Plant Circular RNA Database

Detail information of Os08g0129700_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os08g0129700_circ_g.3
					
						ID in PlantcircBase
						osa_circ_035730
					
						Alias
						Os_ciR11396
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr8: 1667466-1669955  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer, find_circ
					
						Parent gene
						
							Os08g0129700						
					
						Parent gene annotation
						
							NAD(P)-binding domain containing protein. (Os08t0129700-01);NAD(
P)-binding domain containing protein. (Os08t0129700-02)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os08g0129700_circ_g.4 Os08g0129700_circ_g.5 Os08g0129700_circ_g.6 						
					
						Support reads
						2/1
					
						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
						Os08t0129700-01:5
Os08t0129700-02:5

General Information
CircRNA Name	Os08g0129700_circ_g.3
ID in PlantcircBase	osa_circ_035730
Alias	Os_ciR11396
Organism	Oryza sativa
Position	chr8: 1667466-1669955 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ue-circRNA
Identification method	CIRCexplorer, find_circ
Parent gene	Os08g0129700
Parent gene annotation	NAD(P)-binding domain containing protein. (Os08t0129700-01);NAD( P)-binding domain containing protein. (Os08t0129700-02)
Parent gene strand	+
Alternative splicing	Os08g0129700_circ_g.4 Os08g0129700_circ_g.5 Os08g0129700_circ_g.6
Support reads	2/1
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	Os08t0129700-01:5 Os08t0129700-02:5

			
						 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  
						
							GCTCCCAGGTCAACAAGATCTTTGCCGAAAATGCGTTTGATGCTGTTATGCACTTTGCTGCTGT
TGCCTATGTGGGTGAGAGTACATTGGAACCCCTTAGttcatcttctggctggacgaattcaatt
cacggacggtggtggtggtggtgttgactagggatttatttttttaccattggcggctcggctg
catcccca

									
								

					

						Assembled circRNA sequence  
						
							NA
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
						
							NA						
					

						Genomic sequence
						
							TTCATCTTCTGGCTGGACGAATTCAATTCACGGACGGTGGTGGTGGTGGTGTTGACTAGGGATT
TATTTTTTTACCATTGGCGGCTCGGCTGCATCCCCAAGTGAAGAAGAGAATTCGTACATGATTC
CGCTAAACAGGAGGGCGAGTCAGACTAGGGGTGGTAGATCTCGATGCCCTTTCTTTCTCTTTGG
TTATTTACTGTTGCTTTAGATATATGTATATGCGTCTAAATAATGTTGTTGCCTTTTTGATCCC
