Plant Circular RNA Database

Detail information of Os11g0461000_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os11g0461000_circ_g.3
					
						ID in PlantcircBase
						osa_circ_009313
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr11: 15721114-15722355  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, KNIFE, PcircRNA_finder
					
						Parent gene
						
							Os11g0461000						
					
						Parent gene annotation
						
							Peptidase S10, serine carboxypeptidase family protein. (Os11t046
1000-01);Hypothetical conserved gene. (Os11t0461000-02);Peptidas
e S10, serine carboxypeptidase family protein. (Os11t0461000-03)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os11g0461000_circ_igg.1 Os11g0461000_circ_igg.2 Os11g0461000_circ_igg.3 Os11g0461000_circ_g.1 Os11g0461000_circ_g.2 Os11g0461000_circ_g.4 Os11g0461000_circ_g.5 Os11g0461000_circ_g.6 Os11g0461000_circ_g.7 Os11g0461000_circ_g.8 						
					
						Support reads
						3
					
						Tissues
						shoot, root, seed
					
						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
						Os11t0461000-01:3

General Information
CircRNA Name	Os11g0461000_circ_g.3
ID in PlantcircBase	osa_circ_009313
Alias	NA
Organism	Oryza sativa
Position	chr11: 15721114-15722355 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, KNIFE, PcircRNA_finder
Parent gene	Os11g0461000
Parent gene annotation	Peptidase S10, serine carboxypeptidase family protein. (Os11t046 1000-01);Hypothetical conserved gene. (Os11t0461000-02);Peptidas e S10, serine carboxypeptidase family protein. (Os11t0461000-03)
Parent gene strand	+
Alternative splicing	Os11g0461000_circ_igg.1 Os11g0461000_circ_igg.2 Os11g0461000_circ_igg.3 Os11g0461000_circ_g.1 Os11g0461000_circ_g.2 Os11g0461000_circ_g.4 Os11g0461000_circ_g.5 Os11g0461000_circ_g.6 Os11g0461000_circ_g.7 Os11g0461000_circ_g.8
Support reads	3
Tissues	shoot, root, seed
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	Os11t0461000-01:3

			
						 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  
						
							GTACGTTGCTGGCAATCCAAGGACCGAACGCCAATTTGATGAAGGTGGTAAAATTCCATTTCTC
CATGGCATGGGACTTATATCCAATGAACTTTATGAGtggcttcatgatcatccccagttcttgc
tgaatccgctgtatattggaggtgactcatatagtggttatattgtacctacacttgcgctagc
gattgatg

									
								

					

						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: 220
Transcript exons: 15721114-15721172,15722195-15722355
TGGCTTCATGATCATCCCCAGTTCTTGCTGAATCCGCTGTATATTGGAGGTGACTCATAGTGGC
CTGCAATTAACTTTTGCCTTCCACCAATTTCTTTACCTTGTGTACATGACGCAGGGGTACGTTG
CTGGCAATCCAAGGACCGAACGCCAATTTGATGAAGGTGGTAAAATTCCATTTCTCCATGGCAT
GGGACTTATATCCAATGAACTTTATGAG
Transcript length: 222
Transcript exons: 15721114-15721206,15722227-15722355
TGGCTTCATGATCATCCCCAGTTCTTGCTGAATCCGCTGTATATTGGAGGTGACTCATATAGTG
GTTATATTGTACCTACACTTGCGCTAGCGTTTCTTTACCTTGTGTACATGACGCAGGGGTACGT
TGCTGGCAATCCAAGGACCGAACGCCAATTTGATGAAGGTGGTAAAATTCCATTTCTCCATGGC
ATGGGACTTATATCCAATGAACTTTATGAG
Transcript length: 243
Transcript exons: 15721114-15721216,15722052-15722089,15722254-15722355
TGGCTTCATGATCATCCCCAGTTCTTGCTGAATCCGCTGTATATTGGAGGTGACTCATATAGTG
GTTATATTGTACCTACACTTGCGCTAGCGATTGATGAAAGCAATGATTCAGGAGATAAACCAAT
TTTGAATCTCATGGGGTACGTTGCTGGCAATCCAAGGACCGAACGCCAATTTGATGAAGGTGGT
AAAATTCCATTTCTCCATGGCATGGGACTTATATCCAATGAACTTTATGAG
Transcript length: 279
Transcript exons: 15721114-15721200,15722164-15722355
TGGCTTCATGATCATCCCCAGTTCTTGCTGAATCCGCTGTATATTGGAGGTGACTCATATAGTG
GTTATATTGTACCTACACTTGCGCATAAATTGCTTGCTAATGTGTAGTACCAATGTGGCCTGCA
ATTAACTTTTGCCTTCCACCAATTTCTTTACCTTGTGTACATGACGCAGGGGTACGTTGCTGGC
AATCCAAGGACCGAACGCCAATTTGATGAAGGTGGTAAAATTCCATTTCTCCATGGCATGGGAC
TTATATCCAATGAACTTTATGAG
						
					

						Genomic sequence
						
							TGGCTTCATGATCATCCCCAGTTCTTGCTGAATCCGCTGTATATTGGAGGTGACTCATATAGTG
GTTATATTGTACCTACACTTGCGCTAGCGATTGATGAAAGTAAGCTTCTTGCATTGTGAATGGA
TAATTTCCTTAGACATCCTCACAGTGTTACACAACATTAAATTTGATCACCTTGCAGTTTCGGA
ATATATTTCAGTAAATAATACCATCTCTCATATGGGTAATGGTGATCACCATATATCAATTACT
ATCACAACAATTACTAGTAAGATTTTTCTTTTGTTACTAACTAAATACTATTGTTTTGGCAATC
ATCTAAATGAGAGAAATCCTTATATGCCACTCAAAATTAGCTCGTTCTCTTATATGCCACTCAA
AATTAGCTCTTTCCATCTATGCCATTGGTTCGAATTTATCCTCTTTTTTGCCACTACCATCACT
CCATCGTCTATTCACAATTAATTCCATTGTAGAAAGATGCAGTTGCCCTTGAAAGTTGCTATAG
AACAAGTTGGTTGTGACCGTGACGAAGTTTCAGCGAGGTCCTGCTTTTTTCCTAGTTTGGCAAC
TTTTGTTTGATGGATCCAGCATTGTTAGAGGGCAATATTGGATTTTAGGCAGAAGATGCACAAG
GAAACGAAAAAGAGGAATTAAACTATGGACAGATAATGGAGTGGTGGTAACAGCACAAGAGGGT
CGAGAAATTTAAACCAGTGGCATAGATGGAAAGAGCTAATTTCGAATGGTATATAAGAGAATGA
GCCAATTTCAAGTGATATATATGGAATTCTCTCCATCTAAATATTAGGACTGAGATATATATTT
TTTATTCATGAATTATTAAAACAAATTTGTTGTTCATTTTCTGCGTGGATTAATATTGTGTGTG
TTTCCAACTACTAACTACGGACCATGTGTCTATATTTTTCAGGCAATGATTCAGGAGATAAACC
AATTTTGAATCTCATGGTCTGATCGATCTTATCAGATAAATATCAATCATGAAATTTTATATTT
GGAATCTTAATTACGTCAATAGTCTACATAAATTGCTTGCTAATGTGTAGTACCAATGTGGCCT
GCAATTAACTTTTGCCTTCCACCAATTTCTTTACCTTGTGTACATGACGCAGGGGTACGTTGCT
GGCAATCCAAGGACCGAACGCCAATTTGATGAAGGTGGTAAAATTCCATTTCTCCATGGCATGG
GACTTATATCCAATGAACTTTATGAG
						
					

			
		

Sequences
Splice junction sequence	GTACGTTGCTGGCAATCCAAGGACCGAACGCCAATTTGATGAAGGTGGTAAAATTCCATTTCTC CATGGCATGGGACTTATATCCAATGAACTTTATGAGtggcttcatgatcatccccagttcttgc tgaatccgctgtatattggaggtgactcatatagtggttatattgtacctacacttgcgctagc gattgatg
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: 220 Transcript exons: 15721114-15721172,15722195-15722355 TGGCTTCATGATCATCCCCAGTTCTTGCTGAATCCGCTGTATATTGGAGGTGACTCATAGTGGC CTGCAATTAACTTTTGCCTTCCACCAATTTCTTTACCTTGTGTACATGACGCAGGGGTACGTTG CTGGCAATCCAAGGACCGAACGCCAATTTGATGAAGGTGGTAAAATTCCATTTCTCCATGGCAT GGGACTTATATCCAATGAACTTTATGAG Transcript length: 222 Transcript exons: 15721114-15721206,15722227-15722355 TGGCTTCATGATCATCCCCAGTTCTTGCTGAATCCGCTGTATATTGGAGGTGACTCATATAGTG GTTATATTGTACCTACACTTGCGCTAGCGTTTCTTTACCTTGTGTACATGACGCAGGGGTACGT TGCTGGCAATCCAAGGACCGAACGCCAATTTGATGAAGGTGGTAAAATTCCATTTCTCCATGGC ATGGGACTTATATCCAATGAACTTTATGAG Transcript length: 243 Transcript exons: 15721114-15721216,15722052-15722089,15722254-15722355 TGGCTTCATGATCATCCCCAGTTCTTGCTGAATCCGCTGTATATTGGAGGTGACTCATATAGTG GTTATATTGTACCTACACTTGCGCTAGCGATTGATGAAAGCAATGATTCAGGAGATAAACCAAT TTTGAATCTCATGGGGTACGTTGCTGGCAATCCAAGGACCGAACGCCAATTTGATGAAGGTGGT AAAATTCCATTTCTCCATGGCATGGGACTTATATCCAATGAACTTTATGAG Transcript length: 279 Transcript exons: 15721114-15721200,15722164-15722355 TGGCTTCATGATCATCCCCAGTTCTTGCTGAATCCGCTGTATATTGGAGGTGACTCATATAGTG GTTATATTGTACCTACACTTGCGCATAAATTGCTTGCTAATGTGTAGTACCAATGTGGCCTGCA ATTAACTTTTGCCTTCCACCAATTTCTTTACCTTGTGTACATGACGCAGGGGTACGTTGCTGGC AATCCAAGGACCGAACGCCAATTTGATGAAGGTGGTAAAATTCCATTTCTCCATGGCATGGGAC TTATATCCAATGAACTTTATGAG
Genomic sequence	TGGCTTCATGATCATCCCCAGTTCTTGCTGAATCCGCTGTATATTGGAGGTGACTCATATAGTG GTTATATTGTACCTACACTTGCGCTAGCGATTGATGAAAGTAAGCTTCTTGCATTGTGAATGGA TAATTTCCTTAGACATCCTCACAGTGTTACACAACATTAAATTTGATCACCTTGCAGTTTCGGA ATATATTTCAGTAAATAATACCATCTCTCATATGGGTAATGGTGATCACCATATATCAATTACT ATCACAACAATTACTAGTAAGATTTTTCTTTTGTTACTAACTAAATACTATTGTTTTGGCAATC ATCTAAATGAGAGAAATCCTTATATGCCACTCAAAATTAGCTCGTTCTCTTATATGCCACTCAA AATTAGCTCTTTCCATCTATGCCATTGGTTCGAATTTATCCTCTTTTTTGCCACTACCATCACT CCATCGTCTATTCACAATTAATTCCATTGTAGAAAGATGCAGTTGCCCTTGAAAGTTGCTATAG AACAAGTTGGTTGTGACCGTGACGAAGTTTCAGCGAGGTCCTGCTTTTTTCCTAGTTTGGCAAC TTTTGTTTGATGGATCCAGCATTGTTAGAGGGCAATATTGGATTTTAGGCAGAAGATGCACAAG GAAACGAAAAAGAGGAATTAAACTATGGACAGATAATGGAGTGGTGGTAACAGCACAAGAGGGT CGAGAAATTTAAACCAGTGGCATAGATGGAAAGAGCTAATTTCGAATGGTATATAAGAGAATGA GCCAATTTCAAGTGATATATATGGAATTCTCTCCATCTAAATATTAGGACTGAGATATATATTT TTTATTCATGAATTATTAAAACAAATTTGTTGTTCATTTTCTGCGTGGATTAATATTGTGTGTG TTTCCAACTACTAACTACGGACCATGTGTCTATATTTTTCAGGCAATGATTCAGGAGATAAACC AATTTTGAATCTCATGGTCTGATCGATCTTATCAGATAAATATCAATCATGAAATTTTATATTT GGAATCTTAATTACGTCAATAGTCTACATAAATTGCTTGCTAATGTGTAGTACCAATGTGGCCT GCAATTAACTTTTGCCTTCCACCAATTTCTTTACCTTGTGTACATGACGCAGGGGTACGTTGCT GGCAATCCAAGGACCGAACGCCAATTTGATGAAGGTGGTAAAATTCCATTTCTCCATGGCATGG GACTTATATCCAATGAACTTTATGAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_008999 						
					
						PMCS
						0.228463795

Conservation Information
Conserved circRNAs	osi_circ_008999
PMCS	0.228463795

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							15722088-15722352(+)
15722295-15721141(+)
15721130-15722062(-)
15721173-15722335(-)
						
						Potential amino acid sequence
						
							MGYVAGNPRTERQFDEGGKIPFLHGMGLISNELYEWLHDHPQFLLNPLYIGGDSYSGYIVPTLA
LAIDESNDSGDKPILNLMGYVAGNPRTERQFDEGGKIPFLHGMGLISNELYEWLHDHPQFLLNP
LYIGGDSYSGYIVPTLALAIDESNDSGDKPILNLMGYVAGNPRTERQFDEGGKIPFLHGMGLIS
NELYEWLHDHPQFLLNPLYIGGDSYSGYIVPTLALAIDESNDSGDKPILNLMGYVAGNPRTERQ
FDEGGKIPFLHGMGLISNELYE(+)
MKVVKFHFSMAWDLYPMNFMSGFMIIPSSC*(+)
MIMKPLIKFIGYKSHAMEKWNFTTFIKLAFGPWIASNVPHEIQNWFIS*(-)
MSHLQYTADSARTGDDHEATHKVHWI*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	15722088-15722352(+) 15722295-15721141(+) 15721130-15722062(-) 15721173-15722335(-)
Potential amino acid sequence	MGYVAGNPRTERQFDEGGKIPFLHGMGLISNELYEWLHDHPQFLLNPLYIGGDSYSGYIVPTLA LAIDESNDSGDKPILNLMGYVAGNPRTERQFDEGGKIPFLHGMGLISNELYEWLHDHPQFLLNP LYIGGDSYSGYIVPTLALAIDESNDSGDKPILNLMGYVAGNPRTERQFDEGGKIPFLHGMGLIS NELYEWLHDHPQFLLNPLYIGGDSYSGYIVPTLALAIDESNDSGDKPILNLMGYVAGNPRTERQ FDEGGKIPFLHGMGLISNELYE(+) MKVVKFHFSMAWDLYPMNFMSGFMIIPSSC(+) MIMKPLIKFIGYKSHAMEKWNFTTFIKLAFGPWIASNVPHEIQNWFIS(-) MSHLQYTADSARTGDDHEATHKVHWI*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os11g0461000_circ_g.3

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