Plant Circular RNA Database

Detail information of Os09g0116400_circ_g.6

			
						 General Information
					
						CircRNA Name
						Os09g0116400_circ_g.6
					
						ID in PlantcircBase
						osa_circ_038440
					
						Alias
						Os_ciR2705
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr9: 1304888-1306160  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, find_circ
					
						Parent gene
						
							Os09g0116400						
					
						Parent gene annotation
						
							CCAAT-binding factor domain containing protein. (Os09t0116400-01
);Similar to predicted protein. (Os09t0116400-02)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os09g0116400_circ_g.3 Os09g0116400_circ_g.4 Os09g0116400_circ_g.5 						
					
						Support reads
						5/1
					
						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
						Os09t0116400-02:4
Os09t0116400-01:4

General Information
CircRNA Name	Os09g0116400_circ_g.6
ID in PlantcircBase	osa_circ_038440
Alias	Os_ciR2705
Organism	Oryza sativa
Position	chr9: 1304888-1306160 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, find_circ
Parent gene	Os09g0116400
Parent gene annotation	CCAAT-binding factor domain containing protein. (Os09t0116400-01 );Similar to predicted protein. (Os09t0116400-02)
Parent gene strand	+
Alternative splicing	Os09g0116400_circ_g.3 Os09g0116400_circ_g.4 Os09g0116400_circ_g.5
Support reads	5/1
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	Os09t0116400-02:4 Os09t0116400-01:4

			
						 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  
						
							TTTGTACCAAATATCTACAAAAAATCAGATCGCAAGCGACCGTTTTTACCGTGCACTGTATGCA
AAACTTTTGAGTCCTGCATCCGTAACCTCGTCAAAGgtcaactttttgagccagatttttctta
ccagtaagggtgatggcccgaaaatagccaagcgtttggtggatgtttacattgcgcttttcaa
ggtttgaa

									
								

					

						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: 501
Transcript exons: 1304888-1304980,1305192-1305371,1305846-1305929,1306017-
1306160
GTCAACTTTTTGAGCCAGATTTTTCTTACCAGTAAGGGTGATGGCCCGAAAATAGCCAAGCGTT
TGGTGGATGTTTACATTGCGCTTTTCAAGGTACTCATGTCTTGCTCTCGTGCTACTGAAGGAGT
TAAACACAGCAAATATGGCAAGAAAACTAATGAAAATGGGAAAAAGGAAAAGGGCAATGACTTC
AATTCTCATGTAAAGCATGAAGACCCTTGTGCAGGATCAGATTTAGAGATGGACTCTAGGATTC
TCTCTGCACTTTTAACTGGGGTTAATAGAGCATTACCATATGTTGCAAGCTCAGAAGTTGATGA
TATTGTGGAAGTTCAGACACCAATTCTTTTTAGATTGGTGCACTCTGTAAATTTCAATGTTGGT
GTACAGGCATTAATGCTTTTGTACCAAATATCTACAAAAAATCAGATCGCAAGCGACCGTTTTT
ACCGTGCACTGTATGCAAAACTTTTGAGTCCTGCATCCGTAACCTCGTCAAAG
						
					

						Genomic sequence
						
							GTCAACTTTTTGAGCCAGATTTTTCTTACCAGTAAGGGTGATGGCCCGAAAATAGCCAAGCGTT
TGGTGGATGTTTACATTGCGCTTTTCAAGGTTTGAAATTTTTTCAGTATTGCATAATTAGACTT
TCTTTAGGGATAGTCTTATAGTGTTTGGCCTTTGTTGTCTTCTCATCATAGTTCCTTGTATTGC
TGCCCCATTTGTCCTTAGAACTTTATATTTGAACTATTTGCCAATACCAAGTTGCCATTTGCCA
ATCTTTTGACCTTAAGGATTTAAGATACAATTTTTGTTGTTATATCAGGTACTCATGTCTTGCT
CTCGTGCTACTGAAGGAGTTAAACACAGCAAATATGGCAAGAAAACTAATGAAAATGGGAAAAA
GGAAAAGGGCAATGACTTCAATTCTCATGTAAAGCATGAAGACCCTTGTGCAGGATCAGATTTA
GAGATGGACTCTAGGATTCTCTCTGCACTTTTAACTGTACGTCTTGCACTCTGCACAGTGTTTA
TTTATGTTAATTGCTTACTTCTTTATAGAAGATGCTTTATGGTACTCCCTCCGTCCTAGAATAT
AAGATGTTTTAGAGTTGGACACGGTTATTAAGAAAGTAGGTAGAGGTGAATGGTGGAGGGTTGT
GATTGGATGAGTAGTGGAGGTAGGTGGGAAAAGTGAATGGTGGAGGGTTGTGATTGGATGATTA
GTGGAGGTAGGTGGGAAAAGTGAATAGTGGAGGGTTGTGAATTTGTGATTGGTTGGGAAGAGAA
TGTTGATGGAGAAGTTATATTTTGGGACAAATCCTGAGGGCTAAAAGTTGTTATATTTTGTGAC
GGAGGGAGTATGTTTTATGCAATATACTTCCTAAAATTATTCTCTTGTCTTTGCTTTTTGTGTG
CTCAAGATAGTTTGCCTTTTCCTCTTCTAATTCCGTAATAATCTTTTCTGTATCTTATCCAGGG
GGTTAATAGAGCATTACCATATGTTGCAAGCTCAGAAGTTGATGATATTGTGGAAGTTCAGACA
CCAATTCTTTTTAGATTGGTGAGCTTGTTAGCTAACGATAAGAAATATTTTACACATTACTGTT
TGGATGACATAATGCCCTGACATCATTGTTGTTTCATTTAGGTGCACTCTGTAAATTTCAATGT
TGGTGTACAGGCATTAATGCTTTTGTACCAAATATCTACAAAAAATCAGATCGCAAGCGACCGT
TTTTACCGTGCACTGTATGCAAAACTTTTGAGTCCTGCATCCGTAACCTCGTCAAAG
						
