Plant Circular RNA Database

Detail information of EPlOSAG00000021630_circ_ig.1

			
						 General Information
					
						CircRNA Name
						EPlOSAG00000021630_circ_ig.1
					
						ID in PlantcircBase
						osa_circ_018063
					
						Alias
						Os03circ04007/Os_ciR2974
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr3: 3238395-3240594  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ig-circRNA							
									
						Identification method
						SMALT, Segemehl, find_circ
					
						Parent gene
						
							NA						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						NA
					
						Alternative splicing
						
							NA						
					
						Support reads
						3/4
					
						Tissues
						leaf and panicle/root
					
						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  
						
							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
						NA

General Information
CircRNA Name	EPlOSAG00000021630_circ_ig.1
ID in PlantcircBase	osa_circ_018063
Alias	Os03circ04007/Os_ciR2974
Organism	Oryza sativa
Position	chr3: 3238395-3240594 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ig-circRNA
Identification method	SMALT, Segemehl, find_circ
Parent gene	NA
Parent gene annotation	NA
Parent gene strand	NA
Alternative splicing	NA
Support reads	3/4
Tissues	leaf and panicle/root
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	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	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  
						
							TGTAAGGCTGTAGATGTTTCTCTGAGCTCCGTTGACTTCCTGCGAAATAGTTTTTCTACTATTC
TTTCACTCGCACGGTGAAAAATTTACTGCTGCAAACctacagtgcccctgagcacgtacagcca
cgcgagggttggatgctcgccatctctgaagcttccaacaaaaaccgtctcaagtggtccatgc
aacttctg

									
								

					

						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: 171
Transcript exons: 3238395-3238494,3240524-3240594
CTACAGTGCCCCTGAGCACGTACAGCCACGCGAGGGTTGGATGCTCGCCATCTCTGAAGCTTCC
AACAAAAACCGTCTCAAGTGGTCCATGCAACTTCTGCGTTGACTTCCTGCGAAATAGTTTTTCT
ACTATTCTTTCACTCGCACGGTGAAAAATTTACTGCTGCAAAC
Transcript length: 220
Transcript exons: 3238395-3238513,3240494-3240594
CTACAGTGCCCCTGAGCACGTACAGCCACGCGAGGGTTGGATGCTCGCCATCTCTGAAGCTTCC
AACAAAAACCGTCTCAAGTGGTCCATGCAACTTCTGAAACCACCGCAGCTGCCAGCTGTAAGGC
TGTAGATGTTTCTCTGAGCTCCGTTGACTTCCTGCGAAATAGTTTTTCTACTATTCTTTCACTC
GCACGGTGAAAAATTTACTGCTGCAAAC
						
					

