Plant Circular RNA Database

Detail information of Os11g0153700_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os11g0153700_circ_g.3
					
						ID in PlantcircBase
						osa_circ_008496
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr11: 2519659-2521402  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os11g0153700						
					
						Parent gene annotation
						
							Similar to Signal recognition particle 54 kDa protein, chloropla
st precursor (SRP54) (54 chloroplast protein) (54CP) (FFC). (Os1
1t0153700-01)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os11g0153700_circ_g.1 Os11g0153700_circ_g.2 Os11g0153700_circ_g.4 						
					
						Support reads
						1
					
						Tissues
						shoot
					
						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
						Os11t0153700-01:6

General Information
CircRNA Name	Os11g0153700_circ_g.3
ID in PlantcircBase	osa_circ_008496
Alias	NA
Organism	Oryza sativa
Position	chr11: 2519659-2521402 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	Os11g0153700
Parent gene annotation	Similar to Signal recognition particle 54 kDa protein, chloropla st precursor (SRP54) (54 chloroplast protein) (54CP) (FFC). (Os1 1t0153700-01)
Parent gene strand	+
Alternative splicing	Os11g0153700_circ_g.1 Os11g0153700_circ_g.2 Os11g0153700_circ_g.4
Support reads	1
Tissues	shoot
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	Os11t0153700-01:6

			
						 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  
						
							CCGAATGCGTGCTCAAATGCAGAAAATGATGGGTGCTATGCAAGGGCAAGACACCCCTGATATG
GAAGGCCTCATGGATTCCATCAAGGCAGAAGAGCAGcattggttagcaccttcaatgttgagat
tggtattactggtgctatactgacaaaactggatggtgattccagaggtggagcagcactaagt
atcaaaga

									
								

					

						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: 671
Transcript exons: 2519659-2519759,2520207-2520344,2520438-2520581,2520725-
2520800,2521073-2521158,2521277-2521402
CATTGGTTAGCACCTTCAATGTTGAGATTGGTATTACTGGTGCTATACTGACAAAACTGGATGG
TGATTCCAGAGGTGGAGCAGCACTAAGTATCAAAGAGGTATCTGGAAAGCCCATCAAGTTTGTA
GGGCGAGGAGAACGCATGGAAGATCTTGAGCCTTTCTATCCTGATCGTATGGCACAACGAATCT
TGGGAATGGGAGATGTACTTTCATTTGTTGAAAAGGCACAGGAAGTGATGCGTCAAGAAGATGC
TGAGGAATTACAGAAGAAGATCCTGAGTGCAAAATTTAACTTCAATGACTTCTTGAAGCAAACA
CAAGCTATCGCACAAATGGGTTCATTTAGTCGTATAATTGGCATGATTCCAGGCATGAACAAGG
TTACCCCTGCTCAAATTCGTGAAGCGGAGAAAAACCTTAAATTTATGGAGTCCATGATCAACGT
AATGACCCCTGAGGAAAGGGAAAGACCAGAGCTACTTGCTGAATCACGCGAGAGGAGGATAAGA
GTGGCCAAGGAATCCGGAAAAAACGAACGACAGGTGAGCCAATTGGTTGCGCAGCTCTTCCGAA
TGCGTGCTCAAATGCAGAAAATGATGGGTGCTATGCAAGGGCAAGACACCCCTGATATGGAAGG
CCTCATGGATTCCATCAAGGCAGAAGAGCAG
						
					

						Genomic sequence
						
							CATTGGTTAGCACCTTCAATGTTGAGATTGGTATTACTGGTGCTATACTGACAAAACTGGATGG
TGATTCCAGAGGTGGAGCAGCACTAAGTATCAAAGAGGTCTGTTGAATGTGAAAAACAAATGTC
CATCATTTTGTTTTTCCATCTAATTATTAGTTCAGAGTTCTTTATTTTCTCGAACAAGTTCAGA
GTTCTTTGTGAAATAATAAAAACCAATTCTGTCCTGAACAATGTATTAATTCTGCTAAGAAGGC
GCAACAATTACTGTTTCCGGTTCATTTTGTTGGATTCCACTTCCTAGATTCCTCGCTTACTGAA
AAAAAAGTTTGGTTGTGTGAGTTCAACTGGTCCTGACAAATTTGTTGTCTAATAAAAAATGTCC
ATAATAGGGTTATATGTTATTTGACTTTGTATCTGTGACTCTTCCAATTGTATCTTTACATGTT
ATTCTGGTACTTTTGTCACACCTACATTTCTCAGCAATTTTACTTTGTGTTCCCTTGGCTGGTA
GCATATAATAAATATGAAGAAATGATGAATCTGTAGGTATCTGGAAAGCCCATCAAGTTTGTAG
GGCGAGGAGAACGCATGGAAGATCTTGAGCCTTTCTATCCTGATCGTATGGCACAACGAATCTT
GGGAATGGGAGATGTACTTTCATTTGTTGAAAAGGCACAGGAAGTGGTAGGCAGGCTTCTGTGA
AATATTCCTTTCTTTTTTTACTTTAATTAAAGAACAATTTGATACTCATAGTGTGTAATCTACT
GGTACAAGTAGATGCGTCAAGAAGATGCTGAGGAATTACAGAAGAAGATCCTGAGTGCAAAATT
TAACTTCAATGACTTCTTGAAGCAAACACAAGCTATCGCACAAATGGGTTCATTTAGTCGTATA
ATTGGCATGATTCCAGGCATGAACAAGGTGCAAACATGAACTTGTTGAACTCATTGGCTCCTTT
ATCACTTTACTTTGGAACTAATCTTCACACTATGGTACACTGGCGCTTATGTTTCAGCTTCATA
CTTGATGTTATTAAGACCATAGCTTTTCCGTGTTTTGAATAGGTTACCCCTGCTCAAATTCGTG
AAGCGGAGAAAAACCTTAAATTTATGGAGTCCATGATCAACGTAATGACCCCTGGTATGTATAG
TCTACCAATGACAGGCATCTTGAAGATATCCTGTTGCTTGTTCCTCCCATTCTCTTGCAATATT
AGTGTAGTGTTCCAAATGTAACTGATATTTTTGAAAATCTGAATCCATCATCTAATTAGTGTTT
CAGCTTGGACTGTATCAAGCGATCCAGGCCTGCCACTGAAATAACACCTTGATGCTAATGGCGT
AGAACATAATAGTGATGGATCTTTGTTACATGAATATTGTCTTGATAATGTTAATCGTGCCTTT
GTGCAGAGGAAAGGGAAAGACCAGAGCTACTTGCTGAATCACGCGAGAGGAGGATAAGAGTGGC
CAAGGAATCCGGAAAAAACGAACGACAGGTTCAATTCTTAACCTTTTCTCTTTTTTTAATCTCA
TCAGCATTTCCATATCTGTCTGCGCTACTACAAACCAAACTGAACCCCATGGACGTCAATTGAC
TGCCCCCTGCACTACTAGGTGAGCCAATTGGTTGCGCAGCTCTTCCGAATGCGTGCTCAAATGC
AGAAAATGATGGGTGCTATGCAAGGGCAAGACACCCCTGATATGGAAGGCCTCATGGATTCCAT
CAAGGCAGAAGAGCAG
						
					

			
		

Sequences
Splice junction sequence	CCGAATGCGTGCTCAAATGCAGAAAATGATGGGTGCTATGCAAGGGCAAGACACCCCTGATATG GAAGGCCTCATGGATTCCATCAAGGCAGAAGAGCAGcattggttagcaccttcaatgttgagat tggtattactggtgctatactgacaaaactggatggtgattccagaggtggagcagcactaagt atcaaaga
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: 671 Transcript exons: 2519659-2519759,2520207-2520344,2520438-2520581,2520725- 2520800,2521073-2521158,2521277-2521402 CATTGGTTAGCACCTTCAATGTTGAGATTGGTATTACTGGTGCTATACTGACAAAACTGGATGG TGATTCCAGAGGTGGAGCAGCACTAAGTATCAAAGAGGTATCTGGAAAGCCCATCAAGTTTGTA GGGCGAGGAGAACGCATGGAAGATCTTGAGCCTTTCTATCCTGATCGTATGGCACAACGAATCT TGGGAATGGGAGATGTACTTTCATTTGTTGAAAAGGCACAGGAAGTGATGCGTCAAGAAGATGC TGAGGAATTACAGAAGAAGATCCTGAGTGCAAAATTTAACTTCAATGACTTCTTGAAGCAAACA CAAGCTATCGCACAAATGGGTTCATTTAGTCGTATAATTGGCATGATTCCAGGCATGAACAAGG TTACCCCTGCTCAAATTCGTGAAGCGGAGAAAAACCTTAAATTTATGGAGTCCATGATCAACGT AATGACCCCTGAGGAAAGGGAAAGACCAGAGCTACTTGCTGAATCACGCGAGAGGAGGATAAGA GTGGCCAAGGAATCCGGAAAAAACGAACGACAGGTGAGCCAATTGGTTGCGCAGCTCTTCCGAA TGCGTGCTCAAATGCAGAAAATGATGGGTGCTATGCAAGGGCAAGACACCCCTGATATGGAAGG CCTCATGGATTCCATCAAGGCAGAAGAGCAG
Genomic sequence	CATTGGTTAGCACCTTCAATGTTGAGATTGGTATTACTGGTGCTATACTGACAAAACTGGATGG TGATTCCAGAGGTGGAGCAGCACTAAGTATCAAAGAGGTCTGTTGAATGTGAAAAACAAATGTC CATCATTTTGTTTTTCCATCTAATTATTAGTTCAGAGTTCTTTATTTTCTCGAACAAGTTCAGA GTTCTTTGTGAAATAATAAAAACCAATTCTGTCCTGAACAATGTATTAATTCTGCTAAGAAGGC GCAACAATTACTGTTTCCGGTTCATTTTGTTGGATTCCACTTCCTAGATTCCTCGCTTACTGAA AAAAAAGTTTGGTTGTGTGAGTTCAACTGGTCCTGACAAATTTGTTGTCTAATAAAAAATGTCC ATAATAGGGTTATATGTTATTTGACTTTGTATCTGTGACTCTTCCAATTGTATCTTTACATGTT ATTCTGGTACTTTTGTCACACCTACATTTCTCAGCAATTTTACTTTGTGTTCCCTTGGCTGGTA GCATATAATAAATATGAAGAAATGATGAATCTGTAGGTATCTGGAAAGCCCATCAAGTTTGTAG GGCGAGGAGAACGCATGGAAGATCTTGAGCCTTTCTATCCTGATCGTATGGCACAACGAATCTT GGGAATGGGAGATGTACTTTCATTTGTTGAAAAGGCACAGGAAGTGGTAGGCAGGCTTCTGTGA AATATTCCTTTCTTTTTTTACTTTAATTAAAGAACAATTTGATACTCATAGTGTGTAATCTACT GGTACAAGTAGATGCGTCAAGAAGATGCTGAGGAATTACAGAAGAAGATCCTGAGTGCAAAATT TAACTTCAATGACTTCTTGAAGCAAACACAAGCTATCGCACAAATGGGTTCATTTAGTCGTATA ATTGGCATGATTCCAGGCATGAACAAGGTGCAAACATGAACTTGTTGAACTCATTGGCTCCTTT ATCACTTTACTTTGGAACTAATCTTCACACTATGGTACACTGGCGCTTATGTTTCAGCTTCATA CTTGATGTTATTAAGACCATAGCTTTTCCGTGTTTTGAATAGGTTACCCCTGCTCAAATTCGTG AAGCGGAGAAAAACCTTAAATTTATGGAGTCCATGATCAACGTAATGACCCCTGGTATGTATAG TCTACCAATGACAGGCATCTTGAAGATATCCTGTTGCTTGTTCCTCCCATTCTCTTGCAATATT AGTGTAGTGTTCCAAATGTAACTGATATTTTTGAAAATCTGAATCCATCATCTAATTAGTGTTT CAGCTTGGACTGTATCAAGCGATCCAGGCCTGCCACTGAAATAACACCTTGATGCTAATGGCGT AGAACATAATAGTGATGGATCTTTGTTACATGAATATTGTCTTGATAATGTTAATCGTGCCTTT GTGCAGAGGAAAGGGAAAGACCAGAGCTACTTGCTGAATCACGCGAGAGGAGGATAAGAGTGGC CAAGGAATCCGGAAAAAACGAACGACAGGTTCAATTCTTAACCTTTTCTCTTTTTTTAATCTCA TCAGCATTTCCATATCTGTCTGCGCTACTACAAACCAAACTGAACCCCATGGACGTCAATTGAC TGCCCCCTGCACTACTAGGTGAGCCAATTGGTTGCGCAGCTCTTCCGAATGCGTGCTCAAATGC AGAAAATGATGGGTGCTATGCAAGGGCAAGACACCCCTGATATGGAAGGCCTCATGGATTCCAT CAAGGCAGAAGAGCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.258610254

Conservation Information
Conserved circRNAs	NA
PMCS	0.258610254

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							2520250-2519706(+)
2520252-2521388(-)
2519663-2521107(-)
						
						Potential amino acid sequence
						
							MEDLEPFYPDRMAQRILGMGDVLSFVEKAQEVMRQEDAEELQKKILSAKFNFNDFLKQTQAIAQ
MGSFSRIIGMIPGMNKVTPAQIREAEKNLKFMESMINVMTPEERERPELLAESRERRIRVAKES
GKNERQVSQLVAQLFRMRAQMQKMMGAMQGQDTPDMEGLMDSIKAEEQHWLAPSMLRLVLLVLY
*(+)
MRSPRPTNLMGFPDTSLILSAAPPLESPSSFVSIAPVIPISTLKVLTNAALLP*(-)
MLLFCLDGIHEAFHIRGVLPLHSTHHFLHLSTHSEELRNQLAHLSFVFSGFLGHSYPPLA*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	2520250-2519706(+) 2520252-2521388(-) 2519663-2521107(-)
Potential amino acid sequence	MEDLEPFYPDRMAQRILGMGDVLSFVEKAQEVMRQEDAEELQKKILSAKFNFNDFLKQTQAIAQ MGSFSRIIGMIPGMNKVTPAQIREAEKNLKFMESMINVMTPEERERPELLAESRERRIRVAKES GKNERQVSQLVAQLFRMRAQMQKMMGAMQGQDTPDMEGLMDSIKAEEQHWLAPSMLRLVLLVLY (+) MRSPRPTNLMGFPDTSLILSAAPPLESPSSFVSIAPVIPISTLKVLTNAALLP(-) MLLFCLDGIHEAFHIRGVLPLHSTHHFLHLSTHSEELRNQLAHLSFVFSGFLGHSYPPLA*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os11g0153700_circ_g.3

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