Plant Circular RNA Database

Detail information of Os06g0538000_circ_g.2

			
						 General Information
					
						CircRNA Name
						Os06g0538000_circ_g.2
					
						ID in PlantcircBase
						osa_circ_031084
					
						Alias
						Os_ciR5508
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr6: 20161112-20163213  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Os06g0538000						
					
						Parent gene annotation
						
							Similar to T-complex protein 1, gamma subunit (TCP-1-gamma) (CCT
-gamma) (Matricin) (mTRiC-P5). (Os06t0538000-01)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os06g0538000_circ_g.1 Os06g0538000_circ_g.3 						
					
						Support reads
						3
					
						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  
						
							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
						Os06t0538000-01:8

General Information
CircRNA Name	Os06g0538000_circ_g.2
ID in PlantcircBase	osa_circ_031084
Alias	Os_ciR5508
Organism	Oryza sativa
Position	chr6: 20161112-20163213 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	find_circ
Parent gene	Os06g0538000
Parent gene annotation	Similar to T-complex protein 1, gamma subunit (TCP-1-gamma) (CCT -gamma) (Matricin) (mTRiC-P5). (Os06t0538000-01)
Parent gene strand	+
Alternative splicing	Os06g0538000_circ_g.1 Os06g0538000_circ_g.3
Support reads	3
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	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	Os06t0538000-01:8

			
						 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  
						
							TTTGAAAAACCCAAAACTTTTACCTGGAGGTGGTGCTACCGAGCTGACTGTATCAGCAGCACTG
AAGCAAAAGAGTTCTTCAGTTGAAGGTGTAGAAAAGgtattgtggttactaatgatggcaatgc
tatattgcgagaaatagatattgcacatcctgctgccaaggtatgtggaacgttagatgttttc
tctctgtt

									
								

					

						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: 1142
Transcript exons: 20161112-20161179,20161316-20161385,20161728-20161796,20
161885-20161956,20162067-20162140,20162240-20162517,2016
2624-20163008,20163088-20163213
GTATTGTGGTTACTAATGATGGCAATGCTATATTGCGAGAAATAGATATTGCACATCCTGCTGC
CAAGTCTATGATTGAGCTAAGCCGTACACAGGATGAAGAAGTTGGTGATGGCACAACATCTGTC
ATTGTTTTAGCTGGTGAGATGCTCCATGTTGCAGAAGCATTCATTGATAAGCACTACCACCCAA
CTGTTATTTGCCGAGCATACACCAAAGCTCTTGAGGATGCTTTAGCTGTCCTTGACAAAATTGC
AATGCATGTTGACGTGAATGACCGTGCTGCTATGCTAGGGCTAGTGAAGAGCTCTATTGGTACA
AAATTCACGGGTCAGTTTGGTGACCTTATTGCTGACCTTGCTATTGATGCTACTACAACAGCAG
GTGTTGACCTAGGTCAAGGTATGCGTGAAGTTGATATCAAGAAATATATCAAAGTGGAGAAGGT
TCCTGGTGGTCAGTTAGAGGATTCACGGGTTCTTAAAGGAGTTATGTTCAATAAAGATGTTGTA
GCTCCTGGAAAAATGAGAAGGAAGATAGTCAACCCCCGCATTATCCTTCTGGATTGCCCTGTTG
AGTACAAGAAAGGAGAAAACCAGACCAATGCTGAACTGATGAAGGAAGAAGATTGGCAGGTTCT
GCTAGAGATGGAGGAAGAATACATAAAGAACCTCTGTGCGCAGATTTTAAAATTCAAGCCTGAT
TTAGTTGTCACAGAGAAAGGTCTCAGTGATCTTGCTATCCATTACCTAAGCAAGGCTGGTGTTA
GTGCAATTCGTAGGCTAAGGAAGACTGATAACAACAGGATTGCTAAGGCTTGTGGAGCAGTCAT
AGTGAACAGGCCAGAGGAGCTTCAAGAATCGGATGTTGGAACAAGAGCTGGCCTCTTTGAGGTC
AAGAAGATAGGTGATGAATTCTTTACCTTCATTGTCGACTGCAAAGATCCCAAGGCATGCACTG
TTCTTTTGAGGGGAGCAAGCAAGGATGTCCTGAATGAGGTTGAGAGGAACCTTCAGGATGCCAT
GTCTGTTGCAAGGAACATTTTGAAAAACCCAAAACTTTTACCTGGAGGTGGTGCTACCGAGCTG
ACTGTATCAGCAGCACTGAAGCAAAAGAGTTCTTCAGTTGAAGGTGTAGAAAAG
						
					

						Genomic sequence
						
							GTATTGTGGTTACTAATGATGGCAATGCTATATTGCGAGAAATAGATATTGCACATCCTGCTGC
CAAGGTATGTGGAACGTTAGATGTTTTCTCTCTGTTGAGTACTACTGATGAAATTATTAGTCTG
ATGTGTTAAATTGCCAATATTTTCTGCTAATGTATGAATTAGTACTTAATCTAACTTTCTTGTC
ACTCTTTGGCAGTCTATGATTGAGCTAAGCCGTACACAGGATGAAGAAGTTGGTGATGGCACAA
CATCTGTCATTGTTTTAGGTATGTGTTCCCTGATTCATTCAGTTTCATTCAGTTTTATTTAAAT
GTCATATGAGATCGCAACACTAGGATATCGTGACATCTCTTTCTGGTCGAACTAAAACACTTGG
CTATTACTATGAGCTGCAAAGTCATCAATAAACGTCTGTGGCAACTGTCAAGGAAAGTTAGCAA
ACCCCACTGCAAATTTTAAGCTAACTCTGCATGATTAAGTAAGATTATTTTGGTGTGTTAGGGG
TAGAATAGCAATAACTTGTAGGTGCTCCATCAGATCAATGTGAGCAACTTTGTTGGATTTTATC
ATTTTCTTCTGATGCACTAACTTTAATTATTATTTTTTAGCTGGTGAGATGCTCCATGTTGCAG
AAGCATTCATTGATAAGCACTACCACCCAACTGTTATTTGCCGAGGTATTGCTTGATCATTGTA
TCAGATGGTGTTATTTCCTTTGTTGATTTTTTAGTCTGTTCTGAAACATTTAGTGTCTCTCATT
TTCAGCATACACCAAAGCTCTTGAGGATGCTTTAGCTGTCCTTGACAAAATTGCAATGCATGTT
GACGTGAATGACCGTAAGTATATGTCAAGCTTATTACAAATATTGCAAATTTTAGTTTGGAGAA
TCTATGTATCGTCTTCTGTGTTTTTGTTACTGATTTGAGTGAGATGTACCATAATGCAGGTGCT
GCTATGCTAGGGCTAGTGAAGAGCTCTATTGGTACAAAATTCACGGGTCAGTTTGGTGACCTTA
TTGCTGTAAGTATTTCTTTTATTCAAGATTTGAGTGCCACACAACTTCTCGGTTAAGTGTGTTC
AGTTTATAGTTTATCTGACGTCTTGTTGTACTATGCTCAGGACCTTGCTATTGATGCTACTACA
ACAGCAGGTGTTGACCTAGGTCAAGGTATGCGTGAAGTTGATATCAAGAAATATATCAAAGTGG
AGAAGGTTCCTGGTGGTCAGTTAGAGGATTCACGGGTTCTTAAAGGAGTTATGTTCAATAAAGA
TGTTGTAGCTCCTGGAAAAATGAGAAGGAAGATAGTCAACCCCCGCATTATCCTTCTGGATTGC
CCTGTTGAGTACAAGAAAGGAGAAAACCAGACCAATGCTGAACTGATGAAGGAAGAAGATTGGT
AAGGGATGGATAAATTCAAATGTTTTGCCAATTTGAATTGTTGAACTATTGTGGTGCTATTGAA
GCAATGTAGCATGGAATAATTTGTAAATATGCTATTTCAGGCAGGTTCTGCTAGAGATGGAGGA
AGAATACATAAAGAACCTCTGTGCGCAGATTTTAAAATTCAAGCCTGATTTAGTTGTCACAGAG
AAAGGTCTCAGTGATCTTGCTATCCATTACCTAAGCAAGGCTGGTGTTAGTGCAATTCGTAGGC
TAAGGAAGACTGATAACAACAGGATTGCTAAGGCTTGTGGAGCAGTCATAGTGAACAGGCCAGA
GGAGCTTCAAGAATCGGATGTTGGAACAAGAGCTGGCCTCTTTGAGGTCAAGAAGATAGGTGAT
GAATTCTTTACCTTCATTGTCGACTGCAAAGATCCCAAGGCATGCACTGTTCTTTTGAGGGGAG
CAAGCAAGGATGTCCTGAATGAGGTTGAGAGGAACCTTCAGGTATTTGTTAATGTTCCTGTGGT
ACCTGTAATTTTGCATGCCATGTTCACCAATAACCATTTCTTATTCTTTTTGACAGGATGCCAT
GTCTGTTGCAAGGAACATTTTGAAAAACCCAAAACTTTTACCTGGAGGTGGTGCTACCGAGCTG
ACTGTATCAGCAGCACTGAAGCAAAAGAGTTCTTCAGTTGAAGGTGTAGAAAAG
						
