Plant Circular RNA Database

Detail information of Os10g0417600_circ_g.2

			
						 General Information
					
						CircRNA Name
						Os10g0417600_circ_g.2
					
						ID in PlantcircBase
						osa_circ_006823
					
						Alias
						Os_ciR6730
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr10: 14641371-14642205  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer, find_circ
					
						Parent gene
						
							Os10g0417600						
					
						Parent gene annotation
						
							NAD(P)-binding domain containing protein. (Os10t0417600-01)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							NA						
					
						Support reads
						2/1
					
						Tissues
						root/root
					
						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
						Os10t0417600-01:3

General Information
CircRNA Name	Os10g0417600_circ_g.2
ID in PlantcircBase	osa_circ_006823
Alias	Os_ciR6730
Organism	Oryza sativa
Position	chr10: 14641371-14642205 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ue-circRNA
Identification method	CIRCexplorer, find_circ
Parent gene	Os10g0417600
Parent gene annotation	NAD(P)-binding domain containing protein. (Os10t0417600-01)
Parent gene strand	+
Alternative splicing	NA
Support reads	2/1
Tissues	root/root
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	Os10t0417600-01:3

			
						 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  
						
							GCAACTGAGGAGCTCTGCAAGCACTACACCAAGGACTTTGGCATTGAGTGCCGTGTTGGCCGCT
TCCACAACATATATGGCCCCTTTGGAACATGGAAAGaatggggagctcggagaagaacggaact
gcttatggcgagtacacctatgctgaactggagagggagcagtactggccgtctgagaagctga
ggatatcg

									
								

					

						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: 641
Transcript exons: 14641371-14641787,14641895-14641988,14642076-14642205
AATGGGGAGCTCGGAGAAGAACGGAACTGCTTATGGCGAGTACACCTATGCTGAACTGGAGAGG
GAGCAGTACTGGCCGTCTGAGAAGCTGAGGATATCGATCACCGGAGCTGGTGGTTTCATTGGAT
CCCACATTGCTCGCCGTCTGAAGAGCGAGGGGCATTACATCATCGCCTCCGACTGGAAGAAGAA
TGAGCACATGACTGAGGACATGTTCTGCCATGAGTTCCACCTTGTTGACCTTAGGGTCATGGAC
AACTGCCTCAAGGTCACCAACGGCGTCGACCATGTGTTCAACCTTGCCGCTGATATGGGTGGTA
TGGGGTTCATTCAGTCCAACCACTCTGTGATCATGTACAACAACACCATGATCAGTTTCAACAT
GCTCGAGGCTGCACGTATCAATGGTGTGAAGAGGTTCTTCTATGCCTCAAGTGCATGCATTTAC
CCTGAATTCAAGCAGCTTGAAACTAACGTTAGCCTGAAGGAATCTGATGCCTGGCCTGCTGAGC
CTCAAGATGCCTATGGTTTGGAGAAGCTTGCAACTGAGGAGCTCTGCAAGCACTACACCAAGGA
CTTTGGCATTGAGTGCCGTGTTGGCCGCTTCCACAACATATATGGCCCCTTTGGAACATGGAAA
G
						
					

						Genomic sequence
						
							AATGGGGAGCTCGGAGAAGAACGGAACTGCTTATGGCGAGTACACCTATGCTGAACTGGAGAGG
GAGCAGTACTGGCCGTCTGAGAAGCTGAGGATATCGATCACCGGAGCTGGTGGTTTCATTGGAT
CCCACATTGCTCGCCGTCTGAAGAGCGAGGGGCATTACATCATCGCCTCCGACTGGAAGAAGAA
TGAGCACATGACTGAGGACATGTTCTGCCATGAGTTCCACCTTGTTGACCTTAGGGTCATGGAC
AACTGCCTCAAGGTCACCAACGGCGTCGACCATGTGTTCAACCTTGCCGCTGATATGGGTGGTA
TGGGGTTCATTCAGTCCAACCACTCTGTGATCATGTACAACAACACCATGATCAGTTTCAACAT
GCTCGAGGCTGCACGTATCAATGGTGTGAAGAGGTCCGGCTCTCTCTTTTTTTTTTACATATTT
TTACTGTTATATCTCAGCTTAGCCTGAGCTTGTTTTATCCATATCAATTCATTTGTTACAACTA
ATGGTCCTACAGGTTCTTCTATGCCTCAAGTGCATGCATTTACCCTGAATTCAAGCAGCTTGAA
ACTAACGTTAGCCTGAAGGAATCTGATGCCTGGCCTGCTGAGGTTTGTCCATCAAAATAATTTT
AGGCTTTAGTGTTATGTTTTAGTAAAACCAGAAGTTGATTTCCTACTGTTTTAACTACTGTCCA
GCCTCAAGATGCCTATGGTTTGGAGAAGCTTGCAACTGAGGAGCTCTGCAAGCACTACACCAAG
GACTTTGGCATTGAGTGCCGTGTTGGCCGCTTCCACAACATATATGGCCCCTTTGGAACATGGA
AAG
						
					

			
		

Sequences
Splice junction sequence	GCAACTGAGGAGCTCTGCAAGCACTACACCAAGGACTTTGGCATTGAGTGCCGTGTTGGCCGCT TCCACAACATATATGGCCCCTTTGGAACATGGAAAGaatggggagctcggagaagaacggaact gcttatggcgagtacacctatgctgaactggagagggagcagtactggccgtctgagaagctga ggatatcg
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: 641 Transcript exons: 14641371-14641787,14641895-14641988,14642076-14642205 AATGGGGAGCTCGGAGAAGAACGGAACTGCTTATGGCGAGTACACCTATGCTGAACTGGAGAGG GAGCAGTACTGGCCGTCTGAGAAGCTGAGGATATCGATCACCGGAGCTGGTGGTTTCATTGGAT CCCACATTGCTCGCCGTCTGAAGAGCGAGGGGCATTACATCATCGCCTCCGACTGGAAGAAGAA TGAGCACATGACTGAGGACATGTTCTGCCATGAGTTCCACCTTGTTGACCTTAGGGTCATGGAC AACTGCCTCAAGGTCACCAACGGCGTCGACCATGTGTTCAACCTTGCCGCTGATATGGGTGGTA TGGGGTTCATTCAGTCCAACCACTCTGTGATCATGTACAACAACACCATGATCAGTTTCAACAT GCTCGAGGCTGCACGTATCAATGGTGTGAAGAGGTTCTTCTATGCCTCAAGTGCATGCATTTAC CCTGAATTCAAGCAGCTTGAAACTAACGTTAGCCTGAAGGAATCTGATGCCTGGCCTGCTGAGC CTCAAGATGCCTATGGTTTGGAGAAGCTTGCAACTGAGGAGCTCTGCAAGCACTACACCAAGGA CTTTGGCATTGAGTGCCGTGTTGGCCGCTTCCACAACATATATGGCCCCTTTGGAACATGGAAA G
Genomic sequence	AATGGGGAGCTCGGAGAAGAACGGAACTGCTTATGGCGAGTACACCTATGCTGAACTGGAGAGG GAGCAGTACTGGCCGTCTGAGAAGCTGAGGATATCGATCACCGGAGCTGGTGGTTTCATTGGAT CCCACATTGCTCGCCGTCTGAAGAGCGAGGGGCATTACATCATCGCCTCCGACTGGAAGAAGAA TGAGCACATGACTGAGGACATGTTCTGCCATGAGTTCCACCTTGTTGACCTTAGGGTCATGGAC AACTGCCTCAAGGTCACCAACGGCGTCGACCATGTGTTCAACCTTGCCGCTGATATGGGTGGTA TGGGGTTCATTCAGTCCAACCACTCTGTGATCATGTACAACAACACCATGATCAGTTTCAACAT GCTCGAGGCTGCACGTATCAATGGTGTGAAGAGGTCCGGCTCTCTCTTTTTTTTTTACATATTT TTACTGTTATATCTCAGCTTAGCCTGAGCTTGTTTTATCCATATCAATTCATTTGTTACAACTA ATGGTCCTACAGGTTCTTCTATGCCTCAAGTGCATGCATTTACCCTGAATTCAAGCAGCTTGAA ACTAACGTTAGCCTGAAGGAATCTGATGCCTGGCCTGCTGAGGTTTGTCCATCAAAATAATTTT AGGCTTTAGTGTTATGTTTTAGTAAAACCAGAAGTTGATTTCCTACTGTTTTAACTACTGTCCA GCCTCAAGATGCCTATGGTTTGGAGAAGCTTGCAACTGAGGAGCTCTGCAAGCACTACACCAAG GACTTTGGCATTGAGTGCCGTGTTGGCCGCTTCCACAACATATATGGCCCCTTTGGAACATGGA AAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_002816* 						
					
						PMCS
						0.452093064

Conservation Information
Conserved circRNAs	osi_circ_002816*
PMCS	0.452093064

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							14642199-14641459(+)
14641373-14641459(+)
14641973-14641421(+)
14641661-14642131(-)
						
						Potential amino acid sequence
						
							MERMGSSEKNGTAYGEYTYAELEREQYWPSEKLRISITGAGGFIGSHIARRLKSEGHYIIASDW
KKNEHMTEDMFCHEFHLVDLRVMDNCLKVTNGVDHVFNLAADMGGMGFIQSNHSVIMYNNTMIS
FNMLEAARINGVKRFFYASSACIYPEFKQLETNVSLKESDAWPAEPQDAYGLEKLATEELCKHY
TKDFGIECRVGRFHNIYGPFGTWKEWGARRRTELLMASTPMLNWRGSSTGRLRS*(+)
MGSSEKNGTAYGEYTYAELEREQYWPSEKLRISITGAGGFIGSHIARRLKSEGHYIIASDWKKN
EHMTEDMFCHEFHLVDLRVMDNCLKVTNGVDHVFNLAADMGGMGFIQSNHSVIMYNNTMISFNM
LEAARINGVKRFFYASSACIYPEFKQLETNVSLKESDAWPAEPQDAYGLEKLATEELCKHYTKD
FGIECRVGRFHNIYGPFGTWKEWGARRRTELLMASTPMLNWRGSSTGRLRS*(+)
MPGLLSLKMPMVWRSLQLRSSASTTPRTLALSAVLAASTTYMAPLEHGKNGELGEERNCLWRVH
LC*(+)
MVDAVGDLEAVVHDPKVNKVELMAEHVLSHVLILLPVGGDDVMPLALQTASNVGSNETTSSGDR
YPQLLRRPVLLPLQFSIGVLAISSSVLLRAPHSFHVPKGPYMLWKRPTRHSMPKSLV*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	14642199-14641459(+) 14641373-14641459(+) 14641973-14641421(+) 14641661-14642131(-)
Potential amino acid sequence	MERMGSSEKNGTAYGEYTYAELEREQYWPSEKLRISITGAGGFIGSHIARRLKSEGHYIIASDW KKNEHMTEDMFCHEFHLVDLRVMDNCLKVTNGVDHVFNLAADMGGMGFIQSNHSVIMYNNTMIS FNMLEAARINGVKRFFYASSACIYPEFKQLETNVSLKESDAWPAEPQDAYGLEKLATEELCKHY TKDFGIECRVGRFHNIYGPFGTWKEWGARRRTELLMASTPMLNWRGSSTGRLRS(+) MGSSEKNGTAYGEYTYAELEREQYWPSEKLRISITGAGGFIGSHIARRLKSEGHYIIASDWKKN EHMTEDMFCHEFHLVDLRVMDNCLKVTNGVDHVFNLAADMGGMGFIQSNHSVIMYNNTMISFNM LEAARINGVKRFFYASSACIYPEFKQLETNVSLKESDAWPAEPQDAYGLEKLATEELCKHYTKD FGIECRVGRFHNIYGPFGTWKEWGARRRTELLMASTPMLNWRGSSTGRLRS(+) MPGLLSLKMPMVWRSLQLRSSASTTPRTLALSAVLAASTTYMAPLEHGKNGELGEERNCLWRVH LC(+) MVDAVGDLEAVVHDPKVNKVELMAEHVLSHVLILLPVGGDDVMPLALQTASNVGSNETTSSGDR YPQLLRRPVLLPLQFSIGVLAISSSVLLRAPHSFHVPKGPYMLWKRPTRHSMPKSLV(-)
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 Os10g0417600_circ_g.2

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