CTTTGGCCCTTGAGCATGTGTACCAACCAATAGTGGCATTTTTTTTAATGTTTAGTTTGTCCAT
CTAATCTATGTGCCCCATGAAGGAAACTGTTTTTTTTTTAAGAATTGCTCCACCTGAAAAAGCT
GTCCTTTTTTCTTTGCCATGGGATTCACTTGGTGTACAAGCACATGAACACCTTTCAGAGGTCA
TTTCACATGCATATGTATGGGCTAGATATTTCATATGGCAAGCAGTAGTGTGTCTTTTGATGGT
ATGCACTATTGCCAGCAGTGAAGAATTTCTTAGCAAAAATTCCTTTTCAGTAGATGATCCCAGC
CCATTTCTTCTGCCTTAAGTAATGCTTGTTATGTGCACATTAAGATTTCAGTCACTACACAGAT
AGGCAAGTTGAACTAAAGCTATTAGGTGCAATATTTCAACTGAAGTCAACTAAGACATGCAACC
ATATCGATCTTGTTTTTGGTAGATAAATCTTTAAGCAAGCAGTTGCCACTTTGCTGATATCGCA
TTTCAAGTCAAAGCCAGAGTTTGCTTGCTGTGTAGTTTCATTATCAATGAGGACTGGTTCATTT
GTTTGTGCGGAACAGGGGATCCATATATCTGACATTAATTAGGTTGCTCTTTTGTTTGACCATG
GGTATGCTTTAATTTATTCAACTGTTGTAATGGTTAAATGTTTGGTCATTCCCTTTATGTTGTA
AGTTCATCATGTTGATAGGGATGGAGTACTTCGATGCTAGGCGGAAGCCTCATAATGTTGGGAA
AGTTATTGCAGCTCTGGTCCTCACAACACTATGTATATTTATTTTGAAGCAATCTCCTGGTTTT
GGTGGCAGTAGTGTGGTAAGATGTCTATATTTCTTTTTTTCTCTTCTTCTTCTTTCATCCTTAT
TCCTTTAAATCTGCTTTTAAGATCAGCCTTTCCTCACGTTTTCATGTTTTGATTTGTAAGTCAC
TTTCTGCTACCTATAGGTTTAACTTTTGGACTTTTCTCAACTTACTTTCTCTTATGTTTTTCTT
GTTACACAAAAAGCAATTTTAATTTTGAGTATCACCTGTATTATAGAATATGTCCTTGTATAAC
TAGCATAAAACAAAATGATGACTGCTATTGTAGTTGTTTCAATACACATATCTTCATTTCTGCT
CTCAGTGCTAACAAGCAGGTGAGGAAAGTGACATCTCTCCATCCAATTGCCTTTGTTATTGCAA
TGTCTATTACATTAGTTCATGTTCCAACTTGATATTTCAATACACATATCTTCATTAGTTGTTT
GCCACTTCTCGTTGCGGCAAGTTGATGCCTAAATGGCATCCTAACAAACTGTAGCTTTCAGCCA
CGAGACCTTCTGACAGCTAATCAATCTGCATAATAATTTTGACATGTTCCTGTTCAAGAAAACT
ACGATATGATTTGCAGATGTAAATATATCACATCTCTAAAACTACAGGCTAACTATCCAGTTCT
TTAGAATAAAATGTTAAGAGACTGTTGCAGAGTGAAGGTCAAACATAGCACATTACTTTTGTTG
TCTAGAAACATGTATAAGCTGCGATGCAGACCTAGTATGTGTATGGCTAAACTTGGATATGTTC
CATCTGTTTTGACTTCTGTTGCTTAATCTTTCAACTCTTCATGCAAATCCGCCTGTTATGTTTC
TTATGCTGCAATTATTATTATGCCATTCTTATATTTCCCCTATTTTTAATTCAACTGTATAACT
GATTGTGGGGTTATGTATCTTGCAGTTTTCTCGCCATGAACCTGGTGTTACTCATGTCTTAGTA
ACAGGAGGAGCTGGCTATATTGGGTCACATGCTTCATTACGCCTGTTAAAGGACAATTATCGAG
TTACCATTGTGGTAATTAAGTTTTCCTTTGTACTGAATTTCTGAACTGGTTTGTTCTTCAAATG
CCACCCTTGATGGTTAATTGTGATTTTTAGGACAATCTTTCTAGAGGAAACATGGGAGCAGTAA
AGGTTCTCCAAGAGTTGTTCCCCCAGCCAGGAAGACTTCAGTTTATCTATGCTGATCTTGGAGA
TCAAAAAACTGTATCCTCATTTTGTACTTCTAAATTACCTCCTCGTAATTTTTAAAATGTTCAA
ATGCCAGTTTTTCACTTAACTGGCTCCCAGGTCAACAAGATCTTTGCCGAAAATGCGTTTGATG
CTGTTATGCACTTTGCTGCTGTTGCCTATGTGGGTGAGAGTACATTGGAACCCCTTAG
						
					

			
		

Sequences
Splice junction sequence	GCTCCCAGGTCAACAAGATCTTTGCCGAAAATGCGTTTGATGCTGTTATGCACTTTGCTGCTGT TGCCTATGTGGGTGAGAGTACATTGGAACCCCTTAGttcatcttctggctggacgaattcaatt cacggacggtggtggtggtggtgttgactagggatttatttttttaccattggcggctcggctg catcccca
Assembled circRNA sequence	NA 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	NA
Genomic sequence	TTCATCTTCTGGCTGGACGAATTCAATTCACGGACGGTGGTGGTGGTGGTGTTGACTAGGGATT TATTTTTTTACCATTGGCGGCTCGGCTGCATCCCCAAGTGAAGAAGAGAATTCGTACATGATTC CGCTAAACAGGAGGGCGAGTCAGACTAGGGGTGGTAGATCTCGATGCCCTTTCTTTCTCTTTGG TTATTTACTGTTGCTTTAGATATATGTATATGCGTCTAAATAATGTTGTTGCCTTTTTGATCCC CTTTGGCCCTTGAGCATGTGTACCAACCAATAGTGGCATTTTTTTTAATGTTTAGTTTGTCCAT CTAATCTATGTGCCCCATGAAGGAAACTGTTTTTTTTTTAAGAATTGCTCCACCTGAAAAAGCT GTCCTTTTTTCTTTGCCATGGGATTCACTTGGTGTACAAGCACATGAACACCTTTCAGAGGTCA TTTCACATGCATATGTATGGGCTAGATATTTCATATGGCAAGCAGTAGTGTGTCTTTTGATGGT ATGCACTATTGCCAGCAGTGAAGAATTTCTTAGCAAAAATTCCTTTTCAGTAGATGATCCCAGC CCATTTCTTCTGCCTTAAGTAATGCTTGTTATGTGCACATTAAGATTTCAGTCACTACACAGAT AGGCAAGTTGAACTAAAGCTATTAGGTGCAATATTTCAACTGAAGTCAACTAAGACATGCAACC ATATCGATCTTGTTTTTGGTAGATAAATCTTTAAGCAAGCAGTTGCCACTTTGCTGATATCGCA TTTCAAGTCAAAGCCAGAGTTTGCTTGCTGTGTAGTTTCATTATCAATGAGGACTGGTTCATTT GTTTGTGCGGAACAGGGGATCCATATATCTGACATTAATTAGGTTGCTCTTTTGTTTGACCATG GGTATGCTTTAATTTATTCAACTGTTGTAATGGTTAAATGTTTGGTCATTCCCTTTATGTTGTA AGTTCATCATGTTGATAGGGATGGAGTACTTCGATGCTAGGCGGAAGCCTCATAATGTTGGGAA AGTTATTGCAGCTCTGGTCCTCACAACACTATGTATATTTATTTTGAAGCAATCTCCTGGTTTT GGTGGCAGTAGTGTGGTAAGATGTCTATATTTCTTTTTTTCTCTTCTTCTTCTTTCATCCTTAT TCCTTTAAATCTGCTTTTAAGATCAGCCTTTCCTCACGTTTTCATGTTTTGATTTGTAAGTCAC TTTCTGCTACCTATAGGTTTAACTTTTGGACTTTTCTCAACTTACTTTCTCTTATGTTTTTCTT GTTACACAAAAAGCAATTTTAATTTTGAGTATCACCTGTATTATAGAATATGTCCTTGTATAAC TAGCATAAAACAAAATGATGACTGCTATTGTAGTTGTTTCAATACACATATCTTCATTTCTGCT CTCAGTGCTAACAAGCAGGTGAGGAAAGTGACATCTCTCCATCCAATTGCCTTTGTTATTGCAA TGTCTATTACATTAGTTCATGTTCCAACTTGATATTTCAATACACATATCTTCATTAGTTGTTT GCCACTTCTCGTTGCGGCAAGTTGATGCCTAAATGGCATCCTAACAAACTGTAGCTTTCAGCCA CGAGACCTTCTGACAGCTAATCAATCTGCATAATAATTTTGACATGTTCCTGTTCAAGAAAACT ACGATATGATTTGCAGATGTAAATATATCACATCTCTAAAACTACAGGCTAACTATCCAGTTCT TTAGAATAAAATGTTAAGAGACTGTTGCAGAGTGAAGGTCAAACATAGCACATTACTTTTGTTG TCTAGAAACATGTATAAGCTGCGATGCAGACCTAGTATGTGTATGGCTAAACTTGGATATGTTC CATCTGTTTTGACTTCTGTTGCTTAATCTTTCAACTCTTCATGCAAATCCGCCTGTTATGTTTC TTATGCTGCAATTATTATTATGCCATTCTTATATTTCCCCTATTTTTAATTCAACTGTATAACT GATTGTGGGGTTATGTATCTTGCAGTTTTCTCGCCATGAACCTGGTGTTACTCATGTCTTAGTA ACAGGAGGAGCTGGCTATATTGGGTCACATGCTTCATTACGCCTGTTAAAGGACAATTATCGAG TTACCATTGTGGTAATTAAGTTTTCCTTTGTACTGAATTTCTGAACTGGTTTGTTCTTCAAATG CCACCCTTGATGGTTAATTGTGATTTTTAGGACAATCTTTCTAGAGGAAACATGGGAGCAGTAA AGGTTCTCCAAGAGTTGTTCCCCCAGCCAGGAAGACTTCAGTTTATCTATGCTGATCTTGGAGA TCAAAAAACTGTATCCTCATTTTGTACTTCTAAATTACCTCCTCGTAATTTTTAAAATGTTCAA ATGCCAGTTTTTCACTTAACTGGCTCCCAGGTCAACAAGATCTTTGCCGAAAATGCGTTTGATG CTGTTATGCACTTTGCTGCTGTTGCCTATGTGGGTGAGAGTACATTGGAACCCCTTAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.130951928

Conservation Information
Conserved circRNAs	NA
PMCS	0.130951928

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							1667588-1667517(+)
1669755-1667521(+)
						
						Potential amino acid sequence
						
							MIPLNRRASQTRGGMEYFDARRKPHNVGKVIAALVLTTLCIFILKQSPGFGGSSVFSRHEPGVT
HVLVTGGAGYIGSHASLRLLKDNYRVTIVDNLSRGNMGAVKVLQELFPQPGRLQFIYADLGDQK
TVNKIFAENAFDAVMHFAAVAYVGESTLEPLSSSSGWTNSIHGRWWWWC*(+)
MLILEIKKLSTRSLPKMRLMLLCTLLLLPMWVRVHWNPLVHLLAGRIQFTDGGGGGVD*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	1667588-1667517(+) 1669755-1667521(+)
Potential amino acid sequence	MIPLNRRASQTRGGMEYFDARRKPHNVGKVIAALVLTTLCIFILKQSPGFGGSSVFSRHEPGVT HVLVTGGAGYIGSHASLRLLKDNYRVTIVDNLSRGNMGAVKVLQELFPQPGRLQFIYADLGDQK TVNKIFAENAFDAVMHFAAVAYVGESTLEPLSSSSGWTNSIHGRWWWWC(+) MLILEIKKLSTRSLPKMRLMLLCTLLLLPMWVRVHWNPLVHLLAGRIQFTDGGGGGVD(+)
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 Os08g0129700_circ_g.3

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