					

			
		

Sequences
Splice junction sequence	TTTGAAAAACCCAAAACTTTTACCTGGAGGTGGTGCTACCGAGCTGACTGTATCAGCAGCACTG AAGCAAAAGAGTTCTTCAGTTGAAGGTGTAGAAAAGgtattgtggttactaatgatggcaatgc tatattgcgagaaatagatattgcacatcctgctgccaaggtatgtggaacgttagatgttttc tctctgtt
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: 1142 Transcript exons: 20161112-20161179,20161316-20161385,20161728-20161796,20 161885-20161956,20162067-20162140,20162240-20162517,2016 2624-20163008,20163088-20163213 GTATTGTGGTTACTAATGATGGCAATGCTATATTGCGAGAAATAGATATTGCACATCCTGCTGC CAAGTCTATGATTGAGCTAAGCCGTACACAGGATGAAGAAGTTGGTGATGGCACAACATCTGTC ATTGTTTTAGCTGGTGAGATGCTCCATGTTGCAGAAGCATTCATTGATAAGCACTACCACCCAA CTGTTATTTGCCGAGCATACACCAAAGCTCTTGAGGATGCTTTAGCTGTCCTTGACAAAATTGC AATGCATGTTGACGTGAATGACCGTGCTGCTATGCTAGGGCTAGTGAAGAGCTCTATTGGTACA AAATTCACGGGTCAGTTTGGTGACCTTATTGCTGACCTTGCTATTGATGCTACTACAACAGCAG GTGTTGACCTAGGTCAAGGTATGCGTGAAGTTGATATCAAGAAATATATCAAAGTGGAGAAGGT TCCTGGTGGTCAGTTAGAGGATTCACGGGTTCTTAAAGGAGTTATGTTCAATAAAGATGTTGTA GCTCCTGGAAAAATGAGAAGGAAGATAGTCAACCCCCGCATTATCCTTCTGGATTGCCCTGTTG AGTACAAGAAAGGAGAAAACCAGACCAATGCTGAACTGATGAAGGAAGAAGATTGGCAGGTTCT GCTAGAGATGGAGGAAGAATACATAAAGAACCTCTGTGCGCAGATTTTAAAATTCAAGCCTGAT TTAGTTGTCACAGAGAAAGGTCTCAGTGATCTTGCTATCCATTACCTAAGCAAGGCTGGTGTTA GTGCAATTCGTAGGCTAAGGAAGACTGATAACAACAGGATTGCTAAGGCTTGTGGAGCAGTCAT AGTGAACAGGCCAGAGGAGCTTCAAGAATCGGATGTTGGAACAAGAGCTGGCCTCTTTGAGGTC AAGAAGATAGGTGATGAATTCTTTACCTTCATTGTCGACTGCAAAGATCCCAAGGCATGCACTG TTCTTTTGAGGGGAGCAAGCAAGGATGTCCTGAATGAGGTTGAGAGGAACCTTCAGGATGCCAT GTCTGTTGCAAGGAACATTTTGAAAAACCCAAAACTTTTACCTGGAGGTGGTGCTACCGAGCTG ACTGTATCAGCAGCACTGAAGCAAAAGAGTTCTTCAGTTGAAGGTGTAGAAAAG
