Plant Circular RNA Database

Detail information of Os09g0509300_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os09g0509300_circ_g.3
					
						ID in PlantcircBase
						osa_circ_039763
					
						Alias
						Os_ciR11878
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr9: 19761797-19765665  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer, find_circ
					
						Parent gene
						
							Os09g0509350						
					
						Parent gene annotation
						
							Hypothetical protein. (Os09t0509350-00)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os09g0509300_circ_g.1 Os09g0509300_circ_g.2 Os09g0509300_circ_g.4 Os09g0509300_circ_g.5 Os09g0509300_circ_g.6 						
					
						Support reads
						2/1
					
						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
						Os09t0509300-01:8
Os09t0509350-00:6
Os09t0509300-01:8

General Information
CircRNA Name	Os09g0509300_circ_g.3
ID in PlantcircBase	osa_circ_039763
Alias	Os_ciR11878
Organism	Oryza sativa
Position	chr9: 19761797-19765665 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ue-circRNA
Identification method	CIRCexplorer, find_circ
Parent gene	Os09g0509350
Parent gene annotation	Hypothetical protein. (Os09t0509350-00)
Parent gene strand	-
Alternative splicing	Os09g0509300_circ_g.1 Os09g0509300_circ_g.2 Os09g0509300_circ_g.4 Os09g0509300_circ_g.5 Os09g0509300_circ_g.6
Support reads	2/1
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	Os09t0509300-01:8 Os09t0509350-00:6 Os09t0509300-01:8

			
						 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  
						
							CCTGCCAGAATGAGCCTTTCTAGTCTTCCTTCAGCACAAACATCGTTGGAGGATCATCGGCCAT
TGTCAGGAGCTACCGAGTCAGTTAGCAAAACATAGGgatatggcagatatgaggagctgttatg
acaatctgctttctgttgcagcagcgattgcaaatagtgcatatggtatgtttattccccaata
gtacattt

									
								

					

