Plant Circular RNA Database

Detail information of Os11g0545300_circ_g.2

			
						 General Information
					
						CircRNA Name
						Os11g0545300_circ_g.2
					
						ID in PlantcircBase
						osa_circ_009547
					
						Alias
						Os11circ06823/Os_ciR1218
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr11: 20067783-20068141  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRCexplorer, SMALT, Segemehl, find_circ
					
						Parent gene
						
							Os11g0545300						
					
						Parent gene annotation
						
							Similar to Topoisomerase 6 subunit A-like protein. (Os11t0545300
-01);Hypothetical gene. (Os11t0545300-02)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							NA						
					
						Support reads
						2/20/5
					
						Tissues
						leaf/root/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
						Os11t0545300-01:2
Os11t0545300-02:2

General Information
CircRNA Name	Os11g0545300_circ_g.2
ID in PlantcircBase	osa_circ_009547
Alias	Os11circ06823/Os_ciR1218
Organism	Oryza sativa
Position	chr11: 20067783-20068141 JBrowse»
Reference genome	IRGSP-1.0.38
Type	u-circRNA
Identification method	CIRCexplorer, SMALT, Segemehl, find_circ
Parent gene	Os11g0545300
Parent gene annotation	Similar to Topoisomerase 6 subunit A-like protein. (Os11t0545300 -01);Hypothetical gene. (Os11t0545300-02)
Parent gene strand	+
Alternative splicing	NA
Support reads	2/20/5
Tissues	leaf/root/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	Os11t0545300-01:2 Os11t0545300-02:2

			
						 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  
						
							ATAAGAAAGCTGAGATGAAATCGGCTATCCCTACATGAGAGGGAAGTCCGGTTCGGGGTGTCTA
CAATTTTCCCTCCACGTCGAAAGAACAGAACATTTGaataacggtgatggcaatgatatcgatg
aaaataagttgtcgccatgcatccattcttcagatagatcgtcgccatgacctctccaatgaag
ggggtaag

						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: 254
Transcript exons: 20067783-20067871,20067972-20068072,20068078-20068141
AATAACGGTGATGGCAATGATATCGATGAAAATAAGTTGTCGCCATGCATCCATTCTTCAGATA
GATCGTCGCCATGACCTCTCCAATGTTTATGTAGGATTTTGGCTGGGTATTGCGCTCTGCATCA
TCCATGCATCGCCGTCCTAGGTCTAGAACTTATAAGAAAGCTGAGATGAAATCGGCTATCCCGA
GAGGGAAGTCCGGTTCGGGGTGTCTACAATTTTCCCTCCACGTCGAAAGAACAGAACATTTG
Transcript length: 296
Transcript exons: 20067783-20067877,20067941-20068141
AATAACGGTGATGGCAATGATATCGATGAAAATAAGTTGTCGCCATGCATCCATTCTTCAGATA
GATCGTCGCCATGACCTCTCCAATGAAGGGGTGGCAGTTTGCGTGCAGGGGCTTGGGACATCTT
TATGTAGGATTTTGGCTGGGTATTGCGCTCTGCATCATCCATGCATCGCCGTCCTAGGTCTAGA
ACTTATAAGAAAGCTGAGATGAAATCGGCTATCCCTACATGAGAGGGAAGTCCGGTTCGGGGTG
TCTACAATTTTCCCTCCACGTCGAAAGAACAGAACATTTG
						
						Genomic sequence
						
							AATAACGGTGATGGCAATGATATCGATGAAAATAAGTTGTCGCCATGCATCCATTCTTCAGATA
GATCGTCGCCATGACCTCTCCAATGAAGGGGGTAAGTTGCTATTTCTTGTTCAGTCAGTTTTCC
TTATTTGTGTTTTCTAACGTTTAGCTATAGTGGCAGTTTGCGTGCAGGGGCTTGGGACATCTTT
ATGTAGGATTTTGGCTGGGTATTGCGCTCTGCATCATCCATGCATCGCCGTCCTAGGTCTAGAA
CTTATAAGAAAGCTGAGATGAAATCGGCTATCCCTACATGAGAGGGAAGTCCGGTTCGGGGTGT
CTACAATTTTCCCTCCACGTCGAAAGAACAGAACATTTG

