Plant Circular RNA Database

Detail information of Os01g0961600_circ_g.1

			
						 General Information
					
						CircRNA Name
						Os01g0961600_circ_g.1
					
						ID in PlantcircBase
						osa_circ_005935
					
						Alias
						Os_ciR4535
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr1: 42396003-42397250  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer, find_circ
					
						Parent gene
						
							Os01g0961600						
					
						Parent gene annotation
						
							Conserved hypothetical protein. (Os01t0961600-01);Conserved hypo
thetical protein. (Os01t0961600-02)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							NA						
					
						Support reads
						4/1
					
						Tissues
						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  
						
							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
						Os01t0961600-01:8
Os01t0961600-02:8

General Information
CircRNA Name	Os01g0961600_circ_g.1
ID in PlantcircBase	osa_circ_005935
Alias	Os_ciR4535
Organism	Oryza sativa
Position	chr1: 42396003-42397250 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ue-circRNA
Identification method	CIRCexplorer, find_circ
Parent gene	Os01g0961600
Parent gene annotation	Conserved hypothetical protein. (Os01t0961600-01);Conserved hypo thetical protein. (Os01t0961600-02)
Parent gene strand	-
Alternative splicing	NA
Support reads	4/1
Tissues	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	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	Os01t0961600-01:8 Os01t0961600-02:8

			
						 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  
						
							TTGGTAGTTCTTCACAATATTTGACATAATCCTCATCAACTTCATATGTATTAAAACATGAGTG
GTAGTCATCCCTGGCAAGGAATTCAGTGCTATCATCcagctagaccaaaccaatctttttcgcc
atatccatcttcttcgccgcatacccacacatggtctgagtgtgatgaaactgaaaacaaaatc
aattagaa

									
								

					

						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: 615
Transcript exons: 42396003-42396080,42396157-42396207,42396298-42396330,42
396434-42396547,42396653-42396742,42396815-42396910,4239
7005-42397046,42397140-42397250
CAGCTAGACCAAACCAATCTTTTTCGCCATATCCATCTTCTTCGCCGCATACCCACACATGGTC
TGAGTGTGATGAAATTCTCTGTAAACTGCCTTTGTAATCAAATCTAGAGCTTTACCCTCTTCAA
CATCACCAGAAATATCCTTAGAGCACATAGAGAACCTATATTCCAATCCAAACAATTTGTCCCC
ATTTAGTTCAGCCTCCACTGCAAATTTGAAACTATGAAACATATCCATTTCATAGACTACCTTC
AAAGCATCATTGAAATTCATCTTTTGCTTAGCAACTAGCTTCCAAATCTCATGTAAGAAATAAG
GCCATTCCTTAAGGCGACTAATTTCACGCAGGTCCCATACATACTCCATGTATGCAAATTGGGC
TAAACCAACAGTCATATGGCAAAAGTTTGTTGCAATCTTTAACGCTTGGAAAAACGTAGTGTTG
TCCATTTTTGACCACTCCTGAGAAGACCGATCCAAATCTACATAGTCTCCAATCCACTTGATTT
TCTTTGGTAGTTCTTCACAATATTTGACATAATCCTCATCAACTTCATATGTATTAAAACATGA
GTGGTAGTCATCCCTGGCAAGGAATTCAGTGCTATCATC
						
					

						Genomic sequence
						
							CAGCTAGACCAAACCAATCTTTTTCGCCATATCCATCTTCTTCGCCGCATACCCACACATGGTC
TGAGTGTGATGAAACTGAAAACAAAATCAATTAGAACTGTGCAGGGTGTAGAATAAGAAACATT
TTTAGCTTAAGTGTTTCACTGATTACTTCTCTGTAAACTGCCTTTGTAATCAAATCTAGAGCTT
TACCCTCTTCAACCTAAAATAACAATATATTATATTATATGACATTATCGTCATAAAAAATGTA
TTTCAACTACACATATATGCTATACGACATTGTACTTACATCACCAGAAATATCCTTAGAGCAC
ATAGAGAACTAGACGTGGAGAAAAAAAAATTAAATATTAGCAAGATGAGCAAAATAATTATTAA
TCGGATCTTAAAAGATGAGCTTGCAGAATAGCCAAAATAAAAGTTACCCTATATTCCAATCCAA
ACAATTTGTCCCCATTTAGTTCAGCCTCCACTGCAAATTTGAAACTATGAAACATATCCATTTC
ATAGACTACCTTCAAAGCATCATTGAAATTCATCTGAAATGTTCATATAAAGGAAACAAACAAT
AATATATAACCAGCTGATAGACACCCATTAGTGATTTATTTATAAATAACAATGGATTAAACTA
GGATGCTAACCTTTTGCTTAGCAACTAGCTTCCAAATCTCATGTAAGAAATAAGGCCATTCCTT
AAGGCGACTAATTTCACGCAGGTCCCATACATACTCCTGAATTGAAAGGATATAATTGTTAAAA
CCAGCCATGAAAACCAAAACTAAATAGAACAGAAAAATTCTTACCATGTATGCAAATTGGGCTA
AACCAACAGTCATATGGCAAAAGTTTGTTGCAATCTTTAACGCTTGGAAAAACGTAGTGTTGTC
CATTTTTGACCACTAAAGAGCAAAGTTAATCATCCTGATATGCACTATGTATGGACAAATACAC
CTATAAATCATAATTTTCTATAGGCCAGCTTTATATTAGTACCTCCTGAGAAGACCGATCCAAA
TCTACATAGTCTCCAATCCACTGTCCAAGGATAAAAGATTATTAGCACAAAAACAAATCCATGT
TACTGGCTAAGTTTACCAACTATTAATAACTTGATCACATGGTTGATACCTTGATTTTCTTTGG
TAGTTCTTCACAATATTTGACATAATCCTCATCAACTTCATATGTATTAAAACATGAGTGGTAG
TCATCCCTGGCAAGGAATTCAGTGCTATCATC
						
