Plant Circular RNA Database

Detail information of EPlOSAG00000019803_circ_ig.3

			
						 General Information
					
						CircRNA Name
						EPlOSAG00000019803_circ_ig.3
					
						ID in PlantcircBase
						osa_circ_004624
					
						Alias
						Os_ciR3548
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr1: 34939020-34940362  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ig-circRNA							
									
						Identification method
						CIRCexplorer, circseq_cup, find_circ
					
						Parent gene
						
							NA						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						NA
					
						Alternative splicing
						
							Os01g0819400_circ_igg.1 EPlOSAG00000019803_circ_ig.1 EPlOSAG00000019803_circ_ig.2 EPlOSAG00000019803_circ_ig.4 EPlOSAG00000019803_circ_ig.5 EPlOSAG00000019803_circ_ig.6 EPlOSAG00000019803_circ_ig.7 						
					
						Support reads
						2/7/11
					
						Tissues
						root/root/shoot, root
					
						Exon boundary  
						
							No-No							"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
						NA

General Information
CircRNA Name	EPlOSAG00000019803_circ_ig.3
ID in PlantcircBase	osa_circ_004624
Alias	Os_ciR3548
Organism	Oryza sativa
Position	chr1: 34939020-34940362 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ig-circRNA
Identification method	CIRCexplorer, circseq_cup, find_circ
Parent gene	NA
Parent gene annotation	NA
Parent gene strand	NA
Alternative splicing	Os01g0819400_circ_igg.1 EPlOSAG00000019803_circ_ig.1 EPlOSAG00000019803_circ_ig.2 EPlOSAG00000019803_circ_ig.4 EPlOSAG00000019803_circ_ig.5 EPlOSAG00000019803_circ_ig.6 EPlOSAG00000019803_circ_ig.7
Support reads	2/7/11
Tissues	root/root/shoot, root
Exon boundary	No-No "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	NA

			
						 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  
						
							TTTCAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAAGCATATGCCTTGACATTCTT
AAGGAGCAATGGAGCCCTGCTTTGACAATTTCTAAGgggcatatcatggcatcgaagcggatcc
tcaaggaactaaaggacctgcagaaagatcctccaacatcatgcagtgcaggtatgagaaagat
ttatcagt

									
								

					

						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: 232
Transcript exons: 34939020-34939100,34939652-34939725,34940286-34940362
GGGCATATCATGGCATCGAAGCGGATCCTCAAGGAACTAAAGGACCTGCAGAAAGATCCTCCAA
CATCATGCAGTGCAGGTAGGTCCTGCTGGTGAGGATATGTTCCATTGGCAGGCGACCATTATGG
GTCCTCCAGATAGTCCCTATGCTGGTGCAAACATCAATAGCAATGGAAGCATATGCCTTGACAT
TCTTAAGGAGCAATGGAGCCCTGCTTTGACAATTTCTAAG
Transcript length: 312
Transcript exons: 34939020-34940362
GGGCATATCATGGCATCGAAGCGGATCCTCAAGGAACTAAAGGACCTGCAGAAAGATCCTCCAA
CATCATGCAGTGCAGGTCCTGCTGGTGAGGATATGTTCCATTGGCAGGCGACCATTATGGGTCC
TCCAGATAGTCCCTATGCTGGTGGAGTTTTCTTAGTGAATATTCATTTCCCCCCGGACTACCCC
TTCAAGCCTCCAAAGGTATCTTTCAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAA
GCATATGCCTTGACATTCTTAAGGAGCAATGGAGCCCTGCTTTGACAATTTCTAAG
						
					

						Genomic sequence
						
							GGGCATATCATGGCATCGAAGCGGATCCTCAAGGAACTAAAGGACCTGCAGAAAGATCCTCCAA
CATCATGCAGTGCAGGTATGAGAAAGATTTATCAGTGGAACCATGGCTGATTGGCTGGTAGACA
GTGTGAACTTGAACGTTGATATGATAATGACTCTGTTGGTAGTAATCCATGTTTTCATGTCTGA
TGGAATTGTACAGGTTGTTTATAATGGGTTTCCTTATTATTGGAATATTGCGAACTCATCCAAT
GGTGTGGTTGTCCATACATTAATCTTTAATTTATTGTATTGTATTCCATGTTTGATTCATGCCG
AAATTGAACTATCAGTGTTCTGAATGTATAGGGTTTATCTAGTACTCTTACAAGAGAATGCACA
ATCTTGTCAGTTGCAGTCTTGATGCCTTTGTGTTGTTGGTTAGGCAGTTGTTATGTTTGTAATT
TCCAATGAGTGAAGTGCTTACATTTTAAACTGAAAACCTTAATGAATTATCGACAACAATGAAC
CACTGCAATTGATCATCTGTTCTTATGTAATCAATGAACTATTTTGGTCAGTTTGGTCTTGCTT
ACCTTTTTGCCCTTTGGCTTGTACAAGCTCTGGCATTGATGAGATCTTATAAATTTAGGTCCTG
CTGGTGAGGATATGTTCCATTGGCAGGCGACCATTATGGGTCCTCCAGATAGTCCCTATGCTGG
TGGAGTTTTCTTAGTGAATATTCATTTCCCCCCGGACTACCCCTTCAAGCCTCCAAAGGTTAGC
AGTTAGTCTTATTCTGGGGCAAACTTTTCCTATATTTGCTACTTTTATTGAAGATGAACCCTCT
CTCCGTCTCATGGATTCTCACTACTACTTCTTTTAATGTATATTGATCTTAAGGGGCAATTGTC
TTAAATTCACTGTCCTGTTACTGATTACATCACTCAATATCATAAATGATCTTCGATGTTTGTG
AATTTTTAGCTCTATAAACTGGAATCCCCAGCTGCACCTTTGTTTTCCTTATGTTTACTCCAAG
TAGAATCATTGTAGTTCTTTTCCTTTAGTGTACTAGAGTATGTTCCTGTTTTGGACTTTCTTTC
TAAGCCATGTAATGAAAATTACCTGATTTCCCTCCAAAAAAAAGGAAAAATAAACTTGTTCACT
TTTGATTCTGCCTTGTGATGGATTCTTTTGTGTATATTTTTCTTTATCTCTGCTGTTACGCATT
AAGTTGTGTCCTTTTTTTTCAGGTATCTTTCAAGACAAAGGTCTTCCATCCAAACATCAATAGC
AATGGAAGCATATGCCTTGACATTCTTAAGGAGCAATGGAGCCCTGCTTTGACAATTTCTAAG
						