Genomic sequence	GTATTGTGGTTACTAATGATGGCAATGCTATATTGCGAGAAATAGATATTGCACATCCTGCTGC CAAGGTATGTGGAACGTTAGATGTTTTCTCTCTGTTGAGTACTACTGATGAAATTATTAGTCTG ATGTGTTAAATTGCCAATATTTTCTGCTAATGTATGAATTAGTACTTAATCTAACTTTCTTGTC ACTCTTTGGCAGTCTATGATTGAGCTAAGCCGTACACAGGATGAAGAAGTTGGTGATGGCACAA CATCTGTCATTGTTTTAGGTATGTGTTCCCTGATTCATTCAGTTTCATTCAGTTTTATTTAAAT GTCATATGAGATCGCAACACTAGGATATCGTGACATCTCTTTCTGGTCGAACTAAAACACTTGG CTATTACTATGAGCTGCAAAGTCATCAATAAACGTCTGTGGCAACTGTCAAGGAAAGTTAGCAA ACCCCACTGCAAATTTTAAGCTAACTCTGCATGATTAAGTAAGATTATTTTGGTGTGTTAGGGG TAGAATAGCAATAACTTGTAGGTGCTCCATCAGATCAATGTGAGCAACTTTGTTGGATTTTATC ATTTTCTTCTGATGCACTAACTTTAATTATTATTTTTTAGCTGGTGAGATGCTCCATGTTGCAG AAGCATTCATTGATAAGCACTACCACCCAACTGTTATTTGCCGAGGTATTGCTTGATCATTGTA TCAGATGGTGTTATTTCCTTTGTTGATTTTTTAGTCTGTTCTGAAACATTTAGTGTCTCTCATT TTCAGCATACACCAAAGCTCTTGAGGATGCTTTAGCTGTCCTTGACAAAATTGCAATGCATGTT GACGTGAATGACCGTAAGTATATGTCAAGCTTATTACAAATATTGCAAATTTTAGTTTGGAGAA TCTATGTATCGTCTTCTGTGTTTTTGTTACTGATTTGAGTGAGATGTACCATAATGCAGGTGCT GCTATGCTAGGGCTAGTGAAGAGCTCTATTGGTACAAAATTCACGGGTCAGTTTGGTGACCTTA TTGCTGTAAGTATTTCTTTTATTCAAGATTTGAGTGCCACACAACTTCTCGGTTAAGTGTGTTC AGTTTATAGTTTATCTGACGTCTTGTTGTACTATGCTCAGGACCTTGCTATTGATGCTACTACA ACAGCAGGTGTTGACCTAGGTCAAGGTATGCGTGAAGTTGATATCAAGAAATATATCAAAGTGG AGAAGGTTCCTGGTGGTCAGTTAGAGGATTCACGGGTTCTTAAAGGAGTTATGTTCAATAAAGA TGTTGTAGCTCCTGGAAAAATGAGAAGGAAGATAGTCAACCCCCGCATTATCCTTCTGGATTGC CCTGTTGAGTACAAGAAAGGAGAAAACCAGACCAATGCTGAACTGATGAAGGAAGAAGATTGGT AAGGGATGGATAAATTCAAATGTTTTGCCAATTTGAATTGTTGAACTATTGTGGTGCTATTGAA GCAATGTAGCATGGAATAATTTGTAAATATGCTATTTCAGGCAGGTTCTGCTAGAGATGGAGGA AGAATACATAAAGAACCTCTGTGCGCAGATTTTAAAATTCAAGCCTGATTTAGTTGTCACAGAG AAAGGTCTCAGTGATCTTGCTATCCATTACCTAAGCAAGGCTGGTGTTAGTGCAATTCGTAGGC TAAGGAAGACTGATAACAACAGGATTGCTAAGGCTTGTGGAGCAGTCATAGTGAACAGGCCAGA GGAGCTTCAAGAATCGGATGTTGGAACAAGAGCTGGCCTCTTTGAGGTCAAGAAGATAGGTGAT GAATTCTTTACCTTCATTGTCGACTGCAAAGATCCCAAGGCATGCACTGTTCTTTTGAGGGGAG CAAGCAAGGATGTCCTGAATGAGGTTGAGAGGAACCTTCAGGTATTTGTTAATGTTCCTGTGGT ACCTGTAATTTTGCATGCCATGTTCACCAATAACCATTTCTTATTCTTTTTGACAGGATGCCAT GTCTGTTGCAAGGAACATTTTGAAAAACCCAAAACTTTTACCTGGAGGTGGTGCTACCGAGCTG ACTGTATCAGCAGCACTGAAGCAAAAGAGTTCTTCAGTTGAAGGTGTAGAAAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.337251915

