Plant Circular RNA Database

Detail information of Os05g0556600_circ_g.1

			
						 General Information
					
						CircRNA Name
						Os05g0556600_circ_g.1
					
						ID in PlantcircBase
						osa_circ_028862
					
						Alias
						Os05circ17990/Os_ciR655
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr5: 27678093-27678621  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI, SMALT, Segemehl, circRNA_finder, circseq_cup, find_circ
					
						Parent gene
						
							Os05g0556600						
					
						Parent gene annotation
						
							Hypothetical conserved gene. (Os05t0556600-01)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os05g0555800_circ_ag.1 Os05g0555800_circ_ig.1 Os05g0556000_circ_g.1 Os05g0556000_circ_g.2 Os05g0556000_circ_g.3 Os05g0556100_circ_g.1 Os05g0556100_circ_g.2 Os05g0556100_circ_g.3 Os05g0556100_circ_g.4 Os05g0556100_circ_g.5 Os05g0556100_circ_g.6 Os05g0556100_circ_g.7 Os05g0556100_circ_g.8 Os05g0556100_circ_g.9 Os05g0556100_circ_g.10 Os05g0556100_circ_g.11 Os05g0556100_circ_g.12 Os05g0556100_circ_g.13 Os05g0556100_circ_g.14 Os05g0556300_circ_g.1 Os05g0556400_circ_g.1 Os05g0556400_circ_g.2 Os05g0556400_circ_g.3 Os05g0556600_circ_g.2 EPlOSAG00000016487_circ_ig.1 Os05g0556700_circ_igg.1 Os05g0556700_circ_igg.2 Os05g0556650_circ_g.1 Os05g0556700_circ_g.1 						
					
						Support reads
						17/36/38/2
					
						Tissues
						leaf and panicle/root/root/shoot, anther, pistil
					
						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
						Os05t0556600-01:2

General Information
CircRNA Name	Os05g0556600_circ_g.1
ID in PlantcircBase	osa_circ_028862
Alias	Os05circ17990/Os_ciR655
Organism	Oryza sativa
Position	chr5: 27678093-27678621 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRI, SMALT, Segemehl, circRNA_finder, circseq_cup, find_circ
Parent gene	Os05g0556600
Parent gene annotation	Hypothetical conserved gene. (Os05t0556600-01)
Parent gene strand	+
Alternative splicing	Os05g0555800_circ_ag.1 Os05g0555800_circ_ig.1 Os05g0556000_circ_g.1 Os05g0556000_circ_g.2 Os05g0556000_circ_g.3 Os05g0556100_circ_g.1 Os05g0556100_circ_g.2 Os05g0556100_circ_g.3 Os05g0556100_circ_g.4 Os05g0556100_circ_g.5 Os05g0556100_circ_g.6 Os05g0556100_circ_g.7 Os05g0556100_circ_g.8 Os05g0556100_circ_g.9 Os05g0556100_circ_g.10 Os05g0556100_circ_g.11 Os05g0556100_circ_g.12 Os05g0556100_circ_g.13 Os05g0556100_circ_g.14 Os05g0556300_circ_g.1 Os05g0556400_circ_g.1 Os05g0556400_circ_g.2 Os05g0556400_circ_g.3 Os05g0556600_circ_g.2 EPlOSAG00000016487_circ_ig.1 Os05g0556700_circ_igg.1 Os05g0556700_circ_igg.2 Os05g0556650_circ_g.1 Os05g0556700_circ_g.1
Support reads	17/36/38/2
Tissues	leaf and panicle/root/root/shoot, anther, pistil
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	Os05t0556600-01:2

			
						 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  
						
							TTTTTGTTCTGTATTTGTGCAGTTCGTCTGCCCAGGAATGTGGCTCTCGGATGTGACCAGATCC
AAGTATATCGTCCGCGAGAAGAAGTCCACCAAGAAGatccggcgagcagtcggcggcggcgacg
aaggcggagaagcagcagcagcggccggcggcgcacagggtggcggaggccggtggggtggtca
tggcgctg

									
								

					

						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: 168
Transcript exons: 27678093-27678200,27678562-27678621
ATCCGGCGAGCAGTCGGCGGCGGCGACGAAGGCGGAGAAGCAGCAGCAGCGGCCGGCGGCGCAC
AGGGTGGCGGAGGCCGGTGGGGTGGTCATGGCGCTGGCCAAGACTGGCTCTCGGATGTGACCAG
ATCCAAGTATATCGTCCGCGAGAAGAAGTCCACCAAGAAG
Transcript length: 225
Transcript exons: 27678093-27678149,27678175-27678297,27678577-27678621
ATCCGGCGAGCAGTCGGCGGCGGCGACGAAGGCGGAGAAGCAGCAGCAGCGGCCGGCGGGGTGG
TCATGGCGCTGGCCAAGACGGACTCCAAGTATCAGCACCACACCGGCCATGGCGGCCACGGCCA
GGCCGCCGACCACCATGGGCCCAGCTCGTCGTCGAAGGCGGCGACAGCGGCGACCAGATCCAAG
TATATCGTCCGCGAGAAGAAGTCCACCAAGAAG
Transcript length: 421
Transcript exons: 27678093-27678435,27678544-27678621
ATCCGGCGAGCAGTCGGCGGCGGCGACGAAGGCGGAGAAGCAGCAGCAGCGGCCGGCGGCGCAC
AGGGTGGCGGAGGCCGGTGGGGTGGTCATGGCGCTGGCCAAGACGGACTCCAAGTATCAGCACC
ACACCGGCCATGGCGGCCACGGCCAGGCCGCCGACCACCATGGGCCCAGCTCGTCGTCGAAGGC
GGCGACAGCGGCGGCGCAGAAGATCGAGCTGCCGCGGATCTACACGACGCTGTCGCGCAAGGAG
AAGGAGGAGGACTTCATGGCCATGAAAGGCACCAAGCTGCCCCAGCGACCCAAGAAGAGGCCCA
AGCTTGTCGAGAAGCAAGTCAACTTCGTCTGCCCAGGAATGTGGCTCTCGGATGTGACCAGATC
CAAGTATATCGTCCGCGAGAAGAAGTCCACCAAGAAG
						
					

						Genomic sequence
						
							ATCCGGCGAGCAGTCGGCGGCGGCGACGAAGGCGGAGAAGCAGCAGCAGCGGCCGGCGGCGCAC
AGGGTGGCGGAGGCCGGTGGGGTGGTCATGGCGCTGGCCAAGACGGACTCCAAGTATCAGCACC
ACACCGGCCATGGCGGCCACGGCCAGGCCGCCGACCACCATGGGCCCAGCTCGTCGTCGAAGGC
GGCGACAGCGGCGGCGCAGAAGATCGAGCTGCCGCGGATCTACACGACGCTGTCGCGCAAGGAG
AAGGAGGAGGACTTCATGGCCATGAAAGGCACCAAGCTGCCCCAGCGACCCAAGAAGAGGCCCA
AGCTTGTCGAGAAGCAAGTCAACGTATGGATAAATTATGCTACCTAATCAAACTGTGTTTTACT
ACCATCTTTTTGCTTGATGGTCTTGATGAGAAAACTGACATGATTTTTTTGTTCTGTATTTGTG
CAGTTCGTCTGCCCAGGAATGTGGCTCTCGGATGTGACCAGATCCAAGTATATCGTCCGCGAGA
AGAAGTCCACCAAGAAG
						
					

			
		

Sequences
Splice junction sequence	TTTTTGTTCTGTATTTGTGCAGTTCGTCTGCCCAGGAATGTGGCTCTCGGATGTGACCAGATCC AAGTATATCGTCCGCGAGAAGAAGTCCACCAAGAAGatccggcgagcagtcggcggcggcgacg aaggcggagaagcagcagcagcggccggcggcgcacagggtggcggaggccggtggggtggtca tggcgctg
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: 168 Transcript exons: 27678093-27678200,27678562-27678621 ATCCGGCGAGCAGTCGGCGGCGGCGACGAAGGCGGAGAAGCAGCAGCAGCGGCCGGCGGCGCAC AGGGTGGCGGAGGCCGGTGGGGTGGTCATGGCGCTGGCCAAGACTGGCTCTCGGATGTGACCAG ATCCAAGTATATCGTCCGCGAGAAGAAGTCCACCAAGAAG Transcript length: 225 Transcript exons: 27678093-27678149,27678175-27678297,27678577-27678621 ATCCGGCGAGCAGTCGGCGGCGGCGACGAAGGCGGAGAAGCAGCAGCAGCGGCCGGCGGGGTGG TCATGGCGCTGGCCAAGACGGACTCCAAGTATCAGCACCACACCGGCCATGGCGGCCACGGCCA GGCCGCCGACCACCATGGGCCCAGCTCGTCGTCGAAGGCGGCGACAGCGGCGACCAGATCCAAG TATATCGTCCGCGAGAAGAAGTCCACCAAGAAG Transcript length: 421 Transcript exons: 27678093-27678435,27678544-27678621 ATCCGGCGAGCAGTCGGCGGCGGCGACGAAGGCGGAGAAGCAGCAGCAGCGGCCGGCGGCGCAC AGGGTGGCGGAGGCCGGTGGGGTGGTCATGGCGCTGGCCAAGACGGACTCCAAGTATCAGCACC ACACCGGCCATGGCGGCCACGGCCAGGCCGCCGACCACCATGGGCCCAGCTCGTCGTCGAAGGC GGCGACAGCGGCGGCGCAGAAGATCGAGCTGCCGCGGATCTACACGACGCTGTCGCGCAAGGAG AAGGAGGAGGACTTCATGGCCATGAAAGGCACCAAGCTGCCCCAGCGACCCAAGAAGAGGCCCA AGCTTGTCGAGAAGCAAGTCAACTTCGTCTGCCCAGGAATGTGGCTCTCGGATGTGACCAGATC CAAGTATATCGTCCGCGAGAAGAAGTCCACCAAGAAG
Genomic sequence	ATCCGGCGAGCAGTCGGCGGCGGCGACGAAGGCGGAGAAGCAGCAGCAGCGGCCGGCGGCGCAC AGGGTGGCGGAGGCCGGTGGGGTGGTCATGGCGCTGGCCAAGACGGACTCCAAGTATCAGCACC ACACCGGCCATGGCGGCCACGGCCAGGCCGCCGACCACCATGGGCCCAGCTCGTCGTCGAAGGC GGCGACAGCGGCGGCGCAGAAGATCGAGCTGCCGCGGATCTACACGACGCTGTCGCGCAAGGAG AAGGAGGAGGACTTCATGGCCATGAAAGGCACCAAGCTGCCCCAGCGACCCAAGAAGAGGCCCA AGCTTGTCGAGAAGCAAGTCAACGTATGGATAAATTATGCTACCTAATCAAACTGTGTTTTACT ACCATCTTTTTGCTTGATGGTCTTGATGAGAAAACTGACATGATTTTTTTGTTCTGTATTTGTG CAGTTCGTCTGCCCAGGAATGTGGCTCTCGGATGTGACCAGATCCAAGTATATCGTCCGCGAGA AGAAGTCCACCAAGAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_006382* osi_circ_015742 						
					
						PMCS
						0.360989445

Conservation Information
Conserved circRNAs	osi_circ_006382* osi_circ_015742
PMCS	0.360989445

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							27678185-27678370(+)
27678263-27678433(-)
27678187-27678433(-)
						
						Potential amino acid sequence
						
							MALAKTDSKYQHHTGHGGHGQAADHHGPSSSSKAATAAAQKIELPRIYTTLSRKEKEEDFMAMK
GTKLPQRPKKRPKLVEKQVNFVCPGMWLSDVTRSKYIVREKKSTKKIRRAVGGGDEGGEAAAAA
GGAQGGGGRWGGHGAGQDGLQVSAPHRPWRPRPGRRPPWAQLVVEGGDSGGAEDRAAADLHDAV
AQGEGGGLHGHERHQAAPATQEEAQACREASQLRLPRNVALGCDQIQVYRPREEVHQEDPASSR
RRRRRRRSSSSGRRRTGWRRPVGWSWRWPRRTPSISTTPAMAATARPPTTMGPARRRRRRQRRR
RRSSCRGSTRRCRARRRRRTSWP*(+)
MVVGGLAVAAMAGVVLILGVRLGQRHDHPTGLRHPVRRRPLLLLLRLRRRRRLLAGSSWWTSSR
GRYTWIWSHPRATFLGRRS*(-)
MTTPPASATLCAAGRCCCFSAFVAAADCSPDLLGGLLLADDILGSGHIREPHSWADEVDLLLDK
LGPLLGSLGQLGAFHGHEVLLLLLARQRRVDPRQLDLLRRRCRRLRRRAGPMVVGGLAVAAMAG
VVLILGVRLGQRHDHPTGLRHPVRRRPLLLLLRLRRRRRLLAGSSWWTSSRGRYTWIWSHPRAT
FLGRRS*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	27678185-27678370(+) 27678263-27678433(-) 27678187-27678433(-)
Potential amino acid sequence	MALAKTDSKYQHHTGHGGHGQAADHHGPSSSSKAATAAAQKIELPRIYTTLSRKEKEEDFMAMK GTKLPQRPKKRPKLVEKQVNFVCPGMWLSDVTRSKYIVREKKSTKKIRRAVGGGDEGGEAAAAA GGAQGGGGRWGGHGAGQDGLQVSAPHRPWRPRPGRRPPWAQLVVEGGDSGGAEDRAAADLHDAV AQGEGGGLHGHERHQAAPATQEEAQACREASQLRLPRNVALGCDQIQVYRPREEVHQEDPASSR RRRRRRRSSSSGRRRTGWRRPVGWSWRWPRRTPSISTTPAMAATARPPTTMGPARRRRRRQRRR RRSSCRGSTRRCRARRRRRTSWP(+) MVVGGLAVAAMAGVVLILGVRLGQRHDHPTGLRHPVRRRPLLLLLRLRRRRRLLAGSSWWTSSR GRYTWIWSHPRATFLGRRS(-) MTTPPASATLCAAGRCCCFSAFVAAADCSPDLLGGLLLADDILGSGHIREPHSWADEVDLLLDK LGPLLGSLGQLGAFHGHEVLLLLLARQRRVDPRQLDLLRRRCRRLRRRAGPMVVGGLAVAAMAG VVLILGVRLGQRHDHPTGLRHPVRRRPLLLLLRLRRRRRLLAGSSWWTSSRGRYTWIWSHPRAT FLGRRS*(-)
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 Os05g0556600_circ_g.1

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