Plant Circular RNA Database

Detail information of Os01g0349400_circ_g.1

			
						 General Information
					
						CircRNA Name
						Os01g0349400_circ_g.1
					
						ID in PlantcircBase
						osa_circ_001666
					
						Alias
						Os01circ10854
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr1: 13923815-13924640  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, SMALT, Segemehl
					
						Parent gene
						
							Os01g0349400						
					
						Parent gene annotation
						
							Similar to Serine/threonine protein phosphatase PP1 (EC 3.1.3.16
) (Fragment). (Os01t0349400-01)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							NA						
					
						Support reads
						2/1
					
						Tissues
						leaf/shoot
					
						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
						Os01t0349400-01:2

General Information
CircRNA Name	Os01g0349400_circ_g.1
ID in PlantcircBase	osa_circ_001666
Alias	Os01circ10854
Organism	Oryza sativa
Position	chr1: 13923815-13924640 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, SMALT, Segemehl
Parent gene	Os01g0349400
Parent gene annotation	Similar to Serine/threonine protein phosphatase PP1 (EC 3.1.3.16 ) (Fragment). (Os01t0349400-01)
Parent gene strand	-
Alternative splicing	NA
Support reads	2/1
Tissues	leaf/shoot
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	Os01t0349400-01:2

			
						 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  
						
							CTGTCCACATAATCTCCAAGGAAAAGATAAGTGGAAGTTGGAGGATAACCGCCCAAATCAAACA
GCCTCAGAAGATCAACAAATTGCCCATGGATATCACcttgtttgaagttggtttccttgaatgt
ggagcccctgtatcatttggcttcaagatttgaaaagaacacattaaactttcatctatgctca
acagagca

									
								

					

						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: 752
Transcript exons: 13923815-13924006,13924081-13924640
CTTGTTTGAAGTTGGTTTCCTTGAATGTGGAGCCCCTGTATCATTTGGCTTCAAGATTTGAAAA
GAACACATTAAACTTTCATCTATGCTCAACAGAGCACCCGCATTATCAAATTCCCCACAATAGT
TTGGAGCTGAAAAGATTGTCACTAATCTCCTTTGCGCAAAGAACTCGTAGCCATCCTCAACAAC
CTGATGAGCGCGGCATATAAGATCAAGATCATTCTTCTCCAAAAATTCTACAAGCTTATCTGCA
CCAAAAGTGCAGGAAACACCTCTGTCACTCTCTCCCCACCCTTCTGAGTCAGGACTAGGATCAG
ACCAAACTAAATCACACAAAAGACCATAGTCAGGAATCTCAGTGGGCCTCTCGATATCCTTTAT
TTGATCCAAGCTATTCAGTTCAGGTGAGAGGCCACCATGCATGCAGAGTATCTTATCGTCAATG
AGTGCTGCCATAGGCAAGCAGTTGAAGCAATCACAGAAAATCTTCCACAGTCGAACATTGAATC
GCCTCTTACATTCATCATAGAAACCATACACTCTGTTAATTTTCGCATCTTCATGGTTTCCCCT
TAACAGGAAAATCTTATCAGGATACTTCACTTTGTATGCCAGAAGCAAGCATATGGTTTCCAAG
CTTTGTTTGCCTCTGTCCACATAATCTCCAAGGAAAAGATAAGTGGAAGTTGGAGGATAACCGC
CCAAATCAAACAGCCTCAGAAGATCAACAAATTGCCCATGGATATCAC
						
					

						Genomic sequence
						
							CTTGTTTGAAGTTGGTTTCCTTGAATGTGGAGCCCCTGTATCATTTGGCTTCAAGATTTGAAAA
GAACACATTAAACTTTCATCTATGCTCAACAGAGCACCCGCATTATCAAATTCCCCACAATAGT
TTGGAGCTGAAAAGATTGTCACTAATCTCCTTTGCGCAAAGAACTCGTAGCCATCCTCAACAAC
CTAAAGACATTCATGCTGAAATTGTTATATAGATCTCAACAGACAAAATAAAGATCAAAATAAT
TAGTGCTTACCTGATGAGCGCGGCATATAAGATCAAGATCATTCTTCTCCAAAAATTCTACAAG
CTTATCTGCACCAAAAGTGCAGGAAACACCTCTGTCACTCTCTCCCCACCCTTCTGAGTCAGGA
CTAGGATCAGACCAAACTAAATCACACAAAAGACCATAGTCAGGAATCTCAGTGGGCCTCTCGA
TATCCTTTATTTGATCCAAGCTATTCAGTTCAGGTGAGAGGCCACCATGCATGCAGAGTATCTT
ATCGTCAATGAGTGCTGCCATAGGCAAGCAGTTGAAGCAATCACAGAAAATCTTCCACAGTCGA
ACATTGAATCGCCTCTTACATTCATCATAGAAACCATACACTCTGTTAATTTTCGCATCTTCAT
GGTTTCCCCTTAACAGGAAAATCTTATCAGGATACTTCACTTTGTATGCCAGAAGCAAGCATAT
GGTTTCCAAGCTTTGTTTGCCTCTGTCCACATAATCTCCAAGGAAAAGATAAGTGGAAGTTGGA
GGATAACCGCCCAAATCAAACAGCCTCAGAAGATCAACAAATTGCCCATGGATATCAC
						
					

			
		

Sequences
Splice junction sequence	CTGTCCACATAATCTCCAAGGAAAAGATAAGTGGAAGTTGGAGGATAACCGCCCAAATCAAACA GCCTCAGAAGATCAACAAATTGCCCATGGATATCACcttgtttgaagttggtttccttgaatgt ggagcccctgtatcatttggcttcaagatttgaaaagaacacattaaactttcatctatgctca acagagca
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: 752 Transcript exons: 13923815-13924006,13924081-13924640 CTTGTTTGAAGTTGGTTTCCTTGAATGTGGAGCCCCTGTATCATTTGGCTTCAAGATTTGAAAA GAACACATTAAACTTTCATCTATGCTCAACAGAGCACCCGCATTATCAAATTCCCCACAATAGT TTGGAGCTGAAAAGATTGTCACTAATCTCCTTTGCGCAAAGAACTCGTAGCCATCCTCAACAAC CTGATGAGCGCGGCATATAAGATCAAGATCATTCTTCTCCAAAAATTCTACAAGCTTATCTGCA CCAAAAGTGCAGGAAACACCTCTGTCACTCTCTCCCCACCCTTCTGAGTCAGGACTAGGATCAG ACCAAACTAAATCACACAAAAGACCATAGTCAGGAATCTCAGTGGGCCTCTCGATATCCTTTAT TTGATCCAAGCTATTCAGTTCAGGTGAGAGGCCACCATGCATGCAGAGTATCTTATCGTCAATG AGTGCTGCCATAGGCAAGCAGTTGAAGCAATCACAGAAAATCTTCCACAGTCGAACATTGAATC GCCTCTTACATTCATCATAGAAACCATACACTCTGTTAATTTTCGCATCTTCATGGTTTCCCCT TAACAGGAAAATCTTATCAGGATACTTCACTTTGTATGCCAGAAGCAAGCATATGGTTTCCAAG CTTTGTTTGCCTCTGTCCACATAATCTCCAAGGAAAAGATAAGTGGAAGTTGGAGGATAACCGC CCAAATCAAACAGCCTCAGAAGATCAACAAATTGCCCATGGATATCAC
Genomic sequence	CTTGTTTGAAGTTGGTTTCCTTGAATGTGGAGCCCCTGTATCATTTGGCTTCAAGATTTGAAAA GAACACATTAAACTTTCATCTATGCTCAACAGAGCACCCGCATTATCAAATTCCCCACAATAGT TTGGAGCTGAAAAGATTGTCACTAATCTCCTTTGCGCAAAGAACTCGTAGCCATCCTCAACAAC CTAAAGACATTCATGCTGAAATTGTTATATAGATCTCAACAGACAAAATAAAGATCAAAATAAT TAGTGCTTACCTGATGAGCGCGGCATATAAGATCAAGATCATTCTTCTCCAAAAATTCTACAAG CTTATCTGCACCAAAAGTGCAGGAAACACCTCTGTCACTCTCTCCCCACCCTTCTGAGTCAGGA CTAGGATCAGACCAAACTAAATCACACAAAAGACCATAGTCAGGAATCTCAGTGGGCCTCTCGA TATCCTTTATTTGATCCAAGCTATTCAGTTCAGGTGAGAGGCCACCATGCATGCAGAGTATCTT ATCGTCAATGAGTGCTGCCATAGGCAAGCAGTTGAAGCAATCACAGAAAATCTTCCACAGTCGA ACATTGAATCGCCTCTTACATTCATCATAGAAACCATACACTCTGTTAATTTTCGCATCTTCAT GGTTTCCCCTTAACAGGAAAATCTTATCAGGATACTTCACTTTGTATGCCAGAAGCAAGCATAT GGTTTCCAAGCTTTGTTTGCCTCTGTCCACATAATCTCCAAGGAAAAGATAAGTGGAAGTTGGA GGATAACCGCCCAAATCAAACAGCCTCAGAAGATCAACAAATTGCCCATGGATATCAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.685474102

Conservation Information
Conserved circRNAs	NA
PMCS	0.685474102

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							13924631-13923872(+)
13924501-13923820(+)
13924349-13924610(-)
						
						Potential amino acid sequence
						
							MDITLFEVGFLECGAPVSFGFKI*(+)
MPEASIWFPSFVCLCPHNLQGKDKWKLEDNRPNQTASEDQQIAHGYHLV*(+)
MAALIDDKILCMHGGLSPELNSLDQIKDIERPTEIPDYGLLCDLVWSDPSPDSEGWGESDRGVS
CTFGADKLVEFLEKNDLDLICRAHQVVEDGYEFFAQRRLVTIFSAPNYCGEFDNAGALLSIDES
LMCSFQILKPNDTGAPHSRKPTSNKVISMGNLLIF*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	13924631-13923872(+) 13924501-13923820(+) 13924349-13924610(-)
Potential amino acid sequence	MDITLFEVGFLECGAPVSFGFKI(+) MPEASIWFPSFVCLCPHNLQGKDKWKLEDNRPNQTASEDQQIAHGYHLV(+) MAALIDDKILCMHGGLSPELNSLDQIKDIERPTEIPDYGLLCDLVWSDPSPDSEGWGESDRGVS CTFGADKLVEFLEKNDLDLICRAHQVVEDGYEFFAQRRLVTIFSAPNYCGEFDNAGALLSIDES LMCSFQILKPNDTGAPHSRKPTSNKVISMGNLLIF*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

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

circRNA

Detail information of Os01g0349400_circ_g.1

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