Plant Circular RNA Database

Detail information of Os06g0656566_circ_g.1

			
						 General Information
					
						CircRNA Name
						Os06g0656566_circ_g.1
					
						ID in PlantcircBase
						osa_circ_031826
					
						Alias
						Os06circ15559/Os_ciR3108
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr6: 26948161-26948514  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, PcircRNA_finder, SMALT, Segemehl, circseq_cup, find_circ
					
						Parent gene
						
							Os06g0656500						
					
						Parent gene annotation
						
							4-coumarate:coenzyme A ligase, Lignin biosynthesis, Defense agai
nst wounding (Os06t0656500-01);Similar to cDNA clone:J023002B16,
 full insert sequence. (Os06t0656500-02)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os06g0656500_circ_g.1 Os06g0656500_circ_g.2 Os06g0656566_circ_g.2 						
					
						Support reads
						4/4/8/11
					
						Tissues
						leaf and panicle/root/root/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  
						
							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
						Os06t0656566-00:1
Os06t0656500-02:1
Os06t0656566-00:1
Os06t0656500-01:1

General Information
CircRNA Name	Os06g0656566_circ_g.1
ID in PlantcircBase	osa_circ_031826
Alias	Os06circ15559/Os_ciR3108
Organism	Oryza sativa
Position	chr6: 26948161-26948514 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, PcircRNA_finder, SMALT, Segemehl, circseq_cup, find_circ
Parent gene	Os06g0656500
Parent gene annotation	4-coumarate:coenzyme A ligase, Lignin biosynthesis, Defense agai nst wounding (Os06t0656500-01);Similar to cDNA clone:J023002B16, full insert sequence. (Os06t0656500-02)
Parent gene strand	-
Alternative splicing	Os06g0656500_circ_g.1 Os06g0656500_circ_g.2 Os06g0656566_circ_g.2
Support reads	4/4/8/11
Tissues	leaf and panicle/root/root/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	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	Os06t0656566-00:1 Os06t0656500-02:1 Os06t0656566-00:1 Os06t0656500-01:1

			
						 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  
						
							CCAGCAGCACGGAGTTGAGCGAGTAGATGTGGAACAGCGGCAGCAAGCACAGCACCACGTCCTC
CCTCCTGAAGTACAGGTTCGGGTTCTCCCCGTCCACctgtcccaggacggcgttggggatcttg
gccatgaaggcgtcctggaggtccttccccatgggggcggcgccggacataaccatgcggatgg
aggcgagg

						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: 275
Transcript exons: 26948161-26948308,26948388-26948514
CTGTCCCAGGACGGCGTTGGGGATCTTGGCCATGAAGGCGTCCTGGAGGTCCTTCCCCATGGGG
GCGGCGCCGGACATAACCATGCGGATGGAGGCGAGGTCGTCGGCGGTGACGCGGGGGCTCTTGG
CGATCTCCACCACGATGGGCCGATCGCCGACCCGGCTCGCAGCCCCGCCAGCAGCACGGAGTTG
AGCGAGTAGATGTGGAACAGCGGCAGCAAGCACAGCACCACGTCCTCCCTCCTGAAGTACAGGT
TCGGGTTCTCCCCGTCCAC
Transcript length: 354
Transcript exons: 26948161-26948514
CTGTCCCAGGACGGCGTTGGGGATCTTGGCCATGAAGGCGTCCTGGAGGTCCTTCCCCATGGGG
GCGGCGCCGGACATAACCATGCGGATGGAGGCGAGGTCGTCGGCGGTGACGCGGGGGCTCTTGG
CGATCTCCACCACGATGGGCGGCACGAACGGCGCGACGGTGACGCCGTGCCTCCGCGTCAGGTC
CACCAGCGCGCCCAGGTCGAACTTGCGCATGATCACGATCGCCGACCCGGCTCGCAGCCCCGCC
AGCAGCACGGAGTTGAGCGAGTAGATGTGGAACAGCGGCAGCAAGCACAGCACCACGTCCTCCC
TCCTGAAGTACAGGTTCGGGTTCTCCCCGTCCAC
						
						Genomic sequence
						
							CTGTCCCAGGACGGCGTTGGGGATCTTGGCCATGAAGGCGTCCTGGAGGTCCTTCCCCATGGGG
GCGGCGCCGGACATAACCATGCGGATGGAGGCGAGGTCGTCGGCGGTGACGCGGGGGCTCTTGG
CGATCTCCACCACGATGGGCGGCACGAACGGCGCGACGGTGACGCCGTGCCTCCGCGTCAGGTC
CACCAGCGCGCCCAGGTCGAACTTGCGCATGATCACGATCGCCGACCCGGCTCGCAGCCCCGCC
AGCAGCACGGAGTTGAGCGAGTAGATGTGGAACAGCGGCAGCAAGCACAGCACCACGTCCTCCC
TCCTGAAGTACAGGTTCGGGTTCTCCCCGTCCAC

