Plant Circular RNA Database

Detail information of Os07g0404900_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os07g0404900_circ_g.3
					
						ID in PlantcircBase
						osa_circ_033441
					
						Alias
						Os07circ06255/Os_ciR10864
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr7: 12426152-12429197  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						SMALT, Segemehl, find_circ
					
						Parent gene
						
							Os07g0405100						
					
						Parent gene annotation
						
							Similar to F-box-like/WD-repeat protein ebi. (Os07t0405100-01)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							EPlOSAG00000019021_circ_ig.1 Os07g0404900_circ_g.1 Os07g0404900_circ_g.2 Os07g0404900_circ_g.4 Os07g0404900_circ_g.5 Os07g0404900_circ_g.6 Os07g0404900_circ_g.7 Os07g0404900_circ_g.8 						
					
						Support reads
						2/2
					
						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  
						
							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
						Os07t0404900-00:2
Os07t0405100-01:4
Os07t0404900-00:2

General Information
CircRNA Name	Os07g0404900_circ_g.3
ID in PlantcircBase	osa_circ_033441
Alias	Os07circ06255/Os_ciR10864
Organism	Oryza sativa
Position	chr7: 12426152-12429197 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	SMALT, Segemehl, find_circ
Parent gene	Os07g0405100
Parent gene annotation	Similar to F-box-like/WD-repeat protein ebi. (Os07t0405100-01)
Parent gene strand	+
Alternative splicing	EPlOSAG00000019021_circ_ig.1 Os07g0404900_circ_g.1 Os07g0404900_circ_g.2 Os07g0404900_circ_g.4 Os07g0404900_circ_g.5 Os07g0404900_circ_g.6 Os07g0404900_circ_g.7 Os07g0404900_circ_g.8
Support reads	2/2
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	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	Os07t0404900-00:2 Os07t0405100-01:4 Os07t0404900-00:2

			
						 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  
						
							AGTACTAGAAAGCATGTTCTCTTACTGCTTCTTTCAAATTTCTTTGTATTTAGGTGTTCGCTTG
TGCATGGAGTCCAGCTGGTTCCCTTCTAGCGTCTGGgtttcattcatgccgcattcacattagg
gtatgaagcagggatccataagggtgggattgatggaaatctagttccacctggtgctcttatc
actatcgt

									
								

					

						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: 160
Transcript exons: 12426152-12426292,12429179-12429197
GTTTCATTCATGCCGCATTCACATTAGGGTATGAAGCAGGGATCCATAAGGGTGGGATTGATGG
AAATCTAGTTCCACCTGGTGCTCTTATCACTATCGTGCAGAAAGGCCTCCAATACATAGAACTA
GAAGCAAATACGGGTTCCCTTCTAGCGTCTGG
Transcript length: 613
Transcript exons: 12426152-12426297,12426372-12426708,12428969-12429051,12
429151-12429197
GTTTCATTCATGCCGCATTCACATTAGGGTATGAAGCAGGGATCCATAAGGGTGGGATTGATGG
AAATCTAGTTCCACCTGGTGCTCTTATCACTATCGTGCAGAAAGGCCTCCAATACATAGAACTA
GAAGCAAATACGGATGAAAATGATGAAGATCTTGCGAAGGATTTTGCCCTTCTTGAACCTCTTG
AAATAATCACAAAAAATGTTGAAGAGTTGCAACAGATTGTTAAGAAAAGGAAAAGGGAGAAGAC
TCAAAGTGACCGTGACAAGGACAAGGGAAAAGAAAAGGAACGTATGGAGGAGCATGAACGACGC
CCTGGGGGTGAACGGGAGAGGGAGCGCCATGACCAAGAAAAAGAGTTAGAGAAGGAGAAAGACA
GAGCTGAAAGAGACAGGGATCAAGATAAAGAGAAAGAAAAGCTGCACACAGAGCGTATTGATAA
GGTTAAGGCTGAAGAAGATTCTCTTGCTGGTGGAGGTCCCACACCAATGGATGTAAGCACAACT
GCTCATGAAATTTCTAGTGCTGATGTGACTGTTTTGGAAGGACACAGCTCAGAGGTGTTCGCTT
GTGCATGGAGTCCAGCTGGTTCCCTTCTAGCGTCTGG
						
					

						Genomic sequence
						
							GTTTCATTCATGCCGCATTCACATTAGGGTATGAAGCAGGGATCCATAAGGGTGGGATTGATGG
AAATCTAGTTCCACCTGGTGCTCTTATCACTATCGTGCAGAAAGGCCTCCAATACATAGAACTA
GAAGCAAATACGGATGAAGTAAGTTTGTTTGTCTTCTAGTGTTCATTACCTTTTCTGATGCATG
CTACATCATGCTCTTTATCTTGTTGCAGAATGATGAAGATCTTGCGAAGGATTTTGCCCTTCTT
GAACCTCTTGAAATAATCACAAAAAATGTTGAAGAGTTGCAACAGATTGTTAAGAAAAGGAAAA
GGGAGAAGACTCAAAGTGACCGTGACAAGGACAAGGGAAAAGAAAAGGAACGTATGGAGGAGCA
TGAACGACGCCCTGGGGGTGAACGGGAGAGGGAGCGCCATGACCAAGAAAAAGAGTTAGAGAAG
GAGAAAGACAGAGCTGAAAGAGACAGGGATCAAGATAAAGAGAAAGAAAAGCTGCACACAGAGC
GTATTGATAAGGTTAAGGCTGAAGAAGATTCTCTTGCTGGTGGAGGTAATTAACTAATATCTGT
TTGCTGCATTTCCCTTACGATTCCATCTTACAGTTTTCAGCATACTGTGAGTAAACTTTAGTAG
CTACAGTCTACAGATGATTGAATCTTGATAACTTTATTTGTTAACTTGAGAAATGTTTTTGTGA
CAGTTGTTTGATATGTGCGTGTCTTTTCTTTGCGATAAATATGTTAATTACTGATTATTTTACA
ATGTTGACAAGTTTTCATTTGTTGCGGATCAGCAGAGCATTTGCAAGATAATGCTTGAAAATGT
CCTTATGTAATTATGTCCATCGGTTTTCTGTATGTTTTACTATAAATATTACAGTCAAAGCAAC
ATGCAAATTAATATGATGATTTGACGAATTATGCAAGAGTTACCACATTTATCTTTCACTTGGT
TCGCGAAAGTTTTGGGTAACATGCCACATTAGCTCTCCAGTTCATTTATGAAGACATACTTACC
AAACTGGTTACCTTTTTTTTTGGTAATGTCAAGTTTTTTGACTTGGTTTTCTTTGTGTAATAGC
CAATATTAGCCCGAAACCAAACAGGACCATCAAAGAATTATCTTATTGCATCTAAAAGCGTGAG
ATTGCTCAATTTAATATAACACTTGTGCTTGCAAAGAATGCAGACACCAGAATGACAATTGAAC
ATGCATTTGGTGTATTTTGGAAGTCGGAGAATGACAATTGCGACTTGAGAAATGTGGACAAAGT
ACTAAGTATCATTTTCAGCTTATAAATTTTCTTAGTTAAAATCCAATATATTGTCACAGTAGGG
ATTTGATTGTATGGAAGCAATTCAATAAGCTTTCCAATTCCAGGATATGCCACTCCGCAGAATT
GAATCGGTTTTTTTGCTCGTCATCAGATGTGATTAGTATGAGCTCCCACTTTTGACCAACTAGT
TTCATGCCCGTATGTTGTAACGGGTCAGGCCCCCATATAATTAGGGATAAACTGGGAGCCCGTA
