Plant Circular RNA Database

Detail information of EPlOSAG00000043371_circ_ig.1

			
						 General Information
					
						CircRNA Name
						EPlOSAG00000043371_circ_ig.1
					
						ID in PlantcircBase
						osa_circ_009104
					
						Alias
						Os11circ04502, 
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr11: 10702213-10702460  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ig-circRNA							
									
						Identification method
						SMALT, Segemehl, circRNA_finder, circseq_cup, find_circ, CIRI-long
					
						Parent gene
						
							NA						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						NA
					
						Alternative splicing
						
							NA						
					
						Support reads
						3/4/2
					
						Tissues
						leaf and panicle/root/seed, leaf
					
						Exon boundary  
						
							No-No							"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
						NA

General Information
CircRNA Name	EPlOSAG00000043371_circ_ig.1
ID in PlantcircBase	osa_circ_009104
Alias	Os11circ04502,
Organism	Oryza sativa
Position	chr11: 10702213-10702460 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ig-circRNA
Identification method	SMALT, Segemehl, circRNA_finder, circseq_cup, find_circ, CIRI-long
Parent gene	NA
Parent gene annotation	NA
Parent gene strand	NA
Alternative splicing	NA
Support reads	3/4/2
Tissues	leaf and panicle/root/seed, leaf
Exon boundary	No-No "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	NA

			
						 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  
						
							TGGGGAACTGGCCTGCGATCATGGCTAGCTACATTGCCGTGAGAGCATGTCGTGGAATCAGAGT
GATGGAGCTGGTGAATCTAAAATAGTTGCCCAAAGGgctggctgcacccgtccgcccgttaatt
agaaccctaggtgtctacatgaaaacccatgctcaccctgtgctgctgccaccgccaccactct
cttcatcg

						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: 227
Transcript exons: 10702213-10702251,10702258-10702360,10702376-10702460
GCTGGCTGCACCCGTCCGCCCGTTAATTAGAACCCTAGGCATGAAAACCCATGCTCACCCTGTG
CTGCTGCCACCGCCACCACTCTCTTCATCGTTCCCAACCAACCCTGACGTCAGGATGAATGACT
GAGCTTGTGCTTCGCGATCATGGCTAGCTACATTGCCGTGAGAGCATGTCGTGGAATCAGAGTG
ATGGAGCTGGTGAATCTAAAATAGTTGCCCAAAGG
Transcript length: 248
Transcript exons: 10702213-10702460
GCTGGCTGCACCCGTCCGCCCGTTAATTAGAACCCTAGGTGTCTACATGAAAACCCATGCTCAC
CCTGTGCTGCTGCCACCGCCACCACTCTCTTCATCGTTCCCAACCAACCCTGACGTCAGGATGA
ATGACTGAGCTTGTGCTTCGTGGGGAACTGGCCTGCGATCATGGCTAGCTACATTGCCGTGAGA
GCATGTCGTGGAATCAGAGTGATGGAGCTGGTGAATCTAAAATAGTTGCCCAAAGG
						
						Genomic sequence
						
							GCTGGCTGCACCCGTCCGCCCGTTAATTAGAACCCTAGGTGTCTACATGAAAACCCATGCTCAC
CCTGTGCTGCTGCCACCGCCACCACTCTCTTCATCGTTCCCAACCAACCCTGACGTCAGGATGA
ATGACTGAGCTTGTGCTTCGTGGGGAACTGGCCTGCGATCATGGCTAGCTACATTGCCGTGAGA
GCATGTCGTGGAATCAGAGTGATGGAGCTGGTGAATCTAAAATAGTTGCCCAAAGG

Sequences
Splice junction sequence	TGGGGAACTGGCCTGCGATCATGGCTAGCTACATTGCCGTGAGAGCATGTCGTGGAATCAGAGT GATGGAGCTGGTGAATCTAAAATAGTTGCCCAAAGGgctggctgcacccgtccgcccgttaatt agaaccctaggtgtctacatgaaaacccatgctcaccctgtgctgctgccaccgccaccactct cttcatcg
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: 227 Transcript exons: 10702213-10702251,10702258-10702360,10702376-10702460 GCTGGCTGCACCCGTCCGCCCGTTAATTAGAACCCTAGGCATGAAAACCCATGCTCACCCTGTG CTGCTGCCACCGCCACCACTCTCTTCATCGTTCCCAACCAACCCTGACGTCAGGATGAATGACT GAGCTTGTGCTTCGCGATCATGGCTAGCTACATTGCCGTGAGAGCATGTCGTGGAATCAGAGTG ATGGAGCTGGTGAATCTAAAATAGTTGCCCAAAGG Transcript length: 248 Transcript exons: 10702213-10702460 GCTGGCTGCACCCGTCCGCCCGTTAATTAGAACCCTAGGTGTCTACATGAAAACCCATGCTCAC CCTGTGCTGCTGCCACCGCCACCACTCTCTTCATCGTTCCCAACCAACCCTGACGTCAGGATGA ATGACTGAGCTTGTGCTTCGTGGGGAACTGGCCTGCGATCATGGCTAGCTACATTGCCGTGAGA GCATGTCGTGGAATCAGAGTGATGGAGCTGGTGAATCTAAAATAGTTGCCCAAAGG
Genomic sequence	GCTGGCTGCACCCGTCCGCCCGTTAATTAGAACCCTAGGTGTCTACATGAAAACCCATGCTCAC CCTGTGCTGCTGCCACCGCCACCACTCTCTTCATCGTTCCCAACCAACCCTGACGTCAGGATGA ATGACTGAGCTTGTGCTTCGTGGGGAACTGGCCTGCGATCATGGCTAGCTACATTGCCGTGAGA GCATGTCGTGGAATCAGAGTGATGGAGCTGGTGAATCTAAAATAGTTGCCCAAAGG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.346611055

Conservation Information
Conserved circRNAs	NA
PMCS	0.346611055

			
						 Functional Information
					
						Coding potential
						N
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	N
Potential coding position	NA
Potential amino acid sequence	NA
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Lu et al., 2015;Ye et al., 2016;Chu et al., 2017; this study

circRNA

Detail information of EPlOSAG00000043371_circ_ig.1

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