Plant Circular RNA Database

Detail information of Os05g0556100_circ_g.4

			
						 General Information
					
						CircRNA Name
						Os05g0556100_circ_g.4
					
						ID in PlantcircBase
						osa_circ_028847
					
						Alias
						Os_ciR3991
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr5: 27650995-27651476  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, find_circ
					
						Parent gene
						
							Os05g0556100						
					
						Parent gene annotation
						
							Similar to SDL5A. (Os05t0556100-01)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os05g0555800_circ_ag.1 Os05g0555800_circ_ig.1 Os05g0556000_circ_g.1 Os05g0556000_circ_g.2 Os05g0556000_circ_g.3 Os05g0556100_circ_g.1 Os05g0556100_circ_g.2 Os05g0556100_circ_g.3 Os05g0556100_circ_g.5 Os05g0556100_circ_g.6 Os05g0556100_circ_g.7 Os05g0556100_circ_g.8 Os05g0556100_circ_g.9 Os05g0556100_circ_g.10 Os05g0556100_circ_g.11 Os05g0556100_circ_g.12 Os05g0556100_circ_g.13 Os05g0556100_circ_g.14 Os05g0556300_circ_g.1 Os05g0556400_circ_g.1 Os05g0556400_circ_g.2 Os05g0556400_circ_g.3 Os05g0556600_circ_g.1 Os05g0556600_circ_g.2 EPlOSAG00000016487_circ_ig.1 Os05g0556700_circ_igg.1 Os05g0556700_circ_igg.2 Os05g0556650_circ_g.1 Os05g0556700_circ_g.1 						
					
						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  
						
							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
						Os05t0556201-00:2
Os05t0556201-00:2
Os05t0556100-01:2

General Information
CircRNA Name	Os05g0556100_circ_g.4
ID in PlantcircBase	osa_circ_028847
Alias	Os_ciR3991
Organism	Oryza sativa
Position	chr5: 27650995-27651476 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, find_circ
Parent gene	Os05g0556100
Parent gene annotation	Similar to SDL5A. (Os05t0556100-01)
Parent gene strand	-
Alternative splicing	Os05g0555800_circ_ag.1 Os05g0555800_circ_ig.1 Os05g0556000_circ_g.1 Os05g0556000_circ_g.2 Os05g0556000_circ_g.3 Os05g0556100_circ_g.1 Os05g0556100_circ_g.2 Os05g0556100_circ_g.3 Os05g0556100_circ_g.5 Os05g0556100_circ_g.6 Os05g0556100_circ_g.7 Os05g0556100_circ_g.8 Os05g0556100_circ_g.9 Os05g0556100_circ_g.10 Os05g0556100_circ_g.11 Os05g0556100_circ_g.12 Os05g0556100_circ_g.13 Os05g0556100_circ_g.14 Os05g0556300_circ_g.1 Os05g0556400_circ_g.1 Os05g0556400_circ_g.2 Os05g0556400_circ_g.3 Os05g0556600_circ_g.1 Os05g0556600_circ_g.2 EPlOSAG00000016487_circ_ig.1 Os05g0556700_circ_igg.1 Os05g0556700_circ_igg.2 Os05g0556650_circ_g.1 Os05g0556700_circ_g.1
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	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	Os05t0556201-00:2 Os05t0556201-00:2 Os05t0556100-01:2

			
						 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  
						
							TTTTAGCAATTAATTTTAGCTGGGAAAAAACTTACATCAACAGCATCGGTGCCCTTGTCCATTA
GATCAATTTTTGTAAGCACACCAAACGTCCTTTCACcttcgagagactctttgctaaatgttct
gatcccatcctatgagcaaggtgcttgtattctggcgtagttgaaaaatattcacgctctctgc
gcctagca

						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: 260
Transcript exons: 27650995-27651189,27651412-27651476
CTTCGAGAGACTCTTTGCTAAATGTTCTGATCCCATCCTATGAGCAAGGTGCTTGTATTCTGGC
GTAGTTGAAAAATATTCACGCTCTCTGCGCCTAGCAGCAATCATGTCCACATTCTTGTTGATAT
CCTGCTGAGATCGATTGACGACACCAATCCATTGTTGTTGGAGCCGGTATGATCTGCCTTCCAA
TATATCAACAGCATCGGTGCCCTTGTCCATTAGATCAATTTTTGTAAGCACACCAAACGTCCTT
TCAC
						
