Plant Circular RNA Database

Detail information of Os03g0212400_circ_g.1

			
						 General Information
					
						CircRNA Name
						Os03g0212400_circ_g.1
					
						ID in PlantcircBase
						osa_circ_018481
					
						Alias
						Os03circ06716/Os_ciR4401
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr3: 5862051-5863345  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer, SMALT, Segemehl, find_circ
					
						Parent gene
						
							Os03g0212400						
					
						Parent gene annotation
						
							Similar to SNAP25 homologous protein SNAP29. (Os03t0212400-01)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os03g0212400_circ_g.2 Os03g0212400_circ_g.3 Os03g0212400_circ_g.4 Os03g0212400_circ_g.5 						
					
						Support reads
						3/5/3
					
						Tissues
						leaf and panicle/root/shoot, 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
						Os03t0212400-01:4

General Information
CircRNA Name	Os03g0212400_circ_g.1
ID in PlantcircBase	osa_circ_018481
Alias	Os03circ06716/Os_ciR4401
Organism	Oryza sativa
Position	chr3: 5862051-5863345 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ue-circRNA
Identification method	CIRCexplorer, SMALT, Segemehl, find_circ
Parent gene	Os03g0212400
Parent gene annotation	Similar to SNAP25 homologous protein SNAP29. (Os03t0212400-01)
Parent gene strand	+
Alternative splicing	Os03g0212400_circ_g.2 Os03g0212400_circ_g.3 Os03g0212400_circ_g.4 Os03g0212400_circ_g.5
Support reads	3/5/3
Tissues	leaf and panicle/root/shoot, 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	Os03t0212400-01:4

			
						 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  
						
							AGGTTGAGATAGCAAAGCAGGATGATGCGCTCTCAGACTTGAGTAACATGTTGGGAGAGCTGAA
GGGTATGGCATTGGATATGGGCACAGAAATTGAAAGattgctgcaaacaactccagtttctgaa
taaagacagtgccgatattaatggataagaaacagacctcgttaggcactcctgtctacaggac
aaatccct

									
								

					

						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: 683
Transcript exons: 5862051-5862419,5862878-5862968,5863047-5863171,5863248-
5863345
ATTGCTGCAAACAACTCCAGTTTCTGAATAAAGACAGTGCCGATATTAATGGATAAGAAACAGA
CCTCGTTAGGCACTCCTGTCTACAGGACAAATCCCTTCGATTCTGACTCTGATTCTGAAGTGCC
CTCAAGACCGTCAAGGGCACAATCTGTCCCAGTGCGACGCACAGATCAATCTATACAAGAGCTG
GAGGACTATGCTGTTGATAAAGTAGAAGAAACATCACGCAAAGTAAATGATTGTGTCAGAGCCG
CTGAAGCAATCAGAGAAGATGCTACAAAAACACTGGTTACTTTGCATCGTCAAGGTGAACAGAT
CACCCGAACTCATCGAGTAGCCGCGGATATTGAACACGATCTTAGTATGAGTGAGAAGCTTTTG
GGAAGTCTAGGGGGGCTGTTTTCCAAGACATGGAAGCCAAAGAGAAACCAACAGATAAAAGGAC
CGATTTCACAAAATAATTCTTTCACAAGTTCAGCGAACCACATGGAACAGAGGCAGAGGCTAGG
TATTTCCTCAACACGTCAGCCATCTCCAAATCAAGTACATCGTTCACCTGCAACTGCAATCGAG
AAAGTTCAGGTTGAGATAGCAAAGCAGGATGATGCGCTCTCAGACTTGAGTAACATGTTGGGAG
AGCTGAAGGGTATGGCATTGGATATGGGCACAGAAATTGAAAG
						
					