TGTTAATGGGCCAAGCCCATATAATTAGGAAGTGATGGTGGTTATTTTTCGCATACGGACATGC
CGCATGCGTTGGATGAGGGGATGGAAGGAGATGGAAGGAGAACTACTCGACTTTTAAGATAGTA
GAGATCACATTTCTTGTACCCTTTTGCTCTTCTTCCTTCCCTCATATTTCTCCACCTCCGGTCT
CTTTGTGCCTGGCGATGGCTAGTGGTGTGGAGCTTTGAGTGGAGGAGGGGATGGATCCCTTGGG
AGGCGAGGCGGGCAAGCAAGAGCGCATGGAGCCAGAGCAGCACTGGCACACGGAAGTGGATGCA
ATACCGCCCTGCAGGGGAGACAAGGTCAGTGAGGGGAGGCAACACGCAGTGCAGAGGAGTTGGA
GAACACAGTACACGGCTGCGGCATGGCTATTCCTGTCAGTGCTTTCACACAGCAATGCCCAGGC
ACTTGTGTCCTTGCTCTGCTGTTTTAACGTGGCGGTTGAGGATAGACCTCCACAACAGATCCAC
CCTGGTGGAGTTTATCCTGGTGTAGTGCTGGAGGAGAGGAGAGACATCACTTAGCTCCCCTTGC
CAACTGACTTTTCCTTCTCACCATCCAGCCATCCATGCTCCTGTTCAGTCATGCATCGTGCTGG
AGAAACCATTGGGCTACCATGGGCAAAACTGGAAAAGAAAGTAGGGTCTAGGTCATGTAATCAC
TGAAATAGAAATCGAAAAAACCAAAATAATTTTAACATGGCAATTCCTAAAGCATTTTTATCTA
ACAGGTGGCAAATAATCAATTAGCTTCTCTGGAGTGACATATCCTAGAGCCCGTGACTTATGGG
TGGTGTATGATCAATTATCCCTGCCAAAAACTCCATAATATCCTTGTGGTACGTGTCATATGTT
CTAGTAACACGAACATACATTTCTATTACATTTGTGAGTGTGTATTACTATTGTGTTTCCTGAT
GGCAATAAATCGCTAAAACTGTGTTCTTAGGTGCATTAATGCTTGATAATAACCATGATTTTAA
CCTCCTGTATGAACCAATATATTGTTTGATTTCTGATATTTGATTTACATAAGTGAAATGACAT
GAATGGTCATGGAACTGATTTAGGATATTGTGCTTTAATTTCCTTATGTAGAATTAGTGTGCTT
CTTGGAGTAGCAACCTCCTTGTGGAATTAGTTGTCACTTGTATGGAGCCTTCATAATATTTTTT
GGATATTTTTGTGTCTATCAGTTTAACGCTACCATGCCAGGGTGTACTAAATCTTATTGCTACA
GGTCCCACACCAATGGATGTAAGCACAACTGCTCATGAAATTTCTAGTGCTGATGTGACTGTTT
TGGAAGGACACAGCTCAGAGGTTTAAATAGCCTTCTGCCATACAGCTATTTGACCTATCATGGA
TTAGTACTAGAAAGCATGTTCTCTTACTGCTTCTTTCAAATTTCTTTGTATTTAGGTGTTCGCT
TGTGCATGGAGTCCAGCTGGTTCCCTTCTAGCGTCTGG
						
					

			
		

Sequences
Splice junction sequence	AGTACTAGAAAGCATGTTCTCTTACTGCTTCTTTCAAATTTCTTTGTATTTAGGTGTTCGCTTG TGCATGGAGTCCAGCTGGTTCCCTTCTAGCGTCTGGgtttcattcatgccgcattcacattagg gtatgaagcagggatccataagggtgggattgatggaaatctagttccacctggtgctcttatc actatcgt
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: 160 Transcript exons: 12426152-12426292,12429179-12429197 GTTTCATTCATGCCGCATTCACATTAGGGTATGAAGCAGGGATCCATAAGGGTGGGATTGATGG AAATCTAGTTCCACCTGGTGCTCTTATCACTATCGTGCAGAAAGGCCTCCAATACATAGAACTA GAAGCAAATACGGGTTCCCTTCTAGCGTCTGG Transcript length: 613 Transcript exons: 12426152-12426297,12426372-12426708,12428969-12429051,12 429151-12429197 GTTTCATTCATGCCGCATTCACATTAGGGTATGAAGCAGGGATCCATAAGGGTGGGATTGATGG AAATCTAGTTCCACCTGGTGCTCTTATCACTATCGTGCAGAAAGGCCTCCAATACATAGAACTA GAAGCAAATACGGATGAAAATGATGAAGATCTTGCGAAGGATTTTGCCCTTCTTGAACCTCTTG AAATAATCACAAAAAATGTTGAAGAGTTGCAACAGATTGTTAAGAAAAGGAAAAGGGAGAAGAC TCAAAGTGACCGTGACAAGGACAAGGGAAAAGAAAAGGAACGTATGGAGGAGCATGAACGACGC CCTGGGGGTGAACGGGAGAGGGAGCGCCATGACCAAGAAAAAGAGTTAGAGAAGGAGAAAGACA GAGCTGAAAGAGACAGGGATCAAGATAAAGAGAAAGAAAAGCTGCACACAGAGCGTATTGATAA GGTTAAGGCTGAAGAAGATTCTCTTGCTGGTGGAGGTCCCACACCAATGGATGTAAGCACAACT GCTCATGAAATTTCTAGTGCTGATGTGACTGTTTTGGAAGGACACAGCTCAGAGGTGTTCGCTT GTGCATGGAGTCCAGCTGGTTCCCTTCTAGCGTCTGG
Genomic sequence	GTTTCATTCATGCCGCATTCACATTAGGGTATGAAGCAGGGATCCATAAGGGTGGGATTGATGG AAATCTAGTTCCACCTGGTGCTCTTATCACTATCGTGCAGAAAGGCCTCCAATACATAGAACTA GAAGCAAATACGGATGAAGTAAGTTTGTTTGTCTTCTAGTGTTCATTACCTTTTCTGATGCATG CTACATCATGCTCTTTATCTTGTTGCAGAATGATGAAGATCTTGCGAAGGATTTTGCCCTTCTT GAACCTCTTGAAATAATCACAAAAAATGTTGAAGAGTTGCAACAGATTGTTAAGAAAAGGAAAA GGGAGAAGACTCAAAGTGACCGTGACAAGGACAAGGGAAAAGAAAAGGAACGTATGGAGGAGCA TGAACGACGCCCTGGGGGTGAACGGGAGAGGGAGCGCCATGACCAAGAAAAAGAGTTAGAGAAG GAGAAAGACAGAGCTGAAAGAGACAGGGATCAAGATAAAGAGAAAGAAAAGCTGCACACAGAGC GTATTGATAAGGTTAAGGCTGAAGAAGATTCTCTTGCTGGTGGAGGTAATTAACTAATATCTGT TTGCTGCATTTCCCTTACGATTCCATCTTACAGTTTTCAGCATACTGTGAGTAAACTTTAGTAG CTACAGTCTACAGATGATTGAATCTTGATAACTTTATTTGTTAACTTGAGAAATGTTTTTGTGA CAGTTGTTTGATATGTGCGTGTCTTTTCTTTGCGATAAATATGTTAATTACTGATTATTTTACA ATGTTGACAAGTTTTCATTTGTTGCGGATCAGCAGAGCATTTGCAAGATAATGCTTGAAAATGT CCTTATGTAATTATGTCCATCGGTTTTCTGTATGTTTTACTATAAATATTACAGTCAAAGCAAC ATGCAAATTAATATGATGATTTGACGAATTATGCAAGAGTTACCACATTTATCTTTCACTTGGT TCGCGAAAGTTTTGGGTAACATGCCACATTAGCTCTCCAGTTCATTTATGAAGACATACTTACC AAACTGGTTACCTTTTTTTTTGGTAATGTCAAGTTTTTTGACTTGGTTTTCTTTGTGTAATAGC CAATATTAGCCCGAAACCAAACAGGACCATCAAAGAATTATCTTATTGCATCTAAAAGCGTGAG ATTGCTCAATTTAATATAACACTTGTGCTTGCAAAGAATGCAGACACCAGAATGACAATTGAAC ATGCATTTGGTGTATTTTGGAAGTCGGAGAATGACAATTGCGACTTGAGAAATGTGGACAAAGT ACTAAGTATCATTTTCAGCTTATAAATTTTCTTAGTTAAAATCCAATATATTGTCACAGTAGGG ATTTGATTGTATGGAAGCAATTCAATAAGCTTTCCAATTCCAGGATATGCCACTCCGCAGAATT GAATCGGTTTTTTTGCTCGTCATCAGATGTGATTAGTATGAGCTCCCACTTTTGACCAACTAGT TTCATGCCCGTATGTTGTAACGGGTCAGGCCCCCATATAATTAGGGATAAACTGGGAGCCCGTA TGTTAATGGGCCAAGCCCATATAATTAGGAAGTGATGGTGGTTATTTTTCGCATACGGACATGC CGCATGCGTTGGATGAGGGGATGGAAGGAGATGGAAGGAGAACTACTCGACTTTTAAGATAGTA GAGATCACATTTCTTGTACCCTTTTGCTCTTCTTCCTTCCCTCATATTTCTCCACCTCCGGTCT CTTTGTGCCTGGCGATGGCTAGTGGTGTGGAGCTTTGAGTGGAGGAGGGGATGGATCCCTTGGG AGGCGAGGCGGGCAAGCAAGAGCGCATGGAGCCAGAGCAGCACTGGCACACGGAAGTGGATGCA ATACCGCCCTGCAGGGGAGACAAGGTCAGTGAGGGGAGGCAACACGCAGTGCAGAGGAGTTGGA GAACACAGTACACGGCTGCGGCATGGCTATTCCTGTCAGTGCTTTCACACAGCAATGCCCAGGC ACTTGTGTCCTTGCTCTGCTGTTTTAACGTGGCGGTTGAGGATAGACCTCCACAACAGATCCAC CCTGGTGGAGTTTATCCTGGTGTAGTGCTGGAGGAGAGGAGAGACATCACTTAGCTCCCCTTGC CAACTGACTTTTCCTTCTCACCATCCAGCCATCCATGCTCCTGTTCAGTCATGCATCGTGCTGG AGAAACCATTGGGCTACCATGGGCAAAACTGGAAAAGAAAGTAGGGTCTAGGTCATGTAATCAC TGAAATAGAAATCGAAAAAACCAAAATAATTTTAACATGGCAATTCCTAAAGCATTTTTATCTA ACAGGTGGCAAATAATCAATTAGCTTCTCTGGAGTGACATATCCTAGAGCCCGTGACTTATGGG TGGTGTATGATCAATTATCCCTGCCAAAAACTCCATAATATCCTTGTGGTACGTGTCATATGTT CTAGTAACACGAACATACATTTCTATTACATTTGTGAGTGTGTATTACTATTGTGTTTCCTGAT GGCAATAAATCGCTAAAACTGTGTTCTTAGGTGCATTAATGCTTGATAATAACCATGATTTTAA CCTCCTGTATGAACCAATATATTGTTTGATTTCTGATATTTGATTTACATAAGTGAAATGACAT GAATGGTCATGGAACTGATTTAGGATATTGTGCTTTAATTTCCTTATGTAGAATTAGTGTGCTT CTTGGAGTAGCAACCTCCTTGTGGAATTAGTTGTCACTTGTATGGAGCCTTCATAATATTTTTT GGATATTTTTGTGTCTATCAGTTTAACGCTACCATGCCAGGGTGTACTAAATCTTATTGCTACA GGTCCCACACCAATGGATGTAAGCACAACTGCTCATGAAATTTCTAGTGCTGATGTGACTGTTT TGGAAGGACACAGCTCAGAGGTTTAAATAGCCTTCTGCCATACAGCTATTTGACCTATCATGGA TTAGTACTAGAAAGCATGTTCTCTTACTGCTTCTTTCAAATTTCTTTGTATTTAGGTGTTCGCT TGTGCATGGAGTCCAGCTGGTTCCCTTCTAGCGTCTGG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_007130* osi_circ_016953 						
					
						PMCS
						0.46780544

Conservation Information
Conserved circRNAs	osi_circ_007130* osi_circ_016953
PMCS	0.46780544

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							12426526-12426182(+)
12426164-12429013(-)
						
						Potential amino acid sequence
						
							MEEHERRPGGERERERHDQEKELEKEKDRAERDRDQDKEKEKLHTERIDKVKAEEDSLAGGGPT
PMDVSTTAHEISSADVTVLEGHSSEVFACAWSPAGSLLASGFHSCRIHIRV*(+)
MNETQTLEGNQLDSMHKRTPLSCVLPKQSHQH*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	12426526-12426182(+) 12426164-12429013(-)
Potential amino acid sequence	MEEHERRPGGERERERHDQEKELEKEKDRAERDRDQDKEKEKLHTERIDKVKAEEDSLAGGGPT PMDVSTTAHEISSADVTVLEGHSSEVFACAWSPAGSLLASGFHSCRIHIRV(+) MNETQTLEGNQLDSMHKRTPLSCVLPKQSHQH(-)
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 Os07g0404900_circ_g.3

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