Sequences
Splice junction sequence	ATAAGAAAGCTGAGATGAAATCGGCTATCCCTACATGAGAGGGAAGTCCGGTTCGGGGTGTCTA CAATTTTCCCTCCACGTCGAAAGAACAGAACATTTGaataacggtgatggcaatgatatcgatg aaaataagttgtcgccatgcatccattcttcagatagatcgtcgccatgacctctccaatgaag ggggtaag
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: 254 Transcript exons: 20067783-20067871,20067972-20068072,20068078-20068141 AATAACGGTGATGGCAATGATATCGATGAAAATAAGTTGTCGCCATGCATCCATTCTTCAGATA GATCGTCGCCATGACCTCTCCAATGTTTATGTAGGATTTTGGCTGGGTATTGCGCTCTGCATCA TCCATGCATCGCCGTCCTAGGTCTAGAACTTATAAGAAAGCTGAGATGAAATCGGCTATCCCGA GAGGGAAGTCCGGTTCGGGGTGTCTACAATTTTCCCTCCACGTCGAAAGAACAGAACATTTG Transcript length: 296 Transcript exons: 20067783-20067877,20067941-20068141 AATAACGGTGATGGCAATGATATCGATGAAAATAAGTTGTCGCCATGCATCCATTCTTCAGATA GATCGTCGCCATGACCTCTCCAATGAAGGGGTGGCAGTTTGCGTGCAGGGGCTTGGGACATCTT TATGTAGGATTTTGGCTGGGTATTGCGCTCTGCATCATCCATGCATCGCCGTCCTAGGTCTAGA ACTTATAAGAAAGCTGAGATGAAATCGGCTATCCCTACATGAGAGGGAAGTCCGGTTCGGGGTG TCTACAATTTTCCCTCCACGTCGAAAGAACAGAACATTTG
Genomic sequence	AATAACGGTGATGGCAATGATATCGATGAAAATAAGTTGTCGCCATGCATCCATTCTTCAGATA GATCGTCGCCATGACCTCTCCAATGAAGGGGGTAAGTTGCTATTTCTTGTTCAGTCAGTTTTCC TTATTTGTGTTTTCTAACGTTTAGCTATAGTGGCAGTTTGCGTGCAGGGGCTTGGGACATCTTT ATGTAGGATTTTGGCTGGGTATTGCGCTCTGCATCATCCATGCATCGCCGTCCTAGGTCTAGAA CTTATAAGAAAGCTGAGATGAAATCGGCTATCCCTACATGAGAGGGAAGTCCGGTTCGGGGTGT CTACAATTTTCCCTCCACGTCGAAAGAACAGAACATTTG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.33082637

Conservation Information
Conserved circRNAs	NA
PMCS	0.33082637

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							20068077-20067857(+)
20068017-20068074(-)
20067860-20068010(-)
20067838-20068105(-)
						
						Potential amino acid sequence
						
							MRGKSGSGCLQFSLHVERTEHLNNGDGNDIDENKLSPCIHSSDRSSP*(+)
MDDAERNTQPKSYIKMSQAPARKLPPLHWRGHGDDLSEEWMHGDNLFSSISLPSPLFKCSVLST
WRENCRHPEPDFPLM*(-)
MATIYLKNGCMATTYFHRYHCHHRYSNVLFFRRGGKIVDTPNRTSLSCRDSRFHLSFLISSRPR
TAMHG*(-)
MDAWRQLIFIDIIAITVIQMFCSFDVEGKL*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	20068077-20067857(+) 20068017-20068074(-) 20067860-20068010(-) 20067838-20068105(-)
Potential amino acid sequence	MRGKSGSGCLQFSLHVERTEHLNNGDGNDIDENKLSPCIHSSDRSSP(+) MDDAERNTQPKSYIKMSQAPARKLPPLHWRGHGDDLSEEWMHGDNLFSSISLPSPLFKCSVLST WRENCRHPEPDFPLM(-) MATIYLKNGCMATTYFHRYHCHHRYSNVLFFRRGGKIVDTPNRTSLSCRDSRFHLSFLISSRPR TAMHG(-) MDAWRQLIFIDIIAITVIQMFCSFDVEGKL(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

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

circRNA

Detail information of Os11g0545300_circ_g.2

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