Plant Circular RNA Database

Detail information of Os04g0611600_circ_g.2

			
						 General Information
					
						CircRNA Name
						Os04g0611600_circ_g.2
					
						ID in PlantcircBase
						osa_circ_025196
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr4: 31009206-31010593  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ie-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os04g0611600						
					
						Parent gene annotation
						
							Hypothetical protein. (Os04t0611600-00)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os04g0611600_circ_g.1 						
					
						Support reads
						1
					
						Tissues
						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
						Os04t0611500-01:3
Os04t0611600-00:3
Os04t0611500-01:3

General Information
CircRNA Name	Os04g0611600_circ_g.2
ID in PlantcircBase	osa_circ_025196
Alias	NA
Organism	Oryza sativa
Position	chr4: 31009206-31010593 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ie-circRNA
Identification method	CIRCexplorer
Parent gene	Os04g0611600
Parent gene annotation	Hypothetical protein. (Os04t0611600-00)
Parent gene strand	+
Alternative splicing	Os04g0611600_circ_g.1
Support reads	1
Tissues	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	Os04t0611500-01:3 Os04t0611600-00:3 Os04t0611500-01:3

			
						 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  
						
							GTGTCTCACCAAGAGCAATACGAACAGCAAGGTCATCTGCTTCTCTATCAAGTAATTCACTTTT
ACTGATTCCATTCTTCCTTGCTATGTTTTCAGCAACctccaccctgtcaggatcaatctcttca
gcactcactccttccacagtttgctctacaattgctttagtaacaatcctgtcaccaacaacat
ccttctca

									
								

					

						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: 561
Transcript exons: 31009206-31009377,31010007-31010071,31010270-31010593
CTCCACCCTGTCAGGATCAATCTCTTCAGCACTCACTCCTTCCACAGTTTGCTCTACAATTGCT
TTAGTAACAATCCTGTCACCAACAACATCCTTCTCATCATCTTCCACAGGTGCTGAGGTGGGAG
ATAAAATATTTTCAGGTGCCCACTCCAAATACAGTGGAGTATCCTTGTATCTTGTGTACAGTAA
CTTTTTGAAAGCATGCCGAGCTTCTGTCGCTTCAACAAAAACTACCAAGGCAAACACTCTGGTT
GGAGGGAGGATGATTTTATCCAGGCTTCCATGTTTGCGAAACATTGTGGCAAGATCTTCCTCAC
AAGAACTATATGGCAAGTTCTTTACCAATATCACATGGTTGCTTCTTTTAAACTTCTCATTTCT
TTTGGAAGCAAGCTCTTCCAGTGCAGCAACATTAACTCCAGACCTTGATAAATATTTCTTGGTC
TCTGCAATGACATGTGTCTCACCAAGAGCAATACGAACAGCAAGGTCATCTGCTTCTCTATCAA
GTAATTCACTTTTACTGATTCCATTCTTCCTTGCTATGTTTTCAGCAAC
						
					

