Plant Circular RNA Database

Detail information of Os01g0923300_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os01g0923300_circ_g.3
					
						ID in PlantcircBase
						osa_circ_005554
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr1: 40386936-40388443  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os01g0923300						
					
						Parent gene annotation
						
							Cystathionine beta-synthase, core domain containing protein. (Os
01t0923300-01)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os01g0923300_circ_g.1 Os01g0923300_circ_g.2 Os01g0923300_circ_g.4 Os01g0923300_circ_g.5 Os01g0923300_circ_g.6 						
					
						Support reads
						1
					
						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  
						
							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
						Os01t0923300-01:8

General Information
CircRNA Name	Os01g0923300_circ_g.3
ID in PlantcircBase	osa_circ_005554
Alias	NA
Organism	Oryza sativa
Position	chr1: 40386936-40388443 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ue-circRNA
Identification method	CIRCexplorer
Parent gene	Os01g0923300
Parent gene annotation	Cystathionine beta-synthase, core domain containing protein. (Os 01t0923300-01)
Parent gene strand	+
Alternative splicing	Os01g0923300_circ_g.1 Os01g0923300_circ_g.2 Os01g0923300_circ_g.4 Os01g0923300_circ_g.5 Os01g0923300_circ_g.6
Support reads	1
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	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	Os01t0923300-01:8

			
						 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  
						
							GCTTCAAACTTCAGAAACGAGCAGCTTGACAGAGTTGATAACCAGCATTCTACAGAGGCTTGGC
GATGACATCGATAGAAAAAACCTACCACAAATTTTGgtcctaatacttttattgagactcttcg
agagcggatgtttaggccatcactatctaccattatttctgagaattcaaagtaggtaatatcc
attccttt

									
								

					

						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
						
							GTCCTAATACTTTTATTGAGACTCTTCGAGAGCGGATGTTTAGGCCATCACTATCTACCATTAT
TTCTGAGAATTCAAAGTAGGTAATATCCATTCCTTTTTCAAGTTTTAGGCTTTTCCAGCATTTC
AGGAATTTAAGTGCCATTGTTGAACAACTGACTTATTGCTGACAAACTTCTTAGAGTGGTGACT
GTTGCACCAACTGACACAGTGTTGACGGCATCAAAAAAGATGCTTGAAGTTAAAGTAAGTTCAG
CGGTTGTAGCAATTGAAAACAAGCCTGGGGGGATTCTGACGTGAGTATCTCTTCTCAGTTTAAT
TATACCATTTTGACTGTTGAACTAACATCTGCTATCTTTCTTACATCAGCTCTAGAGATATTTT
GATGCGTGTTATAGCCCAGAATCTCCCACCTGAATCTACTACTGTTGAGAAGGTAAGGAAGTCT
TAACATGGAATGTCTGCTATGTTTTTCTTAATCTCTTTAACTATCATGGCATCATGCTTGAAAC
TCCTTTCTACAGGTCATGACCCAGACTCCTGAATGTGCCACGGTTGACACTCCAATCCTTGATG
CCCTCCATACAATGCACGACGGAAAGTTTTTACATTTGCCTGTCTTAGACAAGGGTATGTCCAT
GTAGTGCAATGGATTATATCTAATTTATTTATTGGAGGTCTACTAAGTTGTTGACATGTGTTGT
CTATATCCAGATGGAAATGTTGTAACTGTAGTTGATGTCCTTCACATAACCCATGCTGCAATTG
CAACTGTAAGTGAAAAGTTCCAGCTGCTTGATATATTTTCTCTGTGTCCTTGTGCATACAGTCT
TACACAATACTCACTTTGTCAGCATGCATTGTAAAATGCTGAGAGAATGCATCACGATGTGGAA
CCTGTCATTATTACATGTCTTTTGCTTTCATTCTATTAAGATGGATTGAGTATCATGCTGTATG
CAGGTTGGAAACAGCGCGGGATCTGGATCTGAGGCGACATCAGCTATGATGCAGAGATTTTGGG
ATTCAGCAATGTCCATTGGACCTCTTGATGATGATGATGACTCCAGAAGGTTAGTATCTTTGCT
TATATCTTATCATTTTGATAATCTGATGGCATGGTTCTGTCATGATTTATAATTCACTTGGCAT
ATTATCAGTGAAGGATCAACTAAAGTGGCGTCTGAGGCAACAGATGTAGGAAGATCAGCTTTTT
ATCCGGCTTCTGGTTTGTCCAACACATTCGGGTTCAAGATTCAAGACAAACAAGGCAGGATGCA
CAGATTTAACTGCGGTATGCATCTTAGTTTCATGCCAACAGGGAATTGTGTTATCAATGTTCTT
TCTGCCCTTCCTTTTGTTGTATTTCTAATTATTTATATTGTATCCTTGGTTTCATGTGTGATAT
GCTTCAAACTTCAGAAACGAGCAGCTTGACAGAGTTGATAACCAGCATTCTACAGAGGCTTGGC
GATGACATCGATAGAAAAAACCTACCACAAATTTTG
						
					

			
		

Sequences
Splice junction sequence	GCTTCAAACTTCAGAAACGAGCAGCTTGACAGAGTTGATAACCAGCATTCTACAGAGGCTTGGC GATGACATCGATAGAAAAAACCTACCACAAATTTTGgtcctaatacttttattgagactcttcg agagcggatgtttaggccatcactatctaccattatttctgagaattcaaagtaggtaatatcc attccttt
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	GTCCTAATACTTTTATTGAGACTCTTCGAGAGCGGATGTTTAGGCCATCACTATCTACCATTAT TTCTGAGAATTCAAAGTAGGTAATATCCATTCCTTTTTCAAGTTTTAGGCTTTTCCAGCATTTC AGGAATTTAAGTGCCATTGTTGAACAACTGACTTATTGCTGACAAACTTCTTAGAGTGGTGACT GTTGCACCAACTGACACAGTGTTGACGGCATCAAAAAAGATGCTTGAAGTTAAAGTAAGTTCAG CGGTTGTAGCAATTGAAAACAAGCCTGGGGGGATTCTGACGTGAGTATCTCTTCTCAGTTTAAT TATACCATTTTGACTGTTGAACTAACATCTGCTATCTTTCTTACATCAGCTCTAGAGATATTTT GATGCGTGTTATAGCCCAGAATCTCCCACCTGAATCTACTACTGTTGAGAAGGTAAGGAAGTCT TAACATGGAATGTCTGCTATGTTTTTCTTAATCTCTTTAACTATCATGGCATCATGCTTGAAAC TCCTTTCTACAGGTCATGACCCAGACTCCTGAATGTGCCACGGTTGACACTCCAATCCTTGATG CCCTCCATACAATGCACGACGGAAAGTTTTTACATTTGCCTGTCTTAGACAAGGGTATGTCCAT GTAGTGCAATGGATTATATCTAATTTATTTATTGGAGGTCTACTAAGTTGTTGACATGTGTTGT CTATATCCAGATGGAAATGTTGTAACTGTAGTTGATGTCCTTCACATAACCCATGCTGCAATTG CAACTGTAAGTGAAAAGTTCCAGCTGCTTGATATATTTTCTCTGTGTCCTTGTGCATACAGTCT TACACAATACTCACTTTGTCAGCATGCATTGTAAAATGCTGAGAGAATGCATCACGATGTGGAA CCTGTCATTATTACATGTCTTTTGCTTTCATTCTATTAAGATGGATTGAGTATCATGCTGTATG CAGGTTGGAAACAGCGCGGGATCTGGATCTGAGGCGACATCAGCTATGATGCAGAGATTTTGGG ATTCAGCAATGTCCATTGGACCTCTTGATGATGATGATGACTCCAGAAGGTTAGTATCTTTGCT TATATCTTATCATTTTGATAATCTGATGGCATGGTTCTGTCATGATTTATAATTCACTTGGCAT ATTATCAGTGAAGGATCAACTAAAGTGGCGTCTGAGGCAACAGATGTAGGAAGATCAGCTTTTT ATCCGGCTTCTGGTTTGTCCAACACATTCGGGTTCAAGATTCAAGACAAACAAGGCAGGATGCA CAGATTTAACTGCGGTATGCATCTTAGTTTCATGCCAACAGGGAATTGTGTTATCAATGTTCTT TCTGCCCTTCCTTTTGTTGTATTTCTAATTATTTATATTGTATCCTTGGTTTCATGTGTGATAT GCTTCAAACTTCAGAAACGAGCAGCTTGACAGAGTTGATAACCAGCATTCTACAGAGGCTTGGC GATGACATCGATAGAAAAAACCTACCACAAATTTTG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.160267556

Conservation Information
Conserved circRNAs	NA
PMCS	0.160267556

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							40387168-40388440(+)
40387160-40388223(-)
						
						Potential amino acid sequence
						
							MLEVKVSSAVVAIENKPGGILTSRDILMRVIAQNLPPESTTVEKVMTQTPECATVDTPILDALH
TMHDGKFLHLPVLDKDGNVVTVVDVLHITHAAIATVGNSAGSGSEATSAMMQRFWDSAMSIGPL
DDDDDSRSEGSTKVASEATDVGRSAFYPASGLSNTFGFKIQDKQGRMHRFNCETSSLTELITSI
LQRLGDDIDRKNLPQILVLILLLRLFESGCLGHHYLPLFLRIQSRVVTVAPTDTVLTASKKMLE
VKVSSAVVAIENKPGGILTSRDILMRVIAQNLPPESTTVEKVMTQTPECATVDTPILDALHTMH
DGKFLHLPVLDKDGNVVTVVDVLHITHAAIATVGNSAGSGSEATSAMMQRFWDSAMSIGPLDDD
DDSRSEGSTKVASEATDVGRSAFYPASGLSNTFGFKIQDKQGRMHRFNCETSSLTELITSILQR
LGDDIDRKNLPQILVLILLLRLFESGCLGHHYLPLFLRIQSRVVTVAPTDTVLTASKKMLEVKV
SSAVVAIENKPGGILTSRDILMRVIAQNLPPESTTVEKVMTQTPECATVDTPILDALHTMHDGK
FLHLPVLDKDGNVVTVVDVLHITHAAIATVGNSAGSGSEATSAMMQRFWDSAMSIGPLDDDDDS
RSEGSTKVASEATDVGRSAFYPASGLSNTFGFKIQDKQGRMHRFNCETSSLTELITSILQRLGD
DIDRKNLPQILVLILLLRLFESGCLGHHYLPLFLRIQSRVVTVAPTDTVLTASKKMLEVKVSSA
VVAIENKPGGILTSRDILMRVIAQNLPPESTTVEKVMTQTPECATVDTPILDALHTMHDGKFLH
LPVLDKDGNVVTVVDVLHITHAAIATVGNSAGSGSEATSAMMQRFWDSAMSIGPLDDDDDSRSE
GSTKVASEATDVGRSAFYPASGLSNTFGFKIQDKQGRMHRFNCETSSLTELITSILQRLGDDID
RKNLPQIL(+)
MPSTLCQLVQQSPLYFEFSEIMVDSDGLNIRSRRVSIKVLGPKFVVGFFYRCHRQASVECWLST
LSSCSFRS*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	40387168-40388440(+) 40387160-40388223(-)
Potential amino acid sequence	MLEVKVSSAVVAIENKPGGILTSRDILMRVIAQNLPPESTTVEKVMTQTPECATVDTPILDALH TMHDGKFLHLPVLDKDGNVVTVVDVLHITHAAIATVGNSAGSGSEATSAMMQRFWDSAMSIGPL DDDDDSRSEGSTKVASEATDVGRSAFYPASGLSNTFGFKIQDKQGRMHRFNCETSSLTELITSI LQRLGDDIDRKNLPQILVLILLLRLFESGCLGHHYLPLFLRIQSRVVTVAPTDTVLTASKKMLE VKVSSAVVAIENKPGGILTSRDILMRVIAQNLPPESTTVEKVMTQTPECATVDTPILDALHTMH DGKFLHLPVLDKDGNVVTVVDVLHITHAAIATVGNSAGSGSEATSAMMQRFWDSAMSIGPLDDD DDSRSEGSTKVASEATDVGRSAFYPASGLSNTFGFKIQDKQGRMHRFNCETSSLTELITSILQR LGDDIDRKNLPQILVLILLLRLFESGCLGHHYLPLFLRIQSRVVTVAPTDTVLTASKKMLEVKV SSAVVAIENKPGGILTSRDILMRVIAQNLPPESTTVEKVMTQTPECATVDTPILDALHTMHDGK FLHLPVLDKDGNVVTVVDVLHITHAAIATVGNSAGSGSEATSAMMQRFWDSAMSIGPLDDDDDS RSEGSTKVASEATDVGRSAFYPASGLSNTFGFKIQDKQGRMHRFNCETSSLTELITSILQRLGD DIDRKNLPQILVLILLLRLFESGCLGHHYLPLFLRIQSRVVTVAPTDTVLTASKKMLEVKVSSA VVAIENKPGGILTSRDILMRVIAQNLPPESTTVEKVMTQTPECATVDTPILDALHTMHDGKFLH LPVLDKDGNVVTVVDVLHITHAAIATVGNSAGSGSEATSAMMQRFWDSAMSIGPLDDDDDSRSE GSTKVASEATDVGRSAFYPASGLSNTFGFKIQDKQGRMHRFNCETSSLTELITSILQRLGDDID RKNLPQIL(+) MPSTLCQLVQQSPLYFEFSEIMVDSDGLNIRSRRVSIKVLGPKFVVGFFYRCHRQASVECWLST LSSCSFRS*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os01g0923300_circ_g.3

Address

Any questions?

Supported by