Plant Circular RNA Database

Detail information of Os01g0885600_circ_g.4

			
						 General Information
					
						CircRNA Name
						Os01g0885600_circ_g.4
					
						ID in PlantcircBase
						osa_circ_005126
					
						Alias
						Os_ciR6321
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr1: 38477711-38478191  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, CIRI, PcircRNA_finder, circRNA_finder, circseq_cup, find_circ
					
						Parent gene
						
							Os01g0885600						
					
						Parent gene annotation
						
							Alpha/beta hydrolase fold-1 domain containing protein. (Os01t088
5600-01)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os01g0885600_circ_g.1 Os01g0885600_circ_g.2 Os01g0885600_circ_g.3 Os01g0885600_circ_g.5 						
					
						Support reads
						2/3/4
					
						Tissues
						root/root/shoot, root, 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  
						
							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
						Os01t0885600-01:3

General Information
CircRNA Name	Os01g0885600_circ_g.4
ID in PlantcircBase	osa_circ_005126
Alias	Os_ciR6321
Organism	Oryza sativa
Position	chr1: 38477711-38478191 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, CIRI, PcircRNA_finder, circRNA_finder, circseq_cup, find_circ
Parent gene	Os01g0885600
Parent gene annotation	Alpha/beta hydrolase fold-1 domain containing protein. (Os01t088 5600-01)
Parent gene strand	+
Alternative splicing	Os01g0885600_circ_g.1 Os01g0885600_circ_g.2 Os01g0885600_circ_g.3 Os01g0885600_circ_g.5
Support reads	2/3/4
Tissues	root/root/shoot, root, 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	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	Os01t0885600-01:3

			
						 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  
						
							GTTCCTCTTGGTTGATTTGCGTTGCCATGGAGATTCAGCGTCAATTAAGAAAAGAGGACCGCAT
ACTGTTGCCTCAACTGCTCTTGATGTTCTAAAGCTGgtgcaatggaactcatttatggacaaat
cagtacctgatccaccaacagctgttctccttcatggcatccttgggagcaggaaaaactgggg
taattgag

									
								

					

						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: 164
Transcript exons: 38477711-38477802,38478120-38478191
GTGCAATGGAACTCATTTATGGACAAATCAGTACCTGATCCACCAACAGCTGTTCTCCTTCATG
GCATCCTTGGGAGCAGGAAAAACTGGGGGGAGATTCAGCGTCAATTAAGAAAAGAGGACCGCAT
ACTGTTGCCTCAACTGCTCTTGATGTTCTAAAGCTG
Transcript length: 168
Transcript exons: 38477711-38477774,38478088-38478191
GTGCAATGGAACTCATTTATGGACAAATCAGTACCTGATCCACCAACAGCTGTTCTCCTTCATG
TGCAGTTCCTCTTGGTTGATTTGCGTTGCCATGGAGATTCAGCGTCAATTAAGAAAAGAGGACC
GCATACTGTTGCCTCAACTGCTCTTGATGTTCTAAAGCTG
Transcript length: 234
Transcript exons: 38477711-38477801,38477965-38478008,38478093-38478191
GTGCAATGGAACTCATTTATGGACAAATCAGTACCTGATCCACCAACAGCTGTTCTCCTTCATG
GCATCCTTGGGAGCAGGAAAAACTGGGGATCTTTTGCAAAGAGGCTGGCTCAGGAATTTCCGAT
GTGGCAGTTCCTCTTGGTTGATTTGCGTTGCCATGGAGATTCAGCGTCAATTAAGAAAAGAGGA
CCGCATACTGTTGCCTCAACTGCTCTTGATGTTCTAAAGCTG
Transcript length: 318
Transcript exons: 38477711-38478191
GTGCAATGGAACTCATTTATGGACAAATCAGTACCTGATCCACCAACAGCTGTTCTCCTTCATG
GCATCCTTGGGAGCAGGAAAAACTGGGGATCTTTTGCAAAGAGGCTGGCTCAGGAATTTCCGAT
GTGGCAGGTTACTTTATCTAAAATTCTGCTCGCAATCTGACTTATTTCACAGCATAAAGAAAGA
AACTGTACCTGCCTTTTCCTCATGCAGTTCCTCTTGGTTGATTTGCGTTGCCATGGAGATTCAG
CGTCAATTAAGAAAAGAGGACCGCATACTGTTGCCTCAACTGCTCTTGATGTTCTAAAGCTG
						
					

						Genomic sequence
						
							GTGCAATGGAACTCATTTATGGACAAATCAGTACCTGATCCACCAACAGCTGTTCTCCTTCATG
GCATCCTTGGGAGCAGGAAAAACTGGGGTAATTGAGAAGTGCTTGCTTTCCTATTGCATACTTT
GTTTCCTGGTGTATTGGGTTTGTTGTTGTGTTCAGTTTGCAGAGTGAAATACTGACACATTTTA
AAGCTGTTTTGGCTGTATAAATGCATTTAATCACAAAATTAATTAACTGTGTTGATTTGAAGGA
TCTTTTGCAAAGAGGCTGGCTCAGGAATTTCCGATGTGGCAGGTTACTTTATCTAAAATTCTGC
TCGCAATCTGACTTATTTCACAGCATAAAGAAAGAAACTGTACCTGCCTTTTCCTCATGCAGTT
CCTCTTGGTTGATTTGCGTTGCCATGGAGATTCAGCGTCAATTAAGAAAAGAGGACCGCATACT
GTTGCCTCAACTGCTCTTGATGTTCTAAAGCTG
						
					

			
		