						Genomic sequence
						
							CTCCACCCTGTCAGGATCAATCTCTTCAGCACTCACTCCTTCCACAGTTTGCTCTACAATTGCT
TTAGTAACAATCCTGTCACCAACAACATCCTTCTCATCATCTTCCACAGGTGCTGAGGTGGGAG
ATAAAATATTTTCAGGTGCCCACTCCAAATACAGTGGAGTATCCCTGCAGTAAATAGTAACACC
AACTTAGGAAATATACATGTGCAGATTTCACAATCACACTAATAGCTAGAATTATATAACATTC
ACAAAAAGTCAGAATAATAAAACATAAAAAAAATAAACCATAAGGATGACAGGGTATAATTCCA
TAGAGAGCATATCGATCTATAACTAGAAAGCATTACAACACCCTTAGATCAAATAGACTAAAAT
ACAAGCATCAAGTATGAATATGCGTCTCTCATGCTACTAAAATACAAGTATCAGATATGAATAT
GCATCTCTCTCTCTTGCGACATGCATGCCAGTGCAAATAGGATCTAGCTGTATCAACGTCGATA
ATGGGTTTTTTCTTTCAGTTCCTAGGCAAACTTTAACTTAGATTACCAGGCACATGCATATGAA
AAGTCGATTAAGAATGGAGAAAACAAACTAAAGAAAACCCCTCATTCTTGAAGTAAATATCGAT
GGCTGCCTAATTTATTTAAAGAAAATATGTTAACTATCATGCATTATTCTATCTTAACAGAAAA
TTTACTACATTGATTTATCCTAAAAGCTCAATAAAACTGTATTCAAACTAGTCATTAAGAGTAT
TAGATGTGGACTAGCACTATTGCAGATACTTACTTGTATCTTGTGTACAGTAACTTTTTGAAAG
CATGCCGAGCTTCTGTCGCTTCAACAAAAACTACCTGACATACAAACTCAAGGGGTGAAATTAT
TCGCAATACAGGTAATAATGTTCACTTGGTAATTTGTAGAGCAAAAGAAATACAAAAGTGAAAC
ATTCCAGACAGTAATGTAGGACACTCAAACACTCAAAAGTGTCATGATATAATGACCAATGACC
AATGAACAATTGAACAAAATAAGCAGAAATAGTTACATACCAAGGCAAACACTCTGGTTGGAGG
GAGGATGATTTTATCCAGGCTTCCATGTTTGCGAAACATTGTGGCAAGATCTTCCTCACAAGAA
CTATATGGCAAGTTCTTTACCAATATCACATGGTTGCTTCTTTTAAACTTCTCATTTCTTTTGG
AAGCAAGCTCTTCCAGTGCAGCAACATTAACTCCAGACCTTGATAAATATTTCTTGGTCTCTGC
AATGACATGTGTCTCACCAAGAGCAATACGAACAGCAAGGTCATCTGCTTCTCTATCAAGTAAT
TCACTTTTACTGATTCCATTCTTCCTTGCTATGTTTTCAGCAAC
						
					

			
		

Sequences
Splice junction sequence	GTGTCTCACCAAGAGCAATACGAACAGCAAGGTCATCTGCTTCTCTATCAAGTAATTCACTTTT ACTGATTCCATTCTTCCTTGCTATGTTTTCAGCAACctccaccctgtcaggatcaatctcttca gcactcactccttccacagtttgctctacaattgctttagtaacaatcctgtcaccaacaacat ccttctca
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: 561 Transcript exons: 31009206-31009377,31010007-31010071,31010270-31010593 CTCCACCCTGTCAGGATCAATCTCTTCAGCACTCACTCCTTCCACAGTTTGCTCTACAATTGCT TTAGTAACAATCCTGTCACCAACAACATCCTTCTCATCATCTTCCACAGGTGCTGAGGTGGGAG ATAAAATATTTTCAGGTGCCCACTCCAAATACAGTGGAGTATCCTTGTATCTTGTGTACAGTAA CTTTTTGAAAGCATGCCGAGCTTCTGTCGCTTCAACAAAAACTACCAAGGCAAACACTCTGGTT GGAGGGAGGATGATTTTATCCAGGCTTCCATGTTTGCGAAACATTGTGGCAAGATCTTCCTCAC AAGAACTATATGGCAAGTTCTTTACCAATATCACATGGTTGCTTCTTTTAAACTTCTCATTTCT TTTGGAAGCAAGCTCTTCCAGTGCAGCAACATTAACTCCAGACCTTGATAAATATTTCTTGGTC TCTGCAATGACATGTGTCTCACCAAGAGCAATACGAACAGCAAGGTCATCTGCTTCTCTATCAA GTAATTCACTTTTACTGATTCCATTCTTCCTTGCTATGTTTTCAGCAAC
Genomic sequence	CTCCACCCTGTCAGGATCAATCTCTTCAGCACTCACTCCTTCCACAGTTTGCTCTACAATTGCT TTAGTAACAATCCTGTCACCAACAACATCCTTCTCATCATCTTCCACAGGTGCTGAGGTGGGAG ATAAAATATTTTCAGGTGCCCACTCCAAATACAGTGGAGTATCCCTGCAGTAAATAGTAACACC AACTTAGGAAATATACATGTGCAGATTTCACAATCACACTAATAGCTAGAATTATATAACATTC ACAAAAAGTCAGAATAATAAAACATAAAAAAAATAAACCATAAGGATGACAGGGTATAATTCCA TAGAGAGCATATCGATCTATAACTAGAAAGCATTACAACACCCTTAGATCAAATAGACTAAAAT ACAAGCATCAAGTATGAATATGCGTCTCTCATGCTACTAAAATACAAGTATCAGATATGAATAT GCATCTCTCTCTCTTGCGACATGCATGCCAGTGCAAATAGGATCTAGCTGTATCAACGTCGATA ATGGGTTTTTTCTTTCAGTTCCTAGGCAAACTTTAACTTAGATTACCAGGCACATGCATATGAA AAGTCGATTAAGAATGGAGAAAACAAACTAAAGAAAACCCCTCATTCTTGAAGTAAATATCGAT GGCTGCCTAATTTATTTAAAGAAAATATGTTAACTATCATGCATTATTCTATCTTAACAGAAAA TTTACTACATTGATTTATCCTAAAAGCTCAATAAAACTGTATTCAAACTAGTCATTAAGAGTAT TAGATGTGGACTAGCACTATTGCAGATACTTACTTGTATCTTGTGTACAGTAACTTTTTGAAAG CATGCCGAGCTTCTGTCGCTTCAACAAAAACTACCTGACATACAAACTCAAGGGGTGAAATTAT TCGCAATACAGGTAATAATGTTCACTTGGTAATTTGTAGAGCAAAAGAAATACAAAAGTGAAAC ATTCCAGACAGTAATGTAGGACACTCAAACACTCAAAAGTGTCATGATATAATGACCAATGACC AATGAACAATTGAACAAAATAAGCAGAAATAGTTACATACCAAGGCAAACACTCTGGTTGGAGG GAGGATGATTTTATCCAGGCTTCCATGTTTGCGAAACATTGTGGCAAGATCTTCCTCACAAGAA CTATATGGCAAGTTCTTTACCAATATCACATGGTTGCTTCTTTTAAACTTCTCATTTCTTTTGG AAGCAAGCTCTTCCAGTGCAGCAACATTAACTCCAGACCTTGATAAATATTTCTTGGTCTCTGC AATGACATGTGTCTCACCAAGAGCAATACGAACAGCAAGGTCATCTGCTTCTCTATCAAGTAAT TCACTTTTACTGATTCCATTCTTCCTTGCTATGTTTTCAGCAAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.252142921