						Genomic sequence
						
							CTACAGTGCCCCTGAGCACGTACAGCCACGCGAGGGTTGGATGCTCGCCATCTCTGAAGCTTCC
AACAAAAACCGTCTCAAGTGGTCCATGCAACTTCTGAAACCACCGCAGCTGCCAGTGCCACGCT
CCAGCTTAAAGGCGAAAACCAATCCTGCAACCAGCAATGTATACAAGGACTAGTTACATGTGTC
GCGTGATACACACCGAGCCCACATGTATAGTAGAATTGTAACAAACTTCACCAGTTATAGCATC
GACAACTGACCAGAAGTCCTGCGTCTGAATTGCAGCAGCCAATACGAAAGACTTGAAGATGAAG
TGAGAGCGAAGATTTGATCTCTAAATGTGTAGCAAGGGGAGCAGCTATAAATGGGTTCTGTCAT
TTTCCATTTCACAGTAAAATAATATCATTCCAGGTCTAGAAATAGAGTACATTATTGATGGTTG
TAGGAGCTGAATAAATCCAAGAGTAGTTCCCAGCAGCCTCAAGAGAATTTCTATCCAGGCATCA
TCAGCTTCTGCCATTGTCCAGCATCAAGTTGGGCAGAAACCAGAAATGAGTAAACCAGGTTACA
ACAAAAATGCCTGCATACTTGGCAGGACCAGTACAATAAAGCATGAGTGCATGAGCATGACCAA
GGATTTTAAGATTGAGCTAGTTATTTTGTACTGGAGGACCATTTCTTTGAAGCTTTTTCTATGC
ACTGAGCAAAGACTATATTCTTCTGGTCCATCATAGGATCAAAGTTGTTCTTCACATCAGAATT
TCGGACAGCAAAAGTGAGATTGAACTGACAGTGTATGGTACATAACAAGCAGAGTGTGGTGGCA
TATGCATAAAAATGTGCTCATAATTCAAAGATGAAACAAAAGTATACAGTTTTTCCTTTTCTTT
CAGCCTTTGGCTGTGTACTTAAACCCCTTCTATTAATATAATGCCAATTAATCTGTTTGGCCGT
TTGGAAAAAAAAAAGAAGTATACGTCAATATATTCTATGACTTGTAAAACACATATAAGTCAAG
AATCAGTGCTGATAGAAGGTGTCAGCTGTCGAGAACTCTGTGGATACGAATGACCATACCGAAA
GAAATAGCCAAGCGATCCATGAGACAAATGGGCAATAATTGACCTGAGCTTGTACTTAAACAAA
TATACTTTCTGAACAGTGAACTTCTTTTACACAGTAATATATCCCCCATTACAGAACAATATGA
ACCATGATCTGGTATTAGCATGAAGACAAACTATTCACTGATATATGATGAGAGCAAGCATTTT
AGATGCAACATCTGCATACATGGCCATGAACACACTTTTTTGAGAATTGAAGTGATAAAAAGGG
GCAATATCCGGATAAAAGACCAATTTGGAGAGTATGGTCATGCAGTTGAAGAGACAGGGATCTG
GTAAAAAAAAAAAAGAGTACATGGCAACTCAGTATTTCAGCTTACCACACCTAAGCATGATGAA
TGCAATGATATCAAAACTCTCTGTAGCACATGTTCCTCACTTGTTGTGAGGGATAAGGTCAAGA
CCAATAATATCTTGCTCAATAAAATGTAAAAGTTCCCCCAAAAAAATAAAAATGGTAGCCCAGT
TATCCTGAGTCTTTAAGCGGAAACTAAATGGAGCAGCCTGTTGAAGATATTTTAATCAATTACA
GGTTGACTGGTGCAGCTTCCTTTGATAAACATATTTTGGCGTGACGAAATCTTCCACTGAGCAA
ATAAGCAATTATCCTGCATTTTATAAAATGCAAACCCCTAAGAGTGGCAGAATCATTCAGTCAT
TCATTGACAACCCACTGAGGCCGAGAGCATGTATAGTTCGCAGAAAGGTCATCTAGGTATTATT
CTTTGTTATTTATGGTTTTGGCCTTTAGTCTTGCTGTTCATCAAGTATCCTCGATCGATAGCAT
CAGGTAGTCACCTTGAAAGCTACGGACCATACACGTGTAAGAGCCGTGGAATTGGACTAAAATT
CCGGCCCATCCATGAACAGTCTAGCCCCTTGGCTGTACGGTTTGTGTCCATGAGAAATTGAGGG
TTTTCTCAAAAAAAAAAAAACAGAGATGTTGAGAGTATAGTTGAGCATAACCTGTAAGGCTGTA
GATGTTTCTCTGAGCTCCGTTGACTTCCTGCGAAATAGTTTTTCTACTATTCTTTCACTCGCAC
GGTGAAAAATTTACTGCTGCAAAC
						
					

			
		

