Plant Circular RNA Database

Detail information of Os11g0708000_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os11g0708000_circ_g.3
					
						ID in PlantcircBase
						osa_circ_010245
					
						Alias
						Os11circ11984/Os_ciR399
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr11: 28973535-28976848  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						SMALT, Segemehl, circRNA_finder, find_circ
					
						Parent gene
						
							Os11g0708000						
					
						Parent gene annotation
						
							Hypothetical protein. (Os11t0708000-01);Hypothetical gene. (Os11
t0708000-03)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os11g0708000_circ_g.1 Os11g0708000_circ_g.2 Os11g0708000_circ_g.4 Os11g0708000_circ_g.5 						
					
						Support reads
						31/77/2
					
						Tissues
						leaf and panicle/root/leaf
					
						Exon boundary  
						
							No-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
						Os11t0708000-03:3
Os11t0708000-01:3

General Information
CircRNA Name	Os11g0708000_circ_g.3
ID in PlantcircBase	osa_circ_010245
Alias	Os11circ11984/Os_ciR399
Organism	Oryza sativa
Position	chr11: 28973535-28976848 JBrowse»
Reference genome	IRGSP-1.0.38
Type	u-circRNA
Identification method	SMALT, Segemehl, circRNA_finder, find_circ
Parent gene	Os11g0708000
Parent gene annotation	Hypothetical protein. (Os11t0708000-01);Hypothetical gene. (Os11 t0708000-03)
Parent gene strand	-
Alternative splicing	Os11g0708000_circ_g.1 Os11g0708000_circ_g.2 Os11g0708000_circ_g.4 Os11g0708000_circ_g.5
Support reads	31/77/2
Tissues	leaf and panicle/root/leaf
Exon boundary	No-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	Os11t0708000-03:3 Os11t0708000-01:3

			
						 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  
						
							TTGGTAAATGTTAGGAACAGGCATTGAATATACCTTACAATGTGCCAACACGGCATCTGATGCA
TGTGGTACTCCCCAGCAACTGAATTATTGAGATATGctccgtatttccatgcactgcactgcac
tctcaccagctcttagttctccttcccctgccgctggtcacgcagcaaacatggccgtcctgcc
ggagtcac

									
								

					

						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: 163
Transcript exons: 28973535-28973665,28976817-28976848
CTCCGTATTTCCATGCACTGCACTGCACTCTCACCAGCTCTTAGTTCTCCTTCCCCTGCCGCTG
GTCACGCAGCAAACATGGCCGTCCTGCCGGAGTCACGCCGGCTCTCCCTGCTCCTCATGGCCGC
CTGGTACTCCCCAGCAACTGAATTATTGAGATATG
Transcript length: 222
Transcript exons: 28973535-28973695,28976788-28976848
CTCCGTATTTCCATGCACTGCACTGCACTCTCACCAGCTCTTAGTTCTCCTTCCCCTGCCGCTG
GTCACGCAGCAAACATGGCCGTCCTGCCGGAGTCACGCCGGCTCTCCCTGCTCCTCATGGCCGC
CTGCTTCCTGCTTCAGGCTCTCAGCGCCCACGCATGTGCCAACACGGCATCTGATGCATGTGGT
ACTCCCCAGCAACTGAATTATTGAGATATG
Transcript length: 230
Transcript exons: 28973535-28973704,28976789-28976848
CTCCGTATTTCCATGCACTGCACTGCACTCTCACCAGCTCTTAGTTCTCCTTCCCCTGCCGCTG
GTCACGCAGCAAACATGGCCGTCCTGCCGGAGTCACGCCGGCTCTCCCTGCTCCTCATGGCCGC
CTGCTTCCTGCTTCAGGCTCTCAGCGCCCACGCCATCACCCGTGTGCCAACACGGCATCTGATG
CATGTGGTACTCCCCAGCAACTGAATTATTGAGATATG
						
					