Conservation Information
Conserved circRNAs	NA
PMCS	0.252142921

			
				
						 Functional Information
					

				
						Coding potential
						Y
					

						Potential coding position
						
							31010299-31010590(+)
31010334-31009208(-)
						
					

						Potential amino acid sequence
						
							MILSRLPCLRNIVARSSSQELYGKFFTNITWLLLLNFSFLLEASSSSAATLTPDLDKYFLVSAM
TCVSPRAIRTARSSASLSSNSLLLIPFFLAMFSATSTLSGSISSALTPSTVCSTIALVTILSPT
TSFSSSSTGAEVGDKIFSGAHSKYSGVSLYLVYSNFLKACRASVASTKTTKANTLVGGRMILSR
LPCLRNIVARSSSQELYGKFFTNITWLLLLNFSFLLEASSSSAATLTPDLDKYFLVSAMTCVSP
RAIRTARSSASLSSNSLLLIPFFLAMFSATSTLSGSISSALTPSTVCSTIALVTILSPTTSFSS
SSTGAEVGDKIFSGAHSKYSGVSLYLVYSNFLKACRASVASTKTTKANTLVGGRMILSRLPCLR
NIVARSSSQELYGKFFTNITWLLLLNFSFLLEASSSSAATLTPDLDKYFLVSAMTCVSPRAIRT
ARSSASLSSNSLLLIPFFLAMFSATSTLSGSISSALTPSTVCSTIALVTILSPTTSFSSSSTGA
EVGDKIFSGAHSKYSGVSLYLVYSNFLKACRASVASTKTTKANTLVGGRMILSRLPCLRNIVAR
SSSQELYGKFFTNITWLLLLNFSFLLEASSSSAATLTPDLDKYFLVSAMTCVSPRAIRTARSSA
SLSSNSLLLIPFFLAMFSA(+)
MFRKHGSLDKIILPPTRVFALVVFVEATEARHAFKKLLYTRYKDTPLYLEWAPENILSPTSAPV
EDDEKDVVGDRIVTKAIVEQTVEGVSAEEIDPDRVEVAENIARKNGISKSELLDREADDLAVRI
ALGETHVIAETKKYLSRSGVNVAALEELASKRNEKFKRSNHVILVKNLPYSSCEEDLATMFRKH
GSLDKIILPPTRVFALVVFVEATEARHAFKKLLYTRYKDTPLYLEWAPENILSPTSAPVEDDEK
DVVGDRIVTKAIVEQTVEGVSAEEIDPDRVEVAENIARKNGISKSELLDREADDLAVRIALGET
HVIAETKKYLSRSGVNVAALEELASKRNEKFKRSNHVILVKNLPYSSCEEDLATMFRKHGSLDK
IILPPTRVFALVVFVEATEARHAFKKLLYTRYKDTPLYLEWAPENILSPTSAPVEDDEKDVVGD
RIVTKAIVEQTVEGVSAEEIDPDRVEVAENIARKNGISKSELLDREADDLAVRIALGETHVIAE
TKKYLSRSGVNVAALEELASKRNEKFKRSNHVILVKNLPYSSCEEDLATMFRKHGSLDKIILPP
TRVFALVVFVEATEARHAFKKLLYTRYKDTPLYLEWAPENILSPTSAPVEDDEKDVVGDRIVTK
AIVEQTVEGVSAEEIDPDRVE(-)
						
					

						Sponge-miRNAs
						
							NA						
					

						circRNA-miRNA-mRNA network
						 VISUALIZATION
					

						Potential function description
						NA
					

			
		

Functional Information
Coding potential	Y
Potential coding position	31010299-31010590(+) 31010334-31009208(-)
Potential amino acid sequence	MILSRLPCLRNIVARSSSQELYGKFFTNITWLLLLNFSFLLEASSSSAATLTPDLDKYFLVSAM TCVSPRAIRTARSSASLSSNSLLLIPFFLAMFSATSTLSGSISSALTPSTVCSTIALVTILSPT TSFSSSSTGAEVGDKIFSGAHSKYSGVSLYLVYSNFLKACRASVASTKTTKANTLVGGRMILSR LPCLRNIVARSSSQELYGKFFTNITWLLLLNFSFLLEASSSSAATLTPDLDKYFLVSAMTCVSP RAIRTARSSASLSSNSLLLIPFFLAMFSATSTLSGSISSALTPSTVCSTIALVTILSPTTSFSS SSTGAEVGDKIFSGAHSKYSGVSLYLVYSNFLKACRASVASTKTTKANTLVGGRMILSRLPCLR NIVARSSSQELYGKFFTNITWLLLLNFSFLLEASSSSAATLTPDLDKYFLVSAMTCVSPRAIRT ARSSASLSSNSLLLIPFFLAMFSATSTLSGSISSALTPSTVCSTIALVTILSPTTSFSSSSTGA EVGDKIFSGAHSKYSGVSLYLVYSNFLKACRASVASTKTTKANTLVGGRMILSRLPCLRNIVAR SSSQELYGKFFTNITWLLLLNFSFLLEASSSSAATLTPDLDKYFLVSAMTCVSPRAIRTARSSA SLSSNSLLLIPFFLAMFSA(+) MFRKHGSLDKIILPPTRVFALVVFVEATEARHAFKKLLYTRYKDTPLYLEWAPENILSPTSAPV EDDEKDVVGDRIVTKAIVEQTVEGVSAEEIDPDRVEVAENIARKNGISKSELLDREADDLAVRI ALGETHVIAETKKYLSRSGVNVAALEELASKRNEKFKRSNHVILVKNLPYSSCEEDLATMFRKH GSLDKIILPPTRVFALVVFVEATEARHAFKKLLYTRYKDTPLYLEWAPENILSPTSAPVEDDEK DVVGDRIVTKAIVEQTVEGVSAEEIDPDRVEVAENIARKNGISKSELLDREADDLAVRIALGET HVIAETKKYLSRSGVNVAALEELASKRNEKFKRSNHVILVKNLPYSSCEEDLATMFRKHGSLDK IILPPTRVFALVVFVEATEARHAFKKLLYTRYKDTPLYLEWAPENILSPTSAPVEDDEKDVVGD RIVTKAIVEQTVEGVSAEEIDPDRVEVAENIARKNGISKSELLDREADDLAVRIALGETHVIAE TKKYLSRSGVNVAALEELASKRNEKFKRSNHVILVKNLPYSSCEEDLATMFRKHGSLDKIILPP TRVFALVVFVEATEARHAFKKLLYTRYKDTPLYLEWAPENILSPTSAPVEDDEKDVVGDRIVTK AIVEQTVEGVSAEEIDPDRVE(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os04g0611600_circ_g.2

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