Plant Circular RNA Database

Detail information of EPlOSAG00000019416_circ_ig.3

			
						 General Information
					
						CircRNA Name
						EPlOSAG00000019416_circ_ig.3
					
						ID in PlantcircBase
						osa_circ_035020
					
						Alias
						Os07circ18644/Os_ciR1460
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr7: 26954229-26954838  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ig-circRNA							
									
						Identification method
						CIRCexplorer, KNIFE, PcircRNA_finder, SMALT, Segemehl, find_circ
					
						Parent gene
						
							NA						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						NA
					
						Alternative splicing
						
							EPlOSAG00000019416_circ_ig.1 EPlOSAG00000019416_circ_ig.2 						
					
						Support reads
						3/11/3
					
						Tissues
						leaf and panicle/root/shoot, root, seed
					
						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	EPlOSAG00000019416_circ_ig.3
ID in PlantcircBase	osa_circ_035020
Alias	Os07circ18644/Os_ciR1460
Organism	Oryza sativa
Position	chr7: 26954229-26954838 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ig-circRNA
Identification method	CIRCexplorer, KNIFE, PcircRNA_finder, SMALT, Segemehl, find_circ
Parent gene	NA
Parent gene annotation	NA
Parent gene strand	NA
Alternative splicing	EPlOSAG00000019416_circ_ig.1 EPlOSAG00000019416_circ_ig.2
Support reads	3/11/3
Tissues	leaf and panicle/root/shoot, root, seed
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  
						
							Yes							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   
						
							F: CTGCTTTGAACAACAACCGT
 R: TGGTGGTCTAAACTTGCTGG
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	Yes 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	F: CTGCTTTGAACAACAACCGT R: TGGTGGTCTAAACTTGCTGG 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  
						
							CTCCCACGGTGCTTGGTGATGCAAGTCAGTATGATAATTCAACACAATCAGTTATGGCTCGACA
AGAGATGAGCGAACATATGCGACCGGTATCACAAAGggtggtaaactatgcggacccattgttt
gaaaatggaagtgcacctatagaggacatgaggacacagccttcagaatttgggaaaacagcac
gatcacca

									
								

					

						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: 154
Transcript exons: 26954229-26954355,26954812-26954838
GGTGGTAAACTATGCGGACCCATTGTTTGAAAATGGAAGTGCACCTATAGAGGACATGAGGACA
CAGCCTTCAGAATTTGGGAAAACAGCACGATCACCAACTTCAAACATTACCAGCAAGTTTAGAC
GAACATATGCGACCGGTATCACAAAG
Transcript length: 162
Transcript exons: 26954229-26954279,26954728-26954838
GGTGGTAAACTATGCGGACCCATTGTTTGAAAATGGAAGTGCACCTATAGAGGGTGGTGCATCT
CCCACGGTGCTTGGTGATGCAAGTCAGTATGATAATTCAACACAATCAGTTATGGCTCGACAAG
AGATGAGCGAACATATGCGACCGGTATCACAAAG
Transcript length: 199
Transcript exons: 26954229-26954295,26954707-26954838
GGTGGTAAACTATGCGGACCCATTGTTTGAAAATGGAAGTGCACCTATAGAGGACATGAGGACA
CAGCAGACTACGTCCTGCCTTAGGGGGTGGTGCATCTCCCACGGTGCTTGGTGATGCAAGTCAG
TATGATAATTCAACACAATCAGTTATGGCTCGACAAGAGATGAGCGAACATATGCGACCGGTAT
CACAAAG
Transcript length: 228
Transcript exons: 26954229-26954356,26954739-26954838
GGTGGTAAACTATGCGGACCCATTGTTTGAAAATGGAAGTGCACCTATAGAGGACATGAGGACA
CAGCCTTCAGAATTTGGGAAAACAGCACGATCACCAACTTCAAACATTACCAGCAAGTTTAGAC
CTCCCACGGTGCTTGGTGATGCAAGTCAGTATGATAATTCAACACAATCAGTTATGGCTCGACA
AGAGATGAGCGAACATATGCGACCGGTATCACAAAG
Transcript length: 246
Transcript exons: 26954229-26954361,26954726-26954838
GGTGGTAAACTATGCGGACCCATTGTTTGAAAATGGAAGTGCACCTATAGAGGACATGAGGACA
CAGCCTTCAGAATTTGGGAAAACAGCACGATCACCAACTTCAAACATTACCAGCAAGTTTAGAC
CACCAGGGGGTGGTGCATCTCCCACGGTGCTTGGTGATGCAAGTCAGTATGATAATTCAACACA
ATCAGTTATGGCTCGACAAGAGATGAGCGAACATATGCGACCGGTATCACAAAG
Transcript length: 298
Transcript exons: 26954229-26954381,26954669-26954769,26954795-26954838
GGTGGTAAACTATGCGGACCCATTGTTTGAAAATGGAAGTGCACCTATAGAGGACATGAGGACA
CAGCCTTCAGAATTTGGGAAAACAGCACGATCACCAACTTCAAACATTACCAGCAAGTTTAGAC
CACCATCAGGCTTCCAAAATTATCACCTGCTTTGAACAACAACCGTTTAGTTCCTGGAAGTGGC
AGACTACGTCCTGCCTTAGGGGGTGGTGCATCTCCCACGGTGCTTGGTGATGCAAGTCAGTAGC
TCGACAAGAGATGAGCGAACATATGCGACCGGTATCACAAAG
Transcript length: 315
Transcript exons: 26954229-26954356,26954644-26954744,26954753-26954838
GGTGGTAAACTATGCGGACCCATTGTTTGAAAATGGAAGTGCACCTATAGAGGACATGAGGACA
CAGCCTTCAGAATTTGGGAAAACAGCACGATCACCAACTTCAAACATTACCAGCAAGTTTAGAC
CCATGATGTACGAGCAGCTCCCTCTCCTGCTTTGAACAACAACCGTTTAGTTCCTGGAAGTGGC
AGACTACGTCCTGCCTTAGGGGGTGGTGCATCTCCCAGGTGATGCAAGTCAGTATGATAATTCA
ACACAATCAGTTATGGCTCGACAAGAGATGAGCGAACATATGCGACCGGTATCACAAAG
Transcript length: 320
Transcript exons: 26954229-26954365,26954656-26954838
GGTGGTAAACTATGCGGACCCATTGTTTGAAAATGGAAGTGCACCTATAGAGGACATGAGGACA
CAGCCTTCAGAATTTGGGAAAACAGCACGATCACCAACTTCAAACATTACCAGCAAGTTTAGAC
CACCATCAGAGCAGCTCCCTCTCCTGCTTTGAACAACAACCGTTTAGTTCCTGGAAGTGGCAGA
CTACGTCCTGCCTTAGGGGGTGGTGCATCTCCCACGGTGCTTGGTGATGCAAGTCAGTATGATA
ATTCAACACAATCAGTTATGGCTCGACAAGAGATGAGCGAACATATGCGACCGGTATCACAAAG
						
