Plant Circular RNA Database

Detail information of Os09g0121050_circ_g.1

			
						 General Information
					
						CircRNA Name
						Os09g0121050_circ_g.1
					
						ID in PlantcircBase
						osa_circ_038448
					
						Alias
						Os_ciR5652
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr9: 1644035-1646363  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Os09g0121050						
					
						Parent gene annotation
						
							Similar to SMC6 protein. (Os09t0121050-00)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os09g0121050_circ_g.2 						
					
						Support reads
						3
					
						Tissues
						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  
						
							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
						Os09t0121050-00:5

General Information
CircRNA Name	Os09g0121050_circ_g.1
ID in PlantcircBase	osa_circ_038448
Alias	Os_ciR5652
Organism	Oryza sativa
Position	chr9: 1644035-1646363 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	find_circ
Parent gene	Os09g0121050
Parent gene annotation	Similar to SMC6 protein. (Os09t0121050-00)
Parent gene strand	+
Alternative splicing	Os09g0121050_circ_g.2
Support reads	3
Tissues	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	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	Os09t0121050-00:5

			
						 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  
						
							AACATTTGGGGGACAGAGAGTTCGGAACCTCTTGAAGTCAATAGAAAGACAGGAAAGAAGATTC
AACATCCCGCCTCTTGGTCCTATAGGAGTTCATGTGgctgttgcactgaagattgaactagaga
gagagcatgtacgtggtacaaatgtgctaaagaatatgaacaatcgtgtgaaacaactccagaa
acaaattc

									
								

					

						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: 468
Transcript exons: 1644035-1644169,1644817-1644893,1644969-1645044,1646088-
1646162,1646259-1646363
GCTGTTGCACTGAAGATTGAACTAGAGAGAGAGCATGTACGTGGTACAAATGTGCTAAAGAATA
TGAACAATCGTGTGAAACAACTCCAGAAACAAATTCATGATTTCCGGGAGCAGTATATTCAATA
CACGCAGGATGAATCATCTAAAGCTGAGAACGACAAGTGTGAAATACAGAAGGAGATAAATTCT
CTTCATTCAAATGTTACAAGGTTAAAAGAGGAAGAAAGAGGGTTGCATGAAACACAAATGGGCA
TTGTAAAATCCATCCAAAACATGGAAACAGAGATAGTTGAAAACAGAAAGAAGATTACTCAATT
TAAAGCTCACATTCGTGATCTTCAACAACGTCAATCTGATAAGGTATCAACATTTGGGGGACAG
AGAGTTCGGAACCTCTTGAAGTCAATAGAAAGACAGGAAAGAAGATTCAACATCCCGCCTCTTG
GTCCTATAGGAGTTCATGTG
						
					

