Plant Circular RNA Database

Detail information of Os08g0490000_circ_g.1

			
						 General Information
					
						CircRNA Name
						Os08g0490000_circ_g.1
					
						ID in PlantcircBase
						osa_circ_037446
					
						Alias
						Os_ciR11516
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr8: 24223483-24225962  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer, KNIFE, PcircRNA_finder, circRNA_finder, find_circ
					
						Parent gene
						
							Os08g0490000						
					
						Parent gene annotation
						
							Helix-loop-helix DNA-binding domain containing protein. (Os08t04
90000-01);Similar to Transcription factor BIM2. (Os08t0490000-02
)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os08g0490000_circ_g.2 Os08g0490000_circ_g.3 Os08g0490000_circ_g.4 						
					
						Support reads
						2/12
					
						Tissues
						root/root, seed
					
						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
						Os08t0490000-01:2
Os08t0490000-02:2

General Information
CircRNA Name	Os08g0490000_circ_g.1
ID in PlantcircBase	osa_circ_037446
Alias	Os_ciR11516
Organism	Oryza sativa
Position	chr8: 24223483-24225962 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ue-circRNA
Identification method	CIRCexplorer, KNIFE, PcircRNA_finder, circRNA_finder, find_circ
Parent gene	Os08g0490000
Parent gene annotation	Helix-loop-helix DNA-binding domain containing protein. (Os08t04 90000-01);Similar to Transcription factor BIM2. (Os08t0490000-02 )
Parent gene strand	+
Alternative splicing	Os08g0490000_circ_g.2 Os08g0490000_circ_g.3 Os08g0490000_circ_g.4
Support reads	2/12
Tissues	root/root, seed
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	Os08t0490000-01:2 Os08t0490000-02:2

			
						 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  
						
							GGTGGATTCATGGACGCCGGCTCCAGATCCAGTGGCGGCGCGGGCTTCGACGACGACGACGGCC
ATGCCGCGCGCCGCGAGGTCTCCTCCTCGCTGAAAGatttcttcctcaagacacacgacttcct
gccgcaggtagagaagagagccgaccagacaccaccgccgccgccgccgccgccgccccacgcc
gcggtcac

									
								

					

						Assembled circRNA sequence  
						
							NA
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
						
							NA						
					

						Genomic sequence
						
							ATTTCTTCCTCAAGACACACGACTTCCTGCCGCAGGTAGAGAAGAGAGCCGACCAGACACCACC
GCCGCCGCCGCCGCCGCCGCCCCACGCCGCGGTCACCGCCGAGAAGCAGCTGCTCCACCAGCAC
GCGTTGGCCGCCGCCGGCGCGTTCACCATCAACCACGCCGTGGCCGCGGCCGCCACCGCCGTCA
AGCAGGAGCCGCCCTTCGCGCCGTGGTGCCAGCCCGTCGCCGCCGTAGATCCCCGAGGTACGCC
CGTGCTCTCGTCGCTTGCGCCTTCGATCGCGATCGTCGTGAGCCGCGCCGCGCGCGTGGCGGTG
CCCGCCGGTGGTTGGGCGCGCCGCGCGCCACCTCCTCCACGTGCCCGGCGCGGCGCCTTCCTCC
TCCTCCGGTGGTTGGGGCGTCGGCGTCGCCGCCGCGCGGCGAGCACGTCGACGCACGCGCGCGA
CGCGCGTAGCTGGTGGCCACCCGCTGACACGCGGAGGCGGTAGGGGGATGGTAGGGTGGGCGGG
GCTAGGGAGTAGGCGAGTAGGCCTGGCCGGCCGCACGGGGGACGTGGGCTCGCTGGGCCCGGAT
GCGTGTGGGGGACGGGCCTGGACGTGGGCCAGAGGCTGCGTGCTGGGTGCACGTGGATAGCAGC
ATGGGCCCGGGTACGGGCCTGGTTGTGGGCCATGGGACGTGAGCACTAGAGCGCTCGCTTTTCT
GGATAGACCCGGACCACAAGTAATACTGGGACAAGCAGATGAATCCACTTTCAAACTTAAAAAA
GCTTACTTTGTATATGAATTTTATTCTATAGAATGGAGGAGGTAGTAAATCATATTGCCATTTG
TTATATATCATTGTATTATTAGGATTTTATAAGTGAAGCTTGGGCTTTACGATAAGAGTTAATT
AAAGTGTTCATAGTCCACTAAAAAAAGTGTTAATAGATTCTGTAGTATTTTTCACAGGAAACAA
TGTGACTAATGTGAAAATCATTACATCTAAGGGCTTCTTTTGAATCAAAGGAATTATGATGAAT
TTCATAAAATTAAAATTCTATATAGAGTAAATTTCACAAAACTACATATACTATGACAAAATTA
TTACAAAACTACATATTTAACTCAATGTATCACAAAACTATACATTTAACATCAAATTTATCAC
AAAACTACACATTTAAGATGAAGTGTCACAAAATTACATGTTTAGTAACTAAATTATCATAAAA
TTACAGGTTTAGAACCAATTTGATCACAAAGTAATAATGTTTATAACTCCACCATAACAATGGT
GCTAGGGATTTAAACTCCAAAAGTTGTAGTTTTGTGATAAGTTTCATATTAAATATGCATTTTT
GTGATACTTAACCTAAAATCTGCAGTTTTGTGATAAATTTGGTGCTAAATGTGTAGTTTTATGA
TACAACTCCTTAAGTATGTAGTTTTGTGATAATTTGATCAAAATACATGTAGTTTTGTGAAATT
TACTCTTCTATATAAAATTTTCATATGTAGCCCTTTTATTAAAAAGATTGAAGTTTTCCTAATC
CAATAAAATTCCTATAGAGTAATAGAATGGTTCATTACATATAAATTTTGGAGAAAACTTAGTA
AGAGGTTCAACCTCTTGAAAAAATTCTTCTGAGCCTATCTCTCACGTTCAATTTCCGTATTTTT
TCCGTGGTCCAATCAAATAATCATTCTTGTGTTTTTCATGTATTTTACAATCTTCCATTCAGAA
ATCATGTAATTTTACTATTCCTCTATTTTTTAATCATACGATTTAAAGTACCTTGAATGAATCC
TGAACCATGTAACGTGGGTAAACAATTTTTTTACCTTGAGTTTCAACTGGCAAGACTTTTGCTA
GGGCAAAGATTCGGGTTTGGATTTAAAAAAAGGATTCGGGTTTGATTCACAGCACTGTTTACCT
TACGGTTTTCTCTGTGAATATACAAGTAATAGTTGTCCTTTTGTCGTTCAGCTAACTCCTCTTT
CCATCACATGCTTATTACACTTTTTTTTTGTACTACTACAATATTCCAAGTCCAAACAGCACCT
CCAAAGGCGAGTACATGAAGATTAAATATTTAACAAACCGTAGTATCCTAAGACGTGGAAAATA
TATTCAATAATCATCCTGACAATAGACTTTGGAAACATCTAATGATTCTTTCTCTGTTCCAACT
CTTCATCCAAACACACTCCTACTAGTTGTACAGTAGTTCAGAAAAACCGGAGGAAAGGGAGCTA
AAGGCGTGTGCTTTGTGCTGTTTGTTCACCCGGCAGGTCACCAGTGGTCGCTCCCCTTCGCCGC
GCGCGCCGTCGCCGTCGCCTCCTCCAGGCCGCAGCAGCAGCAGCAGCAGCCACCGCCGCCGGAG
AGGAAGGGTGGCGGTGGATTCATGGACGCCGGCTCCAGATCCAGTGGCGGCGCGGGCTTCGACG
ACGACGACGGCCATGCCGCGCGCCGCGAGGTCTCCTCCTCGCTGAAAG
						
					

			
		

Sequences
Splice junction sequence	GGTGGATTCATGGACGCCGGCTCCAGATCCAGTGGCGGCGCGGGCTTCGACGACGACGACGGCC ATGCCGCGCGCCGCGAGGTCTCCTCCTCGCTGAAAGatttcttcctcaagacacacgacttcct gccgcaggtagagaagagagccgaccagacaccaccgccgccgccgccgccgccgccccacgcc gcggtcac
Assembled circRNA sequence	NA 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	NA
Genomic sequence	ATTTCTTCCTCAAGACACACGACTTCCTGCCGCAGGTAGAGAAGAGAGCCGACCAGACACCACC GCCGCCGCCGCCGCCGCCGCCCCACGCCGCGGTCACCGCCGAGAAGCAGCTGCTCCACCAGCAC GCGTTGGCCGCCGCCGGCGCGTTCACCATCAACCACGCCGTGGCCGCGGCCGCCACCGCCGTCA AGCAGGAGCCGCCCTTCGCGCCGTGGTGCCAGCCCGTCGCCGCCGTAGATCCCCGAGGTACGCC CGTGCTCTCGTCGCTTGCGCCTTCGATCGCGATCGTCGTGAGCCGCGCCGCGCGCGTGGCGGTG CCCGCCGGTGGTTGGGCGCGCCGCGCGCCACCTCCTCCACGTGCCCGGCGCGGCGCCTTCCTCC TCCTCCGGTGGTTGGGGCGTCGGCGTCGCCGCCGCGCGGCGAGCACGTCGACGCACGCGCGCGA CGCGCGTAGCTGGTGGCCACCCGCTGACACGCGGAGGCGGTAGGGGGATGGTAGGGTGGGCGGG GCTAGGGAGTAGGCGAGTAGGCCTGGCCGGCCGCACGGGGGACGTGGGCTCGCTGGGCCCGGAT GCGTGTGGGGGACGGGCCTGGACGTGGGCCAGAGGCTGCGTGCTGGGTGCACGTGGATAGCAGC ATGGGCCCGGGTACGGGCCTGGTTGTGGGCCATGGGACGTGAGCACTAGAGCGCTCGCTTTTCT GGATAGACCCGGACCACAAGTAATACTGGGACAAGCAGATGAATCCACTTTCAAACTTAAAAAA GCTTACTTTGTATATGAATTTTATTCTATAGAATGGAGGAGGTAGTAAATCATATTGCCATTTG TTATATATCATTGTATTATTAGGATTTTATAAGTGAAGCTTGGGCTTTACGATAAGAGTTAATT AAAGTGTTCATAGTCCACTAAAAAAAGTGTTAATAGATTCTGTAGTATTTTTCACAGGAAACAA TGTGACTAATGTGAAAATCATTACATCTAAGGGCTTCTTTTGAATCAAAGGAATTATGATGAAT TTCATAAAATTAAAATTCTATATAGAGTAAATTTCACAAAACTACATATACTATGACAAAATTA TTACAAAACTACATATTTAACTCAATGTATCACAAAACTATACATTTAACATCAAATTTATCAC AAAACTACACATTTAAGATGAAGTGTCACAAAATTACATGTTTAGTAACTAAATTATCATAAAA TTACAGGTTTAGAACCAATTTGATCACAAAGTAATAATGTTTATAACTCCACCATAACAATGGT GCTAGGGATTTAAACTCCAAAAGTTGTAGTTTTGTGATAAGTTTCATATTAAATATGCATTTTT GTGATACTTAACCTAAAATCTGCAGTTTTGTGATAAATTTGGTGCTAAATGTGTAGTTTTATGA TACAACTCCTTAAGTATGTAGTTTTGTGATAATTTGATCAAAATACATGTAGTTTTGTGAAATT TACTCTTCTATATAAAATTTTCATATGTAGCCCTTTTATTAAAAAGATTGAAGTTTTCCTAATC CAATAAAATTCCTATAGAGTAATAGAATGGTTCATTACATATAAATTTTGGAGAAAACTTAGTA AGAGGTTCAACCTCTTGAAAAAATTCTTCTGAGCCTATCTCTCACGTTCAATTTCCGTATTTTT TCCGTGGTCCAATCAAATAATCATTCTTGTGTTTTTCATGTATTTTACAATCTTCCATTCAGAA ATCATGTAATTTTACTATTCCTCTATTTTTTAATCATACGATTTAAAGTACCTTGAATGAATCC TGAACCATGTAACGTGGGTAAACAATTTTTTTACCTTGAGTTTCAACTGGCAAGACTTTTGCTA GGGCAAAGATTCGGGTTTGGATTTAAAAAAAGGATTCGGGTTTGATTCACAGCACTGTTTACCT TACGGTTTTCTCTGTGAATATACAAGTAATAGTTGTCCTTTTGTCGTTCAGCTAACTCCTCTTT CCATCACATGCTTATTACACTTTTTTTTTGTACTACTACAATATTCCAAGTCCAAACAGCACCT CCAAAGGCGAGTACATGAAGATTAAATATTTAACAAACCGTAGTATCCTAAGACGTGGAAAATA TATTCAATAATCATCCTGACAATAGACTTTGGAAACATCTAATGATTCTTTCTCTGTTCCAACT CTTCATCCAAACACACTCCTACTAGTTGTACAGTAGTTCAGAAAAACCGGAGGAAAGGGAGCTA AAGGCGTGTGCTTTGTGCTGTTTGTTCACCCGGCAGGTCACCAGTGGTCGCTCCCCTTCGCCGC GCGCGCCGTCGCCGTCGCCTCCTCCAGGCCGCAGCAGCAGCAGCAGCAGCCACCGCCGCCGGAG AGGAAGGGTGGCGGTGGATTCATGGACGCCGGCTCCAGATCCAGTGGCGGCGCGGGCTTCGACG ACGACGACGGCCATGCCGCGCGCCGCGAGGTCTCCTCCTCGCTGAAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.211569699