Sequences
Splice junction sequence	CCAGCAGCACGGAGTTGAGCGAGTAGATGTGGAACAGCGGCAGCAAGCACAGCACCACGTCCTC CCTCCTGAAGTACAGGTTCGGGTTCTCCCCGTCCACctgtcccaggacggcgttggggatcttg gccatgaaggcgtcctggaggtccttccccatgggggcggcgccggacataaccatgcggatgg aggcgagg
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: 275 Transcript exons: 26948161-26948308,26948388-26948514 CTGTCCCAGGACGGCGTTGGGGATCTTGGCCATGAAGGCGTCCTGGAGGTCCTTCCCCATGGGG GCGGCGCCGGACATAACCATGCGGATGGAGGCGAGGTCGTCGGCGGTGACGCGGGGGCTCTTGG CGATCTCCACCACGATGGGCCGATCGCCGACCCGGCTCGCAGCCCCGCCAGCAGCACGGAGTTG AGCGAGTAGATGTGGAACAGCGGCAGCAAGCACAGCACCACGTCCTCCCTCCTGAAGTACAGGT TCGGGTTCTCCCCGTCCAC Transcript length: 354 Transcript exons: 26948161-26948514 CTGTCCCAGGACGGCGTTGGGGATCTTGGCCATGAAGGCGTCCTGGAGGTCCTTCCCCATGGGG GCGGCGCCGGACATAACCATGCGGATGGAGGCGAGGTCGTCGGCGGTGACGCGGGGGCTCTTGG CGATCTCCACCACGATGGGCGGCACGAACGGCGCGACGGTGACGCCGTGCCTCCGCGTCAGGTC CACCAGCGCGCCCAGGTCGAACTTGCGCATGATCACGATCGCCGACCCGGCTCGCAGCCCCGCC AGCAGCACGGAGTTGAGCGAGTAGATGTGGAACAGCGGCAGCAAGCACAGCACCACGTCCTCCC TCCTGAAGTACAGGTTCGGGTTCTCCCCGTCCAC
Genomic sequence	CTGTCCCAGGACGGCGTTGGGGATCTTGGCCATGAAGGCGTCCTGGAGGTCCTTCCCCATGGGG GCGGCGCCGGACATAACCATGCGGATGGAGGCGAGGTCGTCGGCGGTGACGCGGGGGCTCTTGG CGATCTCCACCACGATGGGCGGCACGAACGGCGCGACGGTGACGCCGTGCCTCCGCGTCAGGTC CACCAGCGCGCCCAGGTCGAACTTGCGCATGATCACGATCGCCGACCCGGCTCGCAGCCCCGCC AGCAGCACGGAGTTGAGCGAGTAGATGTGGAACAGCGGCAGCAAGCACAGCACCACGTCCTCCC TCCTGAAGTACAGGTTCGGGTTCTCCCCGTCCAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_016501 zma_circ_002989 						
					
						PMCS
						0.564398917

Conservation Information
Conserved circRNAs	osi_circ_016501 zma_circ_002989
PMCS	0.564398917

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							26948442-26948437(+)
26948384-26948163(-)
						
						Potential amino acid sequence
						
							MWNSGSKHSTTSSLLKYRFGFSPSTCPRTALGILAMKASWRSFPMGAAPDITMRMEARSSAVTR
GLLAISTTMGGTNGATVTPCLRVRSTSAPRSNLRMITIADPARSPASSTELSE*(+)
MRKFDLGALVDLTRRHGVTVAPFVPPIVVEIAKSPRVTADDLASIRMVMSGAAPMGKDLQDAFM
AKIPNAVLGQVDGENPNLYFRREDVVLCLLPLFHIYSLNSVLLAGLRAGSAIVIMRKFDLGALV
DLTRRHGVTVAPFVPPIVVEIAKSPRVTADDLASIRMVMSGAAPMGKDLQDAFMAKIPNAVLGQ
VDGENPNLYFRREDVVLCLLPLFHIYSLNSVLLAGLRAGSAIVIMRKFDLGALVDLTRRHGVTV
APFVPPIVVEIAKSPRVTADDLASIRMVMSGAAPMGKDLQDAFMAKIPNAVLGQVDGENPNLYF
RREDVVLCLLPLFHIYSLNSVLLAGLRAGSAIVIMRKFDLGALVDLTRRHGVTVAPFVPPIVVE
IAKSPRVTADDLASIRMVMSGAAPMGKDLQDAFMAKIPNAVLGQ(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	26948442-26948437(+) 26948384-26948163(-)
Potential amino acid sequence	MWNSGSKHSTTSSLLKYRFGFSPSTCPRTALGILAMKASWRSFPMGAAPDITMRMEARSSAVTR GLLAISTTMGGTNGATVTPCLRVRSTSAPRSNLRMITIADPARSPASSTELSE*(+) MRKFDLGALVDLTRRHGVTVAPFVPPIVVEIAKSPRVTADDLASIRMVMSGAAPMGKDLQDAFM AKIPNAVLGQVDGENPNLYFRREDVVLCLLPLFHIYSLNSVLLAGLRAGSAIVIMRKFDLGALV DLTRRHGVTVAPFVPPIVVEIAKSPRVTADDLASIRMVMSGAAPMGKDLQDAFMAKIPNAVLGQ VDGENPNLYFRREDVVLCLLPLFHIYSLNSVLLAGLRAGSAIVIMRKFDLGALVDLTRRHGVTV APFVPPIVVEIAKSPRVTADDLASIRMVMSGAAPMGKDLQDAFMAKIPNAVLGQVDGENPNLYF RREDVVLCLLPLFHIYSLNSVLLAGLRAGSAIVIMRKFDLGALVDLTRRHGVTVAPFVPPIVVE IAKSPRVTADDLASIRMVMSGAAPMGKDLQDAFMAKIPNAVLGQ(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

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

circRNA

Detail information of Os06g0656566_circ_g.1

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