Plant Circular RNA Database

Detail information of Os12g0640600_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os12g0640600_circ_g.3
					
						ID in PlantcircBase
						osa_circ_012523
					
						Alias
						Os_ciR2666
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr12: 27466128-27467273  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, find_circ
					
						Parent gene
						
							Os12g0640600						
					
						Parent gene annotation
						
							Similar to Carotenoid cleavage dioxygenase (Fragment). (Os12t064
0600-01)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os12g0640600_circ_g.1 Os12g0640600_circ_g.2 Os12g0640600_circ_g.4 Os12g0640600_circ_g.5 Os12g0640600_circ_g.6 Os12g0640600_circ_g.7 Os12g0640600_circ_g.8 Os12g0640600_circ_g.9 Os12g0640600_circ_g.10 Os12g0640600_circ_g.11 						
					
						Support reads
						5/1
					
						Tissues
						root/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
						Os12t0640600-01:3

General Information
CircRNA Name	Os12g0640600_circ_g.3
ID in PlantcircBase	osa_circ_012523
Alias	Os_ciR2666
Organism	Oryza sativa
Position	chr12: 27466128-27467273 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, find_circ
Parent gene	Os12g0640600
Parent gene annotation	Similar to Carotenoid cleavage dioxygenase (Fragment). (Os12t064 0600-01)
Parent gene strand	+
Alternative splicing	Os12g0640600_circ_g.1 Os12g0640600_circ_g.2 Os12g0640600_circ_g.4 Os12g0640600_circ_g.5 Os12g0640600_circ_g.6 Os12g0640600_circ_g.7 Os12g0640600_circ_g.8 Os12g0640600_circ_g.9 Os12g0640600_circ_g.10 Os12g0640600_circ_g.11
Support reads	5/1
Tissues	root/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	Os12t0640600-01:3

			
						 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  
						
							GATGCGTATCAAAGATGGGAAAGCTACCTATGTGTCGAGATATGTGAAGACTTCTCGTCTCAAG
CAAGAAGAGTATTTTGGTGGAGCAAAGTTTATGAAGgagtgcttgaatggagaatttgtcaggg
taggacccaatccaaagtttgtccctgtcgctggctatcattggtattaacccctccctctctc
tctctctc

						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: 198
Transcript exons: 27466128-27466198,27466524-27466538,27467162-27467273
GAGTGCTTGAATGGAGAATTTGTCAGGGTAGGACCCAATCCAAAGTTTGTCCCTGTCGCTGGCT
ATCATTGGTTTGATGGAGATGGAATGATCCATGCGATGCGTATCAAAGATGGGAAAGCTACCTA
TGTGTCGAGATATGTGAAGACTTCTCGTCTCAAGCAAGAAGAGTATTTTGGTGGAGCAAAGTTT
ATGAAG
						
						Genomic sequence
						
							GAGTGCTTGAATGGAGAATTTGTCAGGGTAGGACCCAATCCAAAGTTTGTCCCTGTCGCTGGCT
ATCATTGGTATTAACCCCTCCCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTAGCTTCATCAC
AATTTTCCTTTCTCTTAAAAAGACATTATTGTAAGGATTGCCATCTTGTTTTCATTAGTGCGTC
CAAACAAAAACAAACTGTACAGATTTTAAATTGTCATCCATATGGGTTTGCATTTATGCCTCTG
CTTTGATGCACATATAAGGGACAATTGTACTCTATTTTCTAAAACACAAAATACATATCCTCAT
ACCTGTTGGCCTGTTGCTTCCAATATCTGTGCATAACGTGTTTAATTGATTTCATATTCTCTGT
TTGTTTCCACAGGTTTGATGGAGATGGGTATGTCATATTAGCCTCTCTGTGGTCAGATGCATAT
CCTTAACGGCATACATATCTGCTTCTCTCTAGCTAATACATTTAATTCCCAGATAATTATTGCA
TTATCCACTTCTTTAGCAGTTGACTAAGGTCTTACTGTCTGCCCCTAAATTGGAGTTTTTTCTT
TCCAATAAGAGTCTACATGATAAAATCTATTGTTCCATGTAGTGTTTCTTAGAATTTAATTTTC
GCATGTATATTGTAGTCCATTGTTTAAAGCAAATTTTTTTTCCTCTACTGTTTAAAGATAGTGT
CAGACTGACAGATTTGCACACAGAACATTCTGATCTTCAGAGCAGATATGGCAAAATCGTTCTT
TGATGCAGATCTTACACGTTATATATCTTCATGGTTTCATGGGCATATTTGACGCTATGTATTG
CCATTTTGCAGCACTTTTAGTACTTCTAAATTTTAATGTTTTGGTGACATATTAACAGTACCTC
ATAGTTTTATAACATATTTGCAAACATGATCAAAATGTGTTCTTTTTTTTATTTTCTGGAAGTG
AAAATAGGAGTTTAACAAGGGCACGTGCGTGGAAAAATAAGATTTCAAAATGTGCATAACTTTG
TTTCTTACAGAATGATCCATGCGATGCGTATCAAAGATGGGAAAGCTACCTATGTGTCGAGATA
TGTGAAGACTTCTCGTCTCAAGCAAGAAGAGTATTTTGGTGGAGCAAAGTTTATGAAG

