Plant Circular RNA Database

Detail information of Os03g0107000_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os03g0107000_circ_g.3
					
						ID in PlantcircBase
						osa_circ_017456
					
						Alias
						Os_ciR4231
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr3: 406799-409014  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Os03g0107000						
					
						Parent gene annotation
						
							Similar to ASK20. (Os03t0107000-01)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os03g0107000_circ_g.1 Os03g0107000_circ_g.2 Os03g0107000_circ_g.4 Os03g0107000_circ_g.5 Os03g0107000_circ_g.6 Os03g0107000_circ_g.7 Os03g0107000_circ_g.8 						
					
						Support reads
						7
					
						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  
						
							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
						Os03t0107000-01:6

General Information
CircRNA Name	Os03g0107000_circ_g.3
ID in PlantcircBase	osa_circ_017456
Alias	Os_ciR4231
Organism	Oryza sativa
Position	chr3: 406799-409014 JBrowse»
Reference genome	IRGSP-1.0.38
Type	u-circRNA
Identification method	find_circ
Parent gene	Os03g0107000
Parent gene annotation	Similar to ASK20. (Os03t0107000-01)
Parent gene strand	-
Alternative splicing	Os03g0107000_circ_g.1 Os03g0107000_circ_g.2 Os03g0107000_circ_g.4 Os03g0107000_circ_g.5 Os03g0107000_circ_g.6 Os03g0107000_circ_g.7 Os03g0107000_circ_g.8
Support reads	7
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	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	Os03t0107000-01:6

			
						 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  
						
							TACCCTGTTTTTGGTCTTCAATTGGATAGTGACCTTATTTCTCTTTTGATTCAACAATGGTCTT
TATTTATGACTAATGGAATGAATGATCTTGTTTAGCctgtcaagctcttcctgcattgcaggat
caagtccatcatcaaggtcagcatcttcaaaggggtactcaacatcatcttgcacatctgagct
ttggcaag

									
								

					

						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: 1414
Transcript exons: 406799-406956,407034-407478,407638-407748,407820-408011,
408384-408608,408732-409014
CTGTCAAGCTCTTCCTGCATTGCAGGATCAAGTCCATCATCAAGGTCAGCATCTTCAAAGGGGT
ACTCAACATCATCTTGCACATCTGAGCTTTGGCAAGGTGTTCTAGAAATATTACCAGTACCCGC
ATTGAATGGAACTCCACGAGTAGCTTCCTCCTTGTTTACAGGTTCAGGATTAGCTTTTGGGGGG
TTCTTAGAATGGTCCTTTCTTCTCTTGTTCTTTTTCTTATTCTTAGAAGCTTTCCCACCTCCAG
AACCTATAAAATGGATAAACCTTTATATGAAATTGCTAAGTTTTTTCTATATAGAAATACTCTT
TGAGCAAGCTCTTTGGTTGCATGTTTGCATCTTTGCCTAAATATTGTAACCAGATTAGTTAAAA
TCGACTATAGAATTTGACCCTGGATGACAACTTAGTAGTTTACTGATTGCTCAGCGTTATTCAG
CAGAACAGGATAATCATGGTTGAATGAGACAAGGGAAACAACGAAGTTATATAGTCAATATAAC
TCACTGTAATTATACCTCCATCCCCATTTATAAAACATAGTATCTCATCCAGTGACCGCTCATC
TTTTTGCTCTTCTTGTACTTGAACATCCTTCAGTTTCTGGCGCTCCTGTAGTTCTTTCCGCTTC
TTTGCATATAATCGATTCAACAAACGGATCCTGGGATCATCATTTATATTTTTCAGGGGTTCCA
ATTTCTCTTCCTCTGTTAAGTCATCTGGCAAATGGAAAATATCACGAATTTCCTCAGGTGTCTT
TCCTTCAATTATTCGAGCAAGTGCTCGACTGGTAAGATCAACCAATGGCTTTAATTGGAGACTA
TCAGCCGCCGATGTCAGCTCACATAGTCTTTCTGTATCTATTCTGACAAACTTTTCATCAAATG
ATTTTCGCTCCTTGTTTGAGCGCCCTGGGACTTGATGAAACCGACAATAGTCAAGAATCAAACT
CAAACTTGTAGGGTTAACTCTTTCTGGGAGAGCAATTGCATGATTTTTTGATGATCCTGTTCCA
TTTTTTACTATCTCTCGACATATCATAGGGCAAAACATGGCAACCTCCTCCTCCACTTGTTGTA
TGGAACCATCAAAGCACTGAAGCCAAATATAACTCTTCAACGCCTCTGGCTTTATTACTGCCAA
CTCACTTTCTGACATTATTGCCAATTCCAGAGAAACAACAAAGCCGCCAATACAATACACCAGA
AAATTTACAAGAAACTCCTTTCGGGGTATAACACCTGCCAGTACTCCAATGGCCGGAAATTATG
TCGACAAACTTTTATCCTGTACAACAAATCACAGTACCCTGTTTTTGGTCTTCAATTGGATAGT
GACCTTATTTCTCTTTTGATTCAACAATGGTCTTTATTTATGACTAATGGAATGAATGATCTTG
TTTAGC
						
