Plant Circular RNA Database

Detail information of Os09g0462400_circ_igg.1

			
						 General Information
					
						CircRNA Name
						Os09g0462400_circ_igg.1
					
						ID in PlantcircBase
						osa_circ_039474
					
						Alias
						Os_ciR2539
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr9: 17474772-17477982  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							igg-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							NA						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						NA
					
						Alternative splicing
						
							Os09g0462400_circ_g.1 Os09g0462400_circ_g.2 						
					
						Support reads
						8
					
						Tissues
						root
					
						Exon boundary  
						
							No-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
						NA

General Information
CircRNA Name	Os09g0462400_circ_igg.1
ID in PlantcircBase	osa_circ_039474
Alias	Os_ciR2539
Organism	Oryza sativa
Position	chr9: 17474772-17477982 JBrowse»
Reference genome	IRGSP-1.0.38
Type	igg-circRNA
Identification method	find_circ
Parent gene	NA
Parent gene annotation	NA
Parent gene strand	NA
Alternative splicing	Os09g0462400_circ_g.1 Os09g0462400_circ_g.2
Support reads	8
Tissues	root
Exon boundary	No-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	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  
						
							GAAATTAGGAAGCACCAGGCTGCATCAGACTTTAACAAATGTGGTCATACCAACTTTCGACATC
AAGTGGTTACAACCAACCATTTTCTCTTCCTACGAGtgccagaaagattgacgtggaattgtta
tatggcagattgatagttcatgaggtaagcaaggttactattgtaagaactgcatgagtcatga
gatgatga

									
								

					

						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: 232
Transcript exons: 17474772-17474821,17474846-17474946,17477902-17477982
TGCCAGAAAGATTGACGTGGAATTGTTATATGGCAGATTGATAGTTCATGGAACTGCATGAGTC
ATGAGATGATGAGAATTTGAGAAGAGGTCTCCAATGGTACCAGCAATCGGACAGCATCCTGAAC
TGAAATAGAGCCATCGTCAGCATCTGCATCAGACTTTAACAAATGTGGTCATACCAACTTTCGA
CATCAAGTGGTTACAACCAACCATTTTCTCTTCCTACGAG
						
					

