Plant Circular RNA Database

Detail information of Os07g0578600_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os07g0578600_circ_g.3
					
						ID in PlantcircBase
						osa_circ_034527
					
						Alias
						Os_ciR11049
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr7: 23420070-23420509  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer, find_circ
					
						Parent gene
						
							Os07g0578600						
					
						Parent gene annotation
						
							Similar to 5-formyltetrahydrofolate cycloligase (EC 6.3.3.2). (O
s07t0578600-01);Similar to 5-formyltetrahydrofolate cyclo-ligase
. (Os07t0578600-02);Similar to 5-formyltetrahydrofolate cyclo-li
gase. (Os07t0578600-03)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os07g0578600_circ_g.1 Os07g0578600_circ_g.2 Os07g0578600_circ_g.4 Os07g0578600_circ_g.5 						
					
						Support reads
						2/2
					
						Tissues
						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
						Os07t0578600-02:3
Os07t0578600-03:3
Os07t0578600-01:3

General Information
CircRNA Name	Os07g0578600_circ_g.3
ID in PlantcircBase	osa_circ_034527
Alias	Os_ciR11049
Organism	Oryza sativa
Position	chr7: 23420070-23420509 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ue-circRNA
Identification method	CIRCexplorer, find_circ
Parent gene	Os07g0578600
Parent gene annotation	Similar to 5-formyltetrahydrofolate cycloligase (EC 6.3.3.2). (O s07t0578600-01);Similar to 5-formyltetrahydrofolate cyclo-ligase . (Os07t0578600-02);Similar to 5-formyltetrahydrofolate cyclo-li gase. (Os07t0578600-03)
Parent gene strand	+
Alternative splicing	Os07g0578600_circ_g.1 Os07g0578600_circ_g.2 Os07g0578600_circ_g.4 Os07g0578600_circ_g.5
Support reads	2/2
Tissues	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	Os07t0578600-02:3 Os07t0578600-03:3 Os07t0578600-01:3

			
						 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  
						
							TACACTGCATCCATCACTGAACATTCAATTGAATAATGATTGTTATTCATGTAGGACAAGCTTT
TGATAGGACTGGACGAAGATTAGGACGTGGTGGAGGaacatggacatgcaaaggatctttatgt
tcctcgagtggaagataagaatcgcaatatgcggatgctcaaaatcactaccatggatgattta
gttaaaaa

						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: 247
Transcript exons: 23420070-23420228,23420347-23420388,23420464-23420509
AACATGGACATGCAAAGGATCTTTATGTTCCTCGAGTGGAAGATAAGAATCGCAATATGCGGAT
GCTCAAAATCACTACCATGGATGATTTAGTTAAAAATTCAATGAACATTCTAGAACCATCACCA
CTTGATGCTAGTGGGAATGCTCGTGAAGAAGTGTTGTCAACCTCTTCCCCTGTTGATCTTTTTC
TATTGCCTGGACAAGCTTTTGATAGGACTGGACGAAGATTAGGACGTGGTGGAGG
Transcript length: 264
Transcript exons: 23420070-23420245,23420347-23420388,23420464-23420509
AACATGGACATGCAAAGGATCTTTATGTTCCTCGAGTGGAAGATAAGAATCGCAATATGCGGAT
GCTCAAAATCACTACCATGGATGATTTAGTTAAAAATTCAATGAACATTCTAGAACCATCACCA
CTTGATGCTAGTGGGAATGCTCGTGAAGAAGGTATGAAGTTTATCTAGTGTTGTCAACCTCTTC
CCCTGTTGATCTTTTTCTATTGCCTGGACAAGCTTTTGATAGGACTGGACGAAGATTAGGACGT
GGTGGAGG
						
