Plant Circular RNA Database

Detail information of Os02g0623500_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os02g0623500_circ_g.3
					
						ID in PlantcircBase
						osa_circ_015560
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr2: 24854152-24857425  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os02g0623500						
					
						Parent gene annotation
						
							Lysyl-tRNA synthetase, class II domain containing protein. (Os02
t0623500-01);Similar to Lysyl-tRNA synthetase. (Os02t0623500-02)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os02g0622300_circ_g.1 Os02g0622350_circ_ag.1 Os02g0622300_circ_g.2 Os02g0622350_circ_g.1 Os02g0622400_circ_g.1 Os02g0622400_circ_g.2 Os02g0623400_circ_ig.1 Os02g0623500_circ_igg.1 Os02g0623500_circ_igg.2 Os02g0623500_circ_g.1 Os02g0623500_circ_g.2 Os02g0623500_circ_g.4 						
					
						Support reads
						1
					
						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
						Os02t0623500-01:5
Os02t0623500-02:5

General Information
CircRNA Name	Os02g0623500_circ_g.3
ID in PlantcircBase	osa_circ_015560
Alias	NA
Organism	Oryza sativa
Position	chr2: 24854152-24857425 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	Os02g0623500
Parent gene annotation	Lysyl-tRNA synthetase, class II domain containing protein. (Os02 t0623500-01);Similar to Lysyl-tRNA synthetase. (Os02t0623500-02)
Parent gene strand	-
Alternative splicing	Os02g0622300_circ_g.1 Os02g0622350_circ_ag.1 Os02g0622300_circ_g.2 Os02g0622350_circ_g.1 Os02g0622400_circ_g.1 Os02g0622400_circ_g.2 Os02g0623400_circ_ig.1 Os02g0623500_circ_igg.1 Os02g0623500_circ_igg.2 Os02g0623500_circ_g.1 Os02g0623500_circ_g.2 Os02g0623500_circ_g.4
Support reads	1
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	Os02t0623500-01:5 Os02t0623500-02:5

			
						 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  
						
							TACCGCTTGTCCACATCAGTTAAGCCATGGTACTTATCAGGTAGTGGGAGTAAGGATTTTGTAA
GGATTTCAAAGTTTTTCACGTAAACAGATAGTTCCCctcaattgtggtaaattcaggattatgg
cgagtggaaatgccttcattccgaaatattctcccaatctcataaactttctcaagccctccaa
cctgcatt

									
								

					