						Genomic sequence
						
							TGCCAGAAAGATTGACGTGGAATTGTTATATGGCAGATTGATAGTTCATGAGGTAAGCAAGGTT
ACTATTGTAAGAACTGCATGAGTCATGAGATGATGAGAATTTGAGAAGAGGTCTCCAATGGTAC
CAGCAATCGGACAGCATCCTGAACTGAAATAGAGCCATCGTCAGCATACTTGGTAATTACGGCT
TCAATCTGTTGTGCGAGTCATACATTGCAACTCACAATCTTCTATTAAAACTTATTATAAGATG
TTTGGTTTTCTATTAGACTTTCTTGTAAGCAATCACTCCTCTCATTATTAAAAAAAGAGAGTTA
AAACTGACCAATTACTGCTAACGCCGCAATTAATTTTGATGAACAACATTGGTATGTTACATAT
CATCATTGCTTACAGTTGTGCCCATAAAAGTTTATGGTACCATTTATCAATTATTTATTGTGAT
GAAAATGTGTTGTTTGATGATGAACTGAAATTTGGGATTGGGATTTGTTATATTGGAACTTCAA
AGACAGAGAGAGTATTGTAGCTGTTGAATAAAGGATGCTCCAACATTAGATACTTTGGATTTGT
GACTAGTTTTCTGCAAGTTAGTATTTGTTCTTGTTTCCCTTCCTTTAGTAAATCATTCGATTAT
TCTTCTGACCATTCTTTGTTCAAAAGGTCTTGAATCCTTAAATATTTTCAATATGTAATGTTTG
GTATTATCATGTTGGCCTTTTCTTGGTGCAGAAGATCAGATTAGGCTTATATCTTGATATGCTG
AAAGTTTACACTTCACCCCTCATTTATCTGGGCAAGGAAAGGACATCTTTTTTCTTTACTCAAT
TTGATGTAGAGAATATTGTTTAGCTATAGTGCTATACAATTGTGAGTATGAAAAAAGAGAGCAT
ACCTCACCACTGATGTAACAAAAATCCAGCTAAATAAAGATGGCACCAATGCAATGGAGCTTGT
AACCGTTTTTCTTTCCTGTGGCTGCATACATCCCAAAATCAAATACTACAATGGCGCACCTTCT
TCTGAGCTTCTATGTATGGGCTGGTATTATGATCTTGTTGCTATTTCTTGATCAATTTCGGTCA
ATCAAATGAAGTAGTTCACAAATTGGCCATCTTATTCTTTTCGTAGCGTGCAAAAATGCAAGCT
AGATTGGTTTGAAACAGAGCATATAAGTGAAGGTGAATTTTCCAACATGACCAACATTTTGAAC
TTGGATGTAAGAATTTCCTTTTTTTTTGTTTTGACAGTACCCCCAGCTTCAGGGCACTAAAGCA
TCCCTTAGTCTAAGGGCAACTGAGAAAGAGATGTTTATTTGCATGAAGGGGCATATGCACAGCA
TTTCAAATCAAACTTGCGGATGCAAGCCTCTCATCCATCATGGTGAAGAATATCTCACTTTCCA
TTTTTATAAATTCTCTTAGCAATTATTTTTGTCACATCAGTAGGTTCATTTAACATCCCTAAGC
ACAGCTGGATTAAGTTTCAGCAACCCAGATTCTTTTATGCATACCATATTTGGTTAGTTAATCC
AACTAAGCAATAATAATTACTGATAGCCACCACTATCAATAATAATCCAACTAAGCAATAATAG
CCCAAGTAAGTAATAGTAATCCTTGAAATCCAGTTGCCACCAGTTTGTTTATTGAAAACACCTT
AGCTAGCCACCACTATTGACGATGGTTCAAACAATAAAGTGTGCACTCTTGCAACTTCAGTTCT
ATGTTGCCTCTCATGAGTAAAAGTTTGACATGTTTCCATTTTTATCACACGTTTAGATTGTGCA
TCATGACTTATCCTGAACGTTGTTGACCTTCCCTACCACCGATGCCATGAAATTTCTTGTCGCT
GCATCTATTTATACTTGCTTCTTATGTTCATTTCAGCTCTCAAATCACCACCCTCAGAAATACT
ATTGTATCGTGTGTAACCTATCCTCAAGAGATTAGAAATATGGAGAGTGAAAAACATATCATTT
GTAGACATCCACCAACTTATGGCAACCTCATAACAGTTCTCTCGATTGATGGTGGAGGGATTCG
AGGAATCATTCCAGCTGTTGTTCTTACCTTTCTAGAATCAGAGTTGCAGGTAAATATTTATGTT
ATACTATGAGTTCCATTTCGTGGCCAAGGCAACTCTAACTTGTCGAGAGATAAGTTCCAAGGAC
AAGGGAAAACTGGTGCTCTAGGGTTAGGAAACGGCATTTGTTTGGTTTGCTTGTTTTAAATTTA
AACCATTTAGATTCAAACTTAATTCAGTAACCATATCTTTCTATAAATTAAGACATCCTTTCGT
TTCGAAGTAGATCTTAATTCTTAAAAACCTTTTGCATTAGTGCCAGAATGAGATTTACTGATCT
TTTCTGCCATATGTTCTGTCTTTAGCCATTTCTTTTATGCAGATGTAATTGTTCAACAGTTGCT
CAGGTTTTTCAGCATTTCTTTCTGCATCGAATATTCCGAATTCATTTTTGATACGGCTGGAACA
GCCATAACAATTATTCTGCTAATTGAGAAAATCTGATTGTTATGTCCCATCTATAGATGGTGAA
TTGAATGTTGTGGTACCACCAAAAATAAACTTGGCATGCTAAATTAAATTTCCCTTTTCATTTC
AATCTCTGTTTGATCTACATGCTGACTCTCTCTCTGTAGTAGCATAACCGTGTGTGTGTGCACG
AAATGAACTGTTCAGATTATACACAGTTCATGTTCTTGACTGCTTCTCATGAAATCTTTTCTGT
TTAATTTCTCAAGAAACTTGATGGAGAGGAAGCCCGAATAGCCGACTATTTTGATGTCATTGCT
GGGACTAGCACAGGGGGGTTAGTGACTGCGATGCTGGCTGCACCAAACAAGAAAAGAAGACCAC
TTTTTGCAGCCAAGGATATTAAAGCATTTTATATGAACCATGCTCCAAAAATTTTTCCACAGCT
AAGGTGAATACATGTACTGCAGTTTTTTTTTCTGATATGATTCATAACTTGGCTGGTTGACATT
TTGCTTCTCTCTTTAGGGGTCCATTCGGTAGGATGATGAGGATATTTCGATCAATGTCAGGACC
TTCCTATGATGGCAAGCACCTTCATGAAGTTGTAAGAGAGAAATTAGGAAGCACCAGGCTGCAT
CAGACTTTAACAAATGTGGTCATACCAACTTTCGACATCAAGTGGTTACAACCAACCATTTTCT
CTTCCTACGAG
						
