Plant Circular RNA Database

Detail information of Os02g0173500_circ_g.1

			
						 General Information
					
						CircRNA Name
						Os02g0173500_circ_g.1
					
						ID in PlantcircBase
						osa_circ_013397
					
						Alias
						Os_ciR2588
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr2: 4026262-4027318  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, find_circ
					
						Parent gene
						
							Os02g0173500						
					
						Parent gene annotation
						
							Similar to Cholinephosphate cytidylyltransferase. (Os02t0173500-
01)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os02g0173500_circ_g.2 Os02g0173500_circ_g.3 Os02g0173500_circ_g.4 Os02g0173500_circ_g.5 Os02g0173500_circ_g.6 Os02g0173500_circ_g.7 						
					
						Support reads
						6/2
					
						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
						Os02t0173500-01:5

General Information
CircRNA Name	Os02g0173500_circ_g.1
ID in PlantcircBase	osa_circ_013397
Alias	Os_ciR2588
Organism	Oryza sativa
Position	chr2: 4026262-4027318 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, find_circ
Parent gene	Os02g0173500
Parent gene annotation	Similar to Cholinephosphate cytidylyltransferase. (Os02t0173500- 01)
Parent gene strand	+
Alternative splicing	Os02g0173500_circ_g.2 Os02g0173500_circ_g.3 Os02g0173500_circ_g.4 Os02g0173500_circ_g.5 Os02g0173500_circ_g.6 Os02g0173500_circ_g.7
Support reads	6/2
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	Os02t0173500-01:5

			
						 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  
						
							CTTTGATACATCTTATCAGGAAAAAAGACTGAGAGTTAACATGGGATTAAAAAACCTGCGTGAC
AAAGTGAAGCAGCACCAAGAAAAAGTAGGGGAGAAGgtttcctaacacatatctccttgtcgga
tgctgcaatgatgagttgacacataagtacaaagggagaactgttatgacagaggatgagcgat
atgaatca

									
								

					

						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: 490
Transcript exons: 4026262-4026375,4026485-4026580,4026783-4026825,4026961-
4027114,4027236-4027318
GTTTCCTAACACATATCTCCTTGTCGGATGCTGCAATGATGAGTTGACACATAAGTACAAAGGG
AGAACTGTTATGACAGAGGATGAGCGATATGAATCACTTCGTCACTGCAAGTGGGTGGATGAAG
TCATTCCTGATGCTCCATGGGTGGTAACGGAAGAATTCTTGAATAAACATAACATTGATTTTGT
TGCACATGATTCTCTGCCGTATGCTGATGCTAGTGGAGCTGGTAACGATGTCTATGAATTTGTC
AAAAAACTTGGTAAATTTAAGGAAACCCAGCGCACAGATGGGATATCGACGTCAGATATTATAA
TGCGGATTGTTAAGGATTATAATGAGTATGTTATGCGGAACCTGGCCAGGGGGTACACCAGAAA
GGATCTTGGTGTCAGTTACGTTAAGGAAAAAAGACTGAGAGTTAACATGGGATTAAAAAACCTG
CGTGACAAAGTGAAGCAGCACCAAGAAAAAGTAGGGGAGAAG
						
					

						Genomic sequence
						
							GTTTCCTAACACATATCTCCTTGTCGGATGCTGCAATGATGAGTTGACACATAAGTACAAAGGG
AGAACTGTTATGACAGAGGATGAGCGATATGAATCACTTCGTCACTGCAAGTAATCTTGTCTTA
TGCTTTGTTCTAGTCAATAAGCCACCAATATTATATCTTTCTTTAGTTCTTTTAGTTACTATAC
TATGATAATACATATGCTCTTCTTTTCCTAGGTGGGTGGATGAAGTCATTCCTGATGCTCCATG
GGTGGTAACGGAAGAATTCTTGAATAAACATAACATTGATTTTGTTGCACATGATTCTCTGCCG
TAAGTGTTCTTAACAGATCTCGATGTTTATAACATAGTAATCATTTCTGATGTACTTGTTGTGA
TAATACATATGCTGGTCTTTTCTTTCTTTACATAATATATACAGAGCCTTTGGGCCTTCACAGT
GATGGATCTGAAATTCAAATATCATTATCTTTAATTAATATATTCACCTTATTTTTCCTATTTG
AATATACAGGTATGCTGATGCTAGTGGAGCTGGTAACGATGTCTATGAATTTGTGAGCCCTAAT
TTCACGACTGTTTTCTTCAATTACAATTATTGATTAAAATTTTGTTTGTCGTATCTAGTAACAG
TTATTATTTGTGTAGACTGGCATATTTCTGACAGAGACTAATCTCGTTGTGTCTATCAGGTCAA
AAAACTTGGTAAATTTAAGGAAACCCAGCGCACAGATGGGATATCGACGTCAGATATTATAATG
CGGATTGTTAAGGATTATAATGAGTATGTTATGCGGAACCTGGCCAGGGGGTACACCAGAAAGG
ATCTTGGTGTCAGTTACGTTAAGGCATGTGATATTAACCTGACACTTTCACCTCAATTCCAGCT
TGAATAGGTTGTCTTTATATTTTAACAGTGCTGCGGTAATGTTTTGAACTGGCCACCTGATCTT
TGATACATCTTATCAGGAAAAAAGACTGAGAGTTAACATGGGATTAAAAAACCTGCGTGACAAA
GTGAAGCAGCACCAAGAAAAAGTAGGGGAGAAG
						
					

			
		

Sequences
Splice junction sequence	CTTTGATACATCTTATCAGGAAAAAAGACTGAGAGTTAACATGGGATTAAAAAACCTGCGTGAC AAAGTGAAGCAGCACCAAGAAAAAGTAGGGGAGAAGgtttcctaacacatatctccttgtcgga tgctgcaatgatgagttgacacataagtacaaagggagaactgttatgacagaggatgagcgat atgaatca
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: 490 Transcript exons: 4026262-4026375,4026485-4026580,4026783-4026825,4026961- 4027114,4027236-4027318 GTTTCCTAACACATATCTCCTTGTCGGATGCTGCAATGATGAGTTGACACATAAGTACAAAGGG AGAACTGTTATGACAGAGGATGAGCGATATGAATCACTTCGTCACTGCAAGTGGGTGGATGAAG TCATTCCTGATGCTCCATGGGTGGTAACGGAAGAATTCTTGAATAAACATAACATTGATTTTGT TGCACATGATTCTCTGCCGTATGCTGATGCTAGTGGAGCTGGTAACGATGTCTATGAATTTGTC AAAAAACTTGGTAAATTTAAGGAAACCCAGCGCACAGATGGGATATCGACGTCAGATATTATAA TGCGGATTGTTAAGGATTATAATGAGTATGTTATGCGGAACCTGGCCAGGGGGTACACCAGAAA GGATCTTGGTGTCAGTTACGTTAAGGAAAAAAGACTGAGAGTTAACATGGGATTAAAAAACCTG CGTGACAAAGTGAAGCAGCACCAAGAAAAAGTAGGGGAGAAG
Genomic sequence	GTTTCCTAACACATATCTCCTTGTCGGATGCTGCAATGATGAGTTGACACATAAGTACAAAGGG AGAACTGTTATGACAGAGGATGAGCGATATGAATCACTTCGTCACTGCAAGTAATCTTGTCTTA TGCTTTGTTCTAGTCAATAAGCCACCAATATTATATCTTTCTTTAGTTCTTTTAGTTACTATAC TATGATAATACATATGCTCTTCTTTTCCTAGGTGGGTGGATGAAGTCATTCCTGATGCTCCATG GGTGGTAACGGAAGAATTCTTGAATAAACATAACATTGATTTTGTTGCACATGATTCTCTGCCG TAAGTGTTCTTAACAGATCTCGATGTTTATAACATAGTAATCATTTCTGATGTACTTGTTGTGA TAATACATATGCTGGTCTTTTCTTTCTTTACATAATATATACAGAGCCTTTGGGCCTTCACAGT GATGGATCTGAAATTCAAATATCATTATCTTTAATTAATATATTCACCTTATTTTTCCTATTTG AATATACAGGTATGCTGATGCTAGTGGAGCTGGTAACGATGTCTATGAATTTGTGAGCCCTAAT TTCACGACTGTTTTCTTCAATTACAATTATTGATTAAAATTTTGTTTGTCGTATCTAGTAACAG TTATTATTTGTGTAGACTGGCATATTTCTGACAGAGACTAATCTCGTTGTGTCTATCAGGTCAA AAAACTTGGTAAATTTAAGGAAACCCAGCGCACAGATGGGATATCGACGTCAGATATTATAATG CGGATTGTTAAGGATTATAATGAGTATGTTATGCGGAACCTGGCCAGGGGGTACACCAGAAAGG ATCTTGGTGTCAGTTACGTTAAGGCATGTGATATTAACCTGACACTTTCACCTCAATTCCAGCT TGAATAGGTTGTCTTTATATTTTAACAGTGCTGCGGTAATGTTTTGAACTGGCCACCTGATCTT TGATACATCTTATCAGGAAAAAAGACTGAGAGTTAACATGGGATTAAAAAACCTGCGTGACAAA GTGAAGCAGCACCAAGAAAAAGTAGGGGAGAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.417035186

Conservation Information
Conserved circRNAs	NA
PMCS	0.417035186

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							4026336-4026267(+)
4026315-4027256(-)
						
						Potential amino acid sequence
						
							MTEDERYESLRHCKWVDEVIPDAPWVVTEEFLNKHNIDFVAHDSLPYADASGAGNDVYEFVKKL
GKFKETQRTDGISTSDIIMRIVKDYNEYVMRNLARGYTRKDLGVSYVKEKRLRVNMGLKNLRDK
VKQHQEKVGEKVS*(+)
MCQLIIAASDKEICVRKPSPLLFLGAASLCHAGFLIPC*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	4026336-4026267(+) 4026315-4027256(-)
Potential amino acid sequence	MTEDERYESLRHCKWVDEVIPDAPWVVTEEFLNKHNIDFVAHDSLPYADASGAGNDVYEFVKKL GKFKETQRTDGISTSDIIMRIVKDYNEYVMRNLARGYTRKDLGVSYVKEKRLRVNMGLKNLRDK VKQHQEKVGEKVS(+) MCQLIIAASDKEICVRKPSPLLFLGAASLCHAGFLIPC(-)
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 Os02g0173500_circ_g.1

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