Conservation Information
Conserved circRNAs	NA
PMCS	0.211569699

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							24225873-24225959(+)
24225930-24223485(-)
24223641-24225762(-)
						
						Potential amino acid sequence
						
							MDAGSRSSGGAGFDDDDGHAARREVSSSLKDFFLKTHDFLPQVEKRADQTPPPPPPPPPHAAVT
AEKQLLHQHALAAAGAFTINHAVAAAATAVKQEPPFAPWCQPVAAVDPRGHQWSLPFAARAVAV
ASSRPQQQQQQPPPPERKGGGGFMDAGSRSSGGAGFDDDDGHAARREVSSSLKDFFLKTHDFLP
QVEKRADQTPPPPPPPPPHAAVTAEKQLLHQHALAAAGAFTINHAVAAAATAVKQEPPFAPWCQ
PVAAVDPRGHQWSLPFAARAVAVASSRPQQQQQQPPPPERKGGGGFMDAGSRSSGGAGFDDDDG
HAARREVSSSLKDFFLKTHDFLPQVEKRADQTPPPPPPPPPHAAVTAEKQLLHQHALAAAGAFT
INHAVAAAATAVKQEPPFAPWCQPVAAVDPRGHQWSLPFAARAVAVASSRPQQQQQQPPPPERK
GGGGFMDAGSRSSGGAGFDDDDGHAARREVSSSLK(+)
MAVVVVEARAATGSGAGVHESTATLPLRRRWLLLLLLRPGGGDGDGARGEGERPLVTSGIYGGD
GLAPRREGRLLLDGGGGRGHGVVDGERAGGGQRVLVEQLLLGGDRGVGRRRRRRRWCLVGSLLY
LRQEVVCLEEEIFQRGGDLAARGMAVVVVEARAATGSGAGVHESTATLPLRRRWLLLLLLRPGG
GDGDGARGEGERPLVTSGIYGGDGLAPRREGRLLLDGGGGRGHGVVDGERAGGGQRVLVEQLLL
GGDRGVGRRRRRRRWCLVGSLLYLRQEVVCLEEEIFQRGGDLAARGMAVVVVEARAATGSGAGV
HESTATLPLRRRWLLLLLLRPGGGDGDGARGEGERPLVTSGIYGGDGLAPRREGRLLLDGGGGR
GHGVVDGERAGGGQRVLVEQLLLGGDRGVGRRRRRRRWCLVGSLLYLRQEVVCLEEEIFQRGGD
LAARGMAVVVVEARAATGSGAGVHESTATLPLRRRWLLLLLLRPGGGDGDGARGEGERPLVTSG
IYGGDGLAPRREGRLLLDGGGGRGHGVVDGERAGGGQRVLVEQLLLGGDRGVGRRRRRRRWCLV
GSLLYLRQEVVCLEEE(-)
MVNAPAAANACWWSSCFSAVTAAWGGGGGGGGGVWSALFSTCGRKSCVLRKKSFSEEETSRRAA
WPSSSSKPAPPLDLEPASMNPPPPFLSGGGGCCCCCCGLEEATATARAAKGSDHW*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	24225873-24225959(+) 24225930-24223485(-) 24223641-24225762(-)
