Plant Circular RNA Database

Detail information of Os01g0502400_circ_g.1

			
						 General Information
					
						CircRNA Name
						Os01g0502400_circ_g.1
					
						ID in PlantcircBase
						osa_circ_001843
					
						Alias
						Os01circ13170
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr1: 17398043-17399719  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, SMALT, Segemehl
					
						Parent gene
						
							Os01g0502400						
					
						Parent gene annotation
						
							2OG-Fe(II) oxygenase domain containing protein. (Os01t0502400-01
)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os01g0502400_circ_g.2 Os01g0502400_circ_g.3 Os01g0502400_circ_g.4 Os01g0502400_circ_g.5 						
					
						Support reads
						3/3
					
						Tissues
						leaf and panicle/shoot, 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
						Os01t0502400-01:4

General Information
CircRNA Name	Os01g0502400_circ_g.1
ID in PlantcircBase	osa_circ_001843
Alias	Os01circ13170
Organism	Oryza sativa
Position	chr1: 17398043-17399719 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, SMALT, Segemehl
Parent gene	Os01g0502400
Parent gene annotation	2OG-Fe(II) oxygenase domain containing protein. (Os01t0502400-01 )
Parent gene strand	+
Alternative splicing	Os01g0502400_circ_g.2 Os01g0502400_circ_g.3 Os01g0502400_circ_g.4 Os01g0502400_circ_g.5
Support reads	3/3
Tissues	leaf and panicle/shoot, 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	Os01t0502400-01:4

			
						 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  
						
							TGTTAATCTTCAGTATTATATCCTGAGGTTGGTGGAGGAACATTAGATACACACCATGCTTTTG
TTGTTGAGTATGGGAAAGACAGGGATGTTGAACTCGgttcaaaggcacagagaatacagacaga
gaatactcaaccattataaggttagcgtttcagcatagctgacattattcgaattatctctaaa
tattttga

									
								

					

						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: 463
Transcript exons: 17398043-17398090,17399115-17399291,17399383-17399533,17
399633-17399719
GTTCAAAGGCACAGAGAATACAGACAGAGAATACTCAACCATTATAAGCCACTTCATAAAGAGC
TATACAAAATGCGCCCTTCATCGTTCTTTTTACCAACATTCCTTGAAGCTATTAGGACCAATAC
AGAAGAAAGCTTTAGAAGCATTATGACTGAGCCAGTTCCTGGTGTTTATTCATTTGCTATGTTA
CAGCCTAATTTTTGTGAGATGCTATTACAGGAGGTAGAGAACTTCGAAAAATGGGTCCACACAA
TGAAATTTAAGATAATGAGGCCAAATACAATGAACAAGTATGGTGCTGTCCTTGATGATTTTGG
CCTGGAAGTTATGCTGAACCAATTCATGGAACAGTTCATAGCTCCAATGTCTACAGTATTATAT
CCTGAGGTTGGTGGAGGAACATTAGATACACACCATGCTTTTGTTGTTGAGTATGGGAAAGACA
GGGATGTTGAACTCG
						
					

