Plant Circular RNA Database

Detail information of Os07g0418000_circ_g.1

			
						 General Information
					
						CircRNA Name
						Os07g0418000_circ_g.1
					
						ID in PlantcircBase
						osa_circ_033518
					
						Alias
						Os07circ06526/Os_ciR10877
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr7: 13288292-13289781  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						SMALT, Segemehl, find_circ
					
						Parent gene
						
							Os07g0418000						
					
						Parent gene annotation
						
							Similar to predicted protein. (Os07t0418000-01);HAD-like domain 
domain containing protein. (Os07t0418000-02)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os07g0418000_circ_g.2 Os07g0418000_circ_g.3 						
					
						Support reads
						4/2
					
						Tissues
						leaf/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  
						
							CT-AC							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
						Os07t0418000-01:2
Os07t0418000-02:2

General Information
CircRNA Name	Os07g0418000_circ_g.1
ID in PlantcircBase	osa_circ_033518
Alias	Os07circ06526/Os_ciR10877
Organism	Oryza sativa
Position	chr7: 13288292-13289781 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	SMALT, Segemehl, find_circ
Parent gene	Os07g0418000
Parent gene annotation	Similar to predicted protein. (Os07t0418000-01);HAD-like domain domain containing protein. (Os07t0418000-02)
Parent gene strand	-
Alternative splicing	Os07g0418000_circ_g.2 Os07g0418000_circ_g.3
Support reads	4/2
Tissues	leaf/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	CT-AC 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	Os07t0418000-01:2 Os07t0418000-02:2

			
						 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  
						
							GTACTCAAATTTAATCGGTAAATCAATAGGGGCTTACTGAAGTGTCAGGCCTTGATGCTGTGGC
ATTTGCTGCAGTTGCTGGAGAACTTTTACCTTTGGAccaggtagaggttccattggtccagtgc
tggctctttaatgacattcttcaaagttgcaagacggtcctcaacgaaactggttatgttgcat
cagaaaga

									
								

					

						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: 140
Transcript exons: 13288292-13288368,13289719-13289781
CCAGGTAGAGGTTCCATTGGTCCAGTGCTGGCTCTTTAATGACATTCTTCAAAGTTGCAAGACG
GTCCTCAACGAAATGAAGTGTCAGGCCTTGATGCTGTGGCATTTGCTGCAGTTGCTGGAGAACT
TTTACCTTTGGA
						
					

						Genomic sequence
						
							CCAGGTAGAGGTTCCATTGGTCCAGTGCTGGCTCTTTAATGACATTCTTCAAAGTTGCAAGACG
GTCCTCAACGAAACTGGTTATGTTGCATCAGAAAGAATTAACTTGTTAAGTCTAATTTATTACT
GCTTAACTCTTAACAGTACACGATTATTTGAAGTAAAAAACAGAGTGCTCAAGGAAGTAGTTGT
TCTTTACTTTTGAGTATTATGGAGATAGTATTGTCCATGTTATACATTTGTAAACAATATATCT
AAATAGTTCAAAATATGATTTACAAAGTTATTGTCATCTGACAAGGGAACATCGTTCTTTTGAG
AAATTTGCTCCTTTGCCACAAAGGTCAGTGGCGTACTTATATTTGCCACACACTTCATCGGCTT
TGCTCTTTTGCCACATAATTTGGTGCAAATCCTTTCATTAACTAATAACATTTACCCTAGCAAA
ATATCAAGTTTACTCTTCTCCTTCCTCCAGCACTGAACCTCCTCTTGTTGGCTTACCCACAGCC
ATTGGGCTGGCACTGTGGACCTCTGGCTTCCATGTGCTTGACTGCTTCCAACCTGGCTGACCAA
GGTGGAGCTCAAGCCAAGGGGAAGAAAGTTACTTGGAGCTCGGTCTAGAAAGAAGAGGTGACGA
TTAGCGAAGCAGGACCATTGCTGTCCGGTGGTTGCAGTGGAGCTTGATCAACACCATCAGAGCC
TGAGCTGAGCCGACGCCAGCTCAATTATTGCTCACCAAGACCCACATAGGGCCTCATGTGCCCG
TCCATTCCTACCTGGTGAAACCCAATGGCCTAACCTCCTCATCAACACTAGAGGCACCAGCAAC
AGCTCCTCCGCCTCCAAGCTCACAGCCTTCATCCTGTCCAGCAGTGCGCTTACCATCAAGGCAT
CAAGGTCATGGAGTTCTCCAGCCTTCGCATCCCCATTGCCGCCACATAGTTCCCTTCCATCGCC
ATCCGCAGAAGCTCACATACAGAGTGAAGCTTGTGCAGGATCAGTCGGAGGTCAGCAGCAGTGG
GGACTGGGGAAGTGGCCAGCTCTCCAGCGCAAGCACAGGAGCTGCCTCAGAGATGGAGAACAGA
GGATGGTTTGTAGCGAATGAGTGGATTTTCACCAAACCATGAGGGAAAACAGAAAAGCCAACTA
GGTGCATAGCAAATATCAGCATGCCACTCTTAACTTTGTGGCAAACGAGCAATTTTTTCTAATA
ATTCTCTCACTGGATTTCCATTCTAGTGTAAGGATAAACCATCAGTTCAAGGAGTAAAAACGAA
AAAACAAAAAAGTTATACAGGGCAATTCCAGCTAGCAAATTATGTGCTACCAAATTGATGAGGA
GGGAAATATTGTTCAACAGAAACATTTCAAGAGAAAATAGTATCTCGTACTCAAATTTAATCGG
TAAATCAATAGGGGCTTACTGAAGTGTCAGGCCTTGATGCTGTGGCATTTGCTGCAGTTGCTGG
AGAACTTTTACCTTTGGA
						
					

			
		

Sequences
Splice junction sequence	GTACTCAAATTTAATCGGTAAATCAATAGGGGCTTACTGAAGTGTCAGGCCTTGATGCTGTGGC ATTTGCTGCAGTTGCTGGAGAACTTTTACCTTTGGAccaggtagaggttccattggtccagtgc tggctctttaatgacattcttcaaagttgcaagacggtcctcaacgaaactggttatgttgcat cagaaaga
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: 140 Transcript exons: 13288292-13288368,13289719-13289781 CCAGGTAGAGGTTCCATTGGTCCAGTGCTGGCTCTTTAATGACATTCTTCAAAGTTGCAAGACG GTCCTCAACGAAATGAAGTGTCAGGCCTTGATGCTGTGGCATTTGCTGCAGTTGCTGGAGAACT TTTACCTTTGGA
Genomic sequence	CCAGGTAGAGGTTCCATTGGTCCAGTGCTGGCTCTTTAATGACATTCTTCAAAGTTGCAAGACG GTCCTCAACGAAACTGGTTATGTTGCATCAGAAAGAATTAACTTGTTAAGTCTAATTTATTACT GCTTAACTCTTAACAGTACACGATTATTTGAAGTAAAAAACAGAGTGCTCAAGGAAGTAGTTGT TCTTTACTTTTGAGTATTATGGAGATAGTATTGTCCATGTTATACATTTGTAAACAATATATCT AAATAGTTCAAAATATGATTTACAAAGTTATTGTCATCTGACAAGGGAACATCGTTCTTTTGAG AAATTTGCTCCTTTGCCACAAAGGTCAGTGGCGTACTTATATTTGCCACACACTTCATCGGCTT TGCTCTTTTGCCACATAATTTGGTGCAAATCCTTTCATTAACTAATAACATTTACCCTAGCAAA ATATCAAGTTTACTCTTCTCCTTCCTCCAGCACTGAACCTCCTCTTGTTGGCTTACCCACAGCC ATTGGGCTGGCACTGTGGACCTCTGGCTTCCATGTGCTTGACTGCTTCCAACCTGGCTGACCAA GGTGGAGCTCAAGCCAAGGGGAAGAAAGTTACTTGGAGCTCGGTCTAGAAAGAAGAGGTGACGA TTAGCGAAGCAGGACCATTGCTGTCCGGTGGTTGCAGTGGAGCTTGATCAACACCATCAGAGCC TGAGCTGAGCCGACGCCAGCTCAATTATTGCTCACCAAGACCCACATAGGGCCTCATGTGCCCG TCCATTCCTACCTGGTGAAACCCAATGGCCTAACCTCCTCATCAACACTAGAGGCACCAGCAAC AGCTCCTCCGCCTCCAAGCTCACAGCCTTCATCCTGTCCAGCAGTGCGCTTACCATCAAGGCAT CAAGGTCATGGAGTTCTCCAGCCTTCGCATCCCCATTGCCGCCACATAGTTCCCTTCCATCGCC ATCCGCAGAAGCTCACATACAGAGTGAAGCTTGTGCAGGATCAGTCGGAGGTCAGCAGCAGTGG GGACTGGGGAAGTGGCCAGCTCTCCAGCGCAAGCACAGGAGCTGCCTCAGAGATGGAGAACAGA GGATGGTTTGTAGCGAATGAGTGGATTTTCACCAAACCATGAGGGAAAACAGAAAAGCCAACTA GGTGCATAGCAAATATCAGCATGCCACTCTTAACTTTGTGGCAAACGAGCAATTTTTTCTAATA ATTCTCTCACTGGATTTCCATTCTAGTGTAAGGATAAACCATCAGTTCAAGGAGTAAAAACGAA AAAACAAAAAAGTTATACAGGGCAATTCCAGCTAGCAAATTATGTGCTACCAAATTGATGAGGA GGGAAATATTGTTCAACAGAAACATTTCAAGAGAAAATAGTATCTCGTACTCAAATTTAATCGG TAAATCAATAGGGGCTTACTGAAGTGTCAGGCCTTGATGCTGTGGCATTTGCTGCAGTTGCTGG AGAACTTTTACCTTTGGA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.202893674

Conservation Information
Conserved circRNAs	NA
PMCS	0.202893674

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							13288369-13288296(+)
13288310-13289773(-)
13289749-13289773(-)
13288338-13288362(-)
						
						Potential amino acid sequence
						
							MKCQALMLWHLLQLLENFYLWTR*(+)
MEPLPGPKVKVLQQLQQMPQHQGLTLHFVEDRLATLKNVIKEPALDQWNLYLVQR*(-)
MPQHQGLTLHFVEDRLATLKNVIKEPALDQWNLYLVQR*(-)
MSLKSQHWTNGTSTWSKGKSSPATAANATASRPDTSFR*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	13288369-13288296(+) 13288310-13289773(-) 13289749-13289773(-) 13288338-13288362(-)
Potential amino acid sequence	MKCQALMLWHLLQLLENFYLWTR(+) MEPLPGPKVKVLQQLQQMPQHQGLTLHFVEDRLATLKNVIKEPALDQWNLYLVQR(-) MPQHQGLTLHFVEDRLATLKNVIKEPALDQWNLYLVQR(-) MSLKSQHWTNGTSTWSKGKSSPATAANATASRPDTSFR(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

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

circRNA

Detail information of Os07g0418000_circ_g.1

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