Plant Circular RNA Database

Detail information of Os04g0643300_circ_g.2

			
						 General Information
					
						CircRNA Name
						Os04g0643300_circ_g.2
					
						ID in PlantcircBase
						osa_circ_025591
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr4: 32742736-32745169  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os04g0643300						
					
						Parent gene annotation
						
							Similar to 3-ketoacyl carrier protein synthase III. (Os04t064330
0-01)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os04g0643300_circ_g.1 Os04g0643300_circ_g.3 						
					
						Support reads
						1
					
						Tissues
						shoot
					
						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
						Os04t0643300-01:4

General Information
CircRNA Name	Os04g0643300_circ_g.2
ID in PlantcircBase	osa_circ_025591
Alias	NA
Organism	Oryza sativa
Position	chr4: 32742736-32745169 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	Os04g0643300
Parent gene annotation	Similar to 3-ketoacyl carrier protein synthase III. (Os04t064330 0-01)
Parent gene strand	+
Alternative splicing	Os04g0643300_circ_g.1 Os04g0643300_circ_g.3
Support reads	1
Tissues	shoot
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	Os04t0643300-01:4

			
						 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  
						
							TCTAGTAATTGGTGCCGATGCTCTTTCACAATTTGTGGATTGGACAGACAGAGGTACATGCATC
CTCTTTGGTGATGCTGCTGGTGCTGTTTTGGTTCAGggtcgtcggtatgggttcaaaactcatt
ggatgcggatcggccactccatcgcttagcgtttcaaatgatgacctttctaaaatagttgaaa
catcagat

									
								

					

						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: 508
Transcript exons: 32742736-32742884,32743446-32743582,32744848-32744950,32
745051-32745169
GGTCGTCGGTATGGGTTCAAAACTCATTGGATGCGGATCGGCCACTCCATCGCTTAGCGTTTCA
AATGATGACCTTTCTAAAATAGTTGAAACATCAGATGAATGGATCGCAGCACGGACTGGGATTC
GGAATAGGCGAGTTCTTTCAGGAAATGAGACACTGCGCGAGCTTTCAGTACAGGCAGCAAAAAA
AGCTCTTGAGATGGCTCAAGTAAATGCTGATGATGTTGACCTTGTTCTCCTTTGCACGTCTACC
CCAGATGATCTGTTTGGAGGTGCTGCTCAGGTGCTGGCGGAGGTGGGATGCGCAAATGCATTTG
GCTTTGATATCACTGCTGCATGTAGTGGGTTTATTATTGGTTTAATTACGGCTACTCGTTTTAT
CAAAGGTGGAGGCATCCGGAATATTCTAGTAATTGGTGCCGATGCTCTTTCACAATTTGTGGAT
TGGACAGACAGAGGTACATGCATCCTCTTTGGTGATGCTGCTGGTGCTGTTTTGGTTCAG
						
					