Sequences
Splice junction sequence	GATGCGTATCAAAGATGGGAAAGCTACCTATGTGTCGAGATATGTGAAGACTTCTCGTCTCAAG CAAGAAGAGTATTTTGGTGGAGCAAAGTTTATGAAGgagtgcttgaatggagaatttgtcaggg taggacccaatccaaagtttgtccctgtcgctggctatcattggtattaacccctccctctctc tctctctc
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: 198 Transcript exons: 27466128-27466198,27466524-27466538,27467162-27467273 GAGTGCTTGAATGGAGAATTTGTCAGGGTAGGACCCAATCCAAAGTTTGTCCCTGTCGCTGGCT ATCATTGGTTTGATGGAGATGGAATGATCCATGCGATGCGTATCAAAGATGGGAAAGCTACCTA TGTGTCGAGATATGTGAAGACTTCTCGTCTCAAGCAAGAAGAGTATTTTGGTGGAGCAAAGTTT ATGAAG
Genomic sequence	GAGTGCTTGAATGGAGAATTTGTCAGGGTAGGACCCAATCCAAAGTTTGTCCCTGTCGCTGGCT ATCATTGGTATTAACCCCTCCCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTAGCTTCATCAC AATTTTCCTTTCTCTTAAAAAGACATTATTGTAAGGATTGCCATCTTGTTTTCATTAGTGCGTC CAAACAAAAACAAACTGTACAGATTTTAAATTGTCATCCATATGGGTTTGCATTTATGCCTCTG CTTTGATGCACATATAAGGGACAATTGTACTCTATTTTCTAAAACACAAAATACATATCCTCAT ACCTGTTGGCCTGTTGCTTCCAATATCTGTGCATAACGTGTTTAATTGATTTCATATTCTCTGT TTGTTTCCACAGGTTTGATGGAGATGGGTATGTCATATTAGCCTCTCTGTGGTCAGATGCATAT CCTTAACGGCATACATATCTGCTTCTCTCTAGCTAATACATTTAATTCCCAGATAATTATTGCA TTATCCACTTCTTTAGCAGTTGACTAAGGTCTTACTGTCTGCCCCTAAATTGGAGTTTTTTCTT TCCAATAAGAGTCTACATGATAAAATCTATTGTTCCATGTAGTGTTTCTTAGAATTTAATTTTC GCATGTATATTGTAGTCCATTGTTTAAAGCAAATTTTTTTTCCTCTACTGTTTAAAGATAGTGT CAGACTGACAGATTTGCACACAGAACATTCTGATCTTCAGAGCAGATATGGCAAAATCGTTCTT TGATGCAGATCTTACACGTTATATATCTTCATGGTTTCATGGGCATATTTGACGCTATGTATTG CCATTTTGCAGCACTTTTAGTACTTCTAAATTTTAATGTTTTGGTGACATATTAACAGTACCTC ATAGTTTTATAACATATTTGCAAACATGATCAAAATGTGTTCTTTTTTTTATTTTCTGGAAGTG AAAATAGGAGTTTAACAAGGGCACGTGCGTGGAAAAATAAGATTTCAAAATGTGCATAACTTTG TTTCTTACAGAATGATCCATGCGATGCGTATCAAAGATGGGAAAGCTACCTATGTGTCGAGATA TGTGAAGACTTCTCGTCTCAAGCAAGAAGAGTATTTTGGTGGAGCAAAGTTTATGAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.240916158

Conservation Information
Conserved circRNAs	NA
PMCS	0.240916158

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							27467164-27467270(+)
27467173-27466130(-)
						
						Potential amino acid sequence
						
							MIHAMRIKDGKATYVSRYVKTSRLKQEEYFGGAKFMKECLNGEFVRVGPNPKFVPVAGYHWFDG
DGMIHAMRIKDGKATYVSRYVKTSRLKQEEYFGGAKFMKECLNGEFVRVGPNPKFVPVAGYHWF
DGDGMIHAMRIKDGKATYVSRYVKTSRLKQEEYFGGAKFMKECLNGEFVRVGPNPKFVPVAGYH
WFDGDGMIHAMRIKDGKATYVSRYVKTSRLKQEEYFGGAKFMK(+)
MDHSISIKPMIASDRDKLWIGSYPDKFSIQALLHKLCSTKILFLLETRSLHISRHIGSFPIFDT
HRMDHSISIKPMIASDRDKLWIGSYPDKFSIQALLHKLCSTKILFLLETRSLHISRHIGSFPIF
DTHRMDHSISIKPMIASDRDKLWIGSYPDKFSIQALLHKLCSTKILFLLETRSLHISRHIGSFP
IFDTHRMDHSISIKPMIASDRDKLWIGSYPDKFSIQAL(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	27467164-27467270(+) 27467173-27466130(-)
Potential amino acid sequence	MIHAMRIKDGKATYVSRYVKTSRLKQEEYFGGAKFMKECLNGEFVRVGPNPKFVPVAGYHWFDG DGMIHAMRIKDGKATYVSRYVKTSRLKQEEYFGGAKFMKECLNGEFVRVGPNPKFVPVAGYHWF DGDGMIHAMRIKDGKATYVSRYVKTSRLKQEEYFGGAKFMKECLNGEFVRVGPNPKFVPVAGYH WFDGDGMIHAMRIKDGKATYVSRYVKTSRLKQEEYFGGAKFMK(+) MDHSISIKPMIASDRDKLWIGSYPDKFSIQALLHKLCSTKILFLLETRSLHISRHIGSFPIFDT HRMDHSISIKPMIASDRDKLWIGSYPDKFSIQALLHKLCSTKILFLLETRSLHISRHIGSFPIF DTHRMDHSISIKPMIASDRDKLWIGSYPDKFSIQALLHKLCSTKILFLLETRSLHISRHIGSFP IFDTHRMDHSISIKPMIASDRDKLWIGSYPDKFSIQAL(-)
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 Os12g0640600_circ_g.3

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