					

			
		

Sequences
Splice junction sequence	TTTGTACCAAATATCTACAAAAAATCAGATCGCAAGCGACCGTTTTTACCGTGCACTGTATGCA AAACTTTTGAGTCCTGCATCCGTAACCTCGTCAAAGgtcaactttttgagccagatttttctta ccagtaagggtgatggcccgaaaatagccaagcgtttggtggatgtttacattgcgcttttcaa ggtttgaa
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: 501 Transcript exons: 1304888-1304980,1305192-1305371,1305846-1305929,1306017- 1306160 GTCAACTTTTTGAGCCAGATTTTTCTTACCAGTAAGGGTGATGGCCCGAAAATAGCCAAGCGTT TGGTGGATGTTTACATTGCGCTTTTCAAGGTACTCATGTCTTGCTCTCGTGCTACTGAAGGAGT TAAACACAGCAAATATGGCAAGAAAACTAATGAAAATGGGAAAAAGGAAAAGGGCAATGACTTC AATTCTCATGTAAAGCATGAAGACCCTTGTGCAGGATCAGATTTAGAGATGGACTCTAGGATTC TCTCTGCACTTTTAACTGGGGTTAATAGAGCATTACCATATGTTGCAAGCTCAGAAGTTGATGA TATTGTGGAAGTTCAGACACCAATTCTTTTTAGATTGGTGCACTCTGTAAATTTCAATGTTGGT GTACAGGCATTAATGCTTTTGTACCAAATATCTACAAAAAATCAGATCGCAAGCGACCGTTTTT ACCGTGCACTGTATGCAAAACTTTTGAGTCCTGCATCCGTAACCTCGTCAAAG
Genomic sequence	GTCAACTTTTTGAGCCAGATTTTTCTTACCAGTAAGGGTGATGGCCCGAAAATAGCCAAGCGTT TGGTGGATGTTTACATTGCGCTTTTCAAGGTTTGAAATTTTTTCAGTATTGCATAATTAGACTT TCTTTAGGGATAGTCTTATAGTGTTTGGCCTTTGTTGTCTTCTCATCATAGTTCCTTGTATTGC TGCCCCATTTGTCCTTAGAACTTTATATTTGAACTATTTGCCAATACCAAGTTGCCATTTGCCA ATCTTTTGACCTTAAGGATTTAAGATACAATTTTTGTTGTTATATCAGGTACTCATGTCTTGCT CTCGTGCTACTGAAGGAGTTAAACACAGCAAATATGGCAAGAAAACTAATGAAAATGGGAAAAA GGAAAAGGGCAATGACTTCAATTCTCATGTAAAGCATGAAGACCCTTGTGCAGGATCAGATTTA GAGATGGACTCTAGGATTCTCTCTGCACTTTTAACTGTACGTCTTGCACTCTGCACAGTGTTTA TTTATGTTAATTGCTTACTTCTTTATAGAAGATGCTTTATGGTACTCCCTCCGTCCTAGAATAT AAGATGTTTTAGAGTTGGACACGGTTATTAAGAAAGTAGGTAGAGGTGAATGGTGGAGGGTTGT GATTGGATGAGTAGTGGAGGTAGGTGGGAAAAGTGAATGGTGGAGGGTTGTGATTGGATGATTA GTGGAGGTAGGTGGGAAAAGTGAATAGTGGAGGGTTGTGAATTTGTGATTGGTTGGGAAGAGAA TGTTGATGGAGAAGTTATATTTTGGGACAAATCCTGAGGGCTAAAAGTTGTTATATTTTGTGAC GGAGGGAGTATGTTTTATGCAATATACTTCCTAAAATTATTCTCTTGTCTTTGCTTTTTGTGTG CTCAAGATAGTTTGCCTTTTCCTCTTCTAATTCCGTAATAATCTTTTCTGTATCTTATCCAGGG GGTTAATAGAGCATTACCATATGTTGCAAGCTCAGAAGTTGATGATATTGTGGAAGTTCAGACA CCAATTCTTTTTAGATTGGTGAGCTTGTTAGCTAACGATAAGAAATATTTTACACATTACTGTT TGGATGACATAATGCCCTGACATCATTGTTGTTTCATTTAGGTGCACTCTGTAAATTTCAATGT TGGTGTACAGGCATTAATGCTTTTGTACCAAATATCTACAAAAAATCAGATCGCAAGCGACCGT TTTTACCGTGCACTGTATGCAAAACTTTTGAGTCCTGCATCCGTAACCTCGTCAAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_007942* osi_circ_018404 						
					