						Genomic sequence
						
							GCTGTTGCACTGAAGATTGAACTAGAGAGAGAGCATGTACGTGGTACAAATGTGCTAAAGAATA
TGAACAATCGTGTGAAACAACTCCAGAAACAAATTCATGATTTCCGGGAGCAGTATATTCAATA
CACGCAGGTTACATTTTTGGCGTTTCTTTATATGCTTCAATTTCCATGCTGGTGGGGAAGTCGT
TTAACCTCCTTACCAACTTATTTTACATATTCTAGGACTGGCTCTGCTGTCATTCTCATTTTTT
AATTGAATGTAGTATTCATGGTTAATTTCTGAAATATGTTTGAAGACAATTTGTTAAATAAATT
TTCCAGCAGACAATAGGAATCAATAAAAGTAGTTCATCTGTGTACAAATTCCAATTAAAAGGTC
AATGCAAAGCACAATCTTTTCTGTATTGCATCATATCCTGGCACGCAGGTTATGTATCTTATTG
ACAATTGTGACTAGTCACTAGTCGTAAGGTGACAAAGAGGGTATTTGTATGCAATTTTATTTAC
CTCTTAAAAGAAAGTCTTTGATTTTTCATTTTTTTTACGGTTATTATAAAAAACGAAATAATCA
GTAAAACTGCATACTACCTGTTCTTTAACATATGCTTCCAAGTGCCATGCCTCTTTATTATTTC
TGTACTACCTCCTTCCAAAATATAACAACTTCTAGCTATGTATCTGGACAAGCGCATATTTTGG
GACGGAGGGATTAGTATTTTGGCTGTACATTTTCCAGTTTTCCTATCGTATCTGAACCATTTCT
TTGTTAAACTAAAGGATGAATCATCTAAAGCTGAGAACGACAAGTGTGAAATACAGAAGGAGAT
AAATTCTCTTCATTCAAATGTTACAAGGTAACTCAGTTATCCTTATACTTTAGCAATCCTACCA
TTTCCTGGTTGTGTGATTTTGCATAATGTGCCATTTAGGTTAAAAGAGGAAGAAAGAGGGTTGC
ATGAAACACAAATGGGCATTGTAAAATCCATCCAAAACATGGAAACAGAGGTATTTGTCATCCA
ATGTGGTTACCTCTTACCTCTTACTAGCTGGTGGTAATGTACCCTAAACAAGGTTTATTCATCT
CATCTTACCTCACTATCTGGTGGTTATGTTCTCTGAGTAATGCGCTCTGTTGTATAGCCAGAAA
GTCTGCTTTCCTCTCTGATATATTAAGCTCTTGAAATATTAACAATCTTGACACTATTACCTCA
TCTATATTATACTATGATTAAATCTGATTTCATTATTACTTAATGGCCTCTATTATCTTTTGGC
CTTGTGAATATATACCTTGGATAATGGTATATGGAATATCTTTAACGGTGCGTTCTGATGTGAG
TTTGGCTTTTGCAACTCCCTCGTTGCCTATGAACACACTTCGCAAACTGCTAAACAATGTGTTT
TTTGAAAACAAAATTATATAGAAGTTTCCTTAAAAAAAATCAAATAAACCCATTTTGCAAGTTT
GCAATAATTAATAACACTCAATTAATCATGTGCTAATGGCTTGCCTCAGTTTGCGTGCCACGGA
AAATCCCACTTGAAACGCACTACCGAACTCAGCCTAAGTCATACTACTTCTCAGTCATTTGTTG
TACTTCTTTTTAGTGCTAATTAGTGTTGTTGAGAAGCTACTCGTAGAGTAGGATGCACATAACA
AAACCTCTTTTTGTATATGACATTGTCTTATTTACACGATTGTGACATGGCCCATAAGAAATGT
TGATTTCTTTTTTCTAAATGTTTTTTACGGTGATAACTTTAATGTTGTGCGATAGTACATTTAC
ATGAGAGCACTATCTTGTGAGCTGTTAAACCTGCAAGCTCATTCAGTTTCAAGCTCATTGGGCT
TTGGTTTGTATCAACTACCTTTTGAAGCTGTCTCCCTTTAATGTTTGTGTGAAGAATCATCGTT
TATAAAGTTAGAATTATGTGCACCATATGAAGTTCACAAGGAATTCCATGTTTTTCTGTATTTT
GACCAACTTTTGTCTTTGGACCATGTTGGTCTTTGTCTACAATATTTTCCAATATGTGTTATTT
TGCAGATAGTTGAAAACAGAAAGAAGATTACTCAATTTAAAGCTCACATTCGTGATCTTCAACA
ACGTCAATCTGATAAGGTCCTTTCTGATTATAACCCTGTTTCCCAAGCATAATTTTTAGTTGTA
GATATTTTGTTAGCACCTTATTTATATGCTACTGGTGCTATACCTCAGGTATCAACATTTGGGG
GACAGAGAGTTCGGAACCTCTTGAAGTCAATAGAAAGACAGGAAAGAAGATTCAACATCCCGCC
TCTTGGTCCTATAGGAGTTCATGTG
						
					

			
		