						Genomic sequence
						
							AACATGGACATGCAAAGGATCTTTATGTTCCTCGAGTGGAAGATAAGAATCGCAATATGCGGAT
GCTCAAAATCACTACCATGGATGATTTAGTTAAAAATTCAATGAACATTCTAGAACCATCACCA
CTTGATGCTAGTGGGAATGCTCGTGAAGAAGGTATGAAGTTTATCTAGGTGATACAATGAAACT
TTTCCTCGGTTGATTAAGTTAGTGCATCACTGGGTAGCTAATATGATTTATATGCATTACACTG
ATCCTCTTTTAATGCTTACAGTGTTGTCAACCTCTTCCCCTGTTGATCTTTTTCTATTGCCTGG
TAAGCCCTTCAATCTCTTAATACACTGCATCCATCACTGAACATTCAATTGAATAATGATTGTT
ATTCATGTAGGACAAGCTTTTGATAGGACTGGACGAAGATTAGGACGTGGTGGAGG

Sequences
Splice junction sequence	TACACTGCATCCATCACTGAACATTCAATTGAATAATGATTGTTATTCATGTAGGACAAGCTTT TGATAGGACTGGACGAAGATTAGGACGTGGTGGAGGaacatggacatgcaaaggatctttatgt tcctcgagtggaagataagaatcgcaatatgcggatgctcaaaatcactaccatggatgattta gttaaaaa
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: 247 Transcript exons: 23420070-23420228,23420347-23420388,23420464-23420509 AACATGGACATGCAAAGGATCTTTATGTTCCTCGAGTGGAAGATAAGAATCGCAATATGCGGAT GCTCAAAATCACTACCATGGATGATTTAGTTAAAAATTCAATGAACATTCTAGAACCATCACCA CTTGATGCTAGTGGGAATGCTCGTGAAGAAGTGTTGTCAACCTCTTCCCCTGTTGATCTTTTTC TATTGCCTGGACAAGCTTTTGATAGGACTGGACGAAGATTAGGACGTGGTGGAGG Transcript length: 264 Transcript exons: 23420070-23420245,23420347-23420388,23420464-23420509 AACATGGACATGCAAAGGATCTTTATGTTCCTCGAGTGGAAGATAAGAATCGCAATATGCGGAT GCTCAAAATCACTACCATGGATGATTTAGTTAAAAATTCAATGAACATTCTAGAACCATCACCA CTTGATGCTAGTGGGAATGCTCGTGAAGAAGGTATGAAGTTTATCTAGTGTTGTCAACCTCTTC CCCTGTTGATCTTTTTCTATTGCCTGGACAAGCTTTTGATAGGACTGGACGAAGATTAGGACGT GGTGGAGG
Genomic sequence	AACATGGACATGCAAAGGATCTTTATGTTCCTCGAGTGGAAGATAAGAATCGCAATATGCGGAT GCTCAAAATCACTACCATGGATGATTTAGTTAAAAATTCAATGAACATTCTAGAACCATCACCA CTTGATGCTAGTGGGAATGCTCGTGAAGAAGGTATGAAGTTTATCTAGGTGATACAATGAAACT TTTCCTCGGTTGATTAAGTTAGTGCATCACTGGGTAGCTAATATGATTTATATGCATTACACTG ATCCTCTTTTAATGCTTACAGTGTTGTCAACCTCTTCCCCTGTTGATCTTTTTCTATTGCCTGG TAAGCCCTTCAATCTCTTAATACACTGCATCCATCACTGAACATTCAATTGAATAATGATTGTT ATTCATGTAGGACAAGCTTTTGATAGGACTGGACGAAGATTAGGACGTGGTGGAGG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.297084564

Conservation Information
Conserved circRNAs	NA
PMCS	0.297084564

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							23420127-23420112(+)
23420082-23420207(-)
						
						Potential amino acid sequence
						
							MRMLKITTMDDLVKNSMNILEPSPLDASGNAREEVLSTSSPVDLFLLPGQAFDRTGRRLGRGGG
TWTCKGSLCSSSGR*(+)
MSMFLHHVLIFVQSYQKLVQAIEKDQQGKRLTTLLHEHSH*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	23420127-23420112(+) 23420082-23420207(-)
Potential amino acid sequence	MRMLKITTMDDLVKNSMNILEPSPLDASGNAREEVLSTSSPVDLFLLPGQAFDRTGRRLGRGGG TWTCKGSLCSSSGR(+) MSMFLHHVLIFVQSYQKLVQAIEKDQQGKRLTTLLHEHSH(-)
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 Os07g0578600_circ_g.3

Address

Any questions?

Supported by