					

						Genomic sequence
						
							CTGTCAAGCTCTTCCTGCATTGCAGGATCAAGTCCATCATCAAGGTCAGCATCTTCAAAGGGGT
ACTCAACATCATCTTGCACATCTGAGCTTTGGCAAGGTGTTCTAGAAATATTACCAGTACCCGC
ATTGAATGGAACTCCACGAGTAGCTTCCTCCTATAAGTCAACAGATAAGTAAGAACTTGACTGT
TCTCCACACAACTACTCAACAAAAAACAGTGAGGACACCTAACCTTGTTTACAGGTTCAGGATT
AGCTTTTGGGGGGTTCTTAGAATGGTCCTTTCTTCTCTTGTTCTTTTTCTTATTCTTAGAAGCT
TTCCCACCTCCAGAACCTATAAAATGGATAAACCTTTATATGAAATTGCTAAGTTTTTTCTATA
TAGAAATACTCTTTGAGCAAGCTCTTTGGTTGCATGTTTGCATCTTTGCCTAAATATTGTAACC
AGATTAGTTAAAATCGACTATAGAATTTGACCCTGGATGACAACTTAGTAGTTTACTGATTGCT
CAGCGTTATTCAGCAGAACAGGATAATCATGGTTGAATGAGACAAGGGAAACAACGAAGTTATA
TAGTCAATATAACTCACTGTAATTATACCTCCATCCCCATTTATAAAACATAGTATCTCATCCA
GTGACCGCTCATCTTTTTGCTCTTCTTGTACTTGAACATCCTGAAACAAAATTAGCATAAGATT
CTTAATACATGACATTCAAACATGAACTACACTGCTGAATGGACAGGATAAATATCATTTCACA
TGGCCTACAGGCCTAATATCAGAAAGCATACTCTGATGATAATACAACAGTTTGGATTTTATCA
TATTTACCTTCAGTTTCTGGCGCTCCTGTAGTTCTTTCCGCTTCTTTGCATATAATCGATTCAA
CAAACGGATCCTGGGATCATCATTTATATTTTTCAGGGGTTCCAATTTCTCTTCCTGAATGAAT
GCAAGTTCCACAGTAAGCATCAATACATGCTGATAACTATAAGCAGACATGCGATTTGTACCTC
TGTTAAGTCATCTGGCAAATGGAAAATATCACGAATTTCCTCAGGTGTCTTTCCTTCAATTATT
CGAGCAAGTGCTCGACTGGTAAGATCAACCAATGGCTTTAATTGGAGACTATCAGCCGCCGATG
TCAGCTCACATAGTCTTTCTGTATCTATTCTGACAAACTTTTCATCAAATGATTTTCGCTCCTG
CACAATAAATGTGACCATGATATGATAACTGGAGAAATGTAAATTCATCAAATGATTATTTCCT
CTTATAACATAAAGTAAATGCCTAAGTGGCTAAAAGAATTAGCATCCTCTCCAGAAAGTTTCCC
GAAGTTCATAAGCTGAATCATGCCATGATCCTTATCGATAAAAATAGGAGTATTAAAAGAAGCA
GAATTACCCTTGAGACTATTACTTGTAACAAAACAACTACGGGAATAACATGGCTGTTACAGGA
AGCAAAATTACATAATGGTCTATACTTGCAACAGGTGGACGCCTGAAACAAGCAGAAGAGAGAA
AGCAGTAAAAAGGGAGTTGCCAGAAGACAAAACTTAAATCACGACATACCTTGTTTGAGCGCCC
TGGGACTTGATGAAACCGACAATAGTCAAGAATCAAACTCAAACTTGTAGGGTTAACTCTTTCT
GGGAGAGCAATTGCATGATTTTTTGATGATCCTGTTCCATTTTTTACTATCTCTCGACATATCA
TAGGGCAAAACATGGCAACCTCCTCCTCCACTTGTTGTATGGAACCATCAAAGCACTGAAGCCA
AATATAACTCTTCAACGCCTGTGAGTTCACAATGAAATTAAATTGGAACCAAATGAATAGCTGA
TAAGGCTGGAGAACAATTGTTTCCCCTCCAATAAACAGAAAAAATAGTTATGATCTAGAAATGC
ATAGGGGTCATACCTCTGGCTTTATTACTGCCAACTCACTTTCTGACATTATTGCCAATTCCAG
AGAAACAACAAAGCCGCCAATACAATACACCAGAAAATTTACAAGAAACTCCTTTCGGGGTATA
ACACCTGCCAGTACTCCAATGGCCGGAAATTATGTCGACAAACTTTTATCCTGTACAACAAATC
ACAGTACCCTGTTTTTGGTCTTCAATTGGATAGTGACCTTATTTCTCTTTTGATTCAACAATGG
TCTTTATTTATGACTAATGGAATGAATGATCTTGTTTAGC
						