Sequences
Splice junction sequence	AACATTTGGGGGACAGAGAGTTCGGAACCTCTTGAAGTCAATAGAAAGACAGGAAAGAAGATTC AACATCCCGCCTCTTGGTCCTATAGGAGTTCATGTGgctgttgcactgaagattgaactagaga gagagcatgtacgtggtacaaatgtgctaaagaatatgaacaatcgtgtgaaacaactccagaa acaaattc
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: 468 Transcript exons: 1644035-1644169,1644817-1644893,1644969-1645044,1646088- 1646162,1646259-1646363 GCTGTTGCACTGAAGATTGAACTAGAGAGAGAGCATGTACGTGGTACAAATGTGCTAAAGAATA TGAACAATCGTGTGAAACAACTCCAGAAACAAATTCATGATTTCCGGGAGCAGTATATTCAATA CACGCAGGATGAATCATCTAAAGCTGAGAACGACAAGTGTGAAATACAGAAGGAGATAAATTCT CTTCATTCAAATGTTACAAGGTTAAAAGAGGAAGAAAGAGGGTTGCATGAAACACAAATGGGCA TTGTAAAATCCATCCAAAACATGGAAACAGAGATAGTTGAAAACAGAAAGAAGATTACTCAATT TAAAGCTCACATTCGTGATCTTCAACAACGTCAATCTGATAAGGTATCAACATTTGGGGGACAG AGAGTTCGGAACCTCTTGAAGTCAATAGAAAGACAGGAAAGAAGATTCAACATCCCGCCTCTTG GTCCTATAGGAGTTCATGTG
Genomic sequence	GCTGTTGCACTGAAGATTGAACTAGAGAGAGAGCATGTACGTGGTACAAATGTGCTAAAGAATA TGAACAATCGTGTGAAACAACTCCAGAAACAAATTCATGATTTCCGGGAGCAGTATATTCAATA CACGCAGGTTACATTTTTGGCGTTTCTTTATATGCTTCAATTTCCATGCTGGTGGGGAAGTCGT TTAACCTCCTTACCAACTTATTTTACATATTCTAGGACTGGCTCTGCTGTCATTCTCATTTTTT AATTGAATGTAGTATTCATGGTTAATTTCTGAAATATGTTTGAAGACAATTTGTTAAATAAATT TTCCAGCAGACAATAGGAATCAATAAAAGTAGTTCATCTGTGTACAAATTCCAATTAAAAGGTC AATGCAAAGCACAATCTTTTCTGTATTGCATCATATCCTGGCACGCAGGTTATGTATCTTATTG ACAATTGTGACTAGTCACTAGTCGTAAGGTGACAAAGAGGGTATTTGTATGCAATTTTATTTAC CTCTTAAAAGAAAGTCTTTGATTTTTCATTTTTTTTACGGTTATTATAAAAAACGAAATAATCA GTAAAACTGCATACTACCTGTTCTTTAACATATGCTTCCAAGTGCCATGCCTCTTTATTATTTC TGTACTACCTCCTTCCAAAATATAACAACTTCTAGCTATGTATCTGGACAAGCGCATATTTTGG GACGGAGGGATTAGTATTTTGGCTGTACATTTTCCAGTTTTCCTATCGTATCTGAACCATTTCT TTGTTAAACTAAAGGATGAATCATCTAAAGCTGAGAACGACAAGTGTGAAATACAGAAGGAGAT AAATTCTCTTCATTCAAATGTTACAAGGTAACTCAGTTATCCTTATACTTTAGCAATCCTACCA TTTCCTGGTTGTGTGATTTTGCATAATGTGCCATTTAGGTTAAAAGAGGAAGAAAGAGGGTTGC ATGAAACACAAATGGGCATTGTAAAATCCATCCAAAACATGGAAACAGAGGTATTTGTCATCCA ATGTGGTTACCTCTTACCTCTTACTAGCTGGTGGTAATGTACCCTAAACAAGGTTTATTCATCT CATCTTACCTCACTATCTGGTGGTTATGTTCTCTGAGTAATGCGCTCTGTTGTATAGCCAGAAA GTCTGCTTTCCTCTCTGATATATTAAGCTCTTGAAATATTAACAATCTTGACACTATTACCTCA TCTATATTATACTATGATTAAATCTGATTTCATTATTACTTAATGGCCTCTATTATCTTTTGGC CTTGTGAATATATACCTTGGATAATGGTATATGGAATATCTTTAACGGTGCGTTCTGATGTGAG TTTGGCTTTTGCAACTCCCTCGTTGCCTATGAACACACTTCGCAAACTGCTAAACAATGTGTTT TTTGAAAACAAAATTATATAGAAGTTTCCTTAAAAAAAATCAAATAAACCCATTTTGCAAGTTT GCAATAATTAATAACACTCAATTAATCATGTGCTAATGGCTTGCCTCAGTTTGCGTGCCACGGA AAATCCCACTTGAAACGCACTACCGAACTCAGCCTAAGTCATACTACTTCTCAGTCATTTGTTG TACTTCTTTTTAGTGCTAATTAGTGTTGTTGAGAAGCTACTCGTAGAGTAGGATGCACATAACA AAACCTCTTTTTGTATATGACATTGTCTTATTTACACGATTGTGACATGGCCCATAAGAAATGT TGATTTCTTTTTTCTAAATGTTTTTTACGGTGATAACTTTAATGTTGTGCGATAGTACATTTAC ATGAGAGCACTATCTTGTGAGCTGTTAAACCTGCAAGCTCATTCAGTTTCAAGCTCATTGGGCT TTGGTTTGTATCAACTACCTTTTGAAGCTGTCTCCCTTTAATGTTTGTGTGAAGAATCATCGTT TATAAAGTTAGAATTATGTGCACCATATGAAGTTCACAAGGAATTCCATGTTTTTCTGTATTTT GACCAACTTTTGTCTTTGGACCATGTTGGTCTTTGTCTACAATATTTTCCAATATGTGTTATTT TGCAGATAGTTGAAAACAGAAAGAAGATTACTCAATTTAAAGCTCACATTCGTGATCTTCAACA ACGTCAATCTGATAAGGTCCTTTCTGATTATAACCCTGTTTCCCAAGCATAATTTTTAGTTGTA GATATTTTGTTAGCACCTTATTTATATGCTACTGGTGCTATACCTCAGGTATCAACATTTGGGG GACAGAGAGTTCGGAACCTCTTGAAGTCAATAGAAAGACAGGAAAGAAGATTCAACATCCCGCC TCTTGGTCCTATAGGAGTTCATGTG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.196950487