Sequences
Splice junction sequence	GTTCCTCTTGGTTGATTTGCGTTGCCATGGAGATTCAGCGTCAATTAAGAAAAGAGGACCGCAT ACTGTTGCCTCAACTGCTCTTGATGTTCTAAAGCTGgtgcaatggaactcatttatggacaaat cagtacctgatccaccaacagctgttctccttcatggcatccttgggagcaggaaaaactgggg taattgag
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: 164 Transcript exons: 38477711-38477802,38478120-38478191 GTGCAATGGAACTCATTTATGGACAAATCAGTACCTGATCCACCAACAGCTGTTCTCCTTCATG GCATCCTTGGGAGCAGGAAAAACTGGGGGGAGATTCAGCGTCAATTAAGAAAAGAGGACCGCAT ACTGTTGCCTCAACTGCTCTTGATGTTCTAAAGCTG Transcript length: 168 Transcript exons: 38477711-38477774,38478088-38478191 GTGCAATGGAACTCATTTATGGACAAATCAGTACCTGATCCACCAACAGCTGTTCTCCTTCATG TGCAGTTCCTCTTGGTTGATTTGCGTTGCCATGGAGATTCAGCGTCAATTAAGAAAAGAGGACC GCATACTGTTGCCTCAACTGCTCTTGATGTTCTAAAGCTG Transcript length: 234 Transcript exons: 38477711-38477801,38477965-38478008,38478093-38478191 GTGCAATGGAACTCATTTATGGACAAATCAGTACCTGATCCACCAACAGCTGTTCTCCTTCATG GCATCCTTGGGAGCAGGAAAAACTGGGGATCTTTTGCAAAGAGGCTGGCTCAGGAATTTCCGAT GTGGCAGTTCCTCTTGGTTGATTTGCGTTGCCATGGAGATTCAGCGTCAATTAAGAAAAGAGGA CCGCATACTGTTGCCTCAACTGCTCTTGATGTTCTAAAGCTG Transcript length: 318 Transcript exons: 38477711-38478191 GTGCAATGGAACTCATTTATGGACAAATCAGTACCTGATCCACCAACAGCTGTTCTCCTTCATG GCATCCTTGGGAGCAGGAAAAACTGGGGATCTTTTGCAAAGAGGCTGGCTCAGGAATTTCCGAT GTGGCAGGTTACTTTATCTAAAATTCTGCTCGCAATCTGACTTATTTCACAGCATAAAGAAAGA AACTGTACCTGCCTTTTCCTCATGCAGTTCCTCTTGGTTGATTTGCGTTGCCATGGAGATTCAG CGTCAATTAAGAAAAGAGGACCGCATACTGTTGCCTCAACTGCTCTTGATGTTCTAAAGCTG
Genomic sequence	GTGCAATGGAACTCATTTATGGACAAATCAGTACCTGATCCACCAACAGCTGTTCTCCTTCATG GCATCCTTGGGAGCAGGAAAAACTGGGGTAATTGAGAAGTGCTTGCTTTCCTATTGCATACTTT GTTTCCTGGTGTATTGGGTTTGTTGTTGTGTTCAGTTTGCAGAGTGAAATACTGACACATTTTA AAGCTGTTTTGGCTGTATAAATGCATTTAATCACAAAATTAATTAACTGTGTTGATTTGAAGGA TCTTTTGCAAAGAGGCTGGCTCAGGAATTTCCGATGTGGCAGGTTACTTTATCTAAAATTCTGC TCGCAATCTGACTTATTTCACAGCATAAAGAAAGAAACTGTACCTGCCTTTTCCTCATGCAGTT CCTCTTGGTTGATTTGCGTTGCCATGGAGATTCAGCGTCAATTAAGAAAAGAGGACCGCATACT GTTGCCTCAACTGCTCTTGATGTTCTAAAGCTG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_011024 						
					
						PMCS
						0.42903902

Conservation Information
Conserved circRNAs	osi_circ_011024
PMCS	0.42903902

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							38477730-38478188(+)
38477728-38478138(-)
						
						Potential amino acid sequence
						
							MDKSVPDPPTAVLLHGILGSRKNWGSFAKRLAQEFPMWQFLLVDLRCHGDSASIKKRGPHTVAS
TALDVLKLVQWNSFMDKSVPDPPTAVLLHGILGSRKNWGSFAKRLAQEFPMWQFLLVDLRCHGD
SASIKKRGPHTVASTALDVLKLVQWNSFMDKSVPDPPTAVLLHGILGSRKNWGSFAKRLAQEFP
MWQFLLVDLRCHGDSASIKKRGPHTVASTALDVLKLVQWNSFMDKSVPDPPTAVLLHGILGSRK
NWGSFAKRLAQEFPMWQFLLVDLRCHGDSASIKKRGPHTVASTALDVLKL(+)
MSSIAPALEHQEQLRQQYAVLFS*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	38477730-38478188(+) 38477728-38478138(-)
Potential amino acid sequence	MDKSVPDPPTAVLLHGILGSRKNWGSFAKRLAQEFPMWQFLLVDLRCHGDSASIKKRGPHTVAS TALDVLKLVQWNSFMDKSVPDPPTAVLLHGILGSRKNWGSFAKRLAQEFPMWQFLLVDLRCHGD SASIKKRGPHTVASTALDVLKLVQWNSFMDKSVPDPPTAVLLHGILGSRKNWGSFAKRLAQEFP MWQFLLVDLRCHGDSASIKKRGPHTVASTALDVLKLVQWNSFMDKSVPDPPTAVLLHGILGSRK NWGSFAKRLAQEFPMWQFLLVDLRCHGDSASIKKRGPHTVASTALDVLKL(+) MSSIAPALEHQEQLRQQYAVLFS*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ye et al., 2015;Ye et al., 2016;Chu et al., 2017

circRNA

Detail information of Os01g0885600_circ_g.4

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