Plant Circular RNA Database

Detail information of Os01g0559600_circ_g.2

			
						 General Information
					
						CircRNA Name
						Os01g0559600_circ_g.2
					
						ID in PlantcircBase
						osa_circ_002215
					
						Alias
						Os_ciR4459
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr1: 21231513-21232718  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, find_circ
					
						Parent gene
						
							Os01g0559600						
					
						Parent gene annotation
						
							Similar to C13 endopeptidase NP1 precursor. (Os01t0559600-01);Si
milar to Asparaginyl endopeptidase. (Os01t0559600-02)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os01g0559600_circ_g.1 Os01g0559600_circ_g.3 Os01g0559600_circ_g.4 Os01g0559600_circ_g.5 Os01g0559600_circ_g.6 Os01g0559600_circ_g.7 Os01g0559600_circ_g.8 Os01g0559600_circ_g.9 Os01g0559600_circ_g.10 Os01g0559600_circ_g.11 Os01g0559600_circ_g.12 Os01g0559600_circ_g.13 						
					
						Support reads
						4/1
					
						Tissues
						root/shoot
					
						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
						Os01t0559600-01:4
Os01t0559600-02:1

General Information
CircRNA Name	Os01g0559600_circ_g.2
ID in PlantcircBase	osa_circ_002215
Alias	Os_ciR4459
Organism	Oryza sativa
Position	chr1: 21231513-21232718 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, find_circ
Parent gene	Os01g0559600
Parent gene annotation	Similar to C13 endopeptidase NP1 precursor. (Os01t0559600-01);Si milar to Asparaginyl endopeptidase. (Os01t0559600-02)
Parent gene strand	+
Alternative splicing	Os01g0559600_circ_g.1 Os01g0559600_circ_g.3 Os01g0559600_circ_g.4 Os01g0559600_circ_g.5 Os01g0559600_circ_g.6 Os01g0559600_circ_g.7 Os01g0559600_circ_g.8 Os01g0559600_circ_g.9 Os01g0559600_circ_g.10 Os01g0559600_circ_g.11 Os01g0559600_circ_g.12 Os01g0559600_circ_g.13
Support reads	4/1
Tissues	root/shoot
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	Os01t0559600-01:4 Os01t0559600-02:1

			
						 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  
						
							GCAGCTGGGGAACATACTGCCCTGGGGAGTACCCGAGCCCACCTCCGGAGTACGACACATGCCT
AGGGGACTTGTACAGCGTTGCTTGGATGGAAGACAGgcggatgtctgccatgcctaccagatca
tgaagaggggcgggctcaaggacgagaacatcatcgtcttcatgtacgatgacatcgcgcacaa
cccggaga

									
								

					

						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: 608
Transcript exons: 21231513-21231677,21232073-21232229,21232339-21232424,21
232519-21232718
GCGGATGTCTGCCATGCCTACCAGATCATGAAGAGGGGCGGGCTCAAGGACGAGAACATCATCG
TCTTCATGTACGATGACATCGCGCACAACCCGGAGAATCCGAGGCCTGGTGTCATCATCAACCA
TCCCCAGGGTGGCGATGTCTATGCTGGGGTCCCGAAGGATTACACTGGGAAGGAGGTTAATGTC
AAAAACTTGTTTGCTGTTCTGCTCGGTAACAAAACTGCTGTCAAAGGTGGGAGTGGCAAAGTCC
TGGACAGTGGCCCCAACGATCATATTTTCATTTTTTACAGTGACCATGGGGGTCCTGGTGTCCT
TGGGATGCCAACCTATCCATACCTCTACGGTGATGATCTTGTAGATGTTCTGAAGAAGAAGCAT
GCTGCTGGGACGTACAAAAGCCTGGTCTTTTACCTTGAAGCCTGTGAATCTGGAAGCATCTTTG
AGGGTCTATTGCCAAATGGCATCAATGTTTATGCCACCACTGCATCAAACGCTGATGAGAGCAG
CTGGGGAACATACTGCCCTGGGGAGTACCCGAGCCCACCTCCGGAGTACGACACATGCCTAGGG
GACTTGTACAGCGTTGCTTGGATGGAAGACAG
						
					