					

			
		

Sequences
Splice junction sequence	TACCCTGTTTTTGGTCTTCAATTGGATAGTGACCTTATTTCTCTTTTGATTCAACAATGGTCTT TATTTATGACTAATGGAATGAATGATCTTGTTTAGCctgtcaagctcttcctgcattgcaggat caagtccatcatcaaggtcagcatcttcaaaggggtactcaacatcatcttgcacatctgagct ttggcaag
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: 1414 Transcript exons: 406799-406956,407034-407478,407638-407748,407820-408011, 408384-408608,408732-409014 CTGTCAAGCTCTTCCTGCATTGCAGGATCAAGTCCATCATCAAGGTCAGCATCTTCAAAGGGGT ACTCAACATCATCTTGCACATCTGAGCTTTGGCAAGGTGTTCTAGAAATATTACCAGTACCCGC ATTGAATGGAACTCCACGAGTAGCTTCCTCCTTGTTTACAGGTTCAGGATTAGCTTTTGGGGGG TTCTTAGAATGGTCCTTTCTTCTCTTGTTCTTTTTCTTATTCTTAGAAGCTTTCCCACCTCCAG AACCTATAAAATGGATAAACCTTTATATGAAATTGCTAAGTTTTTTCTATATAGAAATACTCTT TGAGCAAGCTCTTTGGTTGCATGTTTGCATCTTTGCCTAAATATTGTAACCAGATTAGTTAAAA TCGACTATAGAATTTGACCCTGGATGACAACTTAGTAGTTTACTGATTGCTCAGCGTTATTCAG CAGAACAGGATAATCATGGTTGAATGAGACAAGGGAAACAACGAAGTTATATAGTCAATATAAC TCACTGTAATTATACCTCCATCCCCATTTATAAAACATAGTATCTCATCCAGTGACCGCTCATC TTTTTGCTCTTCTTGTACTTGAACATCCTTCAGTTTCTGGCGCTCCTGTAGTTCTTTCCGCTTC TTTGCATATAATCGATTCAACAAACGGATCCTGGGATCATCATTTATATTTTTCAGGGGTTCCA ATTTCTCTTCCTCTGTTAAGTCATCTGGCAAATGGAAAATATCACGAATTTCCTCAGGTGTCTT TCCTTCAATTATTCGAGCAAGTGCTCGACTGGTAAGATCAACCAATGGCTTTAATTGGAGACTA TCAGCCGCCGATGTCAGCTCACATAGTCTTTCTGTATCTATTCTGACAAACTTTTCATCAAATG ATTTTCGCTCCTTGTTTGAGCGCCCTGGGACTTGATGAAACCGACAATAGTCAAGAATCAAACT CAAACTTGTAGGGTTAACTCTTTCTGGGAGAGCAATTGCATGATTTTTTGATGATCCTGTTCCA TTTTTTACTATCTCTCGACATATCATAGGGCAAAACATGGCAACCTCCTCCTCCACTTGTTGTA TGGAACCATCAAAGCACTGAAGCCAAATATAACTCTTCAACGCCTCTGGCTTTATTACTGCCAA CTCACTTTCTGACATTATTGCCAATTCCAGAGAAACAACAAAGCCGCCAATACAATACACCAGA AAATTTACAAGAAACTCCTTTCGGGGTATAACACCTGCCAGTACTCCAATGGCCGGAAATTATG TCGACAAACTTTTATCCTGTACAACAAATCACAGTACCCTGTTTTTGGTCTTCAATTGGATAGT GACCTTATTTCTCTTTTGATTCAACAATGGTCTTTATTTATGACTAATGGAATGAATGATCTTG TTTAGC