					

						Genomic sequence
						
							GGTGGTAAACTATGCGGACCCATTGTTTGAAAATGGAAGTGCACCTATAGAGGACATGAGGACA
CAGCCTTCAGAATTTGGGAAAACAGCACGATCACCAACTTCAAACATTACCAGCAAGTTTAGAC
CACCATCAGGCTTCCAAAATTATCACCCTGTGCAGGCTGCCAATCCTCTTGAATACAAGTAAGT
TTCTTTCAAACAATCTTCCCAATATTATGTACTGTATTTCATTTTAACCTCTGCTTCTCTTATA
GTACAGACTATATCAAAAGATTGTATAGAACTATCTAGCTAGTACATGCAGTATTTTACTACTG
ATTTTGTTTATGGTCATACTTTGCTTCTTATCTCTCTACTGCTGCTGATTTTTCAGACCTAATG
TAACACCTGCGATGTTCGGAAACCAGAACCTCCATGATGTACGAGCAGCTCCCTCTCCTGCTTT
GAACAACAACCGTTTAGTTCCTGGAAGTGGCAGACTACGTCCTGCCTTAGGGGGTGGTGCATCT
CCCACGGTGCTTGGTGATGCAAGTCAGTATGATAATTCAACACAATCAGTTATGGCTCGACAAG
AGATGAGCGAACATATGCGACCGGTATCACAAAG
						
					

			
		