						Genomic sequence
						
							GGTCGTCGGTATGGGTTCAAAACTCATTGGATGCGGATCGGCCACTCCATCGCTTAGCGTTTCA
AATGATGACCTTTCTAAAATAGTTGAAACATCAGATGAATGGATCGCAGCACGGACTGGGATTC
GGAATAGGCGAGTTCTTTCAGGTACTTCTAGTTCACCTTATTCCATCGAGTTTCATGACAAGTT
AGTTTCATTAGCGTCAGTTGTGCCTCCTCTATGTGGATGCATAATAAATATTTGTGGCACATCA
TCATAGTTGATTGGTACATCACACCACCATTGATGATTGAAGTATTTTTACATCGTGGACTTGT
TGATTCTATGAAGAATGTTGATAGATTATAGATGAACATATGTTCTGCTACAAGGCATTTTTGT
GTCTATGGTCTAGGCTTAACAGCATCATTCAGATACCATGGCTCACAGACTATGTACGAAGATA
GATAAGAGTGAATTTTGATAATTTGCTGTTACCAAAGTAAAACTCCAGTAAACATGTATCTTGT
TACTGTTCCAAGATTGTATATAAACAGCGTGGCACTTTTCACATATTTATTCTAGTTATCTTTA
ATACAATAGATGTGAACCACACCATTGAAAGTTGGTCTTTTGTGTTGTGAACGTATTATGATCA
ATAGCTATTCAGGTGTGCAGCGTGCTTCATTTGTTTATTCTCAGGAGTAATTTATAGTTTTCAT
GTTTAGGAAATGAGACACTGCGCGAGCTTTCAGTACAGGCAGCAAAAAAAGCTCTTGAGATGGC
TCAAGTAAATGCTGATGATGTTGACCTTGTTCTCCTTTGCACGTCTACCCCAGATGATCTGTTT
GGAGGTGCTGCTCAGGTATGGCTAGAAATATGCATTAGCATTGTACTATATTGTAGTAGTTATC
GTTCACATGTTTTCTTACTACTACTTACTAAAAATATTAAGAGAAAGTAATTATCTCTCAACCT
AATATATGTCTTCAAAGATCAGAATTGCATGACATTCCCAATTGCAAGTAAGAATATTAGTATG
TTAGATGTAAATTATGTTATGTTCTGTAAAGTAATGATATTGGCCCCAATCCCATGGACCATGG
TCTTGTGTGTATTTACTTCTTAATTAGTTTTACATGTATGCCACCTGTGGGTATTGTGCGAGTT
ACTGCTTATTCCTGGTTTTGATTAAAGTCATCTCATTCTTGATAATCTACATCTGTTTGTATTT
TAATGTATAGCATAACTAGAGTGGAATGGGGTTTTCTTTAGCGTTAGGTTTATTCAATGAATTG
TTGTTCAACTCCAGTTGCTAGTATATATTTCATGTTGGAGATTGACACTTTTATATTTACTCCC
TGACCACTAGTTTTTCTATTATGAGTCTTTTTATCCTTAGGAGACATTGAGTGGTAGAGGTATA
TTCTACTGTTAATCACGATGTATGTACTCCCAAGGAATAGGACCATAAAAATATCTCCTGTTAC
ACTCCCATCTGTTGACTTGTTTTCTCTGTTTTAGACAAACATCTTAAATTTTGACCTCTAATAT
GTAACAAACAATTGAGATTGATCATGTGAAATGGTAGCATAGAAGTTTTTTTGTGGGAAAGATT
CAAAATATTATTAAATTTATACATAGCTATTAAAATGTTACGACAACAAGGTGTTGGAGATCAC
GATAGTATCCAAAACATCATATATTCTTGAATAGAGGAGTATTATGTTGTTATACATGAAGGTA
AGTATATATTACGAAAGTGTGTTTCATATTATATCCTGCAATACACACTTGACCAATCTCGATA
ATTTTTGACATACTGATGGTCAAACTAAAATGTTTGGTTGCACATTTGTATTACTTCCTATATG
TAGCATCAGATGGAGTAGCTATAAAATAATATATACACAATAACACAATGAATCCGGTCTTTGT
ATCTTTCTTATTTCCTTCTATGTTTTCTTGCCTGTTTAGTATTTTAATCGCTTTGAACTACATC
TACCAGTAAAACTATAAATTCCCATCATAAATGTATATTGATTTATTAACTTGACTGCTCTCTT
ATGTTCTTTTAAAAAAAGATGTGCACAATTTTGCATTAAAAACATCTGGTAAAAATATAAACAG
GTGCTGGCGGAGGTGGGATGCGCAAATGCATTTGGCTTTGATATCACTGCTGCATGTAGTGGGT
TTATTATTGGTTTAATTACGGCTACTCGTTTTATCAAAGGTAACTCTTTTTTTTTTCCTTGTGA
GGATTGTTGGCTATCAAACACTCACAGGAGGTTGTTGTTGTCACCTTGTTCGATTAATATATGA
CAATTTCGTAGGTGGAGGCATCCGGAATATTCTAGTAATTGGTGCCGATGCTCTTTCACAATTT
GTGGATTGGACAGACAGAGGTACATGCATCCTCTTTGGTGATGCTGCTGGTGCTGTTTTGGTTC
AG
						
					

			
		

Sequences
Splice junction sequence	TCTAGTAATTGGTGCCGATGCTCTTTCACAATTTGTGGATTGGACAGACAGAGGTACATGCATC CTCTTTGGTGATGCTGCTGGTGCTGTTTTGGTTCAGggtcgtcggtatgggttcaaaactcatt ggatgcggatcggccactccatcgcttagcgtttcaaatgatgacctttctaaaatagttgaaa catcagat
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: 508 Transcript exons: 32742736-32742884,32743446-32743582,32744848-32744950,32 745051-32745169 GGTCGTCGGTATGGGTTCAAAACTCATTGGATGCGGATCGGCCACTCCATCGCTTAGCGTTTCA AATGATGACCTTTCTAAAATAGTTGAAACATCAGATGAATGGATCGCAGCACGGACTGGGATTC GGAATAGGCGAGTTCTTTCAGGAAATGAGACACTGCGCGAGCTTTCAGTACAGGCAGCAAAAAA AGCTCTTGAGATGGCTCAAGTAAATGCTGATGATGTTGACCTTGTTCTCCTTTGCACGTCTACC CCAGATGATCTGTTTGGAGGTGCTGCTCAGGTGCTGGCGGAGGTGGGATGCGCAAATGCATTTG GCTTTGATATCACTGCTGCATGTAGTGGGTTTATTATTGGTTTAATTACGGCTACTCGTTTTAT CAAAGGTGGAGGCATCCGGAATATTCTAGTAATTGGTGCCGATGCTCTTTCACAATTTGTGGAT TGGACAGACAGAGGTACATGCATCCTCTTTGGTGATGCTGCTGGTGCTGTTTTGGTTCAG
Genomic sequence	GGTCGTCGGTATGGGTTCAAAACTCATTGGATGCGGATCGGCCACTCCATCGCTTAGCGTTTCA AATGATGACCTTTCTAAAATAGTTGAAACATCAGATGAATGGATCGCAGCACGGACTGGGATTC GGAATAGGCGAGTTCTTTCAGGTACTTCTAGTTCACCTTATTCCATCGAGTTTCATGACAAGTT AGTTTCATTAGCGTCAGTTGTGCCTCCTCTATGTGGATGCATAATAAATATTTGTGGCACATCA TCATAGTTGATTGGTACATCACACCACCATTGATGATTGAAGTATTTTTACATCGTGGACTTGT TGATTCTATGAAGAATGTTGATAGATTATAGATGAACATATGTTCTGCTACAAGGCATTTTTGT GTCTATGGTCTAGGCTTAACAGCATCATTCAGATACCATGGCTCACAGACTATGTACGAAGATA GATAAGAGTGAATTTTGATAATTTGCTGTTACCAAAGTAAAACTCCAGTAAACATGTATCTTGT TACTGTTCCAAGATTGTATATAAACAGCGTGGCACTTTTCACATATTTATTCTAGTTATCTTTA ATACAATAGATGTGAACCACACCATTGAAAGTTGGTCTTTTGTGTTGTGAACGTATTATGATCA ATAGCTATTCAGGTGTGCAGCGTGCTTCATTTGTTTATTCTCAGGAGTAATTTATAGTTTTCAT GTTTAGGAAATGAGACACTGCGCGAGCTTTCAGTACAGGCAGCAAAAAAAGCTCTTGAGATGGC TCAAGTAAATGCTGATGATGTTGACCTTGTTCTCCTTTGCACGTCTACCCCAGATGATCTGTTT GGAGGTGCTGCTCAGGTATGGCTAGAAATATGCATTAGCATTGTACTATATTGTAGTAGTTATC GTTCACATGTTTTCTTACTACTACTTACTAAAAATATTAAGAGAAAGTAATTATCTCTCAACCT AATATATGTCTTCAAAGATCAGAATTGCATGACATTCCCAATTGCAAGTAAGAATATTAGTATG TTAGATGTAAATTATGTTATGTTCTGTAAAGTAATGATATTGGCCCCAATCCCATGGACCATGG TCTTGTGTGTATTTACTTCTTAATTAGTTTTACATGTATGCCACCTGTGGGTATTGTGCGAGTT ACTGCTTATTCCTGGTTTTGATTAAAGTCATCTCATTCTTGATAATCTACATCTGTTTGTATTT TAATGTATAGCATAACTAGAGTGGAATGGGGTTTTCTTTAGCGTTAGGTTTATTCAATGAATTG TTGTTCAACTCCAGTTGCTAGTATATATTTCATGTTGGAGATTGACACTTTTATATTTACTCCC TGACCACTAGTTTTTCTATTATGAGTCTTTTTATCCTTAGGAGACATTGAGTGGTAGAGGTATA TTCTACTGTTAATCACGATGTATGTACTCCCAAGGAATAGGACCATAAAAATATCTCCTGTTAC ACTCCCATCTGTTGACTTGTTTTCTCTGTTTTAGACAAACATCTTAAATTTTGACCTCTAATAT GTAACAAACAATTGAGATTGATCATGTGAAATGGTAGCATAGAAGTTTTTTTGTGGGAAAGATT CAAAATATTATTAAATTTATACATAGCTATTAAAATGTTACGACAACAAGGTGTTGGAGATCAC GATAGTATCCAAAACATCATATATTCTTGAATAGAGGAGTATTATGTTGTTATACATGAAGGTA AGTATATATTACGAAAGTGTGTTTCATATTATATCCTGCAATACACACTTGACCAATCTCGATA ATTTTTGACATACTGATGGTCAAACTAAAATGTTTGGTTGCACATTTGTATTACTTCCTATATG TAGCATCAGATGGAGTAGCTATAAAATAATATATACACAATAACACAATGAATCCGGTCTTTGT ATCTTTCTTATTTCCTTCTATGTTTTCTTGCCTGTTTAGTATTTTAATCGCTTTGAACTACATC TACCAGTAAAACTATAAATTCCCATCATAAATGTATATTGATTTATTAACTTGACTGCTCTCTT ATGTTCTTTTAAAAAAAGATGTGCACAATTTTGCATTAAAAACATCTGGTAAAAATATAAACAG GTGCTGGCGGAGGTGGGATGCGCAAATGCATTTGGCTTTGATATCACTGCTGCATGTAGTGGGT TTATTATTGGTTTAATTACGGCTACTCGTTTTATCAAAGGTAACTCTTTTTTTTTTCCTTGTGA GGATTGTTGGCTATCAAACACTCACAGGAGGTTGTTGTTGTCACCTTGTTCGATTAATATATGA CAATTTCGTAGGTGGAGGCATCCGGAATATTCTAGTAATTGGTGCCGATGCTCTTTCACAATTT GTGGATTGGACAGACAGAGGTACATGCATCCTCTTTGGTGATGCTGCTGGTGCTGTTTTGGTTC AG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.327932426

Conservation Information
Conserved circRNAs	NA
PMCS	0.327932426

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							32742747-32742789(+)
32745088-32742789(+)
32742764-32745097(-)
						
						Potential amino acid sequence
						
							MGSKLIGCGSATPSLSVSNDDLSKIVETSDEWIAARTGIRNRRVLSGNETLRELSVQAAKKALE
MAQVNADDVDLVLLCTSTPDDLFGGAAQVLAEVGCANAFGFDITAACSGFIIGLITATRFIKGG
GIRNILVIGADALSQFVDWTDRGTCILFGDAAGAVLVQGRRYGFKTHWMRIGHSIA*(+)
MLFHNLWIGQTEVHASSLVMLLVLFWFRVVGMGSKLIGCGSATPSLSVSNDDLSKIVETSDEWI
AARTGIRNRRVLSGNETLRELSVQAAKKALEMAQVNADDVDLVLLCTSTPDDLFGGAAQVLAEV
GCANAFGFDITAACSGFIIGLITATRFIKGGGIRNILVIGADALSQFVDWTDRGTCILFGDAAG
AVLVQGRRYGFKTHWMRIGHSIA*(+)
MSFEPIPTTLNQNSTSSITKEDACTSVCPIHKL*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	32742747-32742789(+) 32745088-32742789(+) 32742764-32745097(-)
Potential amino acid sequence	MGSKLIGCGSATPSLSVSNDDLSKIVETSDEWIAARTGIRNRRVLSGNETLRELSVQAAKKALE MAQVNADDVDLVLLCTSTPDDLFGGAAQVLAEVGCANAFGFDITAACSGFIIGLITATRFIKGG GIRNILVIGADALSQFVDWTDRGTCILFGDAAGAVLVQGRRYGFKTHWMRIGHSIA(+) MLFHNLWIGQTEVHASSLVMLLVLFWFRVVGMGSKLIGCGSATPSLSVSNDDLSKIVETSDEWI AARTGIRNRRVLSGNETLRELSVQAAKKALEMAQVNADDVDLVLLCTSTPDDLFGGAAQVLAEV GCANAFGFDITAACSGFIIGLITATRFIKGGGIRNILVIGADALSQFVDWTDRGTCILFGDAAG AVLVQGRRYGFKTHWMRIGHSIA(+) MSFEPIPTTLNQNSTSSITKEDACTSVCPIHKL*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os04g0643300_circ_g.2

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