						Genomic sequence
						
							GCGGATGTCTGCCATGCCTACCAGATCATGAAGAGGGGCGGGCTCAAGGACGAGAACATCATCG
TCTTCATGTACGATGACATCGCGCACAACCCGGAGAATCCGAGGCCTGGTGTCATCATCAACCA
TCCCCAGGGTGGCGATGTCTATGCTGGGGTCCCGAAGGTAACCGTGCATGTTCATTCTTCAGGA
GAATTATTGATGCTAGCTATAATTTCTTCGGTTACCTTTCTAAAGAAATGTTACAGTGTGACGA
TAAGATTTTGGCACCAAAGATTTCACTAGCAGCTAGTACATCATTGAAAAGGACAGAATGCCCA
AATTTTCGTCCATCTTGACGTCTTTTGGCAACTTGTTGTGAATAAGAAAAGGCAGGATTGGTCC
ACCACAATTTGGAGGCAACAAGGAAAGAATATACTTAATTAACATAGGCTCAACTGTAACTAAT
GTCAACATCTCTCAGCTGAACCAACTCCCTCTTAGGAAAGACTAATGGACAAGTAACCCTTTCC
ATGGTTTTCCTTCCGTTTAACTTTATTATCATCTATTTTTCACTGTAGGATTACACTGGGAAGG
AGGTTAATGTCAAAAACTTGTTTGCTGTTCTGCTCGGTAACAAAACTGCTGTCAAAGGTGGGAG
TGGCAAAGTCCTGGACAGTGGCCCCAACGATCATATTTTCATTTTTTACAGTGACCATGGGGGT
CCTGGTGTCCTTGGTGAGTACTTGCCTGCAATTATATGAAACCAATAGGATCAGATATCGCTAT
ATTCATGCTTGTGAAACAAGAAATGGTCTTATTGTTTTGACTTTTTCCAAAATTTCAGGGATGC
CAACCTATCCATACCTCTACGGTGATGATCTTGTAGATGTTCTGAAGAAGAAGCATGCTGCTGG
GACGTACAAAAGCCTGGTATCAGATTAGTTATTTGGCTATTCTGCACTATATAATTGCTGCTGC
TTGTAGTTGTAGAATTGATTTGATGAATCTGTTATCTCCTTTGCAGGTCTTTTACCTTGAAGCC
TGTGAATCTGGAAGCATCTTTGAGGGTCTATTGCCAAATGGCATCAATGTTTATGCCACCACTG
CATCAAACGCTGATGAGAGCAGCTGGGGAACATACTGCCCTGGGGAGTACCCGAGCCCACCTCC
GGAGTACGACACATGCCTAGGGGACTTGTACAGCGTTGCTTGGATGGAAGACAG
						
					

			
		

Sequences
Splice junction sequence	GCAGCTGGGGAACATACTGCCCTGGGGAGTACCCGAGCCCACCTCCGGAGTACGACACATGCCT AGGGGACTTGTACAGCGTTGCTTGGATGGAAGACAGgcggatgtctgccatgcctaccagatca tgaagaggggcgggctcaaggacgagaacatcatcgtcttcatgtacgatgacatcgcgcacaa cccggaga
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: 608 Transcript exons: 21231513-21231677,21232073-21232229,21232339-21232424,21 232519-21232718 GCGGATGTCTGCCATGCCTACCAGATCATGAAGAGGGGCGGGCTCAAGGACGAGAACATCATCG TCTTCATGTACGATGACATCGCGCACAACCCGGAGAATCCGAGGCCTGGTGTCATCATCAACCA TCCCCAGGGTGGCGATGTCTATGCTGGGGTCCCGAAGGATTACACTGGGAAGGAGGTTAATGTC AAAAACTTGTTTGCTGTTCTGCTCGGTAACAAAACTGCTGTCAAAGGTGGGAGTGGCAAAGTCC TGGACAGTGGCCCCAACGATCATATTTTCATTTTTTACAGTGACCATGGGGGTCCTGGTGTCCT TGGGATGCCAACCTATCCATACCTCTACGGTGATGATCTTGTAGATGTTCTGAAGAAGAAGCAT GCTGCTGGGACGTACAAAAGCCTGGTCTTTTACCTTGAAGCCTGTGAATCTGGAAGCATCTTTG AGGGTCTATTGCCAAATGGCATCAATGTTTATGCCACCACTGCATCAAACGCTGATGAGAGCAG CTGGGGAACATACTGCCCTGGGGAGTACCCGAGCCCACCTCCGGAGTACGACACATGCCTAGGG GACTTGTACAGCGTTGCTTGGATGGAAGACAG
Genomic sequence	GCGGATGTCTGCCATGCCTACCAGATCATGAAGAGGGGCGGGCTCAAGGACGAGAACATCATCG TCTTCATGTACGATGACATCGCGCACAACCCGGAGAATCCGAGGCCTGGTGTCATCATCAACCA TCCCCAGGGTGGCGATGTCTATGCTGGGGTCCCGAAGGTAACCGTGCATGTTCATTCTTCAGGA GAATTATTGATGCTAGCTATAATTTCTTCGGTTACCTTTCTAAAGAAATGTTACAGTGTGACGA TAAGATTTTGGCACCAAAGATTTCACTAGCAGCTAGTACATCATTGAAAAGGACAGAATGCCCA AATTTTCGTCCATCTTGACGTCTTTTGGCAACTTGTTGTGAATAAGAAAAGGCAGGATTGGTCC ACCACAATTTGGAGGCAACAAGGAAAGAATATACTTAATTAACATAGGCTCAACTGTAACTAAT GTCAACATCTCTCAGCTGAACCAACTCCCTCTTAGGAAAGACTAATGGACAAGTAACCCTTTCC ATGGTTTTCCTTCCGTTTAACTTTATTATCATCTATTTTTCACTGTAGGATTACACTGGGAAGG AGGTTAATGTCAAAAACTTGTTTGCTGTTCTGCTCGGTAACAAAACTGCTGTCAAAGGTGGGAG TGGCAAAGTCCTGGACAGTGGCCCCAACGATCATATTTTCATTTTTTACAGTGACCATGGGGGT CCTGGTGTCCTTGGTGAGTACTTGCCTGCAATTATATGAAACCAATAGGATCAGATATCGCTAT ATTCATGCTTGTGAAACAAGAAATGGTCTTATTGTTTTGACTTTTTCCAAAATTTCAGGGATGC CAACCTATCCATACCTCTACGGTGATGATCTTGTAGATGTTCTGAAGAAGAAGCATGCTGCTGG GACGTACAAAAGCCTGGTATCAGATTAGTTATTTGGCTATTCTGCACTATATAATTGCTGCTGC TTGTAGTTGTAGAATTGATTTGATGAATCTGTTATCTCCTTTGCAGGTCTTTTACCTTGAAGCC TGTGAATCTGGAAGCATCTTTGAGGGTCTATTGCCAAATGGCATCAATGTTTATGCCACCACTG CATCAAACGCTGATGAGAGCAGCTGGGGAACATACTGCCCTGGGGAGTACCCGAGCCCACCTCC GGAGTACGACACATGCCTAGGGGACTTGTACAGCGTTGCTTGGATGGAAGACAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_002142* osi_circ_010109 						
					
