Plant Circular RNA Database

Detail information of Os04g0684500_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os04g0684500_circ_g.3
					
						ID in PlantcircBase
						osa_circ_026031
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr4: 34963882-34964682  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os04g0684500						
					
						Parent gene annotation
						
							Pentatricopeptide repeat domain containing protein. (Os04t068450
0-01);Hypothetical conserved gene. (Os04t0684500-02)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os04g0684500_circ_g.2 Os04g0684500_circ_g.4 Os04g0684500_circ_g.5 Os04g0684500_circ_g.6 Os04g0684500_circ_g.7 Os04g0684500_circ_g.8 						
					
						Support reads
						1
					
						Tissues
						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  
						
							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
						Os04t0684500-02:1
Os04t0684500-01:2

General Information
CircRNA Name	Os04g0684500_circ_g.3
ID in PlantcircBase	osa_circ_026031
Alias	NA
Organism	Oryza sativa
Position	chr4: 34963882-34964682 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ue-circRNA
Identification method	CIRCexplorer
Parent gene	Os04g0684500
Parent gene annotation	Pentatricopeptide repeat domain containing protein. (Os04t068450 0-01);Hypothetical conserved gene. (Os04t0684500-02)
Parent gene strand	+
Alternative splicing	Os04g0684500_circ_g.2 Os04g0684500_circ_g.4 Os04g0684500_circ_g.5 Os04g0684500_circ_g.6 Os04g0684500_circ_g.7 Os04g0684500_circ_g.8
Support reads	1
Tissues	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	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	Os04t0684500-02:1 Os04t0684500-01:2

			
						 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  
						
							GCAAATCAGGGAGGATGCAGAGTGCCTTAGCAGTCACTCGTGAGATGAGCTTCCAAAAGATACC
AAGGAATACATTTATATATAATATTTTGATTGATGGataggtaaggttgccaaagcattatcta
ttagcaaagaaatggagtcttgtggcatcaaacataataataaaacatactctatgcttatcaa
tggattta

									
								

					

						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: 725
Transcript exons: 34963882-34964310,34964387-34964682
ATAGGTAAGGTTGCCAAAGCATTATCTATTAGCAAAGAAATGGAGTCTTGTGGCATCAAACATA
ATAATAAAACATACTCTATGCTTATCAATGGATTTATCCATTTGCACGACTTTGCAAATGCTTT
CGCCATATTTGAGGAAATGCTAAGATCAGGTCTACAACCTGATCGTGCCATATACAATTTGCTT
ATAGAGGCATTTTGTAAGATGGGAAACATGGATCGTGCTATTTGCATTTTGGAAAAAATGCAGA
AGGAACGAATGCAACCATCAAATAGAGCATTCAGGCCTATCATAGAGGGATATGCAGTTGCTGG
TGATATGAAAAGTGCTTTGGATACTCTTGATCTGATGCGGCGAAGTGGTTGTGTTCCCACTGTA
ATGACTTACAATGCTCTCATTCACGGGCTAGTTAGAAAGCACAAGGTTCAAAGAGCTGTCTCTG
TGCTTGATAAGATGTCCATCGCTGGCATTACACCAAATGAGCATACATACACAATCATTATGAG
AGGTTATGCTGCCAGTGGAGATATTGGGAAGGCTTTTGAATACTTCACCAAAATAAAAGAGAGT
GGTCTAAAACTCGATGTGTACATTTATGAAACATTGCTCAGAGCCTGTTGCAAATCAGGGAGGA
TGCAGAGTGCCTTAGCAGTCACTCGTGAGATGAGCTTCCAAAAGATACCAAGGAATACATTTAT
ATATAATATTTTGATTGATGG
Transcript length: 801
Transcript exons: 34963882-34964682
ATAGGTAAGGTTGCCAAAGCATTATCTATTAGCAAAGAAATGGAGTCTTGTGGCATCAAACATA
ATAATAAAACATACTCTATGCTTATCAATGGATTTATCCATTTGCACGACTTTGCAAATGCTTT
CGCCATATTTGAGGAAATGCTAAGATCAGGTCTACAACCTGATCGTGCCATATACAATTTGCTT
ATAGAGGCATTTTGTAAGATGGGAAACATGGATCGTGCTATTTGCATTTTGGAAAAAATGCAGA
AGGAACGAATGCAACCATCAAATAGAGCATTCAGGCCTATCATAGAGGGATATGCAGTTGCTGG
TGATATGAAAAGTGCTTTGGATACTCTTGATCTGATGCGGCGAAGTGGTTGTGTTCCCACTGTA
ATGACTTACAATGCTCTCATTCACGGGCTAGTTAGAAAGCACAAGGTATTTTTCAAGTACATGC
TAGTTTCTTCAAATCTAATCCTGTCATGTGGCATTTACTTTAAATTTGTGTTTATAGGTTCAAA
GAGCTGTCTCTGTGCTTGATAAGATGTCCATCGCTGGCATTACACCAAATGAGCATACATACAC
AATCATTATGAGAGGTTATGCTGCCAGTGGAGATATTGGGAAGGCTTTTGAATACTTCACCAAA
ATAAAAGAGAGTGGTCTAAAACTCGATGTGTACATTTATGAAACATTGCTCAGAGCCTGTTGCA
AATCAGGGAGGATGCAGAGTGCCTTAGCAGTCACTCGTGAGATGAGCTTCCAAAAGATACCAAG
GAATACATTTATATATAATATTTTGATTGATGG
						
					

						Genomic sequence
						
							ATAGGTAAGGTTGCCAAAGCATTATCTATTAGCAAAGAAATGGAGTCTTGTGGCATCAAACATA
ATAATAAAACATACTCTATGCTTATCAATGGATTTATCCATTTGCACGACTTTGCAAATGCTTT
CGCCATATTTGAGGAAATGCTAAGATCAGGTCTACAACCTGATCGTGCCATATACAATTTGCTT
ATAGAGGCATTTTGTAAGATGGGAAACATGGATCGTGCTATTTGCATTTTGGAAAAAATGCAGA
AGGAACGAATGCAACCATCAAATAGAGCATTCAGGCCTATCATAGAGGGATATGCAGTTGCTGG
TGATATGAAAAGTGCTTTGGATACTCTTGATCTGATGCGGCGAAGTGGTTGTGTTCCCACTGTA
ATGACTTACAATGCTCTCATTCACGGGCTAGTTAGAAAGCACAAGGTATTTTTCAAGTACATGC
TAGTTTCTTCAAATCTAATCCTGTCATGTGGCATTTACTTTAAATTTGTGTTTATAGGTTCAAA
GAGCTGTCTCTGTGCTTGATAAGATGTCCATCGCTGGCATTACACCAAATGAGCATACATACAC
AATCATTATGAGAGGTTATGCTGCCAGTGGAGATATTGGGAAGGCTTTTGAATACTTCACCAAA
ATAAAAGAGAGTGGTCTAAAACTCGATGTGTACATTTATGAAACATTGCTCAGAGCCTGTTGCA
AATCAGGGAGGATGCAGAGTGCCTTAGCAGTCACTCGTGAGATGAGCTTCCAAAAGATACCAAG
GAATACATTTATATATAATATTTTGATTGATGG
						
					

			
		

Sequences
Splice junction sequence	GCAAATCAGGGAGGATGCAGAGTGCCTTAGCAGTCACTCGTGAGATGAGCTTCCAAAAGATACC AAGGAATACATTTATATATAATATTTTGATTGATGGataggtaaggttgccaaagcattatcta ttagcaaagaaatggagtcttgtggcatcaaacataataataaaacatactctatgcttatcaa tggattta
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: 725 Transcript exons: 34963882-34964310,34964387-34964682 ATAGGTAAGGTTGCCAAAGCATTATCTATTAGCAAAGAAATGGAGTCTTGTGGCATCAAACATA ATAATAAAACATACTCTATGCTTATCAATGGATTTATCCATTTGCACGACTTTGCAAATGCTTT CGCCATATTTGAGGAAATGCTAAGATCAGGTCTACAACCTGATCGTGCCATATACAATTTGCTT ATAGAGGCATTTTGTAAGATGGGAAACATGGATCGTGCTATTTGCATTTTGGAAAAAATGCAGA AGGAACGAATGCAACCATCAAATAGAGCATTCAGGCCTATCATAGAGGGATATGCAGTTGCTGG TGATATGAAAAGTGCTTTGGATACTCTTGATCTGATGCGGCGAAGTGGTTGTGTTCCCACTGTA ATGACTTACAATGCTCTCATTCACGGGCTAGTTAGAAAGCACAAGGTTCAAAGAGCTGTCTCTG TGCTTGATAAGATGTCCATCGCTGGCATTACACCAAATGAGCATACATACACAATCATTATGAG AGGTTATGCTGCCAGTGGAGATATTGGGAAGGCTTTTGAATACTTCACCAAAATAAAAGAGAGT GGTCTAAAACTCGATGTGTACATTTATGAAACATTGCTCAGAGCCTGTTGCAAATCAGGGAGGA TGCAGAGTGCCTTAGCAGTCACTCGTGAGATGAGCTTCCAAAAGATACCAAGGAATACATTTAT ATATAATATTTTGATTGATGG Transcript length: 801 Transcript exons: 34963882-34964682 ATAGGTAAGGTTGCCAAAGCATTATCTATTAGCAAAGAAATGGAGTCTTGTGGCATCAAACATA ATAATAAAACATACTCTATGCTTATCAATGGATTTATCCATTTGCACGACTTTGCAAATGCTTT CGCCATATTTGAGGAAATGCTAAGATCAGGTCTACAACCTGATCGTGCCATATACAATTTGCTT ATAGAGGCATTTTGTAAGATGGGAAACATGGATCGTGCTATTTGCATTTTGGAAAAAATGCAGA AGGAACGAATGCAACCATCAAATAGAGCATTCAGGCCTATCATAGAGGGATATGCAGTTGCTGG TGATATGAAAAGTGCTTTGGATACTCTTGATCTGATGCGGCGAAGTGGTTGTGTTCCCACTGTA ATGACTTACAATGCTCTCATTCACGGGCTAGTTAGAAAGCACAAGGTATTTTTCAAGTACATGC TAGTTTCTTCAAATCTAATCCTGTCATGTGGCATTTACTTTAAATTTGTGTTTATAGGTTCAAA GAGCTGTCTCTGTGCTTGATAAGATGTCCATCGCTGGCATTACACCAAATGAGCATACATACAC AATCATTATGAGAGGTTATGCTGCCAGTGGAGATATTGGGAAGGCTTTTGAATACTTCACCAAA ATAAAAGAGAGTGGTCTAAAACTCGATGTGTACATTTATGAAACATTGCTCAGAGCCTGTTGCA AATCAGGGAGGATGCAGAGTGCCTTAGCAGTCACTCGTGAGATGAGCTTCCAAAAGATACCAAG GAATACATTTATATATAATATTTTGATTGATGG
Genomic sequence	ATAGGTAAGGTTGCCAAAGCATTATCTATTAGCAAAGAAATGGAGTCTTGTGGCATCAAACATA ATAATAAAACATACTCTATGCTTATCAATGGATTTATCCATTTGCACGACTTTGCAAATGCTTT CGCCATATTTGAGGAAATGCTAAGATCAGGTCTACAACCTGATCGTGCCATATACAATTTGCTT ATAGAGGCATTTTGTAAGATGGGAAACATGGATCGTGCTATTTGCATTTTGGAAAAAATGCAGA AGGAACGAATGCAACCATCAAATAGAGCATTCAGGCCTATCATAGAGGGATATGCAGTTGCTGG TGATATGAAAAGTGCTTTGGATACTCTTGATCTGATGCGGCGAAGTGGTTGTGTTCCCACTGTA ATGACTTACAATGCTCTCATTCACGGGCTAGTTAGAAAGCACAAGGTATTTTTCAAGTACATGC TAGTTTCTTCAAATCTAATCCTGTCATGTGGCATTTACTTTAAATTTGTGTTTATAGGTTCAAA GAGCTGTCTCTGTGCTTGATAAGATGTCCATCGCTGGCATTACACCAAATGAGCATACATACAC AATCATTATGAGAGGTTATGCTGCCAGTGGAGATATTGGGAAGGCTTTTGAATACTTCACCAAA ATAAAAGAGAGTGGTCTAAAACTCGATGTGTACATTTATGAAACATTGCTCAGAGCCTGTTGCA AATCAGGGAGGATGCAGAGTGCCTTAGCAGTCACTCGTGAGATGAGCTTCCAAAAGATACCAAG GAATACATTTATATATAATATTTTGATTGATGG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_005853* 						
					
						PMCS
						0.429820391

Conservation Information
Conserved circRNAs	osi_circ_005853*
PMCS	0.429820391

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							34963922-34963882(+)
34964182-34964660(-)
34963905-34964611(-)
						
						Potential amino acid sequence
						
							MESCGIKHNNKTYSMLINGFIHLHDFANAFAIFEEMLRSGLQPDRAIYNLLIEAFCKMGNMDRA
ICILEKMQKERMQPSNRAFRPIIEGYAVAGDMKSALDTLDLMRRSGCVPTVMTYNALIHGLVRK
HKVQRAVSVLDKMSIAGITPNEHTYTIIMRGYAASGDIGKAFEYFTKIKESGLKLDVYIYETLL
RACCKSGRMQSALAVTREMSFQKIPRNTFIYNILIDG*(+)
MIGLNALFDGCIRSFCIFSKMQIARSMFPILQNASISKLYMARSGCRPDLSISSNMAKAFAKSC
KWINPLISIEYVLLLCLMPQDSISLLIDNALATLPIHQSKYYI*(-)
MLWQPYLSINQNIIYKCIPWYLLEAHLTSDC*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	34963922-34963882(+) 34964182-34964660(-) 34963905-34964611(-)
Potential amino acid sequence	MESCGIKHNNKTYSMLINGFIHLHDFANAFAIFEEMLRSGLQPDRAIYNLLIEAFCKMGNMDRA ICILEKMQKERMQPSNRAFRPIIEGYAVAGDMKSALDTLDLMRRSGCVPTVMTYNALIHGLVRK HKVQRAVSVLDKMSIAGITPNEHTYTIIMRGYAASGDIGKAFEYFTKIKESGLKLDVYIYETLL RACCKSGRMQSALAVTREMSFQKIPRNTFIYNILIDG(+) MIGLNALFDGCIRSFCIFSKMQIARSMFPILQNASISKLYMARSGCRPDLSISSNMAKAFAKSC KWINPLISIEYVLLLCLMPQDSISLLIDNALATLPIHQSKYYI(-) MLWQPYLSINQNIIYKCIPWYLLEAHLTSDC*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os04g0684500_circ_g.3

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