25337616(-) 25337619-25337681(-)
Potential amino acid sequence	MPSLQRSPCLFIFLDTMEMLRETFLGLDQDLLLNSHRVTTSSQIIQCLPQIHDWTSSFWNTIRT QASKRI(+) MWLLCGYLTGGPGLNQGKSHEAFPLCLGR(-) MNKQGDLCNEGMLPHILWWKEKMERCRKPSSMQLTQRLVYSNILGLDPTLRNGSLKDGSLNTEM LQFKSKFPREVLLCRVGDFYEAVGFDACILVEHAGLNPFGGLRSDSIPKAGCPVMNLRQTLDDL TRCGYSVAI*(-)
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 Os04g0507000_circ_g.3

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