Sequences
Splice junction sequence	TGTAAGGCTGTAGATGTTTCTCTGAGCTCCGTTGACTTCCTGCGAAATAGTTTTTCTACTATTC TTTCACTCGCACGGTGAAAAATTTACTGCTGCAAACctacagtgcccctgagcacgtacagcca cgcgagggttggatgctcgccatctctgaagcttccaacaaaaaccgtctcaagtggtccatgc aacttctg
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: 171 Transcript exons: 3238395-3238494,3240524-3240594 CTACAGTGCCCCTGAGCACGTACAGCCACGCGAGGGTTGGATGCTCGCCATCTCTGAAGCTTCC AACAAAAACCGTCTCAAGTGGTCCATGCAACTTCTGCGTTGACTTCCTGCGAAATAGTTTTTCT ACTATTCTTTCACTCGCACGGTGAAAAATTTACTGCTGCAAAC Transcript length: 220 Transcript exons: 3238395-3238513,3240494-3240594 CTACAGTGCCCCTGAGCACGTACAGCCACGCGAGGGTTGGATGCTCGCCATCTCTGAAGCTTCC AACAAAAACCGTCTCAAGTGGTCCATGCAACTTCTGAAACCACCGCAGCTGCCAGCTGTAAGGC TGTAGATGTTTCTCTGAGCTCCGTTGACTTCCTGCGAAATAGTTTTTCTACTATTCTTTCACTC GCACGGTGAAAAATTTACTGCTGCAAAC
Genomic sequence	CTACAGTGCCCCTGAGCACGTACAGCCACGCGAGGGTTGGATGCTCGCCATCTCTGAAGCTTCC AACAAAAACCGTCTCAAGTGGTCCATGCAACTTCTGAAACCACCGCAGCTGCCAGTGCCACGCT CCAGCTTAAAGGCGAAAACCAATCCTGCAACCAGCAATGTATACAAGGACTAGTTACATGTGTC GCGTGATACACACCGAGCCCACATGTATAGTAGAATTGTAACAAACTTCACCAGTTATAGCATC GACAACTGACCAGAAGTCCTGCGTCTGAATTGCAGCAGCCAATACGAAAGACTTGAAGATGAAG TGAGAGCGAAGATTTGATCTCTAAATGTGTAGCAAGGGGAGCAGCTATAAATGGGTTCTGTCAT TTTCCATTTCACAGTAAAATAATATCATTCCAGGTCTAGAAATAGAGTACATTATTGATGGTTG TAGGAGCTGAATAAATCCAAGAGTAGTTCCCAGCAGCCTCAAGAGAATTTCTATCCAGGCATCA TCAGCTTCTGCCATTGTCCAGCATCAAGTTGGGCAGAAACCAGAAATGAGTAAACCAGGTTACA ACAAAAATGCCTGCATACTTGGCAGGACCAGTACAATAAAGCATGAGTGCATGAGCATGACCAA GGATTTTAAGATTGAGCTAGTTATTTTGTACTGGAGGACCATTTCTTTGAAGCTTTTTCTATGC ACTGAGCAAAGACTATATTCTTCTGGTCCATCATAGGATCAAAGTTGTTCTTCACATCAGAATT TCGGACAGCAAAAGTGAGATTGAACTGACAGTGTATGGTACATAACAAGCAGAGTGTGGTGGCA TATGCATAAAAATGTGCTCATAATTCAAAGATGAAACAAAAGTATACAGTTTTTCCTTTTCTTT CAGCCTTTGGCTGTGTACTTAAACCCCTTCTATTAATATAATGCCAATTAATCTGTTTGGCCGT TTGGAAAAAAAAAAGAAGTATACGTCAATATATTCTATGACTTGTAAAACACATATAAGTCAAG AATCAGTGCTGATAGAAGGTGTCAGCTGTCGAGAACTCTGTGGATACGAATGACCATACCGAAA GAAATAGCCAAGCGATCCATGAGACAAATGGGCAATAATTGACCTGAGCTTGTACTTAAACAAA TATACTTTCTGAACAGTGAACTTCTTTTACACAGTAATATATCCCCCATTACAGAACAATATGA ACCATGATCTGGTATTAGCATGAAGACAAACTATTCACTGATATATGATGAGAGCAAGCATTTT AGATGCAACATCTGCATACATGGCCATGAACACACTTTTTTGAGAATTGAAGTGATAAAAAGGG GCAATATCCGGATAAAAGACCAATTTGGAGAGTATGGTCATGCAGTTGAAGAGACAGGGATCTG GTAAAAAAAAAAAAGAGTACATGGCAACTCAGTATTTCAGCTTACCACACCTAAGCATGATGAA TGCAATGATATCAAAACTCTCTGTAGCACATGTTCCTCACTTGTTGTGAGGGATAAGGTCAAGA CCAATAATATCTTGCTCAATAAAATGTAAAAGTTCCCCCAAAAAAATAAAAATGGTAGCCCAGT TATCCTGAGTCTTTAAGCGGAAACTAAATGGAGCAGCCTGTTGAAGATATTTTAATCAATTACA GGTTGACTGGTGCAGCTTCCTTTGATAAACATATTTTGGCGTGACGAAATCTTCCACTGAGCAA ATAAGCAATTATCCTGCATTTTATAAAATGCAAACCCCTAAGAGTGGCAGAATCATTCAGTCAT TCATTGACAACCCACTGAGGCCGAGAGCATGTATAGTTCGCAGAAAGGTCATCTAGGTATTATT CTTTGTTATTTATGGTTTTGGCCTTTAGTCTTGCTGTTCATCAAGTATCCTCGATCGATAGCAT CAGGTAGTCACCTTGAAAGCTACGGACCATACACGTGTAAGAGCCGTGGAATTGGACTAAAATT CCGGCCCATCCATGAACAGTCTAGCCCCTTGGCTGTACGGTTTGTGTCCATGAGAAATTGAGGG TTTTCTCAAAAAAAAAAAAACAGAGATGTTGAGAGTATAGTTGAGCATAACCTGTAAGGCTGTA GATGTTTCTCTGAGCTCCGTTGACTTCCTGCGAAATAGTTTTTCTACTATTCTTTCACTCGCAC GGTGAAAAATTTACTGCTGCAAAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.317359254

Conservation Information
Conserved circRNAs	NA
PMCS	0.317359254

			
						 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

circRNA

Detail information of EPlOSAG00000021630_circ_ig.1

Address

Any questions?

Supported by