						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
						
							CTCAATTGTGGTAAATTCAGGATTATGGCGAGTGGAAATGCCTTCATTCCGAAATATTCTCCCA
ATCTCATAAACTTTCTCAAGCCCTCCAACCTGCATTTTTTTTCAGTAGTACTAAATTTGTAAAT
AAATATAAAATAGCTAAACAGTATACAGTTCGCAAAAAATTATGTTATGGTAAGATTAACATGG
CATAACAAGCATATGTGATACTTCCATTTCGATTAGTCAACATAGTAGTCAAATCTGATCCTTC
TGTACTCACAGGAATCATATTCACTACTATGTTGACTAATTGGAATCATATTCACTACTATGTT
GACTAATTGAAATGGAAGTATCACAGAAATGAATACAGATACAGAGCAGGTTAAGAAAAAAGAG
ATAGCTGCCAAACTGAAGAATAAAAACTGAATAGTAACCTCACCAGCATCCTTTTCAAATGCAG
CTCTGTTGCAATCCTCAAGTAAAGATCTCTTTGCAGTGAGTTATGGTGGGTTATAAATGGTCTT
GCTTCAGCACCACCTGCTGCTCCCTGTTTAGCCCGGTTGGAAAAAAAAAGAAAAATGACCAGAC
GATATTAATGATGACCAATAACAGTCAAATAATACAAAACAAACACTGGGGCACTGGGCAAGTC
CATTTTACCACCCCCCCCCCCCCACCCATGCTGATTAAAAAAAATGATTGCTAAGTCCATGTAA
GCTTTAACCACAAAACCATGGTAATCTATCAAAAGTTCAAAACCAGATCAGATGACACCATGGC
TTGATGCCACCCTGGTTTCCAATTCTAGTGACCTAGCATCTGAGGTGGTCTATGTGCTGAGTGC
TAACTTGGTCACTAATGAGTCAATGAGTAAAAACATTTTGTATTTTCTACCTAATTCCCTTGTG
CCAACCATGCTAAGCCAAGCAAGAGCACTGTTTACAAAATAAAAATGGCAGCAAAAAACATTTT
GCGTGCAGTGACACATTTTCGCTTGCCTGAGCAAGCTTAAAGGACGGCACTCTTCCCTTGTGTT
ACACTGTGATTAGTGTTACCACCTGCCAAGATTAAAAAGCATCCAACAAAAACAATTTCACAAT
GATCCCTGCTACATTGTGCGTACATGTCCTTGGAATGTCTATGAATTAGACTATGTAAGTCTGA
ACTGAATTTAGAGAATCTTTAGATGTATTTGCTCTTATATGTAGGTTTTGCGAAGCTCAGATTG
AGTATAACAGATTGGAGATATGTACTGTACAGAAGACTTGAAAGTTCAAAGTACGAAACATTGT
AAGAATTGGACATGGTTGTATGTCCGTTTACACCCCAGCTCCTAGCTACGAAGCAGAAGAAAAA
TTTTAGAGAATACCACCAAGTAAACTAATTTATCTTTAGAGGACTTCAACGCTGCAGCAAACTT
GCGGTAATCTCAGCCACATGGTTGTTTGTGATACCTCAGTTGGATAAGAGCTTCAAACACAAAA
TGTTGTCTTCAAAGAAAACTTAGCAATAGCACTAAAATCAAAGCTAATTGTCCATAAAAAGTAA
TAGGCCTAAAACTTTACCCAGCTAGCTTTTTCCTGAACACAGGATAGAAAAAGAACAAACATGC
CAAAACCAGGTCAGCGGAGAAGCCTCGTTTTATGTTTGGAGGGTATATGTATATTTTACCGCAT
ATTTTGATATGTTGACATAACCTTAAGTTGAAAGAGGAAAACTAAAGTTTTGCACCCTGTTTAC
ATATGTATCACGTTTTGGATCGATACACTCTCCAGCATGAACCCGTGACCTTTAGTATTGTATA
AATATGTTATTGAAAAAATATTAAGTACATTATTACAGTATTATATAATATCAGAATATTTTTA
TGGCAAATCTAATGGTTTCAGTTACACATGATATTCCAAATACCATTTCATATATCGGTAGTTA
AAAGTAAGGAAGATTTAGTAAAAAAATGTCATTGCGTCATACATTTTCAAACACAGAGCTACAT
ACCATTAATCTATTCTGTCTATATGGTCCCAATTTCTATGTTAACTCTGCCTTGTTTCAGATTC
CATGAGAAAAAGTGGATAATCCCAGCATTATCCTCTTACCAAGCCTAGCGATTAGCAATTTAAA
GAATATGCCTAGAGCACACCTGTAGAACTGGCGTTTCAACTTCTATGAAGCCAAATGATTCCAT
TGTCTTGCGGATTTCAGATACAGCCTAGGAAAAAAAACAGTTAAGACAAACTGAAATGTAGAGT
TGGTGAATCACAAATTATGCAATCTCAATAACGAATAATAAATTGCCATCCCTAGTACTATTTA
TCAAAATGAGAGCTTTGTTGAAATAAGGGCATAGAATTTCCCATCCCACAATTTCCCTATTGCC
TCCTGAACAGAAATGTTGTTCTGTACTGCATAAGATTTTACATAAATTTAAATCCCAAGTAAAA
TAATCATTTAAAGCCAAACATCATAGGCAAGTCGACTTTTCATAATTAATTACTATCTAGTCTA
GTTCACAAATTTGTCTCAACCAAAACTAAAAGGTAATTCAGCTCCCTCATGCAGTCAAAATCGC
TACCTTTGCTCTTGTTCGGAATACATCAGCAACCTCAGGATTTGCAATCATGTCAACATACCTA
TCATTGTACAAGTAAAGATAGTATATGTTAAATGTTGGAACAAAGGAATAGGAGTTTCTAGCTG
ATACTAAAACAATAGTATTAATACTCATAATAAGTGATTCGGATTTAATCAAGTACAAAATGCT
TGTATGTAATTCTCAATTTAGACAGCATCCATCATGATCATGAAACACAGGGAATAACCAAATG
AACGCAATAGATAAATATATAGAGAGAACCATTGATGGTTATAAGCCATAATAGGTGGTAACAA
GGTGTGATTGGTAGTGAAAATATGCAAATACTAAAAACGACTGATACACTTCAGGTATATTCTA
AGAGAAGATTTGCCACGCCTATACTCCGTGGGGTATGCCAGAGGTCCATAAAGCAGAATATTTA
GCTATAAAATAATTAGAATAACAATAGAACTTCCAAAGCAGATTAATGGAACAAGAAACAGCCA
AATAAAACATTCTGAGGTCCAAACTCATTATAGATGCACCGATTGTTCCTTTACTTGAAGAAAA
AAATATATAAACACAAAATAAAAGCTAACCTTTGGCGATACCGCTTGTCCACATCAGTTAAGCC
ATGGTACTTATCAGGTAGTGGGAGTAAGGATTTTGTAAGGATTTCAAAGTTTTTCACGTAAACA
GATAGTTCCC
						
