Plant Circular RNA Database

Detail information of Os10g0516800_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os10g0516800_circ_g.3
					
						ID in PlantcircBase
						osa_circ_007679
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr10: 19965760-19967327  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os10g0516800						
					
						Parent gene annotation
						
							Long-chain base kinase, Regulation of disease resistance respons
e and programmed cell death (PCD) (Os10t0516800-01);Diacylglycer
ol kinase, catalytic region domain containing protein. (Os10t051
6800-02)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os10g0516800_circ_g.4 						
					
						Support reads
						2
					
						Tissues
						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
						Os10t0516800-01:3
Os10t0516800-02:3

General Information
CircRNA Name	Os10g0516800_circ_g.3
ID in PlantcircBase	osa_circ_007679
Alias	NA
Organism	Oryza sativa
Position	chr10: 19965760-19967327 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	Os10g0516800
Parent gene annotation	Long-chain base kinase, Regulation of disease resistance respons e and programmed cell death (PCD) (Os10t0516800-01);Diacylglycer ol kinase, catalytic region domain containing protein. (Os10t051 6800-02)
Parent gene strand	+
Alternative splicing	Os10g0516800_circ_g.4
Support reads	2
Tissues	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	Os10t0516800-01:3 Os10t0516800-02:3

			
						 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  
						
							TACCTGAAGTGTTCTACATAACTATTTTGATCATCTGATTCATGTTTGTGCCTGTCTTCTAGGA
ATTGTATGTGTGGGTGGCGATGGGATTGTTAATGAGgtatcatatcattccgggctccgtcact
tcactgtgcatgcatgccctcttgaaaaaagatccagtggactttcctgctttatgaagcctag
aaaaattc

									
								

					

						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: 501
Transcript exons: 19965760-19966128,19967114-19967207,19967290-19967327
GTATCATATCATTCCGGGCTCCGTCACTTCACTGTGCATGCATGCCCTCTTGAAAAAAGATCCA
GTGGACTTTCCTGCTTTATGAAGCCTAGAAAAATTCAAAAGGACTTACGTTTCCTATCCACTTC
TCCACACGAGGCTTTTCGGTGGGTTAATGGTTTTGCAGATCAACAATGCTATGTAAATCTATTA
CCTCACCCCATGGCATCTAGCAAGAAGCATTCATCTGAACTCATTCCATTTGATAATATGTTTG
ATCCATGTGTTAAATGCCGGTCTCCCCCAAAGATACTTGTCATCTTGAATCCTCGATCTGGACA
TGGTAGATCTAGCAAAGTTTTCCACGGAAAAGTGGAACCTATATTCAAGCTTGCAGGTTTCAAG
ATGGAAGTGGTCAAAACTACACATGCTGGTCATGCAAAATCTCTTGTATCAACAATAGATTTCA
GTACCTGTCCAGATGGAATTGTATGTGTGGGTGGCGATGGGATTGTTAATGAG
						
					

						Genomic sequence
						
							GTATCATATCATTCCGGGCTCCGTCACTTCACTGTGCATGCATGCCCTCTTGAAAAAAGATCCA
GTGGACTTTCCTGCTTTATGAAGCCTAGAAAAATTCAAAAGGACTTACGTTTCCTATCCACTTC
TCCACACGAGGCTTTTCGGTGGGTTAATGGTTTTGCAGATCAACAATGCTATGTAAATCTATTA
CCTCACCCCATGGCATCTAGCAAGAAGCATTCATCTGAACTCATTCCATTTGATAATATGTTTG
ATCCATGTGTTAAATGCCGGTCTCCCCCAAAGATACTTGTCATCTTGAATCCTCGATCTGGACA
TGGTAGATCTAGCAAAGTTTTCCACGGAAAAGTGGAACCTATATTCAAGGTATGTCTAGATGAA
TAGAATCATGTGCATTATTTTATAATCAGAGCTGTGATGTCTGCCTCATCAACTCTTAAGCATG
TTTGCAGCATTAGCTATGGTCATATAGTCATTACATAACTTTAAAAAAAATGTTGCAATGAGTG
TCTTTCATGTTTCCTTATTTACCATTGACATTGGTTACCGATAAAAATGCAAGTCATATACCTA
ATCGTGTTGACCTTTTTATTTGTAGTAATCAAGTAAGATGCTAACTTTGCATAGGTAGATGAAA
AGGCACGAACTGTTTCTTTATTATGTTCCTTGATCCATCTCCATAAAAATGAATTCGTTTGTAG
TAGAGGACCATATCAATATTCATGTTGTCAGTATCTTACCAAGATGAGCTTCTCTATGTATAAA
TTCATGTTTGAGTTCATATTGTGCCCTAAGAATCATCTCTCCTGTTGAACTGGAGCATGCTTTG
CTATCCATTTGTTGCCAGGAGCCATTTTGAAGGTTCTCTGGCTCTAGTAGTTCACATTATCTGT
CAAGGTCCGCTGGTTGGTATGATTCATATGTTTGAAATGTTCCTGAACTTTAAGGGATTTTAAA
TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCGCTGTGTGTGTCTGTAGCTGTTGTATCC
TTTCATCCAGTCTATTTGAATCAAGATATTGGTATTACATAGACACGTGTGATGGAGTAATATC
TTGATACACTGTTGTCTCTACTGCGTTACATATCAATCTTGCTGCTTCTAGTGCCATGCCTTGA
AGATTATTTCTGCCATGTCCTATCATCTCTGTAATGCTGAATTTATTAGGGATGAAAATTCGGC
ATCACTATAGTCTTTGACATAAGTGAGCATTCAATTGTATGGAAATACTCATCTTATCATTCCA
GAGCAAAACAACTTGTTTTCAGTGTATCATGTGGTTGTGCTTGTTTTTATAACAATAATAAGTG
CCGGTGACAGCTTGCAGGTTTCAAGATGGAAGTGGTCAAAACTACACATGCTGGTCATGCAAAA
TCTCTTGTATCAACAATAGATTTCAGTACCTGTCCAGATGGTATATATATCTTTACATCTTACC
TGAAGTGTTCTACATAACTATTTTGATCATCTGATTCATGTTTGTGCCTGTCTTCTAGGAATTG
TATGTGTGGGTGGCGATGGGATTGTTAATGAG
						
					

			
		

Sequences
Splice junction sequence	TACCTGAAGTGTTCTACATAACTATTTTGATCATCTGATTCATGTTTGTGCCTGTCTTCTAGGA ATTGTATGTGTGGGTGGCGATGGGATTGTTAATGAGgtatcatatcattccgggctccgtcact tcactgtgcatgcatgccctcttgaaaaaagatccagtggactttcctgctttatgaagcctag aaaaattc
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: 501 Transcript exons: 19965760-19966128,19967114-19967207,19967290-19967327 GTATCATATCATTCCGGGCTCCGTCACTTCACTGTGCATGCATGCCCTCTTGAAAAAAGATCCA GTGGACTTTCCTGCTTTATGAAGCCTAGAAAAATTCAAAAGGACTTACGTTTCCTATCCACTTC TCCACACGAGGCTTTTCGGTGGGTTAATGGTTTTGCAGATCAACAATGCTATGTAAATCTATTA CCTCACCCCATGGCATCTAGCAAGAAGCATTCATCTGAACTCATTCCATTTGATAATATGTTTG ATCCATGTGTTAAATGCCGGTCTCCCCCAAAGATACTTGTCATCTTGAATCCTCGATCTGGACA TGGTAGATCTAGCAAAGTTTTCCACGGAAAAGTGGAACCTATATTCAAGCTTGCAGGTTTCAAG ATGGAAGTGGTCAAAACTACACATGCTGGTCATGCAAAATCTCTTGTATCAACAATAGATTTCA GTACCTGTCCAGATGGAATTGTATGTGTGGGTGGCGATGGGATTGTTAATGAG
Genomic sequence	GTATCATATCATTCCGGGCTCCGTCACTTCACTGTGCATGCATGCCCTCTTGAAAAAAGATCCA GTGGACTTTCCTGCTTTATGAAGCCTAGAAAAATTCAAAAGGACTTACGTTTCCTATCCACTTC TCCACACGAGGCTTTTCGGTGGGTTAATGGTTTTGCAGATCAACAATGCTATGTAAATCTATTA CCTCACCCCATGGCATCTAGCAAGAAGCATTCATCTGAACTCATTCCATTTGATAATATGTTTG ATCCATGTGTTAAATGCCGGTCTCCCCCAAAGATACTTGTCATCTTGAATCCTCGATCTGGACA TGGTAGATCTAGCAAAGTTTTCCACGGAAAAGTGGAACCTATATTCAAGGTATGTCTAGATGAA TAGAATCATGTGCATTATTTTATAATCAGAGCTGTGATGTCTGCCTCATCAACTCTTAAGCATG TTTGCAGCATTAGCTATGGTCATATAGTCATTACATAACTTTAAAAAAAATGTTGCAATGAGTG TCTTTCATGTTTCCTTATTTACCATTGACATTGGTTACCGATAAAAATGCAAGTCATATACCTA ATCGTGTTGACCTTTTTATTTGTAGTAATCAAGTAAGATGCTAACTTTGCATAGGTAGATGAAA AGGCACGAACTGTTTCTTTATTATGTTCCTTGATCCATCTCCATAAAAATGAATTCGTTTGTAG TAGAGGACCATATCAATATTCATGTTGTCAGTATCTTACCAAGATGAGCTTCTCTATGTATAAA TTCATGTTTGAGTTCATATTGTGCCCTAAGAATCATCTCTCCTGTTGAACTGGAGCATGCTTTG CTATCCATTTGTTGCCAGGAGCCATTTTGAAGGTTCTCTGGCTCTAGTAGTTCACATTATCTGT CAAGGTCCGCTGGTTGGTATGATTCATATGTTTGAAATGTTCCTGAACTTTAAGGGATTTTAAA TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCGCTGTGTGTGTCTGTAGCTGTTGTATCC TTTCATCCAGTCTATTTGAATCAAGATATTGGTATTACATAGACACGTGTGATGGAGTAATATC TTGATACACTGTTGTCTCTACTGCGTTACATATCAATCTTGCTGCTTCTAGTGCCATGCCTTGA AGATTATTTCTGCCATGTCCTATCATCTCTGTAATGCTGAATTTATTAGGGATGAAAATTCGGC ATCACTATAGTCTTTGACATAAGTGAGCATTCAATTGTATGGAAATACTCATCTTATCATTCCA GAGCAAAACAACTTGTTTTCAGTGTATCATGTGGTTGTGCTTGTTTTTATAACAATAATAAGTG CCGGTGACAGCTTGCAGGTTTCAAGATGGAAGTGGTCAAAACTACACATGCTGGTCATGCAAAA TCTCTTGTATCAACAATAGATTTCAGTACCTGTCCAGATGGTATATATATCTTTACATCTTACC TGAAGTGTTCTACATAACTATTTTGATCATCTGATTCATGTTTGTGCCTGTCTTCTAGGAATTG TATGTGTGGGTGGCGATGGGATTGTTAATGAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.263438722

Conservation Information
Conserved circRNAs	NA
PMCS	0.263438722

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							19965842-19967324(+)
19967206-19965841(+)
						
						Potential amino acid sequence
						
							MKPRKIQKDLRFLSTSPHEAFRWVNGFADQQCYVNLLPHPMASSKKHSSELIPFDNMFDPCVKC
RSPPKILVILNPRSGHGRSSKVFHGKVEPIFKLAGFKMEVVKTTHAGHAKSLVSTIDFSTCPDG
IVCVGGDGIVNEVSYHSGLRHFTVHACPLEKRSSGLSCFMKPRKIQKDLRFLSTSPHEAFRWVN
GFADQQCYVNLLPHPMASSKKHSSELIPFDNMFDPCVKCRSPPKILVILNPRSGHGRSSKVFHG
KVEPIFKLAGFKMEVVKTTHAGHAKSLVSTIDFSTCPDGIVCVGGDGIVNEVSYHSGLRHFTVH
ACPLEKRSSGLSCFMKPRKIQKDLRFLSTSPHEAFRWVNGFADQQCYVNLLPHPMASSKKHSSE
LIPFDNMFDPCVKCRSPPKILVILNPRSGHGRSSKVFHGKVEPIFKLAGFKMEVVKTTHAGHAK
SLVSTIDFSTCPDGIVCVGGDGIVNEVSYHSGLRHFTVHACPLEKRSSGLSCFMKPRKIQKDLR
FLSTSPHEAFRWVNGFADQQCYVNLLPHPMASSKKHSSELIPFDNMFDPCVKCRSPPKILVILN
PRSGHGRSSKVFHGKVEPIFKLAGFKMEVVKTTHAGHAKSLVSTIDFSTCPDGIVCVGGDGIVN
E(+)
MELYVWVAMGLLMRYHIIPGSVTSLCMHALLKKDPVDFPAL*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	19965842-19967324(+) 19967206-19965841(+)
Potential amino acid sequence	MKPRKIQKDLRFLSTSPHEAFRWVNGFADQQCYVNLLPHPMASSKKHSSELIPFDNMFDPCVKC RSPPKILVILNPRSGHGRSSKVFHGKVEPIFKLAGFKMEVVKTTHAGHAKSLVSTIDFSTCPDG IVCVGGDGIVNEVSYHSGLRHFTVHACPLEKRSSGLSCFMKPRKIQKDLRFLSTSPHEAFRWVN GFADQQCYVNLLPHPMASSKKHSSELIPFDNMFDPCVKCRSPPKILVILNPRSGHGRSSKVFHG KVEPIFKLAGFKMEVVKTTHAGHAKSLVSTIDFSTCPDGIVCVGGDGIVNEVSYHSGLRHFTVH ACPLEKRSSGLSCFMKPRKIQKDLRFLSTSPHEAFRWVNGFADQQCYVNLLPHPMASSKKHSSE LIPFDNMFDPCVKCRSPPKILVILNPRSGHGRSSKVFHGKVEPIFKLAGFKMEVVKTTHAGHAK SLVSTIDFSTCPDGIVCVGGDGIVNEVSYHSGLRHFTVHACPLEKRSSGLSCFMKPRKIQKDLR FLSTSPHEAFRWVNGFADQQCYVNLLPHPMASSKKHSSELIPFDNMFDPCVKCRSPPKILVILN PRSGHGRSSKVFHGKVEPIFKLAGFKMEVVKTTHAGHAKSLVSTIDFSTCPDGIVCVGGDGIVN E(+) MELYVWVAMGLLMRYHIIPGSVTSLCMHALLKKDPVDFPAL*(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os10g0516800_circ_g.3

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