					

			
		

Sequences
Splice junction sequence	GAAATTAGGAAGCACCAGGCTGCATCAGACTTTAACAAATGTGGTCATACCAACTTTCGACATC AAGTGGTTACAACCAACCATTTTCTCTTCCTACGAGtgccagaaagattgacgtggaattgtta tatggcagattgatagttcatgaggtaagcaaggttactattgtaagaactgcatgagtcatga gatgatga
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: 232 Transcript exons: 17474772-17474821,17474846-17474946,17477902-17477982 TGCCAGAAAGATTGACGTGGAATTGTTATATGGCAGATTGATAGTTCATGGAACTGCATGAGTC ATGAGATGATGAGAATTTGAGAAGAGGTCTCCAATGGTACCAGCAATCGGACAGCATCCTGAAC TGAAATAGAGCCATCGTCAGCATCTGCATCAGACTTTAACAAATGTGGTCATACCAACTTTCGA CATCAAGTGGTTACAACCAACCATTTTCTCTTCCTACGAG
Genomic sequence	TGCCAGAAAGATTGACGTGGAATTGTTATATGGCAGATTGATAGTTCATGAGGTAAGCAAGGTT ACTATTGTAAGAACTGCATGAGTCATGAGATGATGAGAATTTGAGAAGAGGTCTCCAATGGTAC CAGCAATCGGACAGCATCCTGAACTGAAATAGAGCCATCGTCAGCATACTTGGTAATTACGGCT TCAATCTGTTGTGCGAGTCATACATTGCAACTCACAATCTTCTATTAAAACTTATTATAAGATG TTTGGTTTTCTATTAGACTTTCTTGTAAGCAATCACTCCTCTCATTATTAAAAAAAGAGAGTTA AAACTGACCAATTACTGCTAACGCCGCAATTAATTTTGATGAACAACATTGGTATGTTACATAT CATCATTGCTTACAGTTGTGCCCATAAAAGTTTATGGTACCATTTATCAATTATTTATTGTGAT GAAAATGTGTTGTTTGATGATGAACTGAAATTTGGGATTGGGATTTGTTATATTGGAACTTCAA AGACAGAGAGAGTATTGTAGCTGTTGAATAAAGGATGCTCCAACATTAGATACTTTGGATTTGT GACTAGTTTTCTGCAAGTTAGTATTTGTTCTTGTTTCCCTTCCTTTAGTAAATCATTCGATTAT TCTTCTGACCATTCTTTGTTCAAAAGGTCTTGAATCCTTAAATATTTTCAATATGTAATGTTTG GTATTATCATGTTGGCCTTTTCTTGGTGCAGAAGATCAGATTAGGCTTATATCTTGATATGCTG AAAGTTTACACTTCACCCCTCATTTATCTGGGCAAGGAAAGGACATCTTTTTTCTTTACTCAAT TTGATGTAGAGAATATTGTTTAGCTATAGTGCTATACAATTGTGAGTATGAAAAAAGAGAGCAT ACCTCACCACTGATGTAACAAAAATCCAGCTAAATAAAGATGGCACCAATGCAATGGAGCTTGT AACCGTTTTTCTTTCCTGTGGCTGCATACATCCCAAAATCAAATACTACAATGGCGCACCTTCT TCTGAGCTTCTATGTATGGGCTGGTATTATGATCTTGTTGCTATTTCTTGATCAATTTCGGTCA ATCAAATGAAGTAGTTCACAAATTGGCCATCTTATTCTTTTCGTAGCGTGCAAAAATGCAAGCT AGATTGGTTTGAAACAGAGCATATAAGTGAAGGTGAATTTTCCAACATGACCAACATTTTGAAC TTGGATGTAAGAATTTCCTTTTTTTTTGTTTTGACAGTACCCCCAGCTTCAGGGCACTAAAGCA TCCCTTAGTCTAAGGGCAACTGAGAAAGAGATGTTTATTTGCATGAAGGGGCATATGCACAGCA TTTCAAATCAAACTTGCGGATGCAAGCCTCTCATCCATCATGGTGAAGAATATCTCACTTTCCA TTTTTATAAATTCTCTTAGCAATTATTTTTGTCACATCAGTAGGTTCATTTAACATCCCTAAGC