						PMCS
						0.320052939

Conservation Information
Conserved circRNAs	osi_circ_007942* osi_circ_018404
PMCS	0.320052939

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							1305199-1306157(+)
1305310-1306157(-)
						
						Potential amino acid sequence
						
							MSCSRATEGVKHSKYGKKTNENGKKEKGNDFNSHVKHEDPCAGSDLEMDSRILSALLTGVNRAL
PYVASSEVDDIVEVQTPILFRLVHSVNFNVGVQALMLLYQISTKNQIASDRFYRALYAKLLSPA
SVTSSKVNFLSQIFLTSKGDGPKIAKRLVDVYIALFKVLMSCSRATEGVKHSKYGKKTNENGKK
EKGNDFNSHVKHEDPCAGSDLEMDSRILSALLTGVNRALPYVASSEVDDIVEVQTPILFRLVHS
VNFNVGVQALMLLYQISTKNQIASDRFYRALYAKLLSPASVTSSKVNFLSQIFLTSKGDGPKIA
KRLVDVYIALFKVLMSCSRATEGVKHSKYGKKTNENGKKEKGNDFNSHVKHEDPCAGSDLEMDS
RILSALLTGVNRALPYVASSEVDDIVEVQTPILFRLVHSVNFNVGVQALMLLYQISTKNQIASD
RFYRALYAKLLSPASVTSSKVNFLSQIFLTSKGDGPKIAKRLVDVYIALFKVLMSCSRATEGVK
HSKYGKKTNENGKKEKGNDFNSHVKHEDPCAGSDLEMDSRILSALLTGVNRALPYVASSEVDDI
VEVQTPILFRLVHSVNFNVGVQALMLLYQISTKNQIASDRFYRALYAKLLSPASVTSSK(+)
MLYMRIEVIALFLFPIFISFLAIFAVFNSFSSTRARHEYLEKRNVNIHQTLGYFRAITLTGKKN
LAQKVDL*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	1305199-1306157(+) 1305310-1306157(-)
Potential amino acid sequence	MSCSRATEGVKHSKYGKKTNENGKKEKGNDFNSHVKHEDPCAGSDLEMDSRILSALLTGVNRAL PYVASSEVDDIVEVQTPILFRLVHSVNFNVGVQALMLLYQISTKNQIASDRFYRALYAKLLSPA SVTSSKVNFLSQIFLTSKGDGPKIAKRLVDVYIALFKVLMSCSRATEGVKHSKYGKKTNENGKK EKGNDFNSHVKHEDPCAGSDLEMDSRILSALLTGVNRALPYVASSEVDDIVEVQTPILFRLVHS VNFNVGVQALMLLYQISTKNQIASDRFYRALYAKLLSPASVTSSKVNFLSQIFLTSKGDGPKIA KRLVDVYIALFKVLMSCSRATEGVKHSKYGKKTNENGKKEKGNDFNSHVKHEDPCAGSDLEMDS RILSALLTGVNRALPYVASSEVDDIVEVQTPILFRLVHSVNFNVGVQALMLLYQISTKNQIASD RFYRALYAKLLSPASVTSSKVNFLSQIFLTSKGDGPKIAKRLVDVYIALFKVLMSCSRATEGVK HSKYGKKTNENGKKEKGNDFNSHVKHEDPCAGSDLEMDSRILSALLTGVNRALPYVASSEVDDI VEVQTPILFRLVHSVNFNVGVQALMLLYQISTKNQIASDRFYRALYAKLLSPASVTSSK(+) MLYMRIEVIALFLFPIFISFLAIFAVFNSFSSTRARHEYLEKRNVNIHQTLGYFRAITLTGKKN LAQKVDL*(-)
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 Os09g0116400_circ_g.6

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