Potential amino acid sequence	MDAGSRSSGGAGFDDDDGHAARREVSSSLKDFFLKTHDFLPQVEKRADQTPPPPPPPPPHAAVT AEKQLLHQHALAAAGAFTINHAVAAAATAVKQEPPFAPWCQPVAAVDPRGHQWSLPFAARAVAV ASSRPQQQQQQPPPPERKGGGGFMDAGSRSSGGAGFDDDDGHAARREVSSSLKDFFLKTHDFLP QVEKRADQTPPPPPPPPPHAAVTAEKQLLHQHALAAAGAFTINHAVAAAATAVKQEPPFAPWCQ PVAAVDPRGHQWSLPFAARAVAVASSRPQQQQQQPPPPERKGGGGFMDAGSRSSGGAGFDDDDG HAARREVSSSLKDFFLKTHDFLPQVEKRADQTPPPPPPPPPHAAVTAEKQLLHQHALAAAGAFT INHAVAAAATAVKQEPPFAPWCQPVAAVDPRGHQWSLPFAARAVAVASSRPQQQQQQPPPPERK GGGGFMDAGSRSSGGAGFDDDDGHAARREVSSSLK(+) MAVVVVEARAATGSGAGVHESTATLPLRRRWLLLLLLRPGGGDGDGARGEGERPLVTSGIYGGD GLAPRREGRLLLDGGGGRGHGVVDGERAGGGQRVLVEQLLLGGDRGVGRRRRRRRWCLVGSLLY LRQEVVCLEEEIFQRGGDLAARGMAVVVVEARAATGSGAGVHESTATLPLRRRWLLLLLLRPGG GDGDGARGEGERPLVTSGIYGGDGLAPRREGRLLLDGGGGRGHGVVDGERAGGGQRVLVEQLLL GGDRGVGRRRRRRRWCLVGSLLYLRQEVVCLEEEIFQRGGDLAARGMAVVVVEARAATGSGAGV HESTATLPLRRRWLLLLLLRPGGGDGDGARGEGERPLVTSGIYGGDGLAPRREGRLLLDGGGGR GHGVVDGERAGGGQRVLVEQLLLGGDRGVGRRRRRRRWCLVGSLLYLRQEVVCLEEEIFQRGGD LAARGMAVVVVEARAATGSGAGVHESTATLPLRRRWLLLLLLRPGGGDGDGARGEGERPLVTSG IYGGDGLAPRREGRLLLDGGGGRGHGVVDGERAGGGQRVLVEQLLLGGDRGVGRRRRRRRWCLV GSLLYLRQEVVCLEEE(-) MVNAPAAANACWWSSCFSAVTAAWGGGGGGGGGVWSALFSTCGRKSCVLRKKSFSEEETSRRAA WPSSSSKPAPPLDLEPASMNPPPPFLSGGGGCCCCCCGLEEATATARAAKGSDHW*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ye et al., 2015;Chu et al., 2017

circRNA

Detail information of Os08g0490000_circ_g.1

Address

Any questions?

Supported by