Plant Circular RNA Database

Detail information of Os04g0278550_circ_g.1

			
						 General Information
					
						CircRNA Name
						Os04g0278550_circ_g.1
					
						ID in PlantcircBase
						osa_circ_023260
					
						Alias
						Os_ciR2122
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr4: 11767566-11768928  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ei-circRNA							
									
						Identification method
						CIRCexplorer, find_circ
					
						Parent gene
						
							Os04g0278550						
					
						Parent gene annotation
						
							Hypothetical protein. (Os04t0278550-00)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os04g0278200_circ_g.1 Os04g0278550_circ_g.2 Os04g0278550_circ_g.3 Os04g0278550_circ_g.4 Os04g0278550_circ_g.5 Os04g0278550_circ_g.6 Os04g0278550_circ_g.7 Os04g0278550_circ_g.8 Os04g0278550_circ_g.9 Os04g0278550_circ_g.10 Os04g0278550_circ_g.11 Os04g0278550_circ_g.12 Os04g0278550_circ_g.13 Os04g0278550_circ_g.14 Os04g0278550_circ_g.15 Os04g0278550_circ_g.16 Os04g0278550_circ_g.17 Os04g0278550_circ_g.18 Os04g0278550_circ_g.19 						
					
						Support reads
						7/2
					
						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
						Os04t0278200-02:2
Os04t0278200-01:2
Os04t0278200-02:2
Os04t0278550-00:2
Os04t0278200-01:2

General Information
CircRNA Name	Os04g0278550_circ_g.1
ID in PlantcircBase	osa_circ_023260
Alias	Os_ciR2122
Organism	Oryza sativa
Position	chr4: 11767566-11768928 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ei-circRNA
Identification method	CIRCexplorer, find_circ
Parent gene	Os04g0278550
Parent gene annotation	Hypothetical protein. (Os04t0278550-00)
Parent gene strand	-
Alternative splicing	Os04g0278200_circ_g.1 Os04g0278550_circ_g.2 Os04g0278550_circ_g.3 Os04g0278550_circ_g.4 Os04g0278550_circ_g.5 Os04g0278550_circ_g.6 Os04g0278550_circ_g.7 Os04g0278550_circ_g.8 Os04g0278550_circ_g.9 Os04g0278550_circ_g.10 Os04g0278550_circ_g.11 Os04g0278550_circ_g.12 Os04g0278550_circ_g.13 Os04g0278550_circ_g.14 Os04g0278550_circ_g.15 Os04g0278550_circ_g.16 Os04g0278550_circ_g.17 Os04g0278550_circ_g.18 Os04g0278550_circ_g.19
Support reads	7/2
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	Os04t0278200-02:2 Os04t0278200-01:2 Os04t0278200-02:2 Os04t0278550-00:2 Os04t0278200-01:2

			
						 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  
						
							CTGAGTTTTATAGGTTAAAGAAAGAATACGAGAAGGCTGAGCTATTGTATCTGGAAGCAATTGA
AATCCTGGAAGAATCATTTGGATCGGACGATATAAGagaaacctagatgaagctgagaagtttt
tccaggcagccctacatgaagcgaaagaaggatttggactgagagatccacatgttgcgtcagc
ccttaaca

									
								

					

						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: 206
Transcript exons: 11767566-11767670,11768828-11768928
AGAAACCTAGATGAAGCTGAGAAGTTTTTCCAGGCAGCCCTACATGAAGCGAAAGAAGGATTTG
GACTGAGAGATCCACATGTTGCGTCAGCCCTTAACAATCTGGCTGAGTTTTATAGGTTAAAGAA
AGAATACGAGAAGGCTGAGCTATTGTATCTGGAAGCAATTGAAATCCTGGAAGAATCATTTGGA
TCGGACGATATAAG
						
					

						Genomic sequence
						
							AGAAACCTAGATGAAGCTGAGAAGTTTTTCCAGGCAGCCCTACATGAAGCGAAAGAAGGATTTG
GACTGAGAGATCCACATGTTGCGTCAGCCCTTAACAATCTGGTAATTGTTAGTTTGGTTATTTA
CTGAAGACTAATATGCTCTTTAATCCATAATATAACCTTGAGTTTTACAAAGTTGAATGGCCTT
GCTTTGCTTTGAATAAATAAATAAACAAATTCATATACACATGCACATTGAATCGGCAACTTAT
TTGTTGTGGTGCTTGGTTTTCTCCGTGACCTCATTCTGTTGTTATCCTTAGAAGAGCTGCATGT
TAGTTGCCATCGCTCCTTCACCATGCTCAACGCTAGTTACATGCTAGCTTCACCACTTTGCCCT
GAACCATAATTTGGTCTAAAGTTATTTTGTTTATTGGGATACATTTTATTATATTTTTGATTTT
TTTTGTTAAGATATACTCCCCCTGTTGTCTTTTAACCGTTGTTAGGACAAGGACATTGTCTCCA
GGGCATTACTTTTCCTATTTTATATTCATAAAAATATTAAAGATATAAACTGCATGGAAGGGAT
TCGAATGAGGTCATTATCAGATACCAAATCTTAATGTTGTTACACATGTTAATGAGTTAAGATT
TCGAGGTTTTACTGCACCACGTTCTAGGGCATCATCTATTTGAGAACACAGGGAGGTGGAAGGG
GGAGGTCAGAGGGATGAACGAACCATTATCACCAACACAAATATTTATAGTAACATAATTGATA
ATAGGTATACATTCTTGCTCTTCTTGAGTACCTTGTTGAGGGTCTCAGTATAGTGTTCGCCTTT
CTCGCTGAACATGTTGGGTGATTTTACATCTAGGGGATAGCATATTCCAAATTGCTTAGGGTTA
CTTACTAATACGTTAAAATTACATGGTAAAATATCCAAATTGCCATGTGGCTATCTGATCTTGG
TTGAAGAGAGCATAACACACACAGATGTCAGCTTACATTCACTTAGCTGAAGCAGATTATTGAT
GCAAGGACAATGGTGGGGAAAAAGAGGGAGTTGATGAGGAGGATTAGGATCTAGTACCATGATA
TGTTTTGCCACCCACAACTACTCTTCATTCTGTTTGCGCTAATCACACTCAAGTTAAATGGGCC
AGGTGTAGACAGGGCTATGTATATGTCAATACTATTAACACCGCAAACAATTAATACTAGGCTG
GATGGAGCCAAATATTTTAATAAATTGTTACTCCCAAATTTTGCAGGCTGAGTTTTATAGGTTA
AAGAAAGAATACGAGAAGGCTGAGCTATTGTATCTGGAAGCAATTGAAATCCTGGAAGAATCAT
TTGGATCGGACGATATAAG
						
					

			
		

Sequences
Splice junction sequence	CTGAGTTTTATAGGTTAAAGAAAGAATACGAGAAGGCTGAGCTATTGTATCTGGAAGCAATTGA AATCCTGGAAGAATCATTTGGATCGGACGATATAAGagaaacctagatgaagctgagaagtttt tccaggcagccctacatgaagcgaaagaaggatttggactgagagatccacatgttgcgtcagc ccttaaca
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: 206 Transcript exons: 11767566-11767670,11768828-11768928 AGAAACCTAGATGAAGCTGAGAAGTTTTTCCAGGCAGCCCTACATGAAGCGAAAGAAGGATTTG GACTGAGAGATCCACATGTTGCGTCAGCCCTTAACAATCTGGCTGAGTTTTATAGGTTAAAGAA AGAATACGAGAAGGCTGAGCTATTGTATCTGGAAGCAATTGAAATCCTGGAAGAATCATTTGGA TCGGACGATATAAG
Genomic sequence	AGAAACCTAGATGAAGCTGAGAAGTTTTTCCAGGCAGCCCTACATGAAGCGAAAGAAGGATTTG GACTGAGAGATCCACATGTTGCGTCAGCCCTTAACAATCTGGTAATTGTTAGTTTGGTTATTTA CTGAAGACTAATATGCTCTTTAATCCATAATATAACCTTGAGTTTTACAAAGTTGAATGGCCTT GCTTTGCTTTGAATAAATAAATAAACAAATTCATATACACATGCACATTGAATCGGCAACTTAT TTGTTGTGGTGCTTGGTTTTCTCCGTGACCTCATTCTGTTGTTATCCTTAGAAGAGCTGCATGT TAGTTGCCATCGCTCCTTCACCATGCTCAACGCTAGTTACATGCTAGCTTCACCACTTTGCCCT GAACCATAATTTGGTCTAAAGTTATTTTGTTTATTGGGATACATTTTATTATATTTTTGATTTT TTTTGTTAAGATATACTCCCCCTGTTGTCTTTTAACCGTTGTTAGGACAAGGACATTGTCTCCA GGGCATTACTTTTCCTATTTTATATTCATAAAAATATTAAAGATATAAACTGCATGGAAGGGAT TCGAATGAGGTCATTATCAGATACCAAATCTTAATGTTGTTACACATGTTAATGAGTTAAGATT TCGAGGTTTTACTGCACCACGTTCTAGGGCATCATCTATTTGAGAACACAGGGAGGTGGAAGGG GGAGGTCAGAGGGATGAACGAACCATTATCACCAACACAAATATTTATAGTAACATAATTGATA ATAGGTATACATTCTTGCTCTTCTTGAGTACCTTGTTGAGGGTCTCAGTATAGTGTTCGCCTTT CTCGCTGAACATGTTGGGTGATTTTACATCTAGGGGATAGCATATTCCAAATTGCTTAGGGTTA CTTACTAATACGTTAAAATTACATGGTAAAATATCCAAATTGCCATGTGGCTATCTGATCTTGG TTGAAGAGAGCATAACACACACAGATGTCAGCTTACATTCACTTAGCTGAAGCAGATTATTGAT GCAAGGACAATGGTGGGGAAAAAGAGGGAGTTGATGAGGAGGATTAGGATCTAGTACCATGATA TGTTTTGCCACCCACAACTACTCTTCATTCTGTTTGCGCTAATCACACTCAAGTTAAATGGGCC AGGTGTAGACAGGGCTATGTATATGTCAATACTATTAACACCGCAAACAATTAATACTAGGCTG GATGGAGCCAAATATTTTAATAAATTGTTACTCCCAAATTTTGCAGGCTGAGTTTTATAGGTTA AAGAAAGAATACGAGAAGGCTGAGCTATTGTATCTGGAAGCAATTGAAATCCTGGAAGAATCAT TTGGATCGGACGATATAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_015162 						
					
						PMCS
						0.223637717

Conservation Information
Conserved circRNAs	osi_circ_015162
PMCS	0.223637717

			
						 Functional Information
					
						Coding potential
						N
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	N
Potential coding position	NA
Potential amino acid sequence	NA
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 Os04g0278550_circ_g.1

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