						Genomic sequence
						
							GTTCAAAGGCACAGAGAATACAGACAGAGAATACTCAACCATTATAAGGTTAGCGTTTCAGCAT
AGCTGACATTATTCGAATTATCTCTAAATATTTTGAAATGGGGGAATATGCATGTTTTTTCTTG
TGCATAACTATATTTGCACATAGAAATATGCAGTCCAGGAATTCAGGAATTATATCATATATTG
TATGATTTGTTATTTCTTTTGAGCGTTAAGCAGGGTGTGATATGAGATGTTTATGGAACAATTG
TATTGGTCCTGTACGACCAGCCATATGTGATTTCCCAGGTGATTGCATGAGCAAAATCTTTGTT
CTTGAAGAGTGCAGCTGGTTCCTGGTACAAAAGGGCACAATTGGTTGGACAAGAGGTCCGTGAA
GAGTGTAGGGTGGTAGGATACTGGAAGATCATAGATAAAAGAATTACAATCCAGGCATCCAGTA
TGCGCTAGTAATTCAATATTTACAACTGTTTGAATCAAGTATGCATGACTGTGACAGAGCACTA
CAGGTACCATGAATAATTTAGTTATGGAGAGCCTTCCGAGATTTGGTTATCCAATCAGCATTTC
CTGTGTTGGTTGCCTTGTGTGCATGATCTTAGAAAGCTGCTTATGGAATATTTATCTTATTATG
TCAAACGAATTTGGAATTAAATTTCTATGTTTACATGGCAAAATATAAAAAAATATACTTCTTT
TATTAAATGAAGTATACTTCTTTTTTATTAAAAAATATACTTCTTTCTATGTCGATATGGCAAA
ATAAATTTCTATGGCATGAGCGGTAATGAATCCCCAGACAGGAGAATTAAATGAATTGTGAGCT
GACGTGGGTTTCAGTCAACAATATGTGGGTTCCTTGATTTCACTAACAGCTAGAGCTCAAGCAA
GTGGAAATATCAATGAAACTAAATGGCACCATGTGTTTGTTACAGTTCATTCATGTGTACACTA
CAGTTGTAGTGTATGGACTGGAAGTCATCAATCTTATTGAGAAATTGAAACTAAATCTATTTGT
TTTTTGTGCTAGTAATAATAACTTATATTTTTTTTATTTTCCTGACAGCCACTTCATAAAGAGC
TATACAAAATGCGCCCTTCATCGTTCTTTTTACCAACATTCCTTGAAGCTATTAGGACCAATAC
AGAAGAAAGCTTTAGAAGCATTATGACTGAGCCAGTTCCTGGTGTTTATTCATTTGCTATGTTA
CAGCCTAATTTTTGTGAGATGCTATTACAGGAGGTATGGTAGCATATAACATACAATTTTGATA
TTGCTATATCATGTTTTGTTACAAACTTACAATGATAAAACAATGTTTTACACCTTGTAGGTAG
AGAACTTCGAAAAATGGGTCCACACAATGAAATTTAAGATAATGAGGCCAAATACAATGAACAA
GTATGGTGCTGTCCTTGATGATTTTGGCCTGGAAGTTATGCTGAACCAATTCATGGAACAGTTC
ATAGCTCCAATGTCTACAGGTTATCTTATCGACTGCTATCCTTGTTAAATAGAGGCAGAATCAC
TAGCATTTTCAAAATATATTTCCTATATTGATTTTATGCTGTGTTAATCTTCAGTATTATATCC
TGAGGTTGGTGGAGGAACATTAGATACACACCATGCTTTTGTTGTTGAGTATGGGAAAGACAGG
GATGTTGAACTCG
						
					

			
		

Sequences
Splice junction sequence	TGTTAATCTTCAGTATTATATCCTGAGGTTGGTGGAGGAACATTAGATACACACCATGCTTTTG TTGTTGAGTATGGGAAAGACAGGGATGTTGAACTCGgttcaaaggcacagagaatacagacaga gaatactcaaccattataaggttagcgtttcagcatagctgacattattcgaattatctctaaa tattttga
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: 463 Transcript exons: 17398043-17398090,17399115-17399291,17399383-17399533,17 399633-17399719 GTTCAAAGGCACAGAGAATACAGACAGAGAATACTCAACCATTATAAGCCACTTCATAAAGAGC TATACAAAATGCGCCCTTCATCGTTCTTTTTACCAACATTCCTTGAAGCTATTAGGACCAATAC AGAAGAAAGCTTTAGAAGCATTATGACTGAGCCAGTTCCTGGTGTTTATTCATTTGCTATGTTA CAGCCTAATTTTTGTGAGATGCTATTACAGGAGGTAGAGAACTTCGAAAAATGGGTCCACACAA TGAAATTTAAGATAATGAGGCCAAATACAATGAACAAGTATGGTGCTGTCCTTGATGATTTTGG CCTGGAAGTTATGCTGAACCAATTCATGGAACAGTTCATAGCTCCAATGTCTACAGTATTATAT CCTGAGGTTGGTGGAGGAACATTAGATACACACCATGCTTTTGTTGTTGAGTATGGGAAAGACA GGGATGTTGAACTCG
Genomic sequence	GTTCAAAGGCACAGAGAATACAGACAGAGAATACTCAACCATTATAAGGTTAGCGTTTCAGCAT AGCTGACATTATTCGAATTATCTCTAAATATTTTGAAATGGGGGAATATGCATGTTTTTTCTTG TGCATAACTATATTTGCACATAGAAATATGCAGTCCAGGAATTCAGGAATTATATCATATATTG TATGATTTGTTATTTCTTTTGAGCGTTAAGCAGGGTGTGATATGAGATGTTTATGGAACAATTG TATTGGTCCTGTACGACCAGCCATATGTGATTTCCCAGGTGATTGCATGAGCAAAATCTTTGTT CTTGAAGAGTGCAGCTGGTTCCTGGTACAAAAGGGCACAATTGGTTGGACAAGAGGTCCGTGAA GAGTGTAGGGTGGTAGGATACTGGAAGATCATAGATAAAAGAATTACAATCCAGGCATCCAGTA TGCGCTAGTAATTCAATATTTACAACTGTTTGAATCAAGTATGCATGACTGTGACAGAGCACTA CAGGTACCATGAATAATTTAGTTATGGAGAGCCTTCCGAGATTTGGTTATCCAATCAGCATTTC CTGTGTTGGTTGCCTTGTGTGCATGATCTTAGAAAGCTGCTTATGGAATATTTATCTTATTATG TCAAACGAATTTGGAATTAAATTTCTATGTTTACATGGCAAAATATAAAAAAATATACTTCTTT TATTAAATGAAGTATACTTCTTTTTTATTAAAAAATATACTTCTTTCTATGTCGATATGGCAAA ATAAATTTCTATGGCATGAGCGGTAATGAATCCCCAGACAGGAGAATTAAATGAATTGTGAGCT GACGTGGGTTTCAGTCAACAATATGTGGGTTCCTTGATTTCACTAACAGCTAGAGCTCAAGCAA GTGGAAATATCAATGAAACTAAATGGCACCATGTGTTTGTTACAGTTCATTCATGTGTACACTA CAGTTGTAGTGTATGGACTGGAAGTCATCAATCTTATTGAGAAATTGAAACTAAATCTATTTGT TTTTTGTGCTAGTAATAATAACTTATATTTTTTTTATTTTCCTGACAGCCACTTCATAAAGAGC TATACAAAATGCGCCCTTCATCGTTCTTTTTACCAACATTCCTTGAAGCTATTAGGACCAATAC AGAAGAAAGCTTTAGAAGCATTATGACTGAGCCAGTTCCTGGTGTTTATTCATTTGCTATGTTA CAGCCTAATTTTTGTGAGATGCTATTACAGGAGGTATGGTAGCATATAACATACAATTTTGATA TTGCTATATCATGTTTTGTTACAAACTTACAATGATAAAACAATGTTTTACACCTTGTAGGTAG AGAACTTCGAAAAATGGGTCCACACAATGAAATTTAAGATAATGAGGCCAAATACAATGAACAA GTATGGTGCTGTCCTTGATGATTTTGGCCTGGAAGTTATGCTGAACCAATTCATGGAACAGTTC ATAGCTCCAATGTCTACAGGTTATCTTATCGACTGCTATCCTTGTTAAATAGAGGCAGAATCAC TAGCATTTTCAAAATATATTTCCTATATTGATTTTATGCTGTGTTAATCTTCAGTATTATATCC TGAGGTTGGTGGAGGAACATTAGATACACACCATGCTTTTGTTGTTGAGTATGGGAAAGACAGG GATGTTGAACTCG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_009524 						
					
						PMCS
						0.274351863

Conservation Information
Conserved circRNAs	osi_circ_009524
PMCS	0.274351863

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							17399140-17398086(+)
17399676-17398086(+)
17399125-17399530(-)
						
						Potential amino acid sequence
						
							MRPSSFFLPTFLEAIRTNTEESFRSIMTEPVPGVYSFAMLQPNFCEMLLQEVENFEKWVHTMKF
KIMRPNTMNKYGAVLDDFGLEVMLNQFMEQFIAPMSTVLYPEVGGGTLDTHHAFVVEYGKDRDV
ELGSKAQRIQTENTQPL*(+)
MLLLLSMGKTGMLNSVQRHREYRQRILNHYKPLHKELYKMRPSSFFLPTFLEAIRTNTEESFRS
IMTEPVPGVYSFAMLQPNFCEMLLQEVENFEKWVHTMKFKIMRPNTMNKYGAVLDDFGLEVMLN
QFMEQFIAPMSTVLYPEVGGGTLDTHHAFVVEYGKDRDVELGSKAQRIQTENTQPL*(+)
MKWLIMVEYSLSVFSVPLNRVQHPCLSHTQQQKHGVYLMFLHQPQDIIL*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	17399140-17398086(+) 17399676-17398086(+) 17399125-17399530(-)
Potential amino acid sequence	MRPSSFFLPTFLEAIRTNTEESFRSIMTEPVPGVYSFAMLQPNFCEMLLQEVENFEKWVHTMKF KIMRPNTMNKYGAVLDDFGLEVMLNQFMEQFIAPMSTVLYPEVGGGTLDTHHAFVVEYGKDRDV ELGSKAQRIQTENTQPL(+) MLLLLSMGKTGMLNSVQRHREYRQRILNHYKPLHKELYKMRPSSFFLPTFLEAIRTNTEESFRS IMTEPVPGVYSFAMLQPNFCEMLLQEVENFEKWVHTMKFKIMRPNTMNKYGAVLDDFGLEVMLN QFMEQFIAPMSTVLYPEVGGGTLDTHHAFVVEYGKDRDVELGSKAQRIQTENTQPL(+) MKWLIMVEYSLSVFSVPLNRVQHPCLSHTQQQKHGVYLMFLHQPQDIIL*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

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

circRNA

Detail information of Os01g0502400_circ_g.1

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