Plant Circular RNA Database

Detail information of Os12g0279000_circ_g.5

			
						 General Information
					
						CircRNA Name
						Os12g0279000_circ_g.5
					
						ID in PlantcircBase
						osa_circ_011116
					
						Alias
						Os12circ04243/Os_ciR1247
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr12: 10464191-10464889  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, SMALT, Segemehl, find_circ
					
						Parent gene
						
							Os12g0279000						
					
						Parent gene annotation
						
							Helicase, C-terminal domain containing protein. (Os12t0279000-01
)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os12g0279000_circ_g.2 Os12g0279000_circ_g.3 Os12g0279000_circ_g.4 Os12g0279000_circ_g.6 						
					
						Support reads
						4/14/4
					
						Tissues
						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
						Os12t0279000-01:3

General Information
CircRNA Name	Os12g0279000_circ_g.5
ID in PlantcircBase	osa_circ_011116
Alias	Os12circ04243/Os_ciR1247
Organism	Oryza sativa
Position	chr12: 10464191-10464889 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, SMALT, Segemehl, find_circ
Parent gene	Os12g0279000
Parent gene annotation	Helicase, C-terminal domain containing protein. (Os12t0279000-01 )
Parent gene strand	+
Alternative splicing	Os12g0279000_circ_g.2 Os12g0279000_circ_g.3 Os12g0279000_circ_g.4 Os12g0279000_circ_g.6
Support reads	4/14/4
Tissues	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	Os12t0279000-01:3

			
						 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  
						
							CAACCAAAATAAAGGCCATTAAAAGAACAATGCGGTCTTCCACTGCTTTAGCCTTCAAGGATGA
GCTCAAGGCCCGAAAACGGGTTCTTCGTAGACTGGGataggaggcctgaggattccgattacac
agttgatgttctcacaagatgttctgtaagcaaggacaaaagtggaaagaagacaatgaagatt
attcctct

									
								

					

						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: 186
Transcript exons: 10464191-10464263,10464777-10464889
ATAGGAGGCCTGAGGATTCCGATTACACAGTTGATGTTCTCACAAGATGTTCTGTAAGCAAGGA
CAAAAGTGGAAGCAAGAATTATCAACCAAAATAAAGGCCATTAAAAGAACAATGCGGTCTTCCA
CTGCTTTAGCCTTCAAGGATGAGCTCAAGGCCCGAAAACGGGTTCTTCGTAGACTGGG
Transcript length: 529
Transcript exons: 10464191-10464336,10464428-10464577,10464657-10464889
ATAGGAGGCCTGAGGATTCCGATTACACAGTTGATGTTCTCACAAGATGTTCTGTAAGCAAGGA
CAAAAGTGGAAAGAAGACAATGAAGATTATTCCTCTGAAAGACCGTGGAGAACCAGTTGTGATT
TCCTTGCCACTTTCTCAGATTGATGGACTAAGCAGCATTCGGATGCACATACCAAAGGATCTTT
TGCCTGTAGAAGCTCGAGAAAACACATTGAGGAAAGTTGATGAAGTTATTTCCAGGTTTGCTAA
AGATGGGATCCCTTTATTGGATCCAGAAGAGGATATGAAAGTACAATCAAGCTCTTTCCGGAAA
GCTTCCAGAAGAATAGAAGCTCTTGAAAGTTTATTTGAGAAGCACGATGTCCACAATTCTCCAC
ATATTAAACAAAAGCTAAAAGTGTTGCATGCTAAGCAAGAATTATCAACCAAAATAAAGGCCAT
TAAAAGAACAATGCGGTCTTCCACTGCTTTAGCCTTCAAGGATGAGCTCAAGGCCCGAAAACGG
GTTCTTCGTAGACTGGG
						
					

						Genomic sequence
						
							ATAGGAGGCCTGAGGATTCCGATTACACAGTTGATGTTCTCACAAGATGTTCTGTAAGCAAGGA
CAAAAGTGGAAAGAAGACAATGAAGATTATTCCTCTGAAAGACCGTGGAGAACCAGTTGTGATT
TCCTTGCCACTTTCTCAGGTTATTTCCTTTTCCTATTTGACCGGTGAACTTTTTATGTTCTAAA
CATTTATAACAATGCAAAGTGGTCTGTTTTCTGTCTAATTCACAGATTGATGGACTAAGCAGCA
TTCGGATGCACATACCAAAGGATCTTTTGCCTGTAGAAGCTCGAGAAAACACATTGAGGAAAGT
TGATGAAGTTATTTCCAGGTTTGCTAAAGATGGGATCCCTTTATTGGATCCAGAAGAGGATATG
AAAGTAAGAAAAAAAATCATGCATATCACTCAGGTTATCTCTATATATGTAGTTCTAACAGCTT
GTTTGTTTTTCTTTTCAGGTACAATCAAGCTCTTTCCGGAAAGCTTCCAGAAGAATAGAAGCTC
TTGAAAGTTTATTTGAGAAGCACGATGTCCACAATTCTCCACATATTAAACAAAAGCTAAAAGT
GTTGCATGCTAAGCAAGAATTATCAACCAAAATAAAGGCCATTAAAAGAACAATGCGGTCTTCC
ACTGCTTTAGCCTTCAAGGATGAGCTCAAGGCCCGAAAACGGGTTCTTCGTAGACTGGG
						
					

			
		

Sequences
Splice junction sequence	CAACCAAAATAAAGGCCATTAAAAGAACAATGCGGTCTTCCACTGCTTTAGCCTTCAAGGATGA GCTCAAGGCCCGAAAACGGGTTCTTCGTAGACTGGGataggaggcctgaggattccgattacac agttgatgttctcacaagatgttctgtaagcaaggacaaaagtggaaagaagacaatgaagatt attcctct
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: 186 Transcript exons: 10464191-10464263,10464777-10464889 ATAGGAGGCCTGAGGATTCCGATTACACAGTTGATGTTCTCACAAGATGTTCTGTAAGCAAGGA CAAAAGTGGAAGCAAGAATTATCAACCAAAATAAAGGCCATTAAAAGAACAATGCGGTCTTCCA CTGCTTTAGCCTTCAAGGATGAGCTCAAGGCCCGAAAACGGGTTCTTCGTAGACTGGG Transcript length: 529 Transcript exons: 10464191-10464336,10464428-10464577,10464657-10464889 ATAGGAGGCCTGAGGATTCCGATTACACAGTTGATGTTCTCACAAGATGTTCTGTAAGCAAGGA CAAAAGTGGAAAGAAGACAATGAAGATTATTCCTCTGAAAGACCGTGGAGAACCAGTTGTGATT TCCTTGCCACTTTCTCAGATTGATGGACTAAGCAGCATTCGGATGCACATACCAAAGGATCTTT TGCCTGTAGAAGCTCGAGAAAACACATTGAGGAAAGTTGATGAAGTTATTTCCAGGTTTGCTAA AGATGGGATCCCTTTATTGGATCCAGAAGAGGATATGAAAGTACAATCAAGCTCTTTCCGGAAA GCTTCCAGAAGAATAGAAGCTCTTGAAAGTTTATTTGAGAAGCACGATGTCCACAATTCTCCAC ATATTAAACAAAAGCTAAAAGTGTTGCATGCTAAGCAAGAATTATCAACCAAAATAAAGGCCAT TAAAAGAACAATGCGGTCTTCCACTGCTTTAGCCTTCAAGGATGAGCTCAAGGCCCGAAAACGG GTTCTTCGTAGACTGGG
Genomic sequence	ATAGGAGGCCTGAGGATTCCGATTACACAGTTGATGTTCTCACAAGATGTTCTGTAAGCAAGGA CAAAAGTGGAAAGAAGACAATGAAGATTATTCCTCTGAAAGACCGTGGAGAACCAGTTGTGATT TCCTTGCCACTTTCTCAGGTTATTTCCTTTTCCTATTTGACCGGTGAACTTTTTATGTTCTAAA CATTTATAACAATGCAAAGTGGTCTGTTTTCTGTCTAATTCACAGATTGATGGACTAAGCAGCA TTCGGATGCACATACCAAAGGATCTTTTGCCTGTAGAAGCTCGAGAAAACACATTGAGGAAAGT TGATGAAGTTATTTCCAGGTTTGCTAAAGATGGGATCCCTTTATTGGATCCAGAAGAGGATATG AAAGTAAGAAAAAAAATCATGCATATCACTCAGGTTATCTCTATATATGTAGTTCTAACAGCTT GTTTGTTTTTCTTTTCAGGTACAATCAAGCTCTTTCCGGAAAGCTTCCAGAAGAATAGAAGCTC TTGAAAGTTTATTTGAGAAGCACGATGTCCACAATTCTCCACATATTAAACAAAAGCTAAAAGT GTTGCATGCTAAGCAAGAATTATCAACCAAAATAAAGGCCATTAAAAGAACAATGCGGTCTTCC ACTGCTTTAGCCTTCAAGGATGAGCTCAAGGCCCGAAAACGGGTTCTTCGTAGACTGGG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_010382 						
					
						PMCS
						0.602416054

Conservation Information
Conserved circRNAs	osi_circ_010382
PMCS	0.602416054

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							10464851-10464191(+)
10464275-10464191(+)
						
						Potential amino acid sequence
						
							MSSRPENGFFVDWDRRPEDSDYTVDVLTRCSVSKDKSGKKTMKIIPLKDRGEPVVISLPLSQID
GLSSIRMHIPKDLLPVEARENTLRKVDEVISRFAKDGIPLLDPEEDMKVQSSSFRKASRRIEAL
ESLFEKHDVHNSPHIKQKLKVLHAKQELSTKIKAIKRTMRSSTALAFKDELKARKRVLRRLG*(
+)
MKIIPLKDRGEPVVISLPLSQIDGLSSIRMHIPKDLLPVEARENTLRKVDEVISRFAKDGIPLL
DPEEDMKVQSSSFRKASRRIEALESLFEKHDVHNSPHIKQKLKVLHAKQELSTKIKAIKRTMRS
STALAFKDELKARKRVLRRLG*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	10464851-10464191(+) 10464275-10464191(+)
Potential amino acid sequence	MSSRPENGFFVDWDRRPEDSDYTVDVLTRCSVSKDKSGKKTMKIIPLKDRGEPVVISLPLSQID GLSSIRMHIPKDLLPVEARENTLRKVDEVISRFAKDGIPLLDPEEDMKVQSSSFRKASRRIEAL ESLFEKHDVHNSPHIKQKLKVLHAKQELSTKIKAIKRTMRSSTALAFKDELKARKRVLRRLG( +) MKIIPLKDRGEPVVISLPLSQIDGLSSIRMHIPKDLLPVEARENTLRKVDEVISRFAKDGIPLL DPEEDMKVQSSSFRKASRRIEALESLFEKHDVHNSPHIKQKLKVLHAKQELSTKIKAIKRTMRS STALAFKDELKARKRVLRRLG(+)
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 Os12g0279000_circ_g.5

Address

Any questions?

Supported by