Plant Circular RNA Database

Detail information of Os01g0685500_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os01g0685500_circ_g.3
					
						ID in PlantcircBase
						osa_circ_003322
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr1: 28263443-28267074  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os01g0685500						
					
						Parent gene annotation
						
							Similar to DNA ligase. (Os01t0685500-01)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os01g0685500_circ_g.1 Os01g0685500_circ_g.2 Os01g0685500_circ_g.4 Os01g0685500_circ_g.5 Os01g0685500_circ_ag.1 						
					
						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  
						
							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
						Os01t0685500-01:7

General Information
CircRNA Name	Os01g0685500_circ_g.3
ID in PlantcircBase	osa_circ_003322
Alias	NA
Organism	Oryza sativa
Position	chr1: 28263443-28267074 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ue-circRNA
Identification method	CIRCexplorer
Parent gene	Os01g0685500
Parent gene annotation	Similar to DNA ligase. (Os01t0685500-01)
Parent gene strand	-
Alternative splicing	Os01g0685500_circ_g.1 Os01g0685500_circ_g.2 Os01g0685500_circ_g.4 Os01g0685500_circ_g.5 Os01g0685500_circ_ag.1
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	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	Os01t0685500-01:7

			
						 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  
						
							CAGATCAGGAAATCGAGAGGTTGACTCTTTCATTTGCCTTGAAAATATTTGCACAGATCCATCA
TTTGATCTGTGAATCTGGGCTCGCTGACCATCATACctctttatagaactcatctgagaaacca
gacataacgcggcagacactttggaactcttcgtattcagggttgtagcacgccataagaaaag
ggctatac

									
								

					

						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
						
							CTCTTTATAGAACTCATCTGAGAAACCAGACATAACGCGGCAGACACTTTGGAACTCTTCGTAT
TCAGGGTTGTAGCACGCCATAAGAAAAGGGCTATACCTGTAAATGTAGAGAAGAGAAGAGCATT
GGGGCAAGAAGTATGGTAAGGGGAAAAGAGAGGTTATATGCACAGGAACCAAACGTACCATCCA
GCTTTCCGACCATTTCCATACCATGCACCAATTGGAACCAAGTCCAGGCTATCACCCAAGCCAA
CATAGTCACGCTTAACCTGCAACAACACACATGGAATACATGATGCATAGTTTTATAGTTTCAG
ATATAATGAAAAACATTCAGATTCAGGCACTTGTTTAGTATAATACATAGGTTGCACCTTTAAC
CATGAATCACAGCGCTTGGAAGCAGAATATCCAGCATCAACATCCAGTATTTTCAGCATAATAC
CCTCACAAGAAGACTGGCATGCCATTTTGAAAAAGGTGTTCATTCTCTCCAAAGTGGTAGAATT
ATCCACAGAAGCTTCATCTGCTTCTACCTGTAAAATTGATTCATGTGTACCATGCATGAACATA
TGATAAAGAAGCAAGCACAGAGATAAAGGCCAAAGTTATTTGCGATGTCAACCAAAATGCAGTA
GGTTATTATTCTAGAACAAGTATGCTAAAAAATTTAAGCTGAGCAGAAGCATATAGTATATGTT
GAGACATTACCCTGAAAACATAACAAAAGCATCACTACAGTGTCCTGCATTGGTACATGCCCCC
CAACACCCCAGGCTACCTATGTCATTTTGTTTCTAGGCACTCCATTACAAAGCGGAGATGCTGA
AGTCCAACATTTCAGGCCATGTGACTAGTTGTTTTACTCATAGTAGTGTAAAAGATGGCAACCA
TGGGTGAATTCTTGATTGGTCCTTTTTTTTTTTGAGATATTGATTGGTCCTTGAAGTTCCCCCC
AAAACTCACATTGGCAACTCAGAAAGGGCCATCTAGGTCCTCTAGCTTTCTGTGCTAGACCAAA
GGACTTATTGGTAATTCACATTGACACATTTGAGTCAAATTTGATTTTATGTGTTCTTGTAGCT
GATTCATCTTGAGCAAATGTCTATTCTACCCTTACATCCTGAAATTGGATTTGCTATTTCGCTC
CCCTTGATTTTATTTATCCCAGTCTCTTTTTTTCAACCATTATGTGCAGCTCTCATTGTGGCAA
TATCCAGCTTTTGCTTATGATGAGGGAGGAATCATTATACATAAGCACCTTGATGCGGAACAAG
ACAACCCAAATGATATGTTTGGCCCAAATAGACAAATTTGAGGGATCTAGGAGGCCAATTTGAA
ACGCAAGGGAGGAAATTAGCCTAGGGGGAAATTCGGGGGACCAAACTGGGCATTTACCTGGCAA
AATTCAAACAAAAGAAAATATGAAAAGGAATGTTCGTATTGCTAAGTGTGTGGTACAACATAGG
GATAATATCCGGTGTAATCATTTTGCCTTGATGAATACAAGTGCTATTCATAACAGTTACCATG
AATCTGCTGCTTTACACTAAGAGGTGCAACGTTTCGAGTATCATACTATCATGAAGGAGCACAG
GAATGGTAGTGGTAATGTTAACGAATTAGTTGTGAGTAGGTAATGTTAAAACTGGTTAGTTCCG
CATCTTGTATTTGCGTTGCTTGAAAAGGCAAGCGCTTTGATTTTGTGTTGTCCATTCTAGTTGA
TTGATTGGTTAAAATTATAGCCTGATTCTTTAATTCATAAAGCCGGTTACCTTCACATCGAAGT
GGAAAAATGCTAAGAAGATGGCAACGTAGCTATTAATCTCATGCAATTTCAATTAACAGAAGGA
AATGAAATGAAAAGGAAGGATGATATTATGGCAAGATGTAAAAGGCGATATCATTAGGTCAAGT
AAGAAGCGAATGTTTAGAACAGTAAATACATCCATAAAAATGCAAGTCAGAAAAGGATACAACT
TACAGTAAGTTGCTGAGCTAACTCAAAATGTCCTGGCTTCTCCTGGAACAAGTCGTGGATGTCT
GCAGTGAAAAATGCAGAAAGAAGTGCTATCACATTTTCTAAGGGATTCACTCAAAAAGTATGCC
CTGCCTTATACATGTTTTTCAAGTACTTTAAGATGGTACTGAAACATACACTTTCTTCTTTGCC
GAAGTGAGCAGTTCAATAGGCTGCAGAAAAACACCGTAAGTTTTCTGATATTGTAAATAAATTC
AACAAATAATTCATATTGATATGCATGTAAAACATTTTTACACCAAGCAAGCAGCGTGTAATTG
CTTTTGCAGCTTAATAGTGGGCGTTTCCGATTACCAAACAATGTATATATAACCTTTGACCAAC
ATGAAATAAGCTTTCTGAGTCATTTACCGTCTAAGCACAAGGTTTTCTCATTTGTGTGTACCAT
TAAATCACTGATGACTTAAAACTAGAAGGTCACGAGCTTGGTAGTTGAAGCGTGGCACAGCCAA
ACTAAATTAAACTAACAACCATAAGAAAATTATGTTTGTGAGTAAAGCAATAAGCTCTCACATC
GACCCATCAGAGAGGGGTGGTTGCAAAAGTACTTTCCTTGTCTTTTTCTTATTTAAAAAAGTGT
CAAGTTTGATATTATATTATATAGGTAGTCTATGTATATGAAATACTCCATAGTGTTACCTTTG
TCCATTGCAGAACATGATATCAAAAACAAACACACAAATGTCTACCTGCAAAGTAGTCAAAATA
TAGTCAGATAAAAAAGACACAGTTACAAAAAAAAAAGATGGATTAGTAAGCATATTATGCATTC
CTAATAGGTACTGCCACTAACTATTTGTCTATCCACACACTTTCTTTCAACTTTCATCACAGGC
ATTTCAGTGCAAATGAACATCCTCTATGCTAGGAAAACTGATTCATGCTATGAACTATGAACCA
CAAAAAAAATATACGTATTTGTGGAACTGTAGGAATATCTACCACAGAAGTTGAAATTTTGTCA
ACTACATATCTGATTATTTTAGTGATAAGTAATAAGCACTGAAAAAACCCGGTAACTGCAAAGG
GACTTGTTCATTCAATTAAAGTTGTTGGTGACAAACATAAACAATTGAGTACAAATTTCTTTGA
TTATGTTTCCTTGTGAAATTCTATAATTATAGGAATTCATCATGCAAAAATATTGCCCGAAAAT
AATGTTCAAGATTCCAAAGTAACAAGCACAATACTTTGTAAATAAAAGAATAATGGCATCACCT
TTATGTTCTGAATTGCAATTGAGGAGTGCTTGCTCCCTCTCTCTCTTGAAGACAGCTCTTGGAA
TGACATCAGTTTGTTTCCTTTCTTCCTATCGATTCCCACAACCTTGTTTTGAATGCACAAGCAC
AAGAAACACAAGCCTAAGGTGAAGGAGTGTTATATTATGAAGAAACAAACAAATGTGAGTTCCT
CACGAACAAAACTTACCTCGGCGTCAAGTATAAAGCTGGATACTTCGATGCTGCACAGCTCTTT
GATCATGCCAACCAGATCAGGAAATCGAGAGGTTGACTCTTTCATTTGCCTTGAAAATATTTGC
ACAGATCCATCATTTGATCTGTGAATCTGGGCTCGCTGACCATCATAC
						
					

			
		

Sequences
Splice junction sequence	CAGATCAGGAAATCGAGAGGTTGACTCTTTCATTTGCCTTGAAAATATTTGCACAGATCCATCA TTTGATCTGTGAATCTGGGCTCGCTGACCATCATACctctttatagaactcatctgagaaacca gacataacgcggcagacactttggaactcttcgtattcagggttgtagcacgccataagaaaag ggctatac
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	CTCTTTATAGAACTCATCTGAGAAACCAGACATAACGCGGCAGACACTTTGGAACTCTTCGTAT TCAGGGTTGTAGCACGCCATAAGAAAAGGGCTATACCTGTAAATGTAGAGAAGAGAAGAGCATT GGGGCAAGAAGTATGGTAAGGGGAAAAGAGAGGTTATATGCACAGGAACCAAACGTACCATCCA GCTTTCCGACCATTTCCATACCATGCACCAATTGGAACCAAGTCCAGGCTATCACCCAAGCCAA CATAGTCACGCTTAACCTGCAACAACACACATGGAATACATGATGCATAGTTTTATAGTTTCAG ATATAATGAAAAACATTCAGATTCAGGCACTTGTTTAGTATAATACATAGGTTGCACCTTTAAC CATGAATCACAGCGCTTGGAAGCAGAATATCCAGCATCAACATCCAGTATTTTCAGCATAATAC CCTCACAAGAAGACTGGCATGCCATTTTGAAAAAGGTGTTCATTCTCTCCAAAGTGGTAGAATT ATCCACAGAAGCTTCATCTGCTTCTACCTGTAAAATTGATTCATGTGTACCATGCATGAACATA TGATAAAGAAGCAAGCACAGAGATAAAGGCCAAAGTTATTTGCGATGTCAACCAAAATGCAGTA GGTTATTATTCTAGAACAAGTATGCTAAAAAATTTAAGCTGAGCAGAAGCATATAGTATATGTT GAGACATTACCCTGAAAACATAACAAAAGCATCACTACAGTGTCCTGCATTGGTACATGCCCCC CAACACCCCAGGCTACCTATGTCATTTTGTTTCTAGGCACTCCATTACAAAGCGGAGATGCTGA AGTCCAACATTTCAGGCCATGTGACTAGTTGTTTTACTCATAGTAGTGTAAAAGATGGCAACCA TGGGTGAATTCTTGATTGGTCCTTTTTTTTTTTGAGATATTGATTGGTCCTTGAAGTTCCCCCC AAAACTCACATTGGCAACTCAGAAAGGGCCATCTAGGTCCTCTAGCTTTCTGTGCTAGACCAAA GGACTTATTGGTAATTCACATTGACACATTTGAGTCAAATTTGATTTTATGTGTTCTTGTAGCT GATTCATCTTGAGCAAATGTCTATTCTACCCTTACATCCTGAAATTGGATTTGCTATTTCGCTC CCCTTGATTTTATTTATCCCAGTCTCTTTTTTTCAACCATTATGTGCAGCTCTCATTGTGGCAA TATCCAGCTTTTGCTTATGATGAGGGAGGAATCATTATACATAAGCACCTTGATGCGGAACAAG ACAACCCAAATGATATGTTTGGCCCAAATAGACAAATTTGAGGGATCTAGGAGGCCAATTTGAA ACGCAAGGGAGGAAATTAGCCTAGGGGGAAATTCGGGGGACCAAACTGGGCATTTACCTGGCAA AATTCAAACAAAAGAAAATATGAAAAGGAATGTTCGTATTGCTAAGTGTGTGGTACAACATAGG GATAATATCCGGTGTAATCATTTTGCCTTGATGAATACAAGTGCTATTCATAACAGTTACCATG AATCTGCTGCTTTACACTAAGAGGTGCAACGTTTCGAGTATCATACTATCATGAAGGAGCACAG GAATGGTAGTGGTAATGTTAACGAATTAGTTGTGAGTAGGTAATGTTAAAACTGGTTAGTTCCG CATCTTGTATTTGCGTTGCTTGAAAAGGCAAGCGCTTTGATTTTGTGTTGTCCATTCTAGTTGA TTGATTGGTTAAAATTATAGCCTGATTCTTTAATTCATAAAGCCGGTTACCTTCACATCGAAGT GGAAAAATGCTAAGAAGATGGCAACGTAGCTATTAATCTCATGCAATTTCAATTAACAGAAGGA AATGAAATGAAAAGGAAGGATGATATTATGGCAAGATGTAAAAGGCGATATCATTAGGTCAAGT AAGAAGCGAATGTTTAGAACAGTAAATACATCCATAAAAATGCAAGTCAGAAAAGGATACAACT TACAGTAAGTTGCTGAGCTAACTCAAAATGTCCTGGCTTCTCCTGGAACAAGTCGTGGATGTCT GCAGTGAAAAATGCAGAAAGAAGTGCTATCACATTTTCTAAGGGATTCACTCAAAAAGTATGCC CTGCCTTATACATGTTTTTCAAGTACTTTAAGATGGTACTGAAACATACACTTTCTTCTTTGCC GAAGTGAGCAGTTCAATAGGCTGCAGAAAAACACCGTAAGTTTTCTGATATTGTAAATAAATTC AACAAATAATTCATATTGATATGCATGTAAAACATTTTTACACCAAGCAAGCAGCGTGTAATTG CTTTTGCAGCTTAATAGTGGGCGTTTCCGATTACCAAACAATGTATATATAACCTTTGACCAAC ATGAAATAAGCTTTCTGAGTCATTTACCGTCTAAGCACAAGGTTTTCTCATTTGTGTGTACCAT TAAATCACTGATGACTTAAAACTAGAAGGTCACGAGCTTGGTAGTTGAAGCGTGGCACAGCCAA ACTAAATTAAACTAACAACCATAAGAAAATTATGTTTGTGAGTAAAGCAATAAGCTCTCACATC GACCCATCAGAGAGGGGTGGTTGCAAAAGTACTTTCCTTGTCTTTTTCTTATTTAAAAAAGTGT CAAGTTTGATATTATATTATATAGGTAGTCTATGTATATGAAATACTCCATAGTGTTACCTTTG TCCATTGCAGAACATGATATCAAAAACAAACACACAAATGTCTACCTGCAAAGTAGTCAAAATA TAGTCAGATAAAAAAGACACAGTTACAAAAAAAAAAGATGGATTAGTAAGCATATTATGCATTC CTAATAGGTACTGCCACTAACTATTTGTCTATCCACACACTTTCTTTCAACTTTCATCACAGGC ATTTCAGTGCAAATGAACATCCTCTATGCTAGGAAAACTGATTCATGCTATGAACTATGAACCA CAAAAAAAATATACGTATTTGTGGAACTGTAGGAATATCTACCACAGAAGTTGAAATTTTGTCA ACTACATATCTGATTATTTTAGTGATAAGTAATAAGCACTGAAAAAACCCGGTAACTGCAAAGG GACTTGTTCATTCAATTAAAGTTGTTGGTGACAAACATAAACAATTGAGTACAAATTTCTTTGA TTATGTTTCCTTGTGAAATTCTATAATTATAGGAATTCATCATGCAAAAATATTGCCCGAAAAT AATGTTCAAGATTCCAAAGTAACAAGCACAATACTTTGTAAATAAAAGAATAATGGCATCACCT TTATGTTCTGAATTGCAATTGAGGAGTGCTTGCTCCCTCTCTCTCTTGAAGACAGCTCTTGGAA TGACATCAGTTTGTTTCCTTTCTTCCTATCGATTCCCACAACCTTGTTTTGAATGCACAAGCAC AAGAAACACAAGCCTAAGGTGAAGGAGTGTTATATTATGAAGAAACAAACAAATGTGAGTTCCT CACGAACAAAACTTACCTCGGCGTCAAGTATAAAGCTGGATACTTCGATGCTGCACAGCTCTTT GATCATGCCAACCAGATCAGGAAATCGAGAGGTTGACTCTTTCATTTGCCTTGAAAATATTTGC ACAGATCCATCATTTGATCTGTGAATCTGGGCTCGCTGACCATCATAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_010571 						
					
						PMCS
						0.347007952

Conservation Information
Conserved circRNAs	osi_circ_010571
PMCS	0.347007952

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							28263703-28266124(-)
28263935-28267071(-)
						
						Potential amino acid sequence
						
							MLAWVIAWTWFQLVHGMEMVGKLDGIALFLWRATTLNTKSSKVSAALCLVSQMSSIKRYDGQRA
QIHRSNDGSVQIFSRQMKESTSRFPDLVGMIKELCSIEVSSFILDAEVVGIDRKKGNKLMSFQE
LSSRERGSKHSSIAIQNIKVDICVFVFDIMFCNGQR*(-)
MNTFFKMACQSSCEGIMLKILDVDAGYSASKRCDSWLKVKRDYVGLGDSLDLVPIGAWYGNGRK
AGWYSPFLMACYNPEYEEFQSVCRVMSGFSDEFYKEV*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	28263703-28266124(-) 28263935-28267071(-)
Potential amino acid sequence	MLAWVIAWTWFQLVHGMEMVGKLDGIALFLWRATTLNTKSSKVSAALCLVSQMSSIKRYDGQRA QIHRSNDGSVQIFSRQMKESTSRFPDLVGMIKELCSIEVSSFILDAEVVGIDRKKGNKLMSFQE LSSRERGSKHSSIAIQNIKVDICVFVFDIMFCNGQR(-) MNTFFKMACQSSCEGIMLKILDVDAGYSASKRCDSWLKVKRDYVGLGDSLDLVPIGAWYGNGRK AGWYSPFLMACYNPEYEEFQSVCRVMSGFSDEFYKEV(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os01g0685500_circ_g.3

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