						PMCS
						0.412720806

Conservation Information
Conserved circRNAs	osi_circ_002142* osi_circ_010109
PMCS	0.412720806

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							21231541-21231540(+)
21232678-21231540(+)
21232402-21232589(-)
						
						Potential amino acid sequence
						
							MKRGGLKDENIIVFMYDDIAHNPENPRPGVIINHPQGGDVYAGVPKDYTGKEVNVKNLFAVLLG
NKTAVKGGSGKVLDSGPNDHIFIFYSDHGGPGVLGMPTYPYLYGDDLVDVLKKKHAAGTYKSLV
FYLEACESGSIFEGLLPNGINVYATTASNADESSWGTYCPGEYPSPPPEYDTCLGDLYSVAWME
DRRMSAMPTRS*(+)
MPRGLVQRCLDGRQADVCHAYQIMKRGGLKDENIIVFMYDDIAHNPENPRPGVIINHPQGGDVY
AGVPKDYTGKEVNVKNLFAVLLGNKTAVKGGSGKVLDSGPNDHIFIFYSDHGGPGVLGMPTYPY
LYGDDLVDVLKKKHAAGTYKSLVFYLEACESGSIFEGLLPNGINVYATTASNADESSWGTYCPG
EYPSPPPEYDTCLGDLYSVAWMEDRRMSAMPTRS*(+)
MLLLQNIYKIITVEVWIGWHPKDTRTPMVTVKNENMIVGATVQDFATPTFDSSFVTEQNSKQVF
DINLLPSVILRDPSIDIATLGMVDDDTRPRILRVVRDVIVHEDDDVLVLEPAPLHDLVGMADIR
LSSIQATLYKSPRHVSYSGGGLGYSPGQYVPQLLSSAFDAVVA*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	21231541-21231540(+) 21232678-21231540(+) 21232402-21232589(-)
Potential amino acid sequence	MKRGGLKDENIIVFMYDDIAHNPENPRPGVIINHPQGGDVYAGVPKDYTGKEVNVKNLFAVLLG NKTAVKGGSGKVLDSGPNDHIFIFYSDHGGPGVLGMPTYPYLYGDDLVDVLKKKHAAGTYKSLV FYLEACESGSIFEGLLPNGINVYATTASNADESSWGTYCPGEYPSPPPEYDTCLGDLYSVAWME DRRMSAMPTRS(+) MPRGLVQRCLDGRQADVCHAYQIMKRGGLKDENIIVFMYDDIAHNPENPRPGVIINHPQGGDVY AGVPKDYTGKEVNVKNLFAVLLGNKTAVKGGSGKVLDSGPNDHIFIFYSDHGGPGVLGMPTYPY LYGDDLVDVLKKKHAAGTYKSLVFYLEACESGSIFEGLLPNGINVYATTASNADESSWGTYCPG EYPSPPPEYDTCLGDLYSVAWMEDRRMSAMPTRS(+) MLLLQNIYKIITVEVWIGWHPKDTRTPMVTVKNENMIVGATVQDFATPTFDSSFVTEQNSKQVF DINLLPSVILRDPSIDIATLGMVDDDTRPRILRVVRDVIVHEDDDVLVLEPAPLHDLVGMADIR LSSIQATLYKSPRHVSYSGGGLGYSPGQYVPQLLSSAFDAVVA*(-)
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 Os01g0559600_circ_g.2

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