ACAGCTGGATTAAGTTTCAGCAACCCAGATTCTTTTATGCATACCATATTTGGTTAGTTAATCC AACTAAGCAATAATAATTACTGATAGCCACCACTATCAATAATAATCCAACTAAGCAATAATAG CCCAAGTAAGTAATAGTAATCCTTGAAATCCAGTTGCCACCAGTTTGTTTATTGAAAACACCTT AGCTAGCCACCACTATTGACGATGGTTCAAACAATAAAGTGTGCACTCTTGCAACTTCAGTTCT ATGTTGCCTCTCATGAGTAAAAGTTTGACATGTTTCCATTTTTATCACACGTTTAGATTGTGCA TCATGACTTATCCTGAACGTTGTTGACCTTCCCTACCACCGATGCCATGAAATTTCTTGTCGCT GCATCTATTTATACTTGCTTCTTATGTTCATTTCAGCTCTCAAATCACCACCCTCAGAAATACT ATTGTATCGTGTGTAACCTATCCTCAAGAGATTAGAAATATGGAGAGTGAAAAACATATCATTT GTAGACATCCACCAACTTATGGCAACCTCATAACAGTTCTCTCGATTGATGGTGGAGGGATTCG AGGAATCATTCCAGCTGTTGTTCTTACCTTTCTAGAATCAGAGTTGCAGGTAAATATTTATGTT ATACTATGAGTTCCATTTCGTGGCCAAGGCAACTCTAACTTGTCGAGAGATAAGTTCCAAGGAC AAGGGAAAACTGGTGCTCTAGGGTTAGGAAACGGCATTTGTTTGGTTTGCTTGTTTTAAATTTA AACCATTTAGATTCAAACTTAATTCAGTAACCATATCTTTCTATAAATTAAGACATCCTTTCGT TTCGAAGTAGATCTTAATTCTTAAAAACCTTTTGCATTAGTGCCAGAATGAGATTTACTGATCT TTTCTGCCATATGTTCTGTCTTTAGCCATTTCTTTTATGCAGATGTAATTGTTCAACAGTTGCT CAGGTTTTTCAGCATTTCTTTCTGCATCGAATATTCCGAATTCATTTTTGATACGGCTGGAACA GCCATAACAATTATTCTGCTAATTGAGAAAATCTGATTGTTATGTCCCATCTATAGATGGTGAA TTGAATGTTGTGGTACCACCAAAAATAAACTTGGCATGCTAAATTAAATTTCCCTTTTCATTTC AATCTCTGTTTGATCTACATGCTGACTCTCTCTCTGTAGTAGCATAACCGTGTGTGTGTGCACG AAATGAACTGTTCAGATTATACACAGTTCATGTTCTTGACTGCTTCTCATGAAATCTTTTCTGT TTAATTTCTCAAGAAACTTGATGGAGAGGAAGCCCGAATAGCCGACTATTTTGATGTCATTGCT GGGACTAGCACAGGGGGGTTAGTGACTGCGATGCTGGCTGCACCAAACAAGAAAAGAAGACCAC TTTTTGCAGCCAAGGATATTAAAGCATTTTATATGAACCATGCTCCAAAAATTTTTCCACAGCT AAGGTGAATACATGTACTGCAGTTTTTTTTTCTGATATGATTCATAACTTGGCTGGTTGACATT TTGCTTCTCTCTTTAGGGGTCCATTCGGTAGGATGATGAGGATATTTCGATCAATGTCAGGACC TTCCTATGATGGCAAGCACCTTCATGAAGTTGTAAGAGAGAAATTAGGAAGCACCAGGCTGCAT CAGACTTTAACAAATGTGGTCATACCAACTTTCGACATCAAGTGGTTACAACCAACCATTTTCT CTTCCTACGAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_008100* osi_circ_018543 						
					
						PMCS
						0.320850462

Conservation Information
Conserved circRNAs	osi_circ_008100* osi_circ_018543
PMCS	0.320850462

			
						 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
						Ye et al., 2015

circRNA

Detail information of Os09g0462400_circ_igg.1

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