					

			
		

Sequences
Splice junction sequence	TTTCAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAAGCATATGCCTTGACATTCTT AAGGAGCAATGGAGCCCTGCTTTGACAATTTCTAAGgggcatatcatggcatcgaagcggatcc tcaaggaactaaaggacctgcagaaagatcctccaacatcatgcagtgcaggtatgagaaagat ttatcagt
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: 232 Transcript exons: 34939020-34939100,34939652-34939725,34940286-34940362 GGGCATATCATGGCATCGAAGCGGATCCTCAAGGAACTAAAGGACCTGCAGAAAGATCCTCCAA CATCATGCAGTGCAGGTAGGTCCTGCTGGTGAGGATATGTTCCATTGGCAGGCGACCATTATGG GTCCTCCAGATAGTCCCTATGCTGGTGCAAACATCAATAGCAATGGAAGCATATGCCTTGACAT TCTTAAGGAGCAATGGAGCCCTGCTTTGACAATTTCTAAG Transcript length: 312 Transcript exons: 34939020-34940362 GGGCATATCATGGCATCGAAGCGGATCCTCAAGGAACTAAAGGACCTGCAGAAAGATCCTCCAA CATCATGCAGTGCAGGTCCTGCTGGTGAGGATATGTTCCATTGGCAGGCGACCATTATGGGTCC TCCAGATAGTCCCTATGCTGGTGGAGTTTTCTTAGTGAATATTCATTTCCCCCCGGACTACCCC TTCAAGCCTCCAAAGGTATCTTTCAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAA GCATATGCCTTGACATTCTTAAGGAGCAATGGAGCCCTGCTTTGACAATTTCTAAG
Genomic sequence	GGGCATATCATGGCATCGAAGCGGATCCTCAAGGAACTAAAGGACCTGCAGAAAGATCCTCCAA CATCATGCAGTGCAGGTATGAGAAAGATTTATCAGTGGAACCATGGCTGATTGGCTGGTAGACA GTGTGAACTTGAACGTTGATATGATAATGACTCTGTTGGTAGTAATCCATGTTTTCATGTCTGA TGGAATTGTACAGGTTGTTTATAATGGGTTTCCTTATTATTGGAATATTGCGAACTCATCCAAT GGTGTGGTTGTCCATACATTAATCTTTAATTTATTGTATTGTATTCCATGTTTGATTCATGCCG AAATTGAACTATCAGTGTTCTGAATGTATAGGGTTTATCTAGTACTCTTACAAGAGAATGCACA ATCTTGTCAGTTGCAGTCTTGATGCCTTTGTGTTGTTGGTTAGGCAGTTGTTATGTTTGTAATT TCCAATGAGTGAAGTGCTTACATTTTAAACTGAAAACCTTAATGAATTATCGACAACAATGAAC CACTGCAATTGATCATCTGTTCTTATGTAATCAATGAACTATTTTGGTCAGTTTGGTCTTGCTT ACCTTTTTGCCCTTTGGCTTGTACAAGCTCTGGCATTGATGAGATCTTATAAATTTAGGTCCTG CTGGTGAGGATATGTTCCATTGGCAGGCGACCATTATGGGTCCTCCAGATAGTCCCTATGCTGG TGGAGTTTTCTTAGTGAATATTCATTTCCCCCCGGACTACCCCTTCAAGCCTCCAAAGGTTAGC AGTTAGTCTTATTCTGGGGCAAACTTTTCCTATATTTGCTACTTTTATTGAAGATGAACCCTCT CTCCGTCTCATGGATTCTCACTACTACTTCTTTTAATGTATATTGATCTTAAGGGGCAATTGTC TTAAATTCACTGTCCTGTTACTGATTACATCACTCAATATCATAAATGATCTTCGATGTTTGTG AATTTTTAGCTCTATAAACTGGAATCCCCAGCTGCACCTTTGTTTTCCTTATGTTTACTCCAAG TAGAATCATTGTAGTTCTTTTCCTTTAGTGTACTAGAGTATGTTCCTGTTTTGGACTTTCTTTC TAAGCCATGTAATGAAAATTACCTGATTTCCCTCCAAAAAAAAGGAAAAATAAACTTGTTCACT TTTGATTCTGCCTTGTGATGGATTCTTTTGTGTATATTTTTCTTTATCTCTGCTGTTACGCATT AAGTTGTGTCCTTTTTTTTCAGGTATCTTTCAAGACAAAGGTCTTCCATCCAAACATCAATAGC AATGGAAGCATATGCCTTGACATTCTTAAGGAGCAATGGAGCCCTGCTTTGACAATTTCTAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.372759165

Conservation Information
Conserved circRNAs	NA
PMCS	0.372759165

			
						 Functional Information
					
						Coding potential
						N
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	N
Potential coding position	NA
Potential amino acid sequence	NA
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 EPlOSAG00000019803_circ_ig.3

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