						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
						
							GATATGGCAGATATGAGGAGCTGTTATGACAATCTGCTTTCTGTTGCAGCAGCGATTGCAAATA
GTGCATATGGTATGTTTATTCCCCAATAGTACATTTTGTCTTTTGAGATCAGTTAAGTATGTGT
TCAATCCTGTAAAAATATTTTTTTGTGTATTGTTGCCATTTCATTTTACACATGCCCTGCAATA
GAACTAACAACTGCCCATTTTCAAATGGATAAAAAACCTCAATGTTTCTTGGTTAATCGAGAAA
GCATTTAAGACGAATATTTCATAGTTTTAATCTAAAGTACAGACTACAGAGGGTGCAGAAACTT
AGGTGTTTTATGAGTTGTTCACCAATTCTTCTCGTGTATAGCCTCAGTTCATTTGCTCTTTTTT
CATATGCTAGCAGCTTTATTAGTTCTTATGCTAATTGTTTATAAGGTTATAGCAGCTAGAAATA
TAGGTGTCTTGACTCTTTTTTGCATATCAATGATCATTTTATCCTTTCATGCATGCAGAGTTCT
CAGAAGCACTGCAGGAAATGGGGACTTGTTTACTTAAAAGAGTCACACCAAACAAGGACGGGAT
TAATGGTAATTATGTTCTGTTGTGATTAATGGTTCTCACTCCCTTGCATAAACACATATCTTGC
AAATTAAGCTCTTCATGAAAACGACAAATTGAGCCAAGGGAAGTTGTTTGTGCCCATTCTCATC
TGCTAGTTGATAGTCACTATCTCAAATTGTGAGGAAAATGAATAAAAATAGGATAATGAGGCCA
TCTTAATGTTATTGATCATTCCATGTAACTTTTGCCTATTATACACTTTGCTGCTTAATGCTTA
CATTGAACAGTATCCCCCAGATAAAGTTTTGCTGTTGCTTGGAAAGGCCCAGTTTGAACTGCGG
AAGCTTGTAGATAGTTATGTAAGTTTTAAGTTGTTTATCGGTGGAGTCACTTATTTACCATAAT
CTTCTACTGCTAATCAAGTCACTATATTTTTCCCAGCGTGTGCATGTTCTTAATACCATCACCA
CTCCATCACAGTCCCTTCTCAATGAACTTCAAACTGTAGAGGTATGTTCTCCCATTCTAATAAT
TTTAGCCATTATGTACAATTTTTTGTGCATATTCCCTCTTATGCTCATGCTCTTTTCTCTGGGG
CCTATTCCTTCCTTGTTCTATGTCGTTTTACTATTTCCCCCCCTGCCCTTTTTACCCTGCTGAT
CATATGTACAATACATGAACTCGCTAAAAACAAAAGTTTGGCTAGTAAACACTGGTCTGTGGCA
TGAAGGAACTCAAATCAACTCTGTAGTCCACTTCATTAATTTGGGTTACATTTTATTATAAAGT
GTATTGCTGATCATTCAAATGTGGTTTTACATAAACTCATTGCAACTCCAATGGATATACATGA
TAATCTGAAATTGTGTGTGTGCGTGTGTGTTTTTTTCCTTTTGCCATTCAGTACAATCCCTGTT
TAAAGGGAGCATTCATTTACTTAAAATATAGTATACATATTTTTTTTGTTTTGTCTACTCCTAT
GCAGATTAACACTTCACAGCTTTGTTTTGTCATGTTCTTCTTGTTGCATTTGTTCTTATTTTTT
GAGTATTTATTATGTATTTGATGCTTGATTACCTAATCGTAGTGAACTGTTCAATAGATAACTA
TGATTTATTCCACTCAGAACTGCAATTAAGCAATAGTGTTTTTTTATTACAGGAAATGAAGCAC
CAGTGTGATGAAAAAAGGTATGCTGACTGTACAGAATGTGGCTTATATTTTTCCCTGTTGACAC
AATTTTTGAGTTTCCAAATGCTTCTTTCAGAGAGTTGTTCGAATTTCTGCTGAATGCACAGAAA
GAAAAGGGAAGATCTAAGAATGCCAAAAGTGACATTGGTGCGTCAGAGCAATTGAAACAAGCTC
AGGACGATTATCAAGAAGAAGCAACTCTTTTTCTATTCCGGTTAAAGTCATTGAAGCAAGGACA
GTTCAGAAGTCTTTTCACACAAGCTGCTCGGCACCATGCTGCTCAGGTGCACATTCTGTCATTT
GGAAATACCCCACTTCCTTTTTTTTTTCTGTGGCAATCTGTACAAAAGCTAATTTTGTGTAAAT
TTGTTTATATTTTACTCCAACCAGCTAAATTTATTCAGAAAGGGGCTCAAATCTCTTGAGGCTG
TAGAGCCACATGTTAGGCTTGCTGCTGAGCAGCAACACATTGACCATCAGTTCAGTGCACTTGA
CGAGGAGGATTACTCTGTGGATGAAGAAAATGAGGATGATTACAATGACAGTCATGAAGATTTA
TCCTTTGATTATGGAGAAAATAAGGAAGGCACAGAAGCTGGTCATGCTTCCAGGAGCCCTACAG
AGGTAACAATGTGGATTTTAATTTGAGCATAATTAACTATCCTACAGAAGGATACTCTAGAATT
TTGCATGGTCTCTTACTATTAGCAATCATAGTTCACCGCGCAGGTGTAAAGTTGCATTGCTTTA
ATGAGTTTAATGCATGACTTTGTATTTCTCACCTTTTTAAGAAATGATGTTACATTTTCAAAAT
TCCATAGCTACTACAAAGTACAAACTGAATAATTATGATGACATAACCAGTAAGAATGGTATAT
CGTTATTCCATCTGTTAGGAAAGAAAGATCTAAGCAGATAAATGGCATTCCATATGTTCAATTA
CAAGACATTGTGCTTCCATGTACTTAATTTGTTAAGTTGAATTTGTATACGGCTACGCATTTCT
TTTCCTTTTTTAGTTGGCTTCCTTTTCTTGTCCCAAAATATACCTGTTTCTTTACAATCATGTT
TTTCTTTTCATGTCTTTGGAGGCCTTAATTTTCTGGATTTGCAGGAACTTCTTGACAGAAGCAA
AGCAGAGTATTCCTCTTTTCCTGGTGAAAGGCAGAGATCTGGAAGTCAGTCAGCCCCACTTTTT
CCTGAAAAAAAACTTGAGGCAGCAGAGAGAATAAAAGAGTTGCGGCGTTCTGCTACGAGGAAGC
TATATACTTATGTTTTGCCTACTCCAAATGATGTTAGAGACACCTCTCAGACAGTTACAGCAAA
TCCTACTAGTGGATCTCCTCTTGGAAACAAAGGTGCATTCTATTCATCTCCACTCCAGCCAAGT
ACAAATGTGGGAGATTTGAGAGACAATAAGCTACCAAGTCCTACCAGATTATCTAATGCACATT
CAGTTTTGAAAGAGAGCAATACCAATACTACAGACACCAGGACAATGCTTGTGCTCCCTTTGGG
TGATCTCTCTTTACCTGGTTATCATGACTCGAAGGCTTCTGACAACAAAAAGGTGAAGAGAGGA
TCCTTTTCTGGTCCTATTGTTCCCAGGTCAAGGTCAACAGAGAATATTGATGTTGTTTCTGTAC
CACCTAGGCACAGCTCTTCACATCAGCCGTCAATACATGTCAGAGTTTCTCCCAATACCTCGCC
ACCACTGTTGTCCTCACCTAAAATCAAGGAGCTTCATGAGCTTCCTCGGCCACCTGCTAATGCA
TCAAAACATACAACATTTCCCAGTTTAGTCGCCCACTCTGCACCGTTGGTGCCAAATTCTGCTC
CTTTGGCACCCAGAGGCCAGGATCATTTTAGGCCGAGGCAAACACCACCAAGTGCTCCCCAAAC
TGCATCACCTTTACCGACACCACCTGGGCCTATATCCCGCAGTTTTTCGATACCTTCTAGGGGC
ATGAGAACATCAGGTATTTCAGATGGTAAAGAGACAGAAGATCTTCAGGATAAAGGGCCTGCCA
GAATGAGCCTTTCTAGTCTTCCTTCAGCACAAACATCGTTGGAGGATCATCGGCCATTGTCAGG
AGCTACCGAGTCAGTTAGCAAAACATAGG
						
					

			
		

Sequences
Splice junction sequence	CCTGCCAGAATGAGCCTTTCTAGTCTTCCTTCAGCACAAACATCGTTGGAGGATCATCGGCCAT TGTCAGGAGCTACCGAGTCAGTTAGCAAAACATAGGgatatggcagatatgaggagctgttatg acaatctgctttctgttgcagcagcgattgcaaatagtgcatatggtatgtttattccccaata gtacattt
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	GATATGGCAGATATGAGGAGCTGTTATGACAATCTGCTTTCTGTTGCAGCAGCGATTGCAAATA GTGCATATGGTATGTTTATTCCCCAATAGTACATTTTGTCTTTTGAGATCAGTTAAGTATGTGT TCAATCCTGTAAAAATATTTTTTTGTGTATTGTTGCCATTTCATTTTACACATGCCCTGCAATA GAACTAACAACTGCCCATTTTCAAATGGATAAAAAACCTCAATGTTTCTTGGTTAATCGAGAAA GCATTTAAGACGAATATTTCATAGTTTTAATCTAAAGTACAGACTACAGAGGGTGCAGAAACTT AGGTGTTTTATGAGTTGTTCACCAATTCTTCTCGTGTATAGCCTCAGTTCATTTGCTCTTTTTT CATATGCTAGCAGCTTTATTAGTTCTTATGCTAATTGTTTATAAGGTTATAGCAGCTAGAAATA TAGGTGTCTTGACTCTTTTTTGCATATCAATGATCATTTTATCCTTTCATGCATGCAGAGTTCT CAGAAGCACTGCAGGAAATGGGGACTTGTTTACTTAAAAGAGTCACACCAAACAAGGACGGGAT TAATGGTAATTATGTTCTGTTGTGATTAATGGTTCTCACTCCCTTGCATAAACACATATCTTGC AAATTAAGCTCTTCATGAAAACGACAAATTGAGCCAAGGGAAGTTGTTTGTGCCCATTCTCATC TGCTAGTTGATAGTCACTATCTCAAATTGTGAGGAAAATGAATAAAAATAGGATAATGAGGCCA TCTTAATGTTATTGATCATTCCATGTAACTTTTGCCTATTATACACTTTGCTGCTTAATGCTTA CATTGAACAGTATCCCCCAGATAAAGTTTTGCTGTTGCTTGGAAAGGCCCAGTTTGAACTGCGG AAGCTTGTAGATAGTTATGTAAGTTTTAAGTTGTTTATCGGTGGAGTCACTTATTTACCATAAT CTTCTACTGCTAATCAAGTCACTATATTTTTCCCAGCGTGTGCATGTTCTTAATACCATCACCA CTCCATCACAGTCCCTTCTCAATGAACTTCAAACTGTAGAGGTATGTTCTCCCATTCTAATAAT TTTAGCCATTATGTACAATTTTTTGTGCATATTCCCTCTTATGCTCATGCTCTTTTCTCTGGGG CCTATTCCTTCCTTGTTCTATGTCGTTTTACTATTTCCCCCCCTGCCCTTTTTACCCTGCTGAT CATATGTACAATACATGAACTCGCTAAAAACAAAAGTTTGGCTAGTAAACACTGGTCTGTGGCA TGAAGGAACTCAAATCAACTCTGTAGTCCACTTCATTAATTTGGGTTACATTTTATTATAAAGT GTATTGCTGATCATTCAAATGTGGTTTTACATAAACTCATTGCAACTCCAATGGATATACATGA TAATCTGAAATTGTGTGTGTGCGTGTGTGTTTTTTTCCTTTTGCCATTCAGTACAATCCCTGTT TAAAGGGAGCATTCATTTACTTAAAATATAGTATACATATTTTTTTTGTTTTGTCTACTCCTAT GCAGATTAACACTTCACAGCTTTGTTTTGTCATGTTCTTCTTGTTGCATTTGTTCTTATTTTTT GAGTATTTATTATGTATTTGATGCTTGATTACCTAATCGTAGTGAACTGTTCAATAGATAACTA TGATTTATTCCACTCAGAACTGCAATTAAGCAATAGTGTTTTTTTATTACAGGAAATGAAGCAC CAGTGTGATGAAAAAAGGTATGCTGACTGTACAGAATGTGGCTTATATTTTTCCCTGTTGACAC AATTTTTGAGTTTCCAAATGCTTCTTTCAGAGAGTTGTTCGAATTTCTGCTGAATGCACAGAAA GAAAAGGGAAGATCTAAGAATGCCAAAAGTGACATTGGTGCGTCAGAGCAATTGAAACAAGCTC AGGACGATTATCAAGAAGAAGCAACTCTTTTTCTATTCCGGTTAAAGTCATTGAAGCAAGGACA GTTCAGAAGTCTTTTCACACAAGCTGCTCGGCACCATGCTGCTCAGGTGCACATTCTGTCATTT GGAAATACCCCACTTCCTTTTTTTTTTCTGTGGCAATCTGTACAAAAGCTAATTTTGTGTAAAT TTGTTTATATTTTACTCCAACCAGCTAAATTTATTCAGAAAGGGGCTCAAATCTCTTGAGGCTG TAGAGCCACATGTTAGGCTTGCTGCTGAGCAGCAACACATTGACCATCAGTTCAGTGCACTTGA CGAGGAGGATTACTCTGTGGATGAAGAAAATGAGGATGATTACAATGACAGTCATGAAGATTTA TCCTTTGATTATGGAGAAAATAAGGAAGGCACAGAAGCTGGTCATGCTTCCAGGAGCCCTACAG AGGTAACAATGTGGATTTTAATTTGAGCATAATTAACTATCCTACAGAAGGATACTCTAGAATT TTGCATGGTCTCTTACTATTAGCAATCATAGTTCACCGCGCAGGTGTAAAGTTGCATTGCTTTA ATGAGTTTAATGCATGACTTTGTATTTCTCACCTTTTTAAGAAATGATGTTACATTTTCAAAAT TCCATAGCTACTACAAAGTACAAACTGAATAATTATGATGACATAACCAGTAAGAATGGTATAT CGTTATTCCATCTGTTAGGAAAGAAAGATCTAAGCAGATAAATGGCATTCCATATGTTCAATTA CAAGACATTGTGCTTCCATGTACTTAATTTGTTAAGTTGAATTTGTATACGGCTACGCATTTCT TTTCCTTTTTTAGTTGGCTTCCTTTTCTTGTCCCAAAATATACCTGTTTCTTTACAATCATGTT TTTCTTTTCATGTCTTTGGAGGCCTTAATTTTCTGGATTTGCAGGAACTTCTTGACAGAAGCAA AGCAGAGTATTCCTCTTTTCCTGGTGAAAGGCAGAGATCTGGAAGTCAGTCAGCCCCACTTTTT CCTGAAAAAAAACTTGAGGCAGCAGAGAGAATAAAAGAGTTGCGGCGTTCTGCTACGAGGAAGC TATATACTTATGTTTTGCCTACTCCAAATGATGTTAGAGACACCTCTCAGACAGTTACAGCAAA TCCTACTAGTGGATCTCCTCTTGGAAACAAAGGTGCATTCTATTCATCTCCACTCCAGCCAAGT ACAAATGTGGGAGATTTGAGAGACAATAAGCTACCAAGTCCTACCAGATTATCTAATGCACATT CAGTTTTGAAAGAGAGCAATACCAATACTACAGACACCAGGACAATGCTTGTGCTCCCTTTGGG TGATCTCTCTTTACCTGGTTATCATGACTCGAAGGCTTCTGACAACAAAAAGGTGAAGAGAGGA TCCTTTTCTGGTCCTATTGTTCCCAGGTCAAGGTCAACAGAGAATATTGATGTTGTTTCTGTAC CACCTAGGCACAGCTCTTCACATCAGCCGTCAATACATGTCAGAGTTTCTCCCAATACCTCGCC ACCACTGTTGTCCTCACCTAAAATCAAGGAGCTTCATGAGCTTCCTCGGCCACCTGCTAATGCA TCAAAACATACAACATTTCCCAGTTTAGTCGCCCACTCTGCACCGTTGGTGCCAAATTCTGCTC CTTTGGCACCCAGAGGCCAGGATCATTTTAGGCCGAGGCAAACACCACCAAGTGCTCCCCAAAC TGCATCACCTTTACCGACACCACCTGGGCCTATATCCCGCAGTTTTTCGATACCTTCTAGGGGC ATGAGAACATCAGGTATTTCAGATGGTAAAGAGACAGAAGATCTTCAGGATAAAGGGCCTGCCA GAATGAGCCTTTCTAGTCTTCCTTCAGCACAAACATCGTTGGAGGATCATCGGCCATTGTCAGG AGCTACCGAGTCAGTTAGCAAAACATAGG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.244584499

Conservation Information
Conserved circRNAs	NA
PMCS	0.244584499

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							19761868-19765621(-)
						
						Potential amino acid sequence
						
							MHYLQSLLQQKADCHNSSSYLPYPYVLLTDSVAPDNGR*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	19761868-19765621(-)
Potential amino acid sequence	MHYLQSLLQQKADCHNSSSYLPYPYVLLTDSVAPDNGR*(-)
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 Os09g0509300_circ_g.3

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