Plant Circular RNA Database

Detail information of Os09g0248900_circ_g.4

			
						 General Information
					
						CircRNA Name
						Os09g0248900_circ_g.4
					
						ID in PlantcircBase
						osa_circ_038544
					
						Alias
						Os_ciR1838
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr9: 3726364-3728751  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Os09g0248900						
					
						Parent gene annotation
						
							Myb/SANT-like domain domain containing protein. (Os09t0248900-01
)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os09g0248900_circ_g.1 Os09g0248900_circ_g.2 Os09g0248900_circ_g.3 Os09g0248900_circ_g.5 Os09g0248900_circ_g.6 						
					
						Support reads
						7
					
						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
						Os09t0248900-01:8

General Information
CircRNA Name	Os09g0248900_circ_g.4
ID in PlantcircBase	osa_circ_038544
Alias	Os_ciR1838
Organism	Oryza sativa
Position	chr9: 3726364-3728751 JBrowse»
Reference genome	IRGSP-1.0.38
Type	u-circRNA
Identification method	find_circ
Parent gene	Os09g0248900
Parent gene annotation	Myb/SANT-like domain domain containing protein. (Os09t0248900-01 )
Parent gene strand	-
Alternative splicing	Os09g0248900_circ_g.1 Os09g0248900_circ_g.2 Os09g0248900_circ_g.3 Os09g0248900_circ_g.5 Os09g0248900_circ_g.6
Support reads	7
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	Os09t0248900-01:8

			
						 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  
						
							GCCTCCCTACATGCATCGTCCAACAATCGGACAACTTGCAGCAAATCCTTGTCATTGGCCATAT
TTGGATCATCGATCTTTTCAACAAGTGGGCTAATGTctcaagggcacatatgtcatcatcttgg
ttaaccaatgtcagaaggcctgtaatataatcaaatgacaaaaatgatcttcatgagtttgata
aacagaaa

									
								

					

						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
						
							CTCAAGGGCACATATGTCATCATCTTGGTTAACCAATGTCAGAAGGCCTGTAATATAATCAAAT
GACAAAAATGATCTTCATGAGTTTGATAAACAGAAATACAGAAAACACGTGAAACTTTTTACAA
TGCATCAAAGCACCTTATGTATGTGTTGTCCATATATAAAAGTCTATTTCGAAAGGAACTTCTG
AAAGATATGTACTAAGTACTAACCATAGTCTGTGTGAGCTCCACTGAATTGATCGCAGAACGGA
TGTGACATAAGAGAAAAACGGTGTCAGATGAATCTAGTAAGTACATTCTAGCACAATATACTAC
CAAATAAATACATAGATACATTTTGCTTACCAGCCAGTGTCAGTGCGATGCTCTTCTAGAATAT
CGGTTGATACAGGATAACCAATCAACCTGCAAACCCAAAAAGGATCTCCTGCGGTTCTACCTTC
AAAAGCATCAACTGGCCCACCCAATGCCAAGGCTATACCTTGCATGATCTTTCTGGAAAGATCT
ATAAGTAAAATTTCCATCAGAAAAAAAAAAGGATAAATAACATAGATGCATAGCTAAGATCTAA
ACTAAGTTCAAAAGTGAACCTCTTAGAAGGCTGATATAGTTTTTTAGTAGTGCATCAAAATTTG
ATGGATATTTTGGCCTGCATCAAAGTAAATGATATGGTTAATTGAATTTGAAATATTTCTAACC
AAAAGTACTCAAGGGAAGGGTACCAAATTAAGTTCAGAACAGCTCTTCAGTAATAGCAAAGTAA
TTCAACTAGTAGTATCAAAATATATAACATGGAATGCTATAATTCAACTATTCAAAATGCTTCT
AGTAACAACAATACATTATATTGAAGCAACATATGCAACAACAAATAATTCACAATTGTAGCCA
TATTGCATAACATGATACATATTGTTATTATTAATATATTGTAAATTAGAAATTCATTTCCTTC
ATTCTTCCAAATAGAGGTGTGCTATAAGCTAAATTAATTATATTATCATAATTATTATCAATGC
ATAGTAAGTGATCAATAAGTAGAATTGTGGTACCATTTTATATGAAAGTCAAGCAAGCAATATC
TCTCACATATGTTAAATAACATGAGCTTTTGTTATAGTACTCCCGGATTATTTTAGGCCATTCA
TTTCATATTGATATTTCTCTTTCCTCATTTAGAGGTAATAGATCTTGAAGTATGAAGAAAAAAG
TATTTTTCACTTGCTACTCCACCCGTTTTGATAATAATCGTCACTAGACACTATTCACTTTCAA
ACTTTCAATCATTTGTTATGTAATTTTAAGTAATTCTTTAAACATATGAACCACTTCAAATTTT
AAGATTTTCTTTTGAGTTTTGAAAACAATGGTGCTAGTATATTTCAAGTAAAATTTCTATTATA
GACACTTTTCATGGTTGCCTGAATTAATTTTGTTTCTTCTAGTGGATGTATGGCAATAATAATT
TCTATATATTGTCATTAATGTTTTCCTCTTTACTGTCATTTTATTACTAAAGATAAGCAAATAT
ATATTTTATAACACAAAACATAACCTAAATAACAGTACCTCTTACCTCCATAAAGGGCTCCAAA
TAATATAGCGCCAAGGTATAAAATGAAAACAAACAAAGATGAAAGGTTGGAAACATACCACAAA
TTAGTTCCTTCCATTGGTTTGGCAAGATCTCCATATTTACCAGGTTCAATAGGCGCATAATACT
GTGACGTTTTTTCTTCTCAGCGATTAACTAGTAACAAGTTAATGGGTCACTAAAAATAAAGAAA
GAAAAATAAACTTACATCAATTGCTTCCTGCATGTCAGGTTTACCGTTGGTAATATTTTCGCCC
AGTCTTTGGTATCCTCTGATGATCAAGAGAACAAAGTTACTCATAGAGAAAGGACGCTTTGAAC
GACCCAAAACGGAGCACGGAAAAATCAATGTTGGAACTTAAAATGGTACTATAAGAAATCACAC
CTATATCCATTCTGAGGTGTCATTTTAATCTTTAGTTTTTCTTCATAAGGAAGTTGGAAGAACT
TGTGTGTGACGTCCCTAACTTCCTTCATTAGCGACTCAGCAATCCCATGGCCTTTCTGTTAATA
ATAATAACATACAGATGAACATTTGCATTACTTAGCTTCGGTAGTAATATAAAAATCATAGCTT
GCAACGCAAGGACACAGCTACATCAAAATATTCTTGTTGATCTGTACCCATTGTACTATAAAGT
GATGCTAAAAAGGTAAGTAAACGTGTAATTACCACATAAAAGAATCCAGCCTCCCTACATGCAT
CGTCCAACAATCGGACAACTTGCAGCAAATCCTTGTCATTGGCCATATTTGGATCATCGATCTT
TTCAACAAGTGGGCTAATGT
						