						Genomic sequence
						
							ATTGCTGCAAACAACTCCAGTTTCTGAATAAAGACAGTGCCGATATTAATGGATAAGAAACAGA
CCTCGTTAGGCACTCCTGTCTACAGGACAAATCCCTTCGATTCTGACTCTGATTCTGAAGTGCC
CTCAAGACCGTCAAGGGCACAATCTGTCCCAGTGCGACGCACAGATCAATCTATACAAGAGCTG
GAGGACTATGCTGTTGATAAAGTAGAAGAAACATCACGCAAAGTAAATGATTGTGTCAGAGCCG
CTGAAGCAATCAGAGAAGATGCTACAAAAACACTGGTTACTTTGCATCGTCAAGGTGAACAGAT
CACCCGAACTCATCGAGTAGCCGCGGATATTGAACACGATCTTAGTATGGTAAGTTATGTTGTG
GAACCCAAGTATCCTTGATCTTCTTCTCATGAGTATTGCTCATAAATATGGGTAGAAGCTCCAT
AGAACTTTTTGGATGTGTTAGTACTAAATTTCAGTCATCATTTCAATATTTCATCCAAACATTA
GACTAAATTTCTATGCACCTCAACGATAAGTTATGTGATGTTTTGCACATATCTATCCTTATCT
CACTATCTTAACTCCCCTCTAGTTTATGTTTCTCTATGTCGTGTCAATTGCTGGGCTAAACCAT
GGAGGATTTACTAAGTACTATTATTATTCCTTTTCTTGCTTGTCTAGATAATTGTGTTTTGCTT
GGCTTGTTTTTAAGATATAAATTACATGATGTATTTTATTTCTGAAGTTATAGAGATTCTTTGC
CTTGTTCTTAATCTCATCAGAAAAAAAAAATCTGAAATCCAAATTTATGGTCTCTTCAGAGTGA
GAAGCTTTTGGGAAGTCTAGGGGGGCTGTTTTCCAAGACATGGAAGCCAAAGAGAAACCAACAG
ATAAAAGGACCGATTTCACAAAGTATGATGGTTTAGATTCTGACTAATTTCTGGGACTCTCTTT
TTTTTTTGCTTAACTGATCCATTTGAGTTATGGCAGATAATTCTTTCACAAGTTCAGCGAACCA
CATGGAACAGAGGCAGAGGCTAGGTATTTCCTCAACACGTCAGCCATCTCCAAATCAAGTACAT
CGTTCACCTGCAACTGCAATCGAGAAAGTTCAGGTCTGCATTCCCATCTAACCATGAATTGTAG
AATGAGTAATTTGTTCTGGAAGTTTACACCACTTTCTTCTTTTAGGTTGAGATAGCAAAGCAGG
ATGATGCGCTCTCAGACTTGAGTAACATGTTGGGAGAGCTGAAGGGTATGGCATTGGATATGGG
CACAGAAATTGAAAG
						
					

			
		

Sequences
Splice junction sequence	AGGTTGAGATAGCAAAGCAGGATGATGCGCTCTCAGACTTGAGTAACATGTTGGGAGAGCTGAA GGGTATGGCATTGGATATGGGCACAGAAATTGAAAGattgctgcaaacaactccagtttctgaa taaagacagtgccgatattaatggataagaaacagacctcgttaggcactcctgtctacaggac aaatccct
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: 683 Transcript exons: 5862051-5862419,5862878-5862968,5863047-5863171,5863248- 5863345 ATTGCTGCAAACAACTCCAGTTTCTGAATAAAGACAGTGCCGATATTAATGGATAAGAAACAGA CCTCGTTAGGCACTCCTGTCTACAGGACAAATCCCTTCGATTCTGACTCTGATTCTGAAGTGCC CTCAAGACCGTCAAGGGCACAATCTGTCCCAGTGCGACGCACAGATCAATCTATACAAGAGCTG GAGGACTATGCTGTTGATAAAGTAGAAGAAACATCACGCAAAGTAAATGATTGTGTCAGAGCCG CTGAAGCAATCAGAGAAGATGCTACAAAAACACTGGTTACTTTGCATCGTCAAGGTGAACAGAT CACCCGAACTCATCGAGTAGCCGCGGATATTGAACACGATCTTAGTATGAGTGAGAAGCTTTTG GGAAGTCTAGGGGGGCTGTTTTCCAAGACATGGAAGCCAAAGAGAAACCAACAGATAAAAGGAC CGATTTCACAAAATAATTCTTTCACAAGTTCAGCGAACCACATGGAACAGAGGCAGAGGCTAGG TATTTCCTCAACACGTCAGCCATCTCCAAATCAAGTACATCGTTCACCTGCAACTGCAATCGAG AAAGTTCAGGTTGAGATAGCAAAGCAGGATGATGCGCTCTCAGACTTGAGTAACATGTTGGGAG AGCTGAAGGGTATGGCATTGGATATGGGCACAGAAATTGAAAG
Genomic sequence	ATTGCTGCAAACAACTCCAGTTTCTGAATAAAGACAGTGCCGATATTAATGGATAAGAAACAGA CCTCGTTAGGCACTCCTGTCTACAGGACAAATCCCTTCGATTCTGACTCTGATTCTGAAGTGCC CTCAAGACCGTCAAGGGCACAATCTGTCCCAGTGCGACGCACAGATCAATCTATACAAGAGCTG GAGGACTATGCTGTTGATAAAGTAGAAGAAACATCACGCAAAGTAAATGATTGTGTCAGAGCCG CTGAAGCAATCAGAGAAGATGCTACAAAAACACTGGTTACTTTGCATCGTCAAGGTGAACAGAT CACCCGAACTCATCGAGTAGCCGCGGATATTGAACACGATCTTAGTATGGTAAGTTATGTTGTG GAACCCAAGTATCCTTGATCTTCTTCTCATGAGTATTGCTCATAAATATGGGTAGAAGCTCCAT AGAACTTTTTGGATGTGTTAGTACTAAATTTCAGTCATCATTTCAATATTTCATCCAAACATTA GACTAAATTTCTATGCACCTCAACGATAAGTTATGTGATGTTTTGCACATATCTATCCTTATCT CACTATCTTAACTCCCCTCTAGTTTATGTTTCTCTATGTCGTGTCAATTGCTGGGCTAAACCAT GGAGGATTTACTAAGTACTATTATTATTCCTTTTCTTGCTTGTCTAGATAATTGTGTTTTGCTT GGCTTGTTTTTAAGATATAAATTACATGATGTATTTTATTTCTGAAGTTATAGAGATTCTTTGC CTTGTTCTTAATCTCATCAGAAAAAAAAAATCTGAAATCCAAATTTATGGTCTCTTCAGAGTGA GAAGCTTTTGGGAAGTCTAGGGGGGCTGTTTTCCAAGACATGGAAGCCAAAGAGAAACCAACAG ATAAAAGGACCGATTTCACAAAGTATGATGGTTTAGATTCTGACTAATTTCTGGGACTCTCTTT TTTTTTTGCTTAACTGATCCATTTGAGTTATGGCAGATAATTCTTTCACAAGTTCAGCGAACCA CATGGAACAGAGGCAGAGGCTAGGTATTTCCTCAACACGTCAGCCATCTCCAAATCAAGTACAT CGTTCACCTGCAACTGCAATCGAGAAAGTTCAGGTCTGCATTCCCATCTAACCATGAATTGTAG AATGAGTAATTTGTTCTGGAAGTTTACACCACTTTCTTCTTTTAGGTTGAGATAGCAAAGCAGG ATGATGCGCTCTCAGACTTGAGTAACATGTTGGGAGAGCTGAAGGGTATGGCATTGGATATGGG CACAGAAATTGAAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_014039 						
					
						PMCS
						0.355666718

Conservation Information
Conserved circRNAs	osi_circ_014039
PMCS	0.355666718

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							5862100-5862078(+)
						
						Potential amino acid sequence
						
							MDKKQTSLGTPVYRTNPFDSDSDSEVPSRPSRAQSVPVRRTDQSIQELEDYAVDKVEETSRKVN
DCVRAAEAIREDATKTLVTLHRQGEQITRTHRVAADIEHDLSMSEKLLGSLGGLFSKTWKPKRN
QQIKGPISQNNSFTSSANHMEQRQRLGISSTRQPSPNQVHRSPATAIEKVQVEIAKQDDALSDL
SNMLGELKGMALDMGTEIERLLQTTPVSE*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	5862100-5862078(+)
Potential amino acid sequence	MDKKQTSLGTPVYRTNPFDSDSDSEVPSRPSRAQSVPVRRTDQSIQELEDYAVDKVEETSRKVN DCVRAAEAIREDATKTLVTLHRQGEQITRTHRVAADIEHDLSMSEKLLGSLGGLFSKTWKPKRN QQIKGPISQNNSFTSSANHMEQRQRLGISSTRQPSPNQVHRSPATAIEKVQVEIAKQDDALSDL SNMLGELKGMALDMGTEIERLLQTTPVSE*(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Lu et al., 2015;Ye et al., 2015;Chu et al., 2017

circRNA

Detail information of Os03g0212400_circ_g.1

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