						Genomic sequence
						
							CTTCGAGAGACTCTTTGCTAAATGTTCTGATCCCATCCTATGAGCAAGGTGCTTGTATTCTGGC
GTAGTTGAAAAATATTCACGCTCTCTGCGCCTAGCAGCAATCATGTCCACATTCTTGTTGATAT
CCTGCTGAGATCGATTGACGACACCAATCCATTGTTGTTGGAGCCGGTATGATCTGCCTTCCAA
TATCTGCAGAAAAGAACCGTAAGAAAATACAGCTCAAAGAACAAACATAACCTTCATTTTCTAC
AACTGTATATCTTCCAACAGATAGAACAGAAGAATATTCAACATAGGAGATTTAAAAGGTCCCA
AAAGCAAGGGAACAATAATCCATGTTGACATCTCCGGGGACAAAATGTATCGATAATAAAGTTT
TTAGCAATTAATTTTAGCTGGGAAAAAACTTACATCAACAGCATCGGTGCCCTTGTCCATTAGA
TCAATTTTTGTAAGCACACCAAACGTCCTTTCAC

Sequences
Splice junction sequence	TTTTAGCAATTAATTTTAGCTGGGAAAAAACTTACATCAACAGCATCGGTGCCCTTGTCCATTA GATCAATTTTTGTAAGCACACCAAACGTCCTTTCACcttcgagagactctttgctaaatgttct gatcccatcctatgagcaaggtgcttgtattctggcgtagttgaaaaatattcacgctctctgc gcctagca
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: 260 Transcript exons: 27650995-27651189,27651412-27651476 CTTCGAGAGACTCTTTGCTAAATGTTCTGATCCCATCCTATGAGCAAGGTGCTTGTATTCTGGC GTAGTTGAAAAATATTCACGCTCTCTGCGCCTAGCAGCAATCATGTCCACATTCTTGTTGATAT CCTGCTGAGATCGATTGACGACACCAATCCATTGTTGTTGGAGCCGGTATGATCTGCCTTCCAA TATATCAACAGCATCGGTGCCCTTGTCCATTAGATCAATTTTTGTAAGCACACCAAACGTCCTT TCAC
Genomic sequence	CTTCGAGAGACTCTTTGCTAAATGTTCTGATCCCATCCTATGAGCAAGGTGCTTGTATTCTGGC GTAGTTGAAAAATATTCACGCTCTCTGCGCCTAGCAGCAATCATGTCCACATTCTTGTTGATAT CCTGCTGAGATCGATTGACGACACCAATCCATTGTTGTTGGAGCCGGTATGATCTGCCTTCCAA TATCTGCAGAAAAGAACCGTAAGAAAATACAGCTCAAAGAACAAACATAACCTTCATTTTCTAC AACTGTATATCTTCCAACAGATAGAACAGAAGAATATTCAACATAGGAGATTTAAAAGGTCCCA AAAGCAAGGGAACAATAATCCATGTTGACATCTCCGGGGACAAAATGTATCGATAATAAAGTTT TTAGCAATTAATTTTAGCTGGGAAAAAACTTACATCAACAGCATCGGTGCCCTTGTCCATTAGA TCAATTTTTGTAAGCACACCAAACGTCCTTTCAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_015737 						
					
						PMCS
						0.515904443

Conservation Information
Conserved circRNAs	osi_circ_015737
PMCS	0.515904443

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							27651440-27651440(-)
						
						Potential amino acid sequence
						
							MDKGTDAVDILEGRSYRLQQQWIGVVNRSQQDINKNVDMIAARRREREYFSTTPEYKHLAHRMG
SEHLAKSLSKVKGRLVCLQKLI*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	27651440-27651440(-)
Potential amino acid sequence	MDKGTDAVDILEGRSYRLQQQWIGVVNRSQQDINKNVDMIAARRREREYFSTTPEYKHLAHRMG SEHLAKSLSKVKGRLVCLQKLI*(-)
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 Os05g0556100_circ_g.4

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