Plant Circular RNA Database

Detail information of Os01g0909500_circ_g.5

			
						 General Information
					
						CircRNA Name
						Os01g0909500_circ_g.5
					
						ID in PlantcircBase
						osa_circ_005382
					
						Alias
						Os01circ30958
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr1: 39622570-39623317  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer, CIRI, PcircRNA_finder, SMALT, Segemehl
					
						Parent gene
						
							Os01g0909500						
					
						Parent gene annotation
						
							Hypothetical conserved gene. (Os01t0909500-02);Similar to cDNA c
lone:J013116D08, full insert sequence. (Os01t0909500-03)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os01g0909500_circ_g.1 Os01g0909500_circ_g.2 Os01g0909500_circ_g.3 Os01g0909500_circ_g.4 Os01g0909500_circ_g.6 Os01g0909500_circ_g.7 						
					
						Support reads
						2/18
					
						Tissues
						leaf/shoot, root, anther, 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
						Os01t0909500-02:4
Os01t0909500-03:4

General Information
CircRNA Name	Os01g0909500_circ_g.5
ID in PlantcircBase	osa_circ_005382
Alias	Os01circ30958
Organism	Oryza sativa
Position	chr1: 39622570-39623317 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ue-circRNA
Identification method	CIRCexplorer, CIRI, PcircRNA_finder, SMALT, Segemehl
Parent gene	Os01g0909500
Parent gene annotation	Hypothetical conserved gene. (Os01t0909500-02);Similar to cDNA c lone:J013116D08, full insert sequence. (Os01t0909500-03)
Parent gene strand	-
Alternative splicing	Os01g0909500_circ_g.1 Os01g0909500_circ_g.2 Os01g0909500_circ_g.3 Os01g0909500_circ_g.4 Os01g0909500_circ_g.6 Os01g0909500_circ_g.7
Support reads	2/18
Tissues	leaf/shoot, root, anther, 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	Os01t0909500-02:4 Os01t0909500-03:4

			
						 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  
						
							GTTATTTAAATACACTAAATTGGAAAGAGGAAACAAACCCCAAAAATCGACGTCCATTGCTGCT
TTTGTTATTTTCTTCCCGAGCTTTTAGAGATTTGGCctggtggaacctcctcatcagattcatc
acctgaaacatcacatctcaagaattgtgattatcatgaagccaagtgtaggggaaacattaga
gatgacca

						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: 392
Transcript exons: 39622570-39622599,39622676-39622904,39623089-39623159,39
623256-39623317
CTGGTGGAACCTCCTCATCAGATTCATCACCTTCAGAATCAGTGAATTTTCCCAAATTCTTTAC
TTGATAGCCACAAAAGGCAACTTTGCTGATTAGTGAGGTGTGGAATAGTTGAAAGTTCTTCTTG
AAACAGAAGTCAACCTTGATATGCGGATGCCTTTTGGAGGAAAGCGTCCCAATCGCAAACTTCT
CATCATTAACTTCGACAAATACTTTCACATTGGAGTCTTTTAGCCCGTAAGCCTCATCAAGGGC
TACCGATGTTAGATGATACAGGGTATCCTCAGGACAAAAGATCTCCTTCTTATTGCACGGCTCA
ATTACCACTCCCCAAAAATCGACGTCCATTGCTGCTTTTGTTATTTTCTTCCCGAGCTTTTAGA
GATTTGGC
						
						Genomic sequence
						
							CTGGTGGAACCTCCTCATCAGATTCATCACCTGAAACATCACATCTCAAGAATTGTGATTATCA
TGAAGCCAAGTGTAGGGGAAACATTAGAGATGACCAATTTACCTTCAGAATCAGTGAATTTTCC
CAAATTCTTTACTTGATAGCCACAAAAGGCAACTTTGCTGATTAGTGAGGTGTGGAATAGTTGA
AAGTTCTTCTTGAAACAGAAGTCAACCTTGATATGCGGATGCCTTTTGGAGGAAAGCGTCCCAA
TCGCAAACTTCTCATCATTAACTTCGACAAATACTTTCACATTGGAGTCTTTTAGCCCGTAAGC
CTCATCAAGGGCTACCTGCGATTTAAGTTATAACAGTAAGATGAGACATCACTATAAATAATGA
GACCTGGTAAGAAAATTGATAATATGAGAGATAACAAGTACTCCCTCTGTCTCCATCCTAGAAT
ATAGCAACCTAGAACCCAACTTATTACAATCCTAGGTTGCTATATTCTGAGATGGAGGGAGTAG
AACATACCGATGTTAGATGATACAGGGTATCCTCAGGACAAAAGATCTCCTTCTTATTGCACGG
CTCAATTACCACTCCTAATAAACAATAACATTAATCACAAAGTTGTTTTTTTTTAATCTTAATG
AGACAGTTGTTATTTAAATACACTAAATTGGAAAGAGGAAACAAACCCCAAAAATCGACGTCCA
TTGCTGCTTTTGTTATTTTCTTCCCGAGCTTTTAGAGATTTGGC

Sequences
Splice junction sequence	GTTATTTAAATACACTAAATTGGAAAGAGGAAACAAACCCCAAAAATCGACGTCCATTGCTGCT TTTGTTATTTTCTTCCCGAGCTTTTAGAGATTTGGCctggtggaacctcctcatcagattcatc acctgaaacatcacatctcaagaattgtgattatcatgaagccaagtgtaggggaaacattaga gatgacca
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: 392 Transcript exons: 39622570-39622599,39622676-39622904,39623089-39623159,39 623256-39623317 CTGGTGGAACCTCCTCATCAGATTCATCACCTTCAGAATCAGTGAATTTTCCCAAATTCTTTAC TTGATAGCCACAAAAGGCAACTTTGCTGATTAGTGAGGTGTGGAATAGTTGAAAGTTCTTCTTG AAACAGAAGTCAACCTTGATATGCGGATGCCTTTTGGAGGAAAGCGTCCCAATCGCAAACTTCT CATCATTAACTTCGACAAATACTTTCACATTGGAGTCTTTTAGCCCGTAAGCCTCATCAAGGGC TACCGATGTTAGATGATACAGGGTATCCTCAGGACAAAAGATCTCCTTCTTATTGCACGGCTCA ATTACCACTCCCCAAAAATCGACGTCCATTGCTGCTTTTGTTATTTTCTTCCCGAGCTTTTAGA GATTTGGC
Genomic sequence	CTGGTGGAACCTCCTCATCAGATTCATCACCTGAAACATCACATCTCAAGAATTGTGATTATCA TGAAGCCAAGTGTAGGGGAAACATTAGAGATGACCAATTTACCTTCAGAATCAGTGAATTTTCC CAAATTCTTTACTTGATAGCCACAAAAGGCAACTTTGCTGATTAGTGAGGTGTGGAATAGTTGA AAGTTCTTCTTGAAACAGAAGTCAACCTTGATATGCGGATGCCTTTTGGAGGAAAGCGTCCCAA TCGCAAACTTCTCATCATTAACTTCGACAAATACTTTCACATTGGAGTCTTTTAGCCCGTAAGC CTCATCAAGGGCTACCTGCGATTTAAGTTATAACAGTAAGATGAGACATCACTATAAATAATGA GACCTGGTAAGAAAATTGATAATATGAGAGATAACAAGTACTCCCTCTGTCTCCATCCTAGAAT ATAGCAACCTAGAACCCAACTTATTACAATCCTAGGTTGCTATATTCTGAGATGGAGGGAGTAG AACATACCGATGTTAGATGATACAGGGTATCCTCAGGACAAAAGATCTCCTTCTTATTGCACGG CTCAATTACCACTCCTAATAAACAATAACATTAATCACAAAGTTGTTTTTTTTTAATCTTAATG AGACAGTTGTTATTTAAATACACTAAATTGGAAAGAGGAAACAAACCCCAAAAATCGACGTCCA TTGCTGCTTTTGTTATTTTCTTCCCGAGCTTTTAGAGATTTGGC

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_011095 						
					
						PMCS
						0.214411664

Conservation Information
Conserved circRNAs	osi_circ_011095
PMCS	0.214411664

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							39623092-39622739(+)
39623099-39622710(+)
39623276-39623288(-)
39622598-39623149(-)
						
						Potential amino acid sequence
						
							MLDDTGYPQDKRSPSYCTAQLPLPKNRRPLLLLLFSSRAFRDLAWWNLLIRFITFRISEFSQIL
YLIATKGNFAD*(+)
MIQGILRTKDLLLIARLNYHSPKIDVHCCFCYFLPELLEIWPGGTSSSDSSPSESVNFPKFFT*
(+)
MDVDFWGVVIEPCNKKEIFCPEDTLYHLTSVALDEAYGLKDSNVKVFVEVNDEKFAIGTLSSKR
HPHIKVDFCFKKNFQLFHTSLISKVAFCGYQVKNLGKFTDSEGDESDEEVPPGQISKSSGRK*(
-)
MNLMRRFHQAKSLKAREENNKSSNGRRFLGSGN*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	39623092-39622739(+) 39623099-39622710(+) 39623276-39623288(-) 39622598-39623149(-)
Potential amino acid sequence	MLDDTGYPQDKRSPSYCTAQLPLPKNRRPLLLLLFSSRAFRDLAWWNLLIRFITFRISEFSQIL YLIATKGNFAD(+) MIQGILRTKDLLLIARLNYHSPKIDVHCCFCYFLPELLEIWPGGTSSSDSSPSESVNFPKFFT (+) MDVDFWGVVIEPCNKKEIFCPEDTLYHLTSVALDEAYGLKDSNVKVFVEVNDEKFAIGTLSSKR HPHIKVDFCFKKNFQLFHTSLISKVAFCGYQVKNLGKFTDSEGDESDEEVPPGQISKSSGRK( -) MNLMRRFHQAKSLKAREENNKSSNGRRFLGSGN(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

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

circRNA

Detail information of Os01g0909500_circ_g.5

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