Conservation Information
Conserved circRNAs	NA
PMCS	0.196950487

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							1644099-1646360(+)
1644828-1646349(-)
						
						Potential amino acid sequence
						
							MNNRVKQLQKQIHDFREQYIQYTQDESSKAENDKCEIQKEINSLHSNVTRLKEEERGLHETQMG
IVKSIQNMETEIVENRKKITQFKAHIRDLQQRQSDKVSTFGGQRVRNLLKSIERQERRFNIPPL
GPIGVHVAVALKIELEREHVRGTNVLKNMNNRVKQLQKQIHDFREQYIQYTQDESSKAENDKCE
IQKEINSLHSNVTRLKEEERGLHETQMGIVKSIQNMETEIVENRKKITQFKAHIRDLQQRQSDK
VSTFGGQRVRNLLKSIERQERRFNIPPLGPIGVHVAVALKIELEREHVRGTNVLKNMNNRVKQL
QKQIHDFREQYIQYTQDESSKAENDKCEIQKEINSLHSNVTRLKEEERGLHETQMGIVKSIQNM
ETEIVENRKKITQFKAHIRDLQQRQSDKVSTFGGQRVRNLLKSIERQERRFNIPPLGPIGVHVA
VALKIELEREHVRGTNVLKNMNNRVKQLQKQIHDFREQYIQYTQDESSKAENDKCEIQKEINSL
HSNVTRLKEEERGLHETQMGIVKSIQNMETEIVENRKKITQFKAHIRDLQQRQSDKVSTFGGQR
VRNLLKSIERQERRFNIPPLGPIGVHV(+)
MIHPACIEYTAPGNHEFVSGVVSHDCSYSLAHLYHVHALSLVQSSVQQPHELL*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	1644099-1646360(+) 1644828-1646349(-)
Potential amino acid sequence	MNNRVKQLQKQIHDFREQYIQYTQDESSKAENDKCEIQKEINSLHSNVTRLKEEERGLHETQMG IVKSIQNMETEIVENRKKITQFKAHIRDLQQRQSDKVSTFGGQRVRNLLKSIERQERRFNIPPL GPIGVHVAVALKIELEREHVRGTNVLKNMNNRVKQLQKQIHDFREQYIQYTQDESSKAENDKCE IQKEINSLHSNVTRLKEEERGLHETQMGIVKSIQNMETEIVENRKKITQFKAHIRDLQQRQSDK VSTFGGQRVRNLLKSIERQERRFNIPPLGPIGVHVAVALKIELEREHVRGTNVLKNMNNRVKQL QKQIHDFREQYIQYTQDESSKAENDKCEIQKEINSLHSNVTRLKEEERGLHETQMGIVKSIQNM ETEIVENRKKITQFKAHIRDLQQRQSDKVSTFGGQRVRNLLKSIERQERRFNIPPLGPIGVHVA VALKIELEREHVRGTNVLKNMNNRVKQLQKQIHDFREQYIQYTQDESSKAENDKCEIQKEINSL HSNVTRLKEEERGLHETQMGIVKSIQNMETEIVENRKKITQFKAHIRDLQQRQSDKVSTFGGQR VRNLLKSIERQERRFNIPPLGPIGVHV(+) MIHPACIEYTAPGNHEFVSGVVSHDCSYSLAHLYHVHALSLVQSSVQQPHELL*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ye et al., 2015

circRNA

Detail information of Os09g0121050_circ_g.1

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