Conservation Information
Conserved circRNAs	NA
PMCS	0.337251915

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							20161320-20161153(+)
20161169-20163007(-)
20161763-20163151(-)
						
						Potential amino acid sequence
						
							MIELSRTQDEEVGDGTTSVIVLAGEMLHVAEAFIDKHYHPTVICRAYTKALEDALAVLDKIAMH
VDVNDRAAMLGLVKSSIGTKFTGQFGDLIADLAIDATTTAGVDLGQGMREVDIKKYIKVEKVPG
GQLEDSRVLKGVMFNKDVVAPGKMRRKIVNPRIILLDCPVEYKKGENQTNAELMKEEDWQVLLE
MEEEYIKNLCAQILKFKPDLVVTEKGLSDLAIHYLSKAGVSAIRRLRKTDNNRIAKACGAVIVN
RPEELQESDVGTRAGLFEVKKIGDEFFTFIVDCKDPKACTVLLRGASKDVLNEVERNLQDAMSV
ARNILKNPKLLPGGGATELTVSAALKQKSSSVEGVEKVLWLLMMAMLYCEK*(+)
MCNIYFSQYSIAIISNHNTFSTPSTEELFCFSAADTVSSVAPPPGKSFGFFKMFLATDMAS*(-
)
MNASATWSISPAKTMTDVVPSPTSSSCVRLSSIIDLAAGCAISISRNIALPSLVTTIPFLHLQL
KNSFASVLLIQSAR*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	20161320-20161153(+) 20161169-20163007(-) 20161763-20163151(-)
Potential amino acid sequence	MIELSRTQDEEVGDGTTSVIVLAGEMLHVAEAFIDKHYHPTVICRAYTKALEDALAVLDKIAMH VDVNDRAAMLGLVKSSIGTKFTGQFGDLIADLAIDATTTAGVDLGQGMREVDIKKYIKVEKVPG GQLEDSRVLKGVMFNKDVVAPGKMRRKIVNPRIILLDCPVEYKKGENQTNAELMKEEDWQVLLE MEEEYIKNLCAQILKFKPDLVVTEKGLSDLAIHYLSKAGVSAIRRLRKTDNNRIAKACGAVIVN RPEELQESDVGTRAGLFEVKKIGDEFFTFIVDCKDPKACTVLLRGASKDVLNEVERNLQDAMSV ARNILKNPKLLPGGGATELTVSAALKQKSSSVEGVEKVLWLLMMAMLYCEK(+) MCNIYFSQYSIAIISNHNTFSTPSTEELFCFSAADTVSSVAPPPGKSFGFFKMFLATDMAS(- ) MNASATWSISPAKTMTDVVPSPTSSSCVRLSSIIDLAAGCAISISRNIALPSLVTTIPFLHLQL KNSFASVLLIQSAR*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ye et al., 2015

circRNA

Detail information of Os06g0538000_circ_g.2

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