Plant Circular RNA Database

Detail information of Os05g0596600_circ_g.9

			
						 General Information
					
						CircRNA Name
						Os05g0596600_circ_g.9
					
						ID in PlantcircBase
						osa_circ_029255
					
						Alias
						Os_ciR3080
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr5: 29735603-29736170  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, KNIFE, PcircRNA_finder, circRNA_finder, find_circ
					
						Parent gene
						
							Os05g0596600						
					
						Parent gene annotation
						
							Similar to SMC5 protein. (Os05t0596600-01);Similar to SMC5 prote
in. (Os05t0596600-02)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os05g0596600_circ_g.3 Os05g0596600_circ_g.4 Os05g0596600_circ_g.5 Os05g0596600_circ_g.6 Os05g0596600_circ_g.7 Os05g0596600_circ_g.8 						
					
						Support reads
						4/2
					
						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
						Os05t0596600-02:3

General Information
CircRNA Name	Os05g0596600_circ_g.9
ID in PlantcircBase	osa_circ_029255
Alias	Os_ciR3080
Organism	Oryza sativa
Position	chr5: 29735603-29736170 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, KNIFE, PcircRNA_finder, circRNA_finder, find_circ
Parent gene	Os05g0596600
Parent gene annotation	Similar to SMC5 protein. (Os05t0596600-01);Similar to SMC5 prote in. (Os05t0596600-02)
Parent gene strand	-
Alternative splicing	Os05g0596600_circ_g.3 Os05g0596600_circ_g.4 Os05g0596600_circ_g.5 Os05g0596600_circ_g.6 Os05g0596600_circ_g.7 Os05g0596600_circ_g.8
Support reads	4/2
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	Os05t0596600-02:3

			
						 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  
						
							ACCTGGACCACCGATAGTGGTTATCTGGGGTCCAAAAGTCAGAAATGCCTAGCTTTGGTACATC
ATCTGCTCTATTGTGTGTTTCATCTGTACCTATATAcaacacgtctccgtgtttcttcttgcct
cttcttctcaaacatcatcgtgtctgtaatctcttcctggaaatatggcaattaaaagatgagc
actatgag

						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: 376
Transcript exons: 29735603-29735666,29735764-29735909,29736005-29736170
CAACACGTCTCCGTGTTTCTTCTTGCCTCTTCTTCTCAAACATCATCGTGTCTGTAATCTCTTC
CTTTTTCCTGCGAATTTTTGCTGCTTCATCTTCTAATTGTCTCTGTTCCTTCAGAAGCTTCTTT
AAGTCTTCATCCATGCCGTCAATATCTTTGATATGCTTATCCTTCTGAGATCGAAGTCTTTCAG
AGTCAATAACATCTAAATTGCACATAAAAAGACGGGAAGGATTGACGGCATCTACAAATGCTGA
CAAATGACCGCCATATCTTGACCTGGACCACCGATAGTGGTTATCTGGGGTCCAAAAGTCAGAA
ATGCCTAGCTTTGGTACATCATCTGCTCTATTGTGTGTTTCATCTGTACCTATATA
						
						Genomic sequence
						
							CAACACGTCTCCGTGTTTCTTCTTGCCTCTTCTTCTCAAACATCATCGTGTCTGTAATCTCTTC
CTGGAAATATGGCAATTAAAAGATGAGCACTATGAGAAACAACTGGGCATTAACTATATCCAAA
TCTAAAAGTGAATAGAGCTTAAATCGATGAAACCTTTTTCCTGCGAATTTTTGCTGCTTCATCT
TCTAATTGTCTCTGTTCCTTCAGAAGCTTCTTTAAGTCTTCATCCATGCCGTCAATATCTTTGA
TATGCTTATCCTTCTGAGATCGAAGTCTTTCAGAGTCAATAACATCTAAATCTGCATAAAAAAT
CTGACAAGCATCAGGCACCACCAGATCAGAATGCACAACCCAAGTAGCTGACAGGCATTAATGT
TGAGATTGTAACACATACTGCACATAAAAAGACGGGAAGGATTGACGGCATCTACAAATGCTGA
CAAATGACCGCCATATCTTGACCTGGACCACCGATAGTGGTTATCTGGGGTCCAAAAGTCAGAA
ATGCCTAGCTTTGGTACATCATCTGCTCTATTGTGTGTTTCATCTGTACCTATATA

Sequences
Splice junction sequence	ACCTGGACCACCGATAGTGGTTATCTGGGGTCCAAAAGTCAGAAATGCCTAGCTTTGGTACATC ATCTGCTCTATTGTGTGTTTCATCTGTACCTATATAcaacacgtctccgtgtttcttcttgcct cttcttctcaaacatcatcgtgtctgtaatctcttcctggaaatatggcaattaaaagatgagc actatgag
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: 376 Transcript exons: 29735603-29735666,29735764-29735909,29736005-29736170 CAACACGTCTCCGTGTTTCTTCTTGCCTCTTCTTCTCAAACATCATCGTGTCTGTAATCTCTTC CTTTTTCCTGCGAATTTTTGCTGCTTCATCTTCTAATTGTCTCTGTTCCTTCAGAAGCTTCTTT AAGTCTTCATCCATGCCGTCAATATCTTTGATATGCTTATCCTTCTGAGATCGAAGTCTTTCAG AGTCAATAACATCTAAATTGCACATAAAAAGACGGGAAGGATTGACGGCATCTACAAATGCTGA CAAATGACCGCCATATCTTGACCTGGACCACCGATAGTGGTTATCTGGGGTCCAAAAGTCAGAA ATGCCTAGCTTTGGTACATCATCTGCTCTATTGTGTGTTTCATCTGTACCTATATA
Genomic sequence	CAACACGTCTCCGTGTTTCTTCTTGCCTCTTCTTCTCAAACATCATCGTGTCTGTAATCTCTTC CTGGAAATATGGCAATTAAAAGATGAGCACTATGAGAAACAACTGGGCATTAACTATATCCAAA TCTAAAAGTGAATAGAGCTTAAATCGATGAAACCTTTTTCCTGCGAATTTTTGCTGCTTCATCT TCTAATTGTCTCTGTTCCTTCAGAAGCTTCTTTAAGTCTTCATCCATGCCGTCAATATCTTTGA TATGCTTATCCTTCTGAGATCGAAGTCTTTCAGAGTCAATAACATCTAAATCTGCATAAAAAAT CTGACAAGCATCAGGCACCACCAGATCAGAATGCACAACCCAAGTAGCTGACAGGCATTAATGT TGAGATTGTAACACATACTGCACATAAAAAGACGGGAAGGATTGACGGCATCTACAAATGCTGA CAAATGACCGCCATATCTTGACCTGGACCACCGATAGTGGTTATCTGGGGTCCAAAAGTCAGAA ATGCCTAGCTTTGGTACATCATCTGCTCTATTGTGTGTTTCATCTGTACCTATATA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.426571785

Conservation Information
Conserved circRNAs	NA
PMCS	0.426571785

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							29736045-29735872(+)
29736116-29735796(+)
29736013-29736156(-)
						
						Potential amino acid sequence
						
							MLTNDRHILTWTTDSGYLGSKSQKCLALVHHLLYCVFHLYLYTTRLRVSSCLFFSNIIVSVISS
FFLRIFAASSSNCLCSFRSFFKSSSMPSISLICLSF*(+)
MPSFGTSSALLCVSSVPIYNTSPCFFLPLLLKHHRVCNLFLFPANFCCFIF*(+)
MCNLDVIDSERLRSQKDKHIKDIDGMDEDLKKLLKEQRQLEDEAAKIRRKKEEITDTMMFEKKR
QEETRRRVVYRYR*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	29736045-29735872(+) 29736116-29735796(+) 29736013-29736156(-)
Potential amino acid sequence	MLTNDRHILTWTTDSGYLGSKSQKCLALVHHLLYCVFHLYLYTTRLRVSSCLFFSNIIVSVISS FFLRIFAASSSNCLCSFRSFFKSSSMPSISLICLSF(+) MPSFGTSSALLCVSSVPIYNTSPCFFLPLLLKHHRVCNLFLFPANFCCFIF(+) MCNLDVIDSERLRSQKDKHIKDIDGMDEDLKKLLKEQRQLEDEAAKIRRKKEEITDTMMFEKKR QEETRRRVVYRYR*(-)
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 Os05g0596600_circ_g.9

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