						Genomic sequence
						
							CTCCGTATTTCCATGCACTGCACTGCACTCTCACCAGCTCTTAGTTCTCCTTCCCCTGCCGCTG
GTCACGCAGCAAACATGGCCGTCCTGCCGGAGTCACGCCGGCTCTCCCTGCTCCTCATGGCCGC
CTGCTTCCTGCTTCAGGCTCTCAGCGCCCACGCCATCACCCGGCATTACAAGTTCAATGTGAGG
ATATATCGTCATCAAACTTTGCCGCATGATAACTGCAAGCATGCATCGCAATTGTCACATACAT
ATACAGGTTGCAGCAGAAATGGCAAGATGGTTTATTACCACGGTTTTGTCTGTCTTTTCTGTGT
CTTGTGCAGGTGGTCATGCGGAACATGACACGGCTTTGCTCAACCAAGCCTATCCTCACTGTCA
ATGGCAAGTTCCCGGGGCCAACCCTGTATGCAAGAGAAGGCGATAATGTCCTAGTCAAGGTCGT
CAATCATGTAGCTCACAATGTTACCATCCACTGGTAAGCAGCTTAGCTAGCTAGCCCATGGCTA
CTCCATGCATATGCTTCAACTCCACGTGTAATTTGCACCACAATTTGAATCACCACCTCAAGGC
TCCTTTGCTCTCTGTAAGTACCCAAAAAGAAAAGGAGAATATCATGCTGTGTTAGTTAAAAGGT
AAAAAGTATGTATAGCTTGCATTAGATCCTCTCTGTTGAACAGAAAACAGAAATGTGCTAGTTA
TTGTTCCCATTTATGCAACAAAAATACACTTGGTGAATAACTTGATAAACAAGCATGTCATACT
AATCAGGCACGGGGTAAGGCAGATCCGGACAGGGTGGTACGATGGGCCAGCTTACATAACACAG
TGCCCAATACAGCCAGGAAGCAGCTTTCTCTATAATTTCACTATAACAGGGCAACGAGGCACAC
TCCTCTGGCATGCTCACATCAATTGGCTAAGGGCTACCGTCCATGGTGCTATCGTCATCCTTCC
AAAGCTTGGCGTGCCCTACCCCTTCCCTGCACCTCACAAGGAGGCTGTTATCGTGTTAGGTATA
TATATACACACACATATATATAGCTGCTTCTCTACATCTTGATGCATCCAGCACTTAATTTATC
AAGTGCTGCATGCAGGAGAATGGTGGAAAGAGGACACAGAAACTGTAATTAACCAGGCCATGCA
GCTAGGAGTGGGACCCAATATTTCTGATTCACACACCATCAATGGTCATCCTGGTCCGCTGTCT
GAGTGTGCTTCTTCACAAGGTAATACTCTTACTCTACATGAACACGAGACAGACAGTGCATGTT
ATGGCTAACTATGTGCTAGTCCTACAACTGAGCCAAAGACCTAACGATTTCCTGATGTATGCTT
GCAATACAATGCACAGATGGGTTCAAGCTCAGCGTCGAAAATGGCAAAACATACATGCTCCGGA
TCATCAACGCTGCACTGAATGATGACCTATTTTTCAAGGTTGCTGGGCACGAATTAACTGTGGT
TGAGGTTGATGCAGTCTATACCAAGCCATTTAAGACCGATACCCTGCTCATCACTCCAGGCCAG
ACCACCAACGTCCTTGTTAGAGCTAACCAAGGCGCTGGCCGTTACCTTCTCTCAGTCTCCCCCT
TCATGGATGCGCCCGTGCAGGTTGACAACAAAACAGGCACCGCTACTTTGCACTACGCCAACAC
AGTCTCGTCAAGCATGGCATCCCTCACTCTCGTCAAGCCACCACCACAAAATGCCACCCATATC
GTATCAAAATTTACTGATTCACTCCATAGTCTCAATTCCAAGGAGTACCCAGCCAATGTGCCAC
AGACAGTAGACCACTCCCTTCTCCTTACCGTTGGCGTAGGTGTCAATCCATGTCCAAGCTGCAT
CAATGGGACAAGGGTGGTGGGCACAATCAACAACGTGACGTTCATCATGCCATCAACCCCAATT
CTTCAAGCCCACTATTACAACATTCCAGGAGTGTTCACAGAAGACTTCCCAGCAACCCCACTGC
ACAAGTTCAACTATACAGGAAGTGGTCCCAAAAACCTTCAAACCATGAATGGAACCAGGGTTTA
CAGGCTGCCATACAATGCTTCAGTGCAGGTTGTACTCCAGGATACGGGAATCATATCACCAGAA
AGCCACCCAATCCATTTACATGGCTTTAATTTTTTTGTGGTTGGGAAAGGGGTCGGGAACTACA
ACCCCAGGACCTCCCCTTCTACATTCAACCTCATCGACCCCATCGAGAGGAACACCATTGGAGT
TCCTACTGGTGGTTGGACGGCAATCAGATTTAGGTCAGACAACCCAGGTATTGATTTTAAAACC
TATGTTTTTTTAAGATAAATAACCCCTTCTGTTTCCAGACACATTGATTGAGCTGTTATATTGC
AGGTGTTTGGTTTATGCATTGTCATTTCGAGGTGCACACATCATGGGGACTCAAGATGGCCTTT
GTGGTGGATAATGGAAAGAGACCTAGTGAGACTCTGATTCCACCACCCAAAGATCTTCCGCAGT
GTTAACAACATGGGATTCAAAACTGCCCCCACGGAGAGGAGCCTATTACAAGAAGGGTAATTGG
CTTTGGTCCGATGTACGGAAAGAATCAACGGTGATTTCTACCATGTGCTACTACTTGACTCTTG
CCACACATTTTTTTCTCCTTTTTGATTTTTTTGGGCTTGTTTACCAAAGATAGTGCATACAGGG
CATTCAGGTTGTAATTAGCTCTTGCCATGACCAACTTGTTCCCCCTTTTTCAATTAATGAAAAT
GTATATGTTGGCATGCCTCATGAATTGAATGTTTGTTGAGAATTAGAGAAAGATGAATCCGCCT
TAAAGTATCTCAGTCACCAAATTTTAGAAATATGTCGCCGCTATCTCCTCCTTTCTAACACCTA
TCCAGTACTCCCTATCTTCTCTGGCTGGACCCACCCCTGTATAGTCTATTTAGTACTAGATCCA
GCTTAGTACTTTAAGTTACTGTAAACCTGTTCACCGACAGCTCAATCCAAAAAATACCAGGCCA
GCCTCGCCATGCCTCTCGGGCCAGGCTTGACCCAGCTTGAGCCTCCACACGACCCCTATATTAA
GCAGCCCTAGTTTCTAGATTTTCTTAGAAAAACCTTCCAAGAAACAAGTGATGGATATCTATTA
TCTTCTAACTTGTAGTATTATGTCCAACACAAATAGTAATCACGTACTAGCCATAATACCAAAG
TAGTCACTAATGAATTGGTAAATGTTAGGAACAGGCATTGAATATACCTTACAATGTGCCAACA
CGGCATCTGATGCATGTGGTACTCCCCAGCAACTGAATTATTGAGATATG
						
					

			
		

Sequences
Splice junction sequence	TTGGTAAATGTTAGGAACAGGCATTGAATATACCTTACAATGTGCCAACACGGCATCTGATGCA TGTGGTACTCCCCAGCAACTGAATTATTGAGATATGctccgtatttccatgcactgcactgcac tctcaccagctcttagttctccttcccctgccgctggtcacgcagcaaacatggccgtcctgcc ggagtcac
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: 163 Transcript exons: 28973535-28973665,28976817-28976848 CTCCGTATTTCCATGCACTGCACTGCACTCTCACCAGCTCTTAGTTCTCCTTCCCCTGCCGCTG GTCACGCAGCAAACATGGCCGTCCTGCCGGAGTCACGCCGGCTCTCCCTGCTCCTCATGGCCGC CTGGTACTCCCCAGCAACTGAATTATTGAGATATG Transcript length: 222 Transcript exons: 28973535-28973695,28976788-28976848 CTCCGTATTTCCATGCACTGCACTGCACTCTCACCAGCTCTTAGTTCTCCTTCCCCTGCCGCTG GTCACGCAGCAAACATGGCCGTCCTGCCGGAGTCACGCCGGCTCTCCCTGCTCCTCATGGCCGC CTGCTTCCTGCTTCAGGCTCTCAGCGCCCACGCATGTGCCAACACGGCATCTGATGCATGTGGT ACTCCCCAGCAACTGAATTATTGAGATATG Transcript length: 230 Transcript exons: 28973535-28973704,28976789-28976848 CTCCGTATTTCCATGCACTGCACTGCACTCTCACCAGCTCTTAGTTCTCCTTCCCCTGCCGCTG GTCACGCAGCAAACATGGCCGTCCTGCCGGAGTCACGCCGGCTCTCCCTGCTCCTCATGGCCGC CTGCTTCCTGCTTCAGGCTCTCAGCGCCCACGCCATCACCCGTGTGCCAACACGGCATCTGATG CATGTGGTACTCCCCAGCAACTGAATTATTGAGATATG
Genomic sequence	CTCCGTATTTCCATGCACTGCACTGCACTCTCACCAGCTCTTAGTTCTCCTTCCCCTGCCGCTG GTCACGCAGCAAACATGGCCGTCCTGCCGGAGTCACGCCGGCTCTCCCTGCTCCTCATGGCCGC CTGCTTCCTGCTTCAGGCTCTCAGCGCCCACGCCATCACCCGGCATTACAAGTTCAATGTGAGG ATATATCGTCATCAAACTTTGCCGCATGATAACTGCAAGCATGCATCGCAATTGTCACATACAT ATACAGGTTGCAGCAGAAATGGCAAGATGGTTTATTACCACGGTTTTGTCTGTCTTTTCTGTGT CTTGTGCAGGTGGTCATGCGGAACATGACACGGCTTTGCTCAACCAAGCCTATCCTCACTGTCA ATGGCAAGTTCCCGGGGCCAACCCTGTATGCAAGAGAAGGCGATAATGTCCTAGTCAAGGTCGT CAATCATGTAGCTCACAATGTTACCATCCACTGGTAAGCAGCTTAGCTAGCTAGCCCATGGCTA CTCCATGCATATGCTTCAACTCCACGTGTAATTTGCACCACAATTTGAATCACCACCTCAAGGC TCCTTTGCTCTCTGTAAGTACCCAAAAAGAAAAGGAGAATATCATGCTGTGTTAGTTAAAAGGT AAAAAGTATGTATAGCTTGCATTAGATCCTCTCTGTTGAACAGAAAACAGAAATGTGCTAGTTA TTGTTCCCATTTATGCAACAAAAATACACTTGGTGAATAACTTGATAAACAAGCATGTCATACT AATCAGGCACGGGGTAAGGCAGATCCGGACAGGGTGGTACGATGGGCCAGCTTACATAACACAG TGCCCAATACAGCCAGGAAGCAGCTTTCTCTATAATTTCACTATAACAGGGCAACGAGGCACAC TCCTCTGGCATGCTCACATCAATTGGCTAAGGGCTACCGTCCATGGTGCTATCGTCATCCTTCC AAAGCTTGGCGTGCCCTACCCCTTCCCTGCACCTCACAAGGAGGCTGTTATCGTGTTAGGTATA TATATACACACACATATATATAGCTGCTTCTCTACATCTTGATGCATCCAGCACTTAATTTATC AAGTGCTGCATGCAGGAGAATGGTGGAAAGAGGACACAGAAACTGTAATTAACCAGGCCATGCA GCTAGGAGTGGGACCCAATATTTCTGATTCACACACCATCAATGGTCATCCTGGTCCGCTGTCT GAGTGTGCTTCTTCACAAGGTAATACTCTTACTCTACATGAACACGAGACAGACAGTGCATGTT ATGGCTAACTATGTGCTAGTCCTACAACTGAGCCAAAGACCTAACGATTTCCTGATGTATGCTT GCAATACAATGCACAGATGGGTTCAAGCTCAGCGTCGAAAATGGCAAAACATACATGCTCCGGA TCATCAACGCTGCACTGAATGATGACCTATTTTTCAAGGTTGCTGGGCACGAATTAACTGTGGT TGAGGTTGATGCAGTCTATACCAAGCCATTTAAGACCGATACCCTGCTCATCACTCCAGGCCAG ACCACCAACGTCCTTGTTAGAGCTAACCAAGGCGCTGGCCGTTACCTTCTCTCAGTCTCCCCCT TCATGGATGCGCCCGTGCAGGTTGACAACAAAACAGGCACCGCTACTTTGCACTACGCCAACAC AGTCTCGTCAAGCATGGCATCCCTCACTCTCGTCAAGCCACCACCACAAAATGCCACCCATATC GTATCAAAATTTACTGATTCACTCCATAGTCTCAATTCCAAGGAGTACCCAGCCAATGTGCCAC AGACAGTAGACCACTCCCTTCTCCTTACCGTTGGCGTAGGTGTCAATCCATGTCCAAGCTGCAT CAATGGGACAAGGGTGGTGGGCACAATCAACAACGTGACGTTCATCATGCCATCAACCCCAATT CTTCAAGCCCACTATTACAACATTCCAGGAGTGTTCACAGAAGACTTCCCAGCAACCCCACTGC ACAAGTTCAACTATACAGGAAGTGGTCCCAAAAACCTTCAAACCATGAATGGAACCAGGGTTTA CAGGCTGCCATACAATGCTTCAGTGCAGGTTGTACTCCAGGATACGGGAATCATATCACCAGAA AGCCACCCAATCCATTTACATGGCTTTAATTTTTTTGTGGTTGGGAAAGGGGTCGGGAACTACA ACCCCAGGACCTCCCCTTCTACATTCAACCTCATCGACCCCATCGAGAGGAACACCATTGGAGT TCCTACTGGTGGTTGGACGGCAATCAGATTTAGGTCAGACAACCCAGGTATTGATTTTAAAACC TATGTTTTTTTAAGATAAATAACCCCTTCTGTTTCCAGACACATTGATTGAGCTGTTATATTGC AGGTGTTTGGTTTATGCATTGTCATTTCGAGGTGCACACATCATGGGGACTCAAGATGGCCTTT GTGGTGGATAATGGAAAGAGACCTAGTGAGACTCTGATTCCACCACCCAAAGATCTTCCGCAGT GTTAACAACATGGGATTCAAAACTGCCCCCACGGAGAGGAGCCTATTACAAGAAGGGTAATTGG CTTTGGTCCGATGTACGGAAAGAATCAACGGTGATTTCTACCATGTGCTACTACTTGACTCTTG CCACACATTTTTTTCTCCTTTTTGATTTTTTTGGGCTTGTTTACCAAAGATAGTGCATACAGGG CATTCAGGTTGTAATTAGCTCTTGCCATGACCAACTTGTTCCCCCTTTTTCAATTAATGAAAAT GTATATGTTGGCATGCCTCATGAATTGAATGTTTGTTGAGAATTAGAGAAAGATGAATCCGCCT TAAAGTATCTCAGTCACCAAATTTTAGAAATATGTCGCCGCTATCTCCTCCTTTCTAACACCTA TCCAGTACTCCCTATCTTCTCTGGCTGGACCCACCCCTGTATAGTCTATTTAGTACTAGATCCA GCTTAGTACTTTAAGTTACTGTAAACCTGTTCACCGACAGCTCAATCCAAAAAATACCAGGCCA GCCTCGCCATGCCTCTCGGGCCAGGCTTGACCCAGCTTGAGCCTCCACACGACCCCTATATTAA GCAGCCCTAGTTTCTAGATTTTCTTAGAAAAACCTTCCAAGAAACAAGTGATGGATATCTATTA TCTTCTAACTTGTAGTATTATGTCCAACACAAATAGTAATCACGTACTAGCCATAATACCAAAG TAGTCACTAATGAATTGGTAAATGTTAGGAACAGGCATTGAATATACCTTACAATGTGCCAACA CGGCATCTGATGCATGTGGTACTCCCCAGCAACTGAATTATTGAGATATG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.52355749

Conservation Information
Conserved circRNAs	NA
PMCS	0.52355749

			
						 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
						Lu et al., 2015;Ye et al., 2015;Chu et al., 2017

circRNA

Detail information of Os11g0708000_circ_g.3

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