					

			
		

Sequences
Splice junction sequence	GCCTCCCTACATGCATCGTCCAACAATCGGACAACTTGCAGCAAATCCTTGTCATTGGCCATAT TTGGATCATCGATCTTTTCAACAAGTGGGCTAATGTctcaagggcacatatgtcatcatcttgg ttaaccaatgtcagaaggcctgtaatataatcaaatgacaaaaatgatcttcatgagtttgata aacagaaa
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	CTCAAGGGCACATATGTCATCATCTTGGTTAACCAATGTCAGAAGGCCTGTAATATAATCAAAT GACAAAAATGATCTTCATGAGTTTGATAAACAGAAATACAGAAAACACGTGAAACTTTTTACAA TGCATCAAAGCACCTTATGTATGTGTTGTCCATATATAAAAGTCTATTTCGAAAGGAACTTCTG AAAGATATGTACTAAGTACTAACCATAGTCTGTGTGAGCTCCACTGAATTGATCGCAGAACGGA TGTGACATAAGAGAAAAACGGTGTCAGATGAATCTAGTAAGTACATTCTAGCACAATATACTAC CAAATAAATACATAGATACATTTTGCTTACCAGCCAGTGTCAGTGCGATGCTCTTCTAGAATAT CGGTTGATACAGGATAACCAATCAACCTGCAAACCCAAAAAGGATCTCCTGCGGTTCTACCTTC AAAAGCATCAACTGGCCCACCCAATGCCAAGGCTATACCTTGCATGATCTTTCTGGAAAGATCT ATAAGTAAAATTTCCATCAGAAAAAAAAAAGGATAAATAACATAGATGCATAGCTAAGATCTAA ACTAAGTTCAAAAGTGAACCTCTTAGAAGGCTGATATAGTTTTTTAGTAGTGCATCAAAATTTG ATGGATATTTTGGCCTGCATCAAAGTAAATGATATGGTTAATTGAATTTGAAATATTTCTAACC AAAAGTACTCAAGGGAAGGGTACCAAATTAAGTTCAGAACAGCTCTTCAGTAATAGCAAAGTAA TTCAACTAGTAGTATCAAAATATATAACATGGAATGCTATAATTCAACTATTCAAAATGCTTCT AGTAACAACAATACATTATATTGAAGCAACATATGCAACAACAAATAATTCACAATTGTAGCCA TATTGCATAACATGATACATATTGTTATTATTAATATATTGTAAATTAGAAATTCATTTCCTTC ATTCTTCCAAATAGAGGTGTGCTATAAGCTAAATTAATTATATTATCATAATTATTATCAATGC ATAGTAAGTGATCAATAAGTAGAATTGTGGTACCATTTTATATGAAAGTCAAGCAAGCAATATC TCTCACATATGTTAAATAACATGAGCTTTTGTTATAGTACTCCCGGATTATTTTAGGCCATTCA TTTCATATTGATATTTCTCTTTCCTCATTTAGAGGTAATAGATCTTGAAGTATGAAGAAAAAAG TATTTTTCACTTGCTACTCCACCCGTTTTGATAATAATCGTCACTAGACACTATTCACTTTCAA ACTTTCAATCATTTGTTATGTAATTTTAAGTAATTCTTTAAACATATGAACCACTTCAAATTTT AAGATTTTCTTTTGAGTTTTGAAAACAATGGTGCTAGTATATTTCAAGTAAAATTTCTATTATA GACACTTTTCATGGTTGCCTGAATTAATTTTGTTTCTTCTAGTGGATGTATGGCAATAATAATT TCTATATATTGTCATTAATGTTTTCCTCTTTACTGTCATTTTATTACTAAAGATAAGCAAATAT ATATTTTATAACACAAAACATAACCTAAATAACAGTACCTCTTACCTCCATAAAGGGCTCCAAA TAATATAGCGCCAAGGTATAAAATGAAAACAAACAAAGATGAAAGGTTGGAAACATACCACAAA TTAGTTCCTTCCATTGGTTTGGCAAGATCTCCATATTTACCAGGTTCAATAGGCGCATAATACT GTGACGTTTTTTCTTCTCAGCGATTAACTAGTAACAAGTTAATGGGTCACTAAAAATAAAGAAA GAAAAATAAACTTACATCAATTGCTTCCTGCATGTCAGGTTTACCGTTGGTAATATTTTCGCCC AGTCTTTGGTATCCTCTGATGATCAAGAGAACAAAGTTACTCATAGAGAAAGGACGCTTTGAAC GACCCAAAACGGAGCACGGAAAAATCAATGTTGGAACTTAAAATGGTACTATAAGAAATCACAC CTATATCCATTCTGAGGTGTCATTTTAATCTTTAGTTTTTCTTCATAAGGAAGTTGGAAGAACT TGTGTGTGACGTCCCTAACTTCCTTCATTAGCGACTCAGCAATCCCATGGCCTTTCTGTTAATA ATAATAACATACAGATGAACATTTGCATTACTTAGCTTCGGTAGTAATATAAAAATCATAGCTT GCAACGCAAGGACACAGCTACATCAAAATATTCTTGTTGATCTGTACCCATTGTACTATAAAGT GATGCTAAAAAGGTAAGTAAACGTGTAATTACCACATAAAAGAATCCAGCCTCCCTACATGCAT CGTCCAACAATCGGACAACTTGCAGCAAATCCTTGTCATTGGCCATATTTGGATCATCGATCTT TTCAACAAGTGGGCTAATGT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.10816607

Conservation Information
Conserved circRNAs	NA
PMCS	0.10816607

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							3728459-3726580(+)
3728715-3728637(-)
						
						Potential amino acid sequence
						
							MAFHIKESSLPTCIVQQSDNLQQILVIGHIWIIDLFNKWANVSRAHMSSSWLTNVRRP*(+)
MANDKDLLQVVRLLDDACREAGFFYVKGHGIAESLMKEVRDVTHKFFQLPYEEKLKIKMTPQNG
YRGYQRLGENITNGKPDMQEAIDYYAPIEPGKYGDLAKPMEGTNLWPKYPSNFDALLKNYISLL
RDLSRKIMQGIALALGGPVDAFEGRTAGDPFWVCRLIGYPVSTDILEEHRTDTGCGAHTDYGLL
TLVNQDDDICALETLAHLLKRSMIQIWPMTRICCKLSDCWTMHVGRLDSFM*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	3728459-3726580(+) 3728715-3728637(-)
Potential amino acid sequence	MAFHIKESSLPTCIVQQSDNLQQILVIGHIWIIDLFNKWANVSRAHMSSSWLTNVRRP(+) MANDKDLLQVVRLLDDACREAGFFYVKGHGIAESLMKEVRDVTHKFFQLPYEEKLKIKMTPQNG YRGYQRLGENITNGKPDMQEAIDYYAPIEPGKYGDLAKPMEGTNLWPKYPSNFDALLKNYISLL RDLSRKIMQGIALALGGPVDAFEGRTAGDPFWVCRLIGYPVSTDILEEHRTDTGCGAHTDYGLL TLVNQDDDICALETLAHLLKRSMIQIWPMTRICCKLSDCWTMHVGRLDSFM(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ye et al., 2015

circRNA

Detail information of Os09g0248900_circ_g.4

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