Sequences
Splice junction sequence	CTCCCACGGTGCTTGGTGATGCAAGTCAGTATGATAATTCAACACAATCAGTTATGGCTCGACA AGAGATGAGCGAACATATGCGACCGGTATCACAAAGggtggtaaactatgcggacccattgttt gaaaatggaagtgcacctatagaggacatgaggacacagccttcagaatttgggaaaacagcac gatcacca
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: 154 Transcript exons: 26954229-26954355,26954812-26954838 GGTGGTAAACTATGCGGACCCATTGTTTGAAAATGGAAGTGCACCTATAGAGGACATGAGGACA CAGCCTTCAGAATTTGGGAAAACAGCACGATCACCAACTTCAAACATTACCAGCAAGTTTAGAC GAACATATGCGACCGGTATCACAAAG Transcript length: 162 Transcript exons: 26954229-26954279,26954728-26954838 GGTGGTAAACTATGCGGACCCATTGTTTGAAAATGGAAGTGCACCTATAGAGGGTGGTGCATCT CCCACGGTGCTTGGTGATGCAAGTCAGTATGATAATTCAACACAATCAGTTATGGCTCGACAAG AGATGAGCGAACATATGCGACCGGTATCACAAAG Transcript length: 199 Transcript exons: 26954229-26954295,26954707-26954838 GGTGGTAAACTATGCGGACCCATTGTTTGAAAATGGAAGTGCACCTATAGAGGACATGAGGACA CAGCAGACTACGTCCTGCCTTAGGGGGTGGTGCATCTCCCACGGTGCTTGGTGATGCAAGTCAG TATGATAATTCAACACAATCAGTTATGGCTCGACAAGAGATGAGCGAACATATGCGACCGGTAT CACAAAG Transcript length: 228 Transcript exons: 26954229-26954356,26954739-26954838 GGTGGTAAACTATGCGGACCCATTGTTTGAAAATGGAAGTGCACCTATAGAGGACATGAGGACA CAGCCTTCAGAATTTGGGAAAACAGCACGATCACCAACTTCAAACATTACCAGCAAGTTTAGAC CTCCCACGGTGCTTGGTGATGCAAGTCAGTATGATAATTCAACACAATCAGTTATGGCTCGACA AGAGATGAGCGAACATATGCGACCGGTATCACAAAG Transcript length: 246 Transcript exons: 26954229-26954361,26954726-26954838 GGTGGTAAACTATGCGGACCCATTGTTTGAAAATGGAAGTGCACCTATAGAGGACATGAGGACA CAGCCTTCAGAATTTGGGAAAACAGCACGATCACCAACTTCAAACATTACCAGCAAGTTTAGAC CACCAGGGGGTGGTGCATCTCCCACGGTGCTTGGTGATGCAAGTCAGTATGATAATTCAACACA ATCAGTTATGGCTCGACAAGAGATGAGCGAACATATGCGACCGGTATCACAAAG Transcript length: 298 Transcript exons: 26954229-26954381,26954669-26954769,26954795-26954838 GGTGGTAAACTATGCGGACCCATTGTTTGAAAATGGAAGTGCACCTATAGAGGACATGAGGACA CAGCCTTCAGAATTTGGGAAAACAGCACGATCACCAACTTCAAACATTACCAGCAAGTTTAGAC CACCATCAGGCTTCCAAAATTATCACCTGCTTTGAACAACAACCGTTTAGTTCCTGGAAGTGGC AGACTACGTCCTGCCTTAGGGGGTGGTGCATCTCCCACGGTGCTTGGTGATGCAAGTCAGTAGC TCGACAAGAGATGAGCGAACATATGCGACCGGTATCACAAAG Transcript length: 315 Transcript exons: 26954229-26954356,26954644-26954744,26954753-26954838 GGTGGTAAACTATGCGGACCCATTGTTTGAAAATGGAAGTGCACCTATAGAGGACATGAGGACA CAGCCTTCAGAATTTGGGAAAACAGCACGATCACCAACTTCAAACATTACCAGCAAGTTTAGAC CCATGATGTACGAGCAGCTCCCTCTCCTGCTTTGAACAACAACCGTTTAGTTCCTGGAAGTGGC AGACTACGTCCTGCCTTAGGGGGTGGTGCATCTCCCAGGTGATGCAAGTCAGTATGATAATTCA ACACAATCAGTTATGGCTCGACAAGAGATGAGCGAACATATGCGACCGGTATCACAAAG Transcript length: 320 Transcript exons: 26954229-26954365,26954656-26954838 GGTGGTAAACTATGCGGACCCATTGTTTGAAAATGGAAGTGCACCTATAGAGGACATGAGGACA CAGCCTTCAGAATTTGGGAAAACAGCACGATCACCAACTTCAAACATTACCAGCAAGTTTAGAC CACCATCAGAGCAGCTCCCTCTCCTGCTTTGAACAACAACCGTTTAGTTCCTGGAAGTGGCAGA CTACGTCCTGCCTTAGGGGGTGGTGCATCTCCCACGGTGCTTGGTGATGCAAGTCAGTATGATA ATTCAACACAATCAGTTATGGCTCGACAAGAGATGAGCGAACATATGCGACCGGTATCACAAAG
Genomic sequence	GGTGGTAAACTATGCGGACCCATTGTTTGAAAATGGAAGTGCACCTATAGAGGACATGAGGACA CAGCCTTCAGAATTTGGGAAAACAGCACGATCACCAACTTCAAACATTACCAGCAAGTTTAGAC CACCATCAGGCTTCCAAAATTATCACCCTGTGCAGGCTGCCAATCCTCTTGAATACAAGTAAGT TTCTTTCAAACAATCTTCCCAATATTATGTACTGTATTTCATTTTAACCTCTGCTTCTCTTATA GTACAGACTATATCAAAAGATTGTATAGAACTATCTAGCTAGTACATGCAGTATTTTACTACTG ATTTTGTTTATGGTCATACTTTGCTTCTTATCTCTCTACTGCTGCTGATTTTTCAGACCTAATG TAACACCTGCGATGTTCGGAAACCAGAACCTCCATGATGTACGAGCAGCTCCCTCTCCTGCTTT GAACAACAACCGTTTAGTTCCTGGAAGTGGCAGACTACGTCCTGCCTTAGGGGGTGGTGCATCT CCCACGGTGCTTGGTGATGCAAGTCAGTATGATAATTCAACACAATCAGTTATGGCTCGACAAG AGATGAGCGAACATATGCGACCGGTATCACAAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_007379* osi_circ_017407 						
					
						PMCS
						0.368644153

Conservation Information
Conserved circRNAs	osi_circ_007379* osi_circ_017407
PMCS	0.368644153

			
						 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., 2015;Chu et al., 2017

circRNA

Detail information of EPlOSAG00000019416_circ_ig.3

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