Plant Circular RNA Database

Detail information of Os01g0859500_circ_g.6

			
						 General Information
					
						CircRNA Name
						Os01g0859500_circ_g.6
					
						ID in PlantcircBase
						osa_circ_004898
					
						Alias
						Os_ciR6278
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr1: 37186147-37187317  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, circseq_cup, find_circ
					
						Parent gene
						
							Os01g0859500						
					
						Parent gene annotation
						
							Similar to Basic leucine zipper protein (Liguleless2). (Os01t085
9500-01)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os01g0859500_circ_g.3 Os01g0859500_circ_g.4 Os01g0859500_circ_g.5 Os01g0859500_circ_g.7 Os01g0859500_circ_g.8 Os01g0859500_circ_g.9 Os01g0859500_circ_g.10 Os01g0859500_circ_g.11 Os01g0859500_circ_g.12 Os01g0859500_circ_g.13 						
					
						Support reads
						2/18/36
					
						Tissues
						root/root/shoot, 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  
						
							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
						Os01t0859500-01:3

General Information
CircRNA Name	Os01g0859500_circ_g.6
ID in PlantcircBase	osa_circ_004898
Alias	Os_ciR6278
Organism	Oryza sativa
Position	chr1: 37186147-37187317 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, circseq_cup, find_circ
Parent gene	Os01g0859500
Parent gene annotation	Similar to Basic leucine zipper protein (Liguleless2). (Os01t085 9500-01)
Parent gene strand	-
Alternative splicing	Os01g0859500_circ_g.3 Os01g0859500_circ_g.4 Os01g0859500_circ_g.5 Os01g0859500_circ_g.7 Os01g0859500_circ_g.8 Os01g0859500_circ_g.9 Os01g0859500_circ_g.10 Os01g0859500_circ_g.11 Os01g0859500_circ_g.12 Os01g0859500_circ_g.13
Support reads	2/18/36
Tissues	root/root/shoot, 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	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	Os01t0859500-01:3

			
						 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  
						
							CATGCCGGGATCGACGACGCCGCCGGCGTTGGCGCCATGGATGAGGGCCTCCTCCAGCTCGCCG
AAGTAGGCAGCTGCCGCGGCAGCAGGCTGGAAGTCCcttgtcatggtctcctcctccgtgcagc
tgctgctgctggtggtgctggagctgatgctgctgctgaaagcttggggaggcagcagcgaggc
ctggcttg

									
								

					

						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: 496
Transcript exons: 37186147-37186416,37186695-37186795,37187193-37187317
CTTGTCATGGTCTCCTCCTCCGTGCAGCTGCTGCTGCTGGTGGTGCTGGAGCTGATGCTGCTGC
TGAAAGCTTGGGGAGGCAGCAGCGAGGCCTGGCTTGTAGCTGTAATCATCAGTGGTCACCATCA
TGACCTCCTGCCCCGGCTGCTGCTGCTGGTGCTGGTGCTCGGAGGAGGCCCTGATACTCGCTGG
GGACACCAACTCCATCTGCGGCATTGTGTTCTGGGCTGAGCTCGAGTCAGTGGTGCTCCCGACT
GACTGCGAATTCCCACTGTGTAGCTGCTGTTGCTGCCTCATTGGCCATGAAGGGAAGATCTCCA
GCGTGGGGGGCCTGGCCGCGAGATATCCTGCCGTCGCTGCCGCTGCCGCCGACTTGCTGTGCAC
GTCGGCTCTGATCATGCCGGGATCGACGACGCCGCCGGCGTTGGCGCCATGGATGAGGGCCTCC
TCCAGCTCGCCGAAGTAGGCAGCTGCCGCGGCAGCAGGCTGGAAGTCC
						
					

						Genomic sequence
						
							CTTGTCATGGTCTCCTCCTCCGTGCAGCTGCTGCTGCTGGTGGTGCTGGAGCTGATGCTGCTGC
TGAAAGCTTGGGGAGGCAGCAGCGAGGCCTGGCTTGTAGCTGTAATCATCAGTGGTCACCATCA
TGACCTCCTGCCCCGGCTGCTGCTGCTGGTGCTGGTGCTCGGAGGAGGCCCTGATACTCGCTGG
GGACACCAACTCCATCTGCGGCATTGTGTTCTGGGCTGAGCTCGAGTCAGTGGTGCTCCCGACT
GACTGCGAATTCCCCTGTTCAGCCATTAATTGAGGCAGCGAGAGACAACAGTGAGCGGTCGGTA
AGCATGAGATTAATGTGCTCTGAATCATCTCTCAGTCTCTCTCTCTCTTTCTCTCTCTGCTCGT
GGTGATGCGAACCAAGAGCCAAGAACAACAGCGGCAACAGTGTCGTCTCGATCTCTTTTCTTGG
GTTCAGCGATGAGCAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGGGGAAGAAGAAGAC
GATGAATGAATGATCATGGGAAGCGCGTCCATTTACACTGTGTAGCTGCTGTTGCTGCCTCATT
GGCCATGAAGGGAAGATCTCCAGCGTGGGGGGCCTGGCCGCGAGATATCCTGCCGTCGCTGCCG
CTGCCGCCGCTGCATGCATACAAAGAGAATTAAAAAGCCCGCCCTCATCGATTCCTACTACTGC
TACCCTGTTCATCTCTCTCTCTCTCTCCAACAAGGCTACAGAGAAACAGGAGAGAGAAGCTGCT
ACTGGTAAATCGCCAATAGTGTGTAGGTGAAGCCGAGCTGGAGGACATGCTTGATCATGTTTCC
ATCTTTGTGGCATCGGCATCTCGCCATTTATGCGGCGCCAACAACAATTTCTCTCTCTCTGTGC
ATGTGGCCGGCCACTGTGTGCTGGATCGCAAAAGGCGAGGCATGTCTCGCCATGTGTGGCAATC
GGACAAGGTTTGGAGAGACACCGAAACATCGATGCAGAGAAAGAGAGAGAGAGAAAACAAGAAA
GAAAGAAGAAAATTTGGCTTACACTTGCTGTGCACGTCGGCTCTGATCATGCCGGGATCGACGA
CGCCGCCGGCGTTGGCGCCATGGATGAGGGCCTCCTCCAGCTCGCCGAAGTAGGCAGCTGCCGC
GGCAGCAGGCTGGAAGTