Plant Circular RNA Database

Detail information of Os09g0542000_circ_g.6

			
						 General Information
					
						CircRNA Name
						Os09g0542000_circ_g.6
					
						ID in PlantcircBase
						osa_circ_040071
					
						Alias
						Os09circ10331/Os_ciR1483, 
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr9: 21344499-21345145  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, KNIFE, PcircRNA_finder, SMALT, Segemehl, find_circ, CIRI-long
					
						Parent gene
						
							Os09g0542000						
					
						Parent gene annotation
						
							Similar to Ribonuclease P. (Os09t0542000-01)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os09g0542000_circ_g.1 Os09g0542000_circ_g.2 Os09g0542000_circ_g.3 Os09g0542000_circ_g.4 Os09g0542000_circ_g.5 Os09g0542000_circ_g.7 Os09g0542000_circ_g.8 						
					
						Support reads
						2/10/6
					
						Tissues
						panicle/root/shoot, root, seed, pistil, leaf
					
						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
						Os09t0542000-01:3

General Information
CircRNA Name	Os09g0542000_circ_g.6
ID in PlantcircBase	osa_circ_040071
Alias	Os09circ10331/Os_ciR1483,
Organism	Oryza sativa
Position	chr9: 21344499-21345145 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, KNIFE, PcircRNA_finder, SMALT, Segemehl, find_circ, CIRI-long
Parent gene	Os09g0542000
Parent gene annotation	Similar to Ribonuclease P. (Os09t0542000-01)
Parent gene strand	-
Alternative splicing	Os09g0542000_circ_g.1 Os09g0542000_circ_g.2 Os09g0542000_circ_g.3 Os09g0542000_circ_g.4 Os09g0542000_circ_g.5 Os09g0542000_circ_g.7 Os09g0542000_circ_g.8
Support reads	2/10/6
Tissues	panicle/root/shoot, root, seed, pistil, leaf
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	Os09t0542000-01:3

			
						 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  
						
							TCACTTCTTACGGGAGCAAGCCTTCCTCCAGTGGCTCCCACATATCAGTGATATCAGTAGATCC
AGTGGTGGTGTTTTGGTGGAGACCAACAATTCTTCTcttcttcgttctcgtattcaaccaaagg
cttaaccttatcagcaggcaacggagattgatatctgtatatacaataattaataaataattaa
catattta

						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: 226
Transcript exons: 21344499-21344560,21344897-21344971,21345057-21345145
CTTCTTCGTTCTCGTATTCAACCAAAGGCTTAACCTTATCAGCAGGCAACGGAGATTGATATCC
GATGGAGGATGTGTCCAGCTCCTTCTTTGAAAGGGTAATAGTTATCATAGATACATGCCTTGTT
GTCTCAAGTGGGAGCAAGCCTTCCTCCAGTGGCTCCCACATATCAGTGATATCAGTAGATCCAG
TGGTGGTGTTTTGGTGGAGACCAACAATTCTTCT
						
						Genomic sequence
						
							CTTCTTCGTTCTCGTATTCAACCAAAGGCTTAACCTTATCAGCAGGCAACGGAGATTGATATCT
GTATATACAATAATTAATAAATAATTAACATATTTATTGCTACTTTGCTATCTTAGAAGTTCAT
ACGGCAAGCTGATCACATTGTATAGATACAGATGTAACAATTACAGTGGTGCCTAAAAACAGAT
CACATTACCACATATTAACCATACACAAATTGATGTTATGTAAAATGTCTAATTGAACAGACTA
CAGCATTATCATTTCACAGCACCAATTGAAAAGGGTCTACATACTCTCCGGACAATCCACTAAA
GCATATAAATGATAGAAACATATTAGAAAAAAAAATCCTCAAGACTCATATACAGTTAAACAAA
AACAGAATACATACCCGATGGAGGATGTGTCCAGCTCCTTCTTTGAAAGGGTAATAGTTATCAT
AGATACATGCCTTGTTGTCTCAAGTCTGCAGAGGAGGAAAAGGGATAAATAAAAGACCAAATAA
ATATCTATACAGCACTACTTGAAATTGGAAAGTGGTCACTTCTTACGGGAGCAAGCCTTCCTCC
AGTGGCTCCCACATATCAGTGATATCAGTAGATCCAGTGGTGGTGTTTTGGTGGAGACCAACAA
TTCTTCT

Sequences
Splice junction sequence	TCACTTCTTACGGGAGCAAGCCTTCCTCCAGTGGCTCCCACATATCAGTGATATCAGTAGATCC AGTGGTGGTGTTTTGGTGGAGACCAACAATTCTTCTcttcttcgttctcgtattcaaccaaagg cttaaccttatcagcaggcaacggagattgatatctgtatatacaataattaataaataattaa catattta
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: 226 Transcript exons: 21344499-21344560,21344897-21344971,21345057-21345145 CTTCTTCGTTCTCGTATTCAACCAAAGGCTTAACCTTATCAGCAGGCAACGGAGATTGATATCC GATGGAGGATGTGTCCAGCTCCTTCTTTGAAAGGGTAATAGTTATCATAGATACATGCCTTGTT GTCTCAAGTGGGAGCAAGCCTTCCTCCAGTGGCTCCCACATATCAGTGATATCAGTAGATCCAG TGGTGGTGTTTTGGTGGAGACCAACAATTCTTCT
Genomic sequence	CTTCTTCGTTCTCGTATTCAACCAAAGGCTTAACCTTATCAGCAGGCAACGGAGATTGATATCT GTATATACAATAATTAATAAATAATTAACATATTTATTGCTACTTTGCTATCTTAGAAGTTCAT ACGGCAAGCTGATCACATTGTATAGATACAGATGTAACAATTACAGTGGTGCCTAAAAACAGAT CACATTACCACATATTAACCATACACAAATTGATGTTATGTAAAATGTCTAATTGAACAGACTA CAGCATTATCATTTCACAGCACCAATTGAAAAGGGTCTACATACTCTCCGGACAATCCACTAAA GCATATAAATGATAGAAACATATTAGAAAAAAAAATCCTCAAGACTCATATACAGTTAAACAAA AACAGAATACATACCCGATGGAGGATGTGTCCAGCTCCTTCTTTGAAAGGGTAATAGTTATCAT AGATACATGCCTTGTTGTCTCAAGTCTGCAGAGGAGGAAAAGGGATAAATAAAAGACCAAATAA ATATCTATACAGCACTACTTGAAATTGGAAAGTGGTCACTTCTTACGGGAGCAAGCCTTCCTCC AGTGGCTCCCACATATCAGTGATATCAGTAGATCCAGTGGTGGTGTTTTGGTGGAGACCAACAA TTCTTCT

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_018722 						
					
						PMCS
						0.387737275

Conservation Information
Conserved circRNAs	osi_circ_018722
PMCS	0.387737275

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							21344954-21344528(+)
21344901-21344925(+)
21345090-21345101(-)
						
						Potential amino acid sequence
						
							MPCCLKWEQAFLQWLPHISDISRSSGGVLVETNNSSLLRSRIQPKA*(+)
MEDVSSSFFERVIVIIDTCLVVSSGSKPSSSGSHISVISVDPVVVFWWRPTILLFFVLVFNQRL
NLISRQRRLISDGGCVQLLL*(+)
MWEPLEEGLLPLETTRHVSMITITLSKKELDTSSIGYQSPLPADKVKPLVEYENEEEKNCWSPP
KHHHWIY*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	21344954-21344528(+) 21344901-21344925(+) 21345090-21345101(-)
Potential amino acid sequence	MPCCLKWEQAFLQWLPHISDISRSSGGVLVETNNSSLLRSRIQPKA(+) MEDVSSSFFERVIVIIDTCLVVSSGSKPSSSGSHISVISVDPVVVFWWRPTILLFFVLVFNQRL NLISRQRRLISDGGCVQLLL(+) MWEPLEEGLLPLETTRHVSMITITLSKKELDTSSIGYQSPLPADKVKPLVEYENEEEKNCWSPP KHHHWIY*(-)
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; this study

circRNA

Detail information of Os09g0542000_circ_g.6

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