Plant Circular RNA Database

Detail information of Os04g0628400_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os04g0628400_circ_g.3
					
						ID in PlantcircBase
						osa_circ_025459
					
						Alias
						Os_ciR9586
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr4: 31980438-31980857  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer, find_circ
					
						Parent gene
						
							Os04g0628400						
					
						Parent gene annotation
						
							Zinc finger, BED-type predicted domain containing protein. (Os04
t0628400-01);Similar to Transposase-related protein b-gary. (Os0
4t0628400-02);Zinc finger, BED-type predicted domain containing 
protein. (Os04t0628400-03);Zinc finger, BED-type predicted domai
n containing protein. (Os04t0628400-04)
							
						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  
						
							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
						Os04t0628400-03:1
Os04t0628400-02:1
Os04t0628400-04:1
Os04t0628400-01:1

General Information
CircRNA Name	Os04g0628400_circ_g.3
ID in PlantcircBase	osa_circ_025459
Alias	Os_ciR9586
Organism	Oryza sativa
Position	chr4: 31980438-31980857 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ue-circRNA
Identification method	CIRCexplorer, find_circ
Parent gene	Os04g0628400
Parent gene annotation	Zinc finger, BED-type predicted domain containing protein. (Os04 t0628400-01);Similar to Transposase-related protein b-gary. (Os0 4t0628400-02);Zinc finger, BED-type predicted domain containing protein. (Os04t0628400-03);Zinc finger, BED-type predicted domai n containing protein. (Os04t0628400-04)
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	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	Os04t0628400-03:1 Os04t0628400-02:1 Os04t0628400-04:1 Os04t0628400-01:1

			
						 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  
						
							TGATCCATTCATGGGCGGATCTAACATGGGGCATGGGGGGTTCAGTTCAACACCCCCAAACTTT
TTGGGAACAAACAAACATCAAGGTTAAGCCAAATTTcgcatgggaagtaggaatccttctgtcg
cctctgcgccgcttcctccttgccagggcagattttctgatgccgccatagatggcttgtgccg
ttggaatc

						Assembled circRNA sequence  
						
							NA
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
						
							NA						
					
						Genomic sequence
						
							CGCATGGGAAGTAGGAATCCTTCTGTCGCCTCTGCGCCGCTTCCTCCTTGCCAGGGCAGATTTT
CTGATGCCGCCATAGATGGCTTGTGCCGTTGGAATCTTTGCAGCTGAGGCGATTATGGCAGTAG
AGACACTCCGCAAACTGAACCTTCCCATTCAGAAAGATGGGCTTGTACTCCTCCCAAACCTTGG
ACCTTTTCTTGTGCCTGTACCGGAACGGGCTGTGCACTCCATCAAATGCCACATCCACTTTCAT
GCTGTTATCCTCCTCATGCTCCTCTCCAGGAACAGGATGCTCCATAGTGTTTTGGAGTGAATCA
TGATCCATTCATGGGCGGATCTAACATGGGGCATGGGGGGTTCAGTTCAACACCCCCAAACTTT
TTGGGAACAAACAAACATCAAGGTTAAGCCAAATTT

Sequences
Splice junction sequence	TGATCCATTCATGGGCGGATCTAACATGGGGCATGGGGGGTTCAGTTCAACACCCCCAAACTTT TTGGGAACAAACAAACATCAAGGTTAAGCCAAATTTcgcatgggaagtaggaatccttctgtcg cctctgcgccgcttcctccttgccagggcagattttctgatgccgccatagatggcttgtgccg ttggaatc
Assembled circRNA sequence	NA 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	NA
Genomic sequence	CGCATGGGAAGTAGGAATCCTTCTGTCGCCTCTGCGCCGCTTCCTCCTTGCCAGGGCAGATTTT CTGATGCCGCCATAGATGGCTTGTGCCGTTGGAATCTTTGCAGCTGAGGCGATTATGGCAGTAG AGACACTCCGCAAACTGAACCTTCCCATTCAGAAAGATGGGCTTGTACTCCTCCCAAACCTTGG ACCTTTTCTTGTGCCTGTACCGGAACGGGCTGTGCACTCCATCAAATGCCACATCCACTTTCAT GCTGTTATCCTCCTCATGCTCCTCTCCAGGAACAGGATGCTCCATAGTGTTTTGGAGTGAATCA TGATCCATTCATGGGCGGATCTAACATGGGGCATGGGGGGTTCAGTTCAACACCCCCAAACTTT TTGGGAACAAACAAACATCAAGGTTAAGCCAAATTT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.198011429

Conservation Information
Conserved circRNAs	NA
PMCS	0.198011429

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							31980758-31980513(+)
31980595-31980806(-)
31980516-31980847(-)
31980767-31980801(-)
						
						Potential amino acid sequence
						
							MIHSWADLTWGMGGSVQHPQTFWEQTNIKVKPNFAWEVGILLSPLRRFLLARADFLMPP*(+)
MGRFSLRSVSTAIIASAAKIPTAQAIYGGIRKSALARRKRRRGDRRIPTSHAKFGLTLMFVCSQ
KVWGC*(-)
MAASENLPWQGGSGAEATEGFLLPMRNLA*(-)
MDHDSLQNTMEHPVPGEEHEEDNSMKVDVAFDGVHSPFRYRHKKRSKVWEEYKPIFLNGKVQFA
ECLYCHNRLSCKDSNGTSHLWRHQKICPGKEEAAQRRQKDSYFPCEIWLNLDVCLFPKSLGVLN
*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	31980758-31980513(+) 31980595-31980806(-) 31980516-31980847(-) 31980767-31980801(-)
Potential amino acid sequence	MIHSWADLTWGMGGSVQHPQTFWEQTNIKVKPNFAWEVGILLSPLRRFLLARADFLMPP(+) MGRFSLRSVSTAIIASAAKIPTAQAIYGGIRKSALARRKRRRGDRRIPTSHAKFGLTLMFVCSQ KVWGC(-) MAASENLPWQGGSGAEATEGFLLPMRNLA(-) MDHDSLQNTMEHPVPGEEHEEDNSMKVDVAFDGVHSPFRYRHKKRSKVWEEYKPIFLNGKVQFA ECLYCHNRLSCKDSNGTSHLWRHQKICPGKEEAAQRRQKDSYFPCEIWLNLDVCLFPKSLGVLN (-)
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 Os04g0628400_circ_g.3

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