					

			
		

Sequences
Splice junction sequence	TTGGTAGTTCTTCACAATATTTGACATAATCCTCATCAACTTCATATGTATTAAAACATGAGTG GTAGTCATCCCTGGCAAGGAATTCAGTGCTATCATCcagctagaccaaaccaatctttttcgcc atatccatcttcttcgccgcatacccacacatggtctgagtgtgatgaaactgaaaacaaaatc aattagaa
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: 615 Transcript exons: 42396003-42396080,42396157-42396207,42396298-42396330,42 396434-42396547,42396653-42396742,42396815-42396910,4239 7005-42397046,42397140-42397250 CAGCTAGACCAAACCAATCTTTTTCGCCATATCCATCTTCTTCGCCGCATACCCACACATGGTC TGAGTGTGATGAAATTCTCTGTAAACTGCCTTTGTAATCAAATCTAGAGCTTTACCCTCTTCAA CATCACCAGAAATATCCTTAGAGCACATAGAGAACCTATATTCCAATCCAAACAATTTGTCCCC ATTTAGTTCAGCCTCCACTGCAAATTTGAAACTATGAAACATATCCATTTCATAGACTACCTTC AAAGCATCATTGAAATTCATCTTTTGCTTAGCAACTAGCTTCCAAATCTCATGTAAGAAATAAG GCCATTCCTTAAGGCGACTAATTTCACGCAGGTCCCATACATACTCCATGTATGCAAATTGGGC TAAACCAACAGTCATATGGCAAAAGTTTGTTGCAATCTTTAACGCTTGGAAAAACGTAGTGTTG TCCATTTTTGACCACTCCTGAGAAGACCGATCCAAATCTACATAGTCTCCAATCCACTTGATTT TCTTTGGTAGTTCTTCACAATATTTGACATAATCCTCATCAACTTCATATGTATTAAAACATGA GTGGTAGTCATCCCTGGCAAGGAATTCAGTGCTATCATC
Genomic sequence	CAGCTAGACCAAACCAATCTTTTTCGCCATATCCATCTTCTTCGCCGCATACCCACACATGGTC TGAGTGTGATGAAACTGAAAACAAAATCAATTAGAACTGTGCAGGGTGTAGAATAAGAAACATT TTTAGCTTAAGTGTTTCACTGATTACTTCTCTGTAAACTGCCTTTGTAATCAAATCTAGAGCTT TACCCTCTTCAACCTAAAATAACAATATATTATATTATATGACATTATCGTCATAAAAAATGTA TTTCAACTACACATATATGCTATACGACATTGTACTTACATCACCAGAAATATCCTTAGAGCAC ATAGAGAACTAGACGTGGAGAAAAAAAAATTAAATATTAGCAAGATGAGCAAAATAATTATTAA TCGGATCTTAAAAGATGAGCTTGCAGAATAGCCAAAATAAAAGTTACCCTATATTCCAATCCAA ACAATTTGTCCCCATTTAGTTCAGCCTCCACTGCAAATTTGAAACTATGAAACATATCCATTTC ATAGACTACCTTCAAAGCATCATTGAAATTCATCTGAAATGTTCATATAAAGGAAACAAACAAT AATATATAACCAGCTGATAGACACCCATTAGTGATTTATTTATAAATAACAATGGATTAAACTA GGATGCTAACCTTTTGCTTAGCAACTAGCTTCCAAATCTCATGTAAGAAATAAGGCCATTCCTT AAGGCGACTAATTTCACGCAGGTCCCATACATACTCCTGAATTGAAAGGATATAATTGTTAAAA CCAGCCATGAAAACCAAAACTAAATAGAACAGAAAAATTCTTACCATGTATGCAAATTGGGCTA AACCAACAGTCATATGGCAAAAGTTTGTTGCAATCTTTAACGCTTGGAAAAACGTAGTGTTGTC CATTTTTGACCACTAAAGAGCAAAGTTAATCATCCTGATATGCACTATGTATGGACAAATACAC CTATAAATCATAATTTTCTATAGGCCAGCTTTATATTAGTACCTCCTGAGAAGACCGATCCAAA TCTACATAGTCTCCAATCCACTGTCCAAGGATAAAAGATTATTAGCACAAAAACAAATCCATGT TACTGGCTAAGTTTACCAACTATTAATAACTTGATCACATGGTTGATACCTTGATTTTCTTTGG TAGTTCTTCACAATATTTGACATAATCCTCATCAACTTCATATGTATTAAAACATGAGTGGTAG TCATCCCTGGCAAGGAATTCAGTGCTATCATC

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_011235 						
					
						PMCS
						0.310245755

Conservation Information
Conserved circRNAs	osi_circ_011235
PMCS	0.310245755

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							42397209-42396176(+)
42396054-42397030(-)
						
						Potential amino acid sequence
						
							MSGSHPWQGIQCYHPARPNQSFSPYPSSSPHTHTWSECDEILCKLPL*(+)
MRRRRWIWRKRLVWSSWMIALNSLPGMTTTHVLIHMKLMRIMSNIVKNYQRKSSGLETM*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	42397209-42396176(+) 42396054-42397030(-)
Potential amino acid sequence	MSGSHPWQGIQCYHPARPNQSFSPYPSSSPHTHTWSECDEILCKLPL(+) MRRRRWIWRKRLVWSSWMIALNSLPGMTTTHVLIHMKLMRIMSNIVKNYQRKSSGLETM(-)
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 Os01g0961600_circ_g.1

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