					

			
		

Sequences
Splice junction sequence	TACCGCTTGTCCACATCAGTTAAGCCATGGTACTTATCAGGTAGTGGGAGTAAGGATTTTGTAA GGATTTCAAAGTTTTTCACGTAAACAGATAGTTCCCctcaattgtggtaaattcaggattatgg cgagtggaaatgccttcattccgaaatattctcccaatctcataaactttctcaagccctccaa cctgcatt
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	CTCAATTGTGGTAAATTCAGGATTATGGCGAGTGGAAATGCCTTCATTCCGAAATATTCTCCCA ATCTCATAAACTTTCTCAAGCCCTCCAACCTGCATTTTTTTTCAGTAGTACTAAATTTGTAAAT AAATATAAAATAGCTAAACAGTATACAGTTCGCAAAAAATTATGTTATGGTAAGATTAACATGG CATAACAAGCATATGTGATACTTCCATTTCGATTAGTCAACATAGTAGTCAAATCTGATCCTTC TGTACTCACAGGAATCATATTCACTACTATGTTGACTAATTGGAATCATATTCACTACTATGTT GACTAATTGAAATGGAAGTATCACAGAAATGAATACAGATACAGAGCAGGTTAAGAAAAAAGAG ATAGCTGCCAAACTGAAGAATAAAAACTGAATAGTAACCTCACCAGCATCCTTTTCAAATGCAG CTCTGTTGCAATCCTCAAGTAAAGATCTCTTTGCAGTGAGTTATGGTGGGTTATAAATGGTCTT GCTTCAGCACCACCTGCTGCTCCCTGTTTAGCCCGGTTGGAAAAAAAAAGAAAAATGACCAGAC GATATTAATGATGACCAATAACAGTCAAATAATACAAAACAAACACTGGGGCACTGGGCAAGTC CATTTTACCACCCCCCCCCCCCCACCCATGCTGATTAAAAAAAATGATTGCTAAGTCCATGTAA GCTTTAACCACAAAACCATGGTAATCTATCAAAAGTTCAAAACCAGATCAGATGACACCATGGC TTGATGCCACCCTGGTTTCCAATTCTAGTGACCTAGCATCTGAGGTGGTCTATGTGCTGAGTGC TAACTTGGTCACTAATGAGTCAATGAGTAAAAACATTTTGTATTTTCTACCTAATTCCCTTGTG CCAACCATGCTAAGCCAAGCAAGAGCACTGTTTACAAAATAAAAATGGCAGCAAAAAACATTTT GCGTGCAGTGACACATTTTCGCTTGCCTGAGCAAGCTTAAAGGACGGCACTCTTCCCTTGTGTT ACACTGTGATTAGTGTTACCACCTGCCAAGATTAAAAAGCATCCAACAAAAACAATTTCACAAT GATCCCTGCTACATTGTGCGTACATGTCCTTGGAATGTCTATGAATTAGACTATGTAAGTCTGA ACTGAATTTAGAGAATCTTTAGATGTATTTGCTCTTATATGTAGGTTTTGCGAAGCTCAGATTG AGTATAACAGATTGGAGATATGTACTGTACAGAAGACTTGAAAGTTCAAAGTACGAAACATTGT AAGAATTGGACATGGTTGTATGTCCGTTTACACCCCAGCTCCTAGCTACGAAGCAGAAGAAAAA TTTTAGAGAATACCACCAAGTAAACTAATTTATCTTTAGAGGACTTCAACGCTGCAGCAAACTT GCGGTAATCTCAGCCACATGGTTGTTTGTGATACCTCAGTTGGATAAGAGCTTCAAACACAAAA TGTTGTCTTCAAAGAAAACTTAGCAATAGCACTAAAATCAAAGCTAATTGTCCATAAAAAGTAA TAGGCCTAAAACTTTACCCAGCTAGCTTTTTCCTGAACACAGGATAGAAAAAGAACAAACATGC CAAAACCAGGTCAGCGGAGAAGCCTCGTTTTATGTTTGGAGGGTATATGTATATTTTACCGCAT ATTTTGATATGTTGACATAACCTTAAGTTGAAAGAGGAAAACTAAAGTTTTGCACCCTGTTTAC ATATGTATCACGTTTTGGATCGATACACTCTCCAGCATGAACCCGTGACCTTTAGTATTGTATA AATATGTTATTGAAAAAATATTAAGTACATTATTACAGTATTATATAATATCAGAATATTTTTA TGGCAAATCTAATGGTTTCAGTTACACATGATATTCCAAATACCATTTCATATATCGGTAGTTA AAAGTAAGGAAGATTTAGTAAAAAAATGTCATTGCGTCATACATTTTCAAACACAGAGCTACAT ACCATTAATCTATTCTGTCTATATGGTCCCAATTTCTATGTTAACTCTGCCTTGTTTCAGATTC CATGAGAAAAAGTGGATAATCCCAGCATTATCCTCTTACCAAGCCTAGCGATTAGCAATTTAAA GAATATGCCTAGAGCACACCTGTAGAACTGGCGTTTCAACTTCTATGAAGCCAAATGATTCCAT TGTCTTGCGGATTTCAGATACAGCCTAGGAAAAAAAACAGTTAAGACAAACTGAAATGTAGAGT TGGTGAATCACAAATTATGCAATCTCAATAACGAATAATAAATTGCCATCCCTAGTACTATTTA TCAAAATGAGAGCTTTGTTGAAATAAGGGCATAGAATTTCCCATCCCACAATTTCCCTATTGCC TCCTGAACAGAAATGTTGTTCTGTACTGCATAAGATTTTACATAAATTTAAATCCCAAGTAAAA TAATCATTTAAAGCCAAACATCATAGGCAAGTCGACTTTTCATAATTAATTACTATCTAGTCTA GTTCACAAATTTGTCTCAACCAAAACTAAAAGGTAATTCAGCTCCCTCATGCAGTCAAAATCGC TACCTTTGCTCTTGTTCGGAATACATCAGCAACCTCAGGATTTGCAATCATGTCAACATACCTA TCATTGTACAAGTAAAGATAGTATATGTTAAATGTTGGAACAAAGGAATAGGAGTTTCTAGCTG ATACTAAAACAATAGTATTAATACTCATAATAAGTGATTCGGATTTAATCAAGTACAAAATGCT TGTATGTAATTCTCAATTTAGACAGCATCCATCATGATCATGAAACACAGGGAATAACCAAATG AACGCAATAGATAAATATATAGAGAGAACCATTGATGGTTATAAGCCATAATAGGTGGTAACAA GGTGTGATTGGTAGTGAAAATATGCAAATACTAAAAACGACTGATACACTTCAGGTATATTCTA AGAGAAGATTTGCCACGCCTATACTCCGTGGGGTATGCCAGAGGTCCATAAAGCAGAATATTTA GCTATAAAATAATTAGAATAACAATAGAACTTCCAAAGCAGATTAATGGAACAAGAAACAGCCA AATAAAACATTCTGAGGTCCAAACTCATTATAGATGCACCGATTGTTCCTTTACTTGAAGAAAA AAATATATAAACACAAAATAAAAGCTAACCTTTGGCGATACCGCTTGTCCACATCAGTTAAGCC ATGGTACTTATCAGGTAGTGGGAGTAAGGATTTTGTAAGGATTTCAAAGTTTTTCACGTAAACA GATAGTTCCC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.212460723

Conservation Information
Conserved circRNAs	NA
PMCS	0.212460723

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							24854224-24857397(-)
24856764-24857407(-)
						
						Potential amino acid sequence
						
							MRLGEYFGMKAFPLAIILNLPQLRGTICLREKL*(-)
MIANPEVADVFRTRAKAVSEIRKTMESFGFIEVETPVLQGAAGGAEARPFITHHNSLQRDLYLR
IATELHLKRMLVGGLEKVYEIGRIFRNEGISTRHNPEFTTIEGNYLFT*(-)
						
						Sponge-miRNAs
						
							osa-miR2864.1 						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	24854224-24857397(-) 24856764-24857407(-)
Potential amino acid sequence	MRLGEYFGMKAFPLAIILNLPQLRGTICLREKL(-) MIANPEVADVFRTRAKAVSEIRKTMESFGFIEVETPVLQGAAGGAEARPFITHHNSLQRDLYLR IATELHLKRMLVGGLEKVYEIGRIFRNEGISTRHNPEFTTIEGNYLFT(-)
Sponge-miRNAs	osa-miR2864.1
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os02g0623500_circ_g.3

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