Genomic sequence	CTGTCAAGCTCTTCCTGCATTGCAGGATCAAGTCCATCATCAAGGTCAGCATCTTCAAAGGGGT ACTCAACATCATCTTGCACATCTGAGCTTTGGCAAGGTGTTCTAGAAATATTACCAGTACCCGC ATTGAATGGAACTCCACGAGTAGCTTCCTCCTATAAGTCAACAGATAAGTAAGAACTTGACTGT TCTCCACACAACTACTCAACAAAAAACAGTGAGGACACCTAACCTTGTTTACAGGTTCAGGATT AGCTTTTGGGGGGTTCTTAGAATGGTCCTTTCTTCTCTTGTTCTTTTTCTTATTCTTAGAAGCT TTCCCACCTCCAGAACCTATAAAATGGATAAACCTTTATATGAAATTGCTAAGTTTTTTCTATA TAGAAATACTCTTTGAGCAAGCTCTTTGGTTGCATGTTTGCATCTTTGCCTAAATATTGTAACC AGATTAGTTAAAATCGACTATAGAATTTGACCCTGGATGACAACTTAGTAGTTTACTGATTGCT CAGCGTTATTCAGCAGAACAGGATAATCATGGTTGAATGAGACAAGGGAAACAACGAAGTTATA TAGTCAATATAACTCACTGTAATTATACCTCCATCCCCATTTATAAAACATAGTATCTCATCCA GTGACCGCTCATCTTTTTGCTCTTCTTGTACTTGAACATCCTGAAACAAAATTAGCATAAGATT CTTAATACATGACATTCAAACATGAACTACACTGCTGAATGGACAGGATAAATATCATTTCACA TGGCCTACAGGCCTAATATCAGAAAGCATACTCTGATGATAATACAACAGTTTGGATTTTATCA TATTTACCTTCAGTTTCTGGCGCTCCTGTAGTTCTTTCCGCTTCTTTGCATATAATCGATTCAA CAAACGGATCCTGGGATCATCATTTATATTTTTCAGGGGTTCCAATTTCTCTTCCTGAATGAAT GCAAGTTCCACAGTAAGCATCAATACATGCTGATAACTATAAGCAGACATGCGATTTGTACCTC TGTTAAGTCATCTGGCAAATGGAAAATATCACGAATTTCCTCAGGTGTCTTTCCTTCAATTATT CGAGCAAGTGCTCGACTGGTAAGATCAACCAATGGCTTTAATTGGAGACTATCAGCCGCCGATG TCAGCTCACATAGTCTTTCTGTATCTATTCTGACAAACTTTTCATCAAATGATTTTCGCTCCTG CACAATAAATGTGACCATGATATGATAACTGGAGAAATGTAAATTCATCAAATGATTATTTCCT CTTATAACATAAAGTAAATGCCTAAGTGGCTAAAAGAATTAGCATCCTCTCCAGAAAGTTTCCC GAAGTTCATAAGCTGAATCATGCCATGATCCTTATCGATAAAAATAGGAGTATTAAAAGAAGCA GAATTACCCTTGAGACTATTACTTGTAACAAAACAACTACGGGAATAACATGGCTGTTACAGGA