Plant Circular RNA Database

Detail information of Os09g0279000_circ_g.2

			
						 General Information
					
						CircRNA Name
						Os09g0279000_circ_g.2
					
						ID in PlantcircBase
						osa_circ_038688
					
						Alias
						Os_ciR11999
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr9: 5841032-5842204  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, PcircRNA_finder, find_circ
					
						Parent gene
						
							Os09g0279000						
					
						Parent gene annotation
						
							Similar to r-interacting factor1. (Os09t0279000-01)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os09g0279000_circ_g.3 						
					
						Support reads
						2/11
					
						Tissues
						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
						Os09t0279000-01:5

General Information
CircRNA Name	Os09g0279000_circ_g.2
ID in PlantcircBase	osa_circ_038688
Alias	Os_ciR11999
Organism	Oryza sativa
Position	chr9: 5841032-5842204 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, PcircRNA_finder, find_circ
Parent gene	Os09g0279000
Parent gene annotation	Similar to r-interacting factor1. (Os09t0279000-01)
Parent gene strand	-
Alternative splicing	Os09g0279000_circ_g.3
Support reads	2/11
Tissues	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	Os09t0279000-01:5

			
						 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  
						
							GAACCAGCAGGAACAATAGCTCTTCCATTACCACTGACACGTCCACTGCCTCTAATACCCCTAT
TGCTTGGATATGGTGGAGGAAGATCATCAGCAGTTCctgtttaagatcaacccactcccatgat
tcattagctgtatttatgtcataagccaatgcatacagatcctgcaatggaatcccttagaaaa
gcccaaag

									
								

					

						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: 857
Transcript exons: 5841032-5841100,5841176-5841400,5841477-5841720,5841795-
5841904,5841996-5842204
CTGTTTAAGATCAACCCACTCCCATGATTCATTAGCTGTATTTATGTCATAAGCCAATGCATAC
AGATCCGTTTCTGGATTATAATCAGTAATAGTTGCTTCGTAAAAACTGTTATCTTCAGGCCACC
GGCTCATGACTTTACGATTAATTAATGGATTAATATGCAGTGCTTCGGAAGGTTCAAAAGAAAC
AAGGCCAACAGGAAAGTTTCTATTCATATGTGGTCCCCTTCCGCTAGGACCAGCTGAAGATGTC
ATGGCCTTGACTGAAGGGCCCCCTGGCACCTTCTGACCTGGTTTGGTCTTTTTGCCTTTAGCTC
CTGATGAAGCTCCCTTTTTAGCTGTTGAAGATGATGGTGGTCCTTGTAAAGCCAACTGCTGTGA
ATGCATAACAGGAGGCGGTGCAGGCAGGGCAGGAAATGATTGCGATGTCTTTTGCCTCTTACGG
CCCGAGGTGGTAGGGCTAGGCGCTAGATCATGCATAGGCTGAGCATTATTGGGTAACATTGCTT
GAGGCCCTCCTGCTGATCTCCATTCCCTTATGCTACGGATAATATCATCACTGTTGACCCGATT
TAGTAGTTCCCTGTGGTCTACATCAGATACCCTTAGCTCTTTCCGAAGTTCTGTTATGAGACCT
TCTTTCTCCCATGTAATGGCGTCAGACTGGGCTTTAAATGCACGAAGAACCGAGCAATATGCTT
CTTGTTCAAGATGATGGATTTGTGTTGCCATATCAGTATGGGCTCTAGTGTATGAACCAGCAGG
AACAATAGCTCTTCCATTACCACTGACACGTCCACTGCCTCTAATACCCCTATTGCTTGGATAT
GGTGGAGGAAGATCATCAGCAGTTC
						
					

						Genomic sequence
						
							CTGTTTAAGATCAACCCACTCCCATGATTCATTAGCTGTATTTATGTCATAAGCCAATGCATAC
AGATCCTGCAATGGAATCCCTTAGAAAAGCCCAAAGGCCTGAATCAACAGAACTGTAGCTATAA
TGAAGTAAGAACAAACCGTTTCTGGATTATAATCAGTAATAGTTGCTTCGTAAAAACTGTTATC
TTCAGGCCACCGGCTCATGACTTTACGATTAATTAATGGATTAATATGCAGTGCTTCGGAAGGT
TCAAAAGAAACAAGGCCAACAGGAAAGTTTCTATTCATATGTGGTCCCCTTCCGCTAGGACCAG
CTGAAGATGTCATGGCCTTGACTGAAGGGCCCCCTGGCACCTTCTGACCCTGGAAGCACATGAA
ACTTCATCAAAGAAACCCGATTTCTTTTTTTAAGAAAGAGACATCAGAATTATGTGCTTACTGG
TTTGGTCTTTTTGCCTTTAGCTCCTGATGAAGCTCCCTTTTTAGCTGTTGAAGATGATGGTGGT
CCTTGTAAAGCCAACTGCTGTGAATGCATAACAGGAGGCGGTGCAGGCAGGGCAGGAAATGATT
GCGATGTCTTTTGCCTCTTACGGCCCGAGGTGGTAGGGCTAGGCGCTAGATCATGCATAGGCTG
AGCATTATTGGGTAACATTGCTTGAGGCCCTCCTGCTGATCTCCATTCCCTTGATTACAAGGAA
GAAAGAAATTCAGAATGTTGAAAACAGAACACACATGAACACTTCTTTATATATTCTACCTTAT
GCTACGGATAATATCATCACTGTTGACCCGATTTAGTAGTTCCCTGTGGTCTACATCAGATACC
CTTAGCTCTTTCCGAAGTTCTGTTATGAGACCTTCTTTCTCCTGGAAATGAGAAACAGCTTTGA
GATATAATGTTCAAGATGAATCAGCACAGACCCAAAGATAATAAAACCATAGTTTAATGGTTAA
CAACCCATGTAATGGCGTCAGACTGGGCTTTAAATGCACGAAGAACCGAGCAATATGCTTCTTG
TTCAAGATGATGGATTTGTGTTGCCATATCAGTATGGGCTCTAGTGTATGAACCAGCAGGAACA
ATAGCTCTTCCATTACCACTGACACGTCCACTGCCTCTAATACCCCTATTGCTTGGATATGGTG
GAGGAAGATCATCAGCAGTTC
						
					

			
		

Sequences
Splice junction sequence	GAACCAGCAGGAACAATAGCTCTTCCATTACCACTGACACGTCCACTGCCTCTAATACCCCTAT TGCTTGGATATGGTGGAGGAAGATCATCAGCAGTTCctgtttaagatcaacccactcccatgat tcattagctgtatttatgtcataagccaatgcatacagatcctgcaatggaatcccttagaaaa gcccaaag
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: 857 Transcript exons: 5841032-5841100,5841176-5841400,5841477-5841720,5841795- 5841904,5841996-5842204 CTGTTTAAGATCAACCCACTCCCATGATTCATTAGCTGTATTTATGTCATAAGCCAATGCATAC AGATCCGTTTCTGGATTATAATCAGTAATAGTTGCTTCGTAAAAACTGTTATCTTCAGGCCACC GGCTCATGACTTTACGATTAATTAATGGATTAATATGCAGTGCTTCGGAAGGTTCAAAAGAAAC AAGGCCAACAGGAAAGTTTCTATTCATATGTGGTCCCCTTCCGCTAGGACCAGCTGAAGATGTC ATGGCCTTGACTGAAGGGCCCCCTGGCACCTTCTGACCTGGTTTGGTCTTTTTGCCTTTAGCTC CTGATGAAGCTCCCTTTTTAGCTGTTGAAGATGATGGTGGTCCTTGTAAAGCCAACTGCTGTGA ATGCATAACAGGAGGCGGTGCAGGCAGGGCAGGAAATGATTGCGATGTCTTTTGCCTCTTACGG CCCGAGGTGGTAGGGCTAGGCGCTAGATCATGCATAGGCTGAGCATTATTGGGTAACATTGCTT GAGGCCCTCCTGCTGATCTCCATTCCCTTATGCTACGGATAATATCATCACTGTTGACCCGATT TAGTAGTTCCCTGTGGTCTACATCAGATACCCTTAGCTCTTTCCGAAGTTCTGTTATGAGACCT TCTTTCTCCCATGTAATGGCGTCAGACTGGGCTTTAAATGCACGAAGAACCGAGCAATATGCTT CTTGTTCAAGATGATGGATTTGTGTTGCCATATCAGTATGGGCTCTAGTGTATGAACCAGCAGG AACAATAGCTCTTCCATTACCACTGACACGTCCACTGCCTCTAATACCCCTATTGCTTGGATAT GGTGGAGGAAGATCATCAGCAGTTC
Genomic sequence	CTGTTTAAGATCAACCCACTCCCATGATTCATTAGCTGTATTTATGTCATAAGCCAATGCATAC AGATCCTGCAATGGAATCCCTTAGAAAAGCCCAAAGGCCTGAATCAACAGAACTGTAGCTATAA TGAAGTAAGAACAAACCGTTTCTGGATTATAATCAGTAATAGTTGCTTCGTAAAAACTGTTATC TTCAGGCCACCGGCTCATGACTTTACGATTAATTAATGGATTAATATGCAGTGCTTCGGAAGGT TCAAAAGAAACAAGGCCAACAGGAAAGTTTCTATTCATATGTGGTCCCCTTCCGCTAGGACCAG CTGAAGATGTCATGGCCTTGACTGAAGGGCCCCCTGGCACCTTCTGACCCTGGAAGCACATGAA ACTTCATCAAAGAAACCCGATTTCTTTTTTTAAGAAAGAGACATCAGAATTATGTGCTTACTGG TTTGGTCTTTTTGCCTTTAGCTCCTGATGAAGCTCCCTTTTTAGCTGTTGAAGATGATGGTGGT CCTTGTAAAGCCAACTGCTGTGAATGCATAACAGGAGGCGGTGCAGGCAGGGCAGGAAATGATT GCGATGTCTTTTGCCTCTTACGGCCCGAGGTGGTAGGGCTAGGCGCTAGATCATGCATAGGCTG AGCATTATTGGGTAACATTGCTTGAGGCCCTCCTGCTGATCTCCATTCCCTTGATTACAAGGAA GAAAGAAATTCAGAATGTTGAAAACAGAACACACATGAACACTTCTTTATATATTCTACCTTAT GCTACGGATAATATCATCACTGTTGACCCGATTTAGTAGTTCCCTGTGGTCTACATCAGATACC CTTAGCTCTTTCCGAAGTTCTGTTATGAGACCTTCTTTCTCCTGGAAATGAGAAACAGCTTTGA GATATAATGTTCAAGATGAATCAGCACAGACCCAAAGATAATAAAACCATAGTTTAATGGTTAA CAACCCATGTAATGGCGTCAGACTGGGCTTTAAATGCACGAAGAACCGAGCAATATGCTTCTTG TTCAAGATGATGGATTTGTGTTGCCATATCAGTATGGGCTCTAGTGTATGAACCAGCAGGAACA ATAGCTCTTCCATTACCACTGACACGTCCACTGCCTCTAATACCCCTATTGCTTGGATATGGTG GAGGAAGATCATCAGCAGTTC

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_007987* osi_circ_018859 						
					
						PMCS
						0.307930527

Conservation Information
Conserved circRNAs	osi_circ_007987* osi_circ_018859
PMCS	0.307930527

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							5842084-5841888(-)
						
						Potential amino acid sequence
						
							MATQIHHLEQEAYCSVLRAFKAQSDAITWEKEGLITELRKELRVSDVDHRELLNRVNSDDIIRS
IREWRSAGGPQAMLPNNAQPMHDLAPSPTTSGRKRQKTSQSFPALPAPPPVMHSQQLALQGPPS
SSTAKKGASSGAKGKKTKPGQKVPGGPSVKAMTSSAGPSGRGPHMNRNFPVGLVSFEPSEALHI
NPLINRKVMSRWPEDNSFYEATITDYNPETDLYALAYDINTANESWEWVDLKQELLMIFLHHIQ
AIGVLEAVDVSVVMEELLFLLVHTLEPILIWQHKSIILNKKHIARFFVHLKPSLTPLHGRKKVS
*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	5842084-5841888(-)
Potential amino acid sequence	MATQIHHLEQEAYCSVLRAFKAQSDAITWEKEGLITELRKELRVSDVDHRELLNRVNSDDIIRS IREWRSAGGPQAMLPNNAQPMHDLAPSPTTSGRKRQKTSQSFPALPAPPPVMHSQQLALQGPPS SSTAKKGASSGAKGKKTKPGQKVPGGPSVKAMTSSAGPSGRGPHMNRNFPVGLVSFEPSEALHI NPLINRKVMSRWPEDNSFYEATITDYNPETDLYALAYDINTANESWEWVDLKQELLMIFLHHIQ AIGVLEAVDVSVVMEELLFLLVHTLEPILIWQHKSIILNKKHIARFFVHLKPSLTPLHGRKKVS *(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

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

circRNA

Detail information of Os09g0279000_circ_g.2

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