Plant Circular RNA Database

Detail information of Os09g0516900_circ_g.2

			
						 General Information
					
						CircRNA Name
						Os09g0516900_circ_g.2
					
						ID in PlantcircBase
						osa_circ_039866
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr9: 20150053-20151894  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os09g0516900						
					
						Parent gene annotation
						
							C2 calcium-dependent membrane targeting domain containing protei
n. (Os09t0516900-01);Similar to GRAM domain containing protein. 
(Os09t0516900-02)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							NA						
					
						Support reads
						5
					
						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
						Os09t0516900-02:5
Os09t0516900-01:5

General Information
CircRNA Name	Os09g0516900_circ_g.2
ID in PlantcircBase	osa_circ_039866
Alias	NA
Organism	Oryza sativa
Position	chr9: 20150053-20151894 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	Os09g0516900
Parent gene annotation	C2 calcium-dependent membrane targeting domain containing protei n. (Os09t0516900-01);Similar to GRAM domain containing protein. (Os09t0516900-02)
Parent gene strand	-
Alternative splicing	NA
Support reads	5
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	Os09t0516900-02:5 Os09t0516900-01:5

			
						 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  
						
							CGTCTGCAAATGACTTGGTTTTTGATGAACTACAGTGGGTCCTTGTTTATCCAAGGAAATTCTT
CTACGAGCACCAGCCTCAGCAGAGCTATTTAGAGCCctgtttctcagcctctatcattgtatgg
aagttcttgacagctcgttgcaatgctctaaatgtatggtttctattccaaaatgatgcaaatt
tatatctg

									
								

					

						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: 478
Transcript exons: 20150053-20150159,20150679-20150778,20150870-20150899,20
151558-20151674,20151771-20151894
CTGTTTCTCAGCCTCTATCATTGTATGGAAGTTCTTGACAGCTCGTTGCAATGCTCTAAATGTA
TGGTTTCTATTCCAAAATGATGCAAATTTATATCTGACTCTTCCATCGGGACTTCCTAAGGGAG
GAACCCCATGTCCTCCAGCTCCCATTCGAAGAAATATCGTGATTGCTGGATTAATAACTGCATG
CTGGCTTCTTCTTATCTCATCAATATCCCTCAACGGAAGCATAACCTTGATCTGCTTAGAGAAG
ACGTTTGAATGGAAGCAAATGTGCCATGAAGAGACATACATGCGCCCGTGATACAGAAATGACC
TCTCAAGTGCACATGAATAACTATGTTCAACAACCTCATCTGGAGGAAGTCCAAATATCGTCTG
CAAATGACTTGGTTTTTGATGAACTACAGTGGGTCCTTGTTTATCCAAGGAAATTCTTCTACGA
GCACCAGCCTCAGCAGAGCTATTTAGAGCC
						
					

						Genomic sequence
						
							CTGTTTCTCAGCCTCTATCATTGTATGGAAGTTCTTGACAGCTCGTTGCAATGCTCTAAATGTA
TGGTTTCTATTCCAAAATGATGCAAATTTATATCTGACTCTTCCTGCAGAAATATACATAAACA
GAGTGTTATGAACTCATGAAGCAGTTCGTCATGTATCAAATCTTACGTCTTCCAGTCCTTTGGC
TGTCTCCAAAAAAATTGCCATATCTTTGCTAAACTTTGGTTATCGGTTCTTTCCATTGTAAGGG
TATTGATCTGCTTCAATAATGACCATTTAGCTTTATCCACATATATGCAATTCTAGCTTGCTAC
CAATTTTGTTGCATCAAGAAAAATATACGACTCAATTTAGGATATGCATGCATTCAGTTCTCAA
GCAAGCTAGAGGGATGTAATTTAGTCCGGTAAGTAGTAACAAACCTTCACAGCACTCAAATTTA
CACTAACTTATGAGTAATAGTGTAATACCAACAACATGTTTTGCTGTTGAGAGCGAGAAGCATG
AAGTGGGATCCAAATAATATAATTCAAGATGAACTTTTGAGTTAGCACTGCTGTCCATGTAGTG
CTAAAAAGAGGAAGAGGCAAAGGTGCAGACTTGCTAGTGTTAGAGCTTACCATCGGGACTTCCT
AAGGGAGGAACCCCATGTCCTCCAGCTCCCATTCGAAGAAATATCGTGATTGCTGGATTAATAA
CTGCATGCTGGCTTCTTCTTATCTGCAGTACTTGTAATAACAGAAAGAAAAGGCAAATTAACAT
GTGCAGCAAGAAATCATGAAGAGATCACAGGAAATAGTATAGTAATCACCTCATCAATATCCCT
CAACGGAAGCATAACCTTCATAAAAATGAAAAGAATTGTTAGTTACATGAGTAAAGCATATATA
TCAACTGAAGTAAATGATAATAGATGGACTTATTTTTAAGACAAACCATCTGGCACAGTGTAAT
TTTCCTAAGCTCGTAAACTACAAATCAATTACAAAAATCTAATTCAATCAGATAATCGCCAGAC
CAGGACCGGTGGCTTCACTGGTTAGGATTTTGGAAGAACTAAAGCATAACAGTTAGTATGGAAA
TCTTGCAACAGTGATAACCATTTAGGTGCAATACTTAGTTTCCAATGATCTATCGGAAGATTTT
GCTGATATTCTGTTGGTTTTTCTGTAAGAACTCAATCAGAAGTGCATGGTTATAACAAGATTTA
ACCAAAAACTACATAAACAAAAATAGCATTATTGTGCTGTTATTGTTAACCCTGAAAAGTGAAC
GCATTAATTATCCACATTTACTCCACTATCCTTTTTTTGATAGTCACAAAGGTCATGTATCCTA
TTATCTTGTTTAGATGGAAACCGCTGGTAAAATCAACAGAACATTCAAAATAACTGAATGATTT
CTGATAAACATAATATAAAAATGAAGTGAAATATAGAACCTAAACTAATTGCATCAACGGAAGG
ATGCCAACTAAAATAATCTGTATATGAGCTAACCTTGATCTGCTTAGAGAAGACGTTTGAATGG
AAGCAAATGTGCCATGAAGAGACATACATGCGCCCGTGATACAGAAATGACCTCTCAAGTGCAC
ATGAATAACTATGTTCAACAACCTGACAAAGGGGAAAGAAATGAACAAGTAAAACTTGCCATTA
GGAATCGTGTTTCTATGCATAAAAACAAGAAGAATAGTTCAGATAGTTACATACCTCATCTGGA
GGAAGTCCAAATATCGTCTGCAAATGACTTGGTTTTTGATGAACTACAGTGGGTCCTTGTTTAT
CCAAGGAAATTCTTCTACGAGCACCAGCCTCAGCAGAGCTATTTAGAGCC
						
					

			
		

Sequences
Splice junction sequence	CGTCTGCAAATGACTTGGTTTTTGATGAACTACAGTGGGTCCTTGTTTATCCAAGGAAATTCTT CTACGAGCACCAGCCTCAGCAGAGCTATTTAGAGCCctgtttctcagcctctatcattgtatgg aagttcttgacagctcgttgcaatgctctaaatgtatggtttctattccaaaatgatgcaaatt tatatctg
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: 478 Transcript exons: 20150053-20150159,20150679-20150778,20150870-20150899,20 151558-20151674,20151771-20151894 CTGTTTCTCAGCCTCTATCATTGTATGGAAGTTCTTGACAGCTCGTTGCAATGCTCTAAATGTA TGGTTTCTATTCCAAAATGATGCAAATTTATATCTGACTCTTCCATCGGGACTTCCTAAGGGAG GAACCCCATGTCCTCCAGCTCCCATTCGAAGAAATATCGTGATTGCTGGATTAATAACTGCATG CTGGCTTCTTCTTATCTCATCAATATCCCTCAACGGAAGCATAACCTTGATCTGCTTAGAGAAG ACGTTTGAATGGAAGCAAATGTGCCATGAAGAGACATACATGCGCCCGTGATACAGAAATGACC TCTCAAGTGCACATGAATAACTATGTTCAACAACCTCATCTGGAGGAAGTCCAAATATCGTCTG CAAATGACTTGGTTTTTGATGAACTACAGTGGGTCCTTGTTTATCCAAGGAAATTCTTCTACGA GCACCAGCCTCAGCAGAGCTATTTAGAGCC
Genomic sequence	CTGTTTCTCAGCCTCTATCATTGTATGGAAGTTCTTGACAGCTCGTTGCAATGCTCTAAATGTA TGGTTTCTATTCCAAAATGATGCAAATTTATATCTGACTCTTCCTGCAGAAATATACATAAACA GAGTGTTATGAACTCATGAAGCAGTTCGTCATGTATCAAATCTTACGTCTTCCAGTCCTTTGGC TGTCTCCAAAAAAATTGCCATATCTTTGCTAAACTTTGGTTATCGGTTCTTTCCATTGTAAGGG TATTGATCTGCTTCAATAATGACCATTTAGCTTTATCCACATATATGCAATTCTAGCTTGCTAC CAATTTTGTTGCATCAAGAAAAATATACGACTCAATTTAGGATATGCATGCATTCAGTTCTCAA GCAAGCTAGAGGGATGTAATTTAGTCCGGTAAGTAGTAACAAACCTTCACAGCACTCAAATTTA CACTAACTTATGAGTAATAGTGTAATACCAACAACATGTTTTGCTGTTGAGAGCGAGAAGCATG AAGTGGGATCCAAATAATATAATTCAAGATGAACTTTTGAGTTAGCACTGCTGTCCATGTAGTG CTAAAAAGAGGAAGAGGCAAAGGTGCAGACTTGCTAGTGTTAGAGCTTACCATCGGGACTTCCT AAGGGAGGAACCCCATGTCCTCCAGCTCCCATTCGAAGAAATATCGTGATTGCTGGATTAATAA CTGCATGCTGGCTTCTTCTTATCTGCAGTACTTGTAATAACAGAAAGAAAAGGCAAATTAACAT GTGCAGCAAGAAATCATGAAGAGATCACAGGAAATAGTATAGTAATCACCTCATCAATATCCCT CAACGGAAGCATAACCTTCATAAAAATGAAAAGAATTGTTAGTTACATGAGTAAAGCATATATA TCAACTGAAGTAAATGATAATAGATGGACTTATTTTTAAGACAAACCATCTGGCACAGTGTAAT TTTCCTAAGCTCGTAAACTACAAATCAATTACAAAAATCTAATTCAATCAGATAATCGCCAGAC CAGGACCGGTGGCTTCACTGGTTAGGATTTTGGAAGAACTAAAGCATAACAGTTAGTATGGAAA TCTTGCAACAGTGATAACCATTTAGGTGCAATACTTAGTTTCCAATGATCTATCGGAAGATTTT GCTGATATTCTGTTGGTTTTTCTGTAAGAACTCAATCAGAAGTGCATGGTTATAACAAGATTTA ACCAAAAACTACATAAACAAAAATAGCATTATTGTGCTGTTATTGTTAACCCTGAAAAGTGAAC GCATTAATTATCCACATTTACTCCACTATCCTTTTTTTGATAGTCACAAAGGTCATGTATCCTA TTATCTTGTTTAGATGGAAACCGCTGGTAAAATCAACAGAACATTCAAAATAACTGAATGATTT CTGATAAACATAATATAAAAATGAAGTGAAATATAGAACCTAAACTAATTGCATCAACGGAAGG ATGCCAACTAAAATAATCTGTATATGAGCTAACCTTGATCTGCTTAGAGAAGACGTTTGAATGG AAGCAAATGTGCCATGAAGAGACATACATGCGCCCGTGATACAGAAATGACCTCTCAAGTGCAC ATGAATAACTATGTTCAACAACCTGACAAAGGGGAAAGAAATGAACAAGTAAAACTTGCCATTA GGAATCGTGTTTCTATGCATAAAAACAAGAAGAATAGTTCAGATAGTTACATACCTCATCTGGA GGAAGTCCAAATATCGTCTGCAAATGACTTGGTTTTTGATGAACTACAGTGGGTCCTTGTTTAT CCAAGGAAATTCTTCTACGAGCACCAGCCTCAGCAGAGCTATTTAGAGCC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.140169607

Conservation Information
Conserved circRNAs	NA
PMCS	0.140169607

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							20151603-20151624(+)
20151619-20151885(-)
						
						Potential amino acid sequence
						
							MKRHTCARDTEMTSQVHMNNYVQQPHLEEVQISSANDLVFDELQWVLVYPRKFFYEHQPQQSYL
EPCFSASIIVWKFLTARCNALNVWFLFQNDANLYLTLPSGLPKGGTPCPPAPIRRNIVIAGLIT
ACWLLLISSISLNGSITLICLEKTFEWKQMCHEETYMRP*(+)
MYVSSWHICFHSNVFSKQIKVMLPLRDIDEIRRSQHAVINPAITIFLRMGAGGHGVPPLGSPDG
RVRYKFASFWNRNHTFRALQRAVKNFHTMIEAEKQGSK*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	20151603-20151624(+) 20151619-20151885(-)
Potential amino acid sequence	MKRHTCARDTEMTSQVHMNNYVQQPHLEEVQISSANDLVFDELQWVLVYPRKFFYEHQPQQSYL EPCFSASIIVWKFLTARCNALNVWFLFQNDANLYLTLPSGLPKGGTPCPPAPIRRNIVIAGLIT ACWLLLISSISLNGSITLICLEKTFEWKQMCHEETYMRP(+) MYVSSWHICFHSNVFSKQIKVMLPLRDIDEIRRSQHAVINPAITIFLRMGAGGHGVPPLGSPDG RVRYKFASFWNRNHTFRALQRAVKNFHTMIEAEKQGSK(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os09g0516900_circ_g.2

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