AGCAAAATTACATAATGGTCTATACTTGCAACAGGTGGACGCCTGAAACAAGCAGAAGAGAGAA AGCAGTAAAAAGGGAGTTGCCAGAAGACAAAACTTAAATCACGACATACCTTGTTTGAGCGCCC TGGGACTTGATGAAACCGACAATAGTCAAGAATCAAACTCAAACTTGTAGGGTTAACTCTTTCT GGGAGAGCAATTGCATGATTTTTTGATGATCCTGTTCCATTTTTTACTATCTCTCGACATATCA TAGGGCAAAACATGGCAACCTCCTCCTCCACTTGTTGTATGGAACCATCAAAGCACTGAAGCCA AATATAACTCTTCAACGCCTGTGAGTTCACAATGAAATTAAATTGGAACCAAATGAATAGCTGA TAAGGCTGGAGAACAATTGTTTCCCCTCCAATAAACAGAAAAAATAGTTATGATCTAGAAATGC ATAGGGGTCATACCTCTGGCTTTATTACTGCCAACTCACTTTCTGACATTATTGCCAATTCCAG AGAAACAACAAAGCCGCCAATACAATACACCAGAAAATTTACAAGAAACTCCTTTCGGGGTATA ACACCTGCCAGTACTCCAATGGCCGGAAATTATGTCGACAAACTTTTATCCTGTACAACAAATC ACAGTACCCTGTTTTTGGTCTTCAATTGGATAGTGACCTTATTTCTCTTTTGATTCAACAATGG TCTTTATTTATGACTAATGGAATGAATGATCTTGTTTAGC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.245273432

Conservation Information
Conserved circRNAs	NA
PMCS	0.245273432

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							409001-407232(+)
406930-409012(-)
						
						Potential amino acid sequence
						
							MILFSLSSSSCIAGSSPSSRSASSKGYSTSSCTSELWQGVLEILPVPALNGTPRVASSLFTGSG
LAFGGFLEWSFLLLFFFLFLEAFPPPEPIKWINLYMKLLSFFYIEILFEQALWLHVCIFA*(+)
MRVLVIFLEHLAKAQMCKMMLSTPLKMLTLMMDLILQCRKSLTG*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	409001-407232(+) 406930-409012(-)
Potential amino acid sequence	MILFSLSSSSCIAGSSPSSRSASSKGYSTSSCTSELWQGVLEILPVPALNGTPRVASSLFTGSG LAFGGFLEWSFLLLFFFLFLEAFPPPEPIKWINLYMKLLSFFYIEILFEQALWLHVCIFA(+) MRVLVIFLEHLAKAQMCKMMLSTPLKMLTLMMDLILQCRKSLTG(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ye et al., 2015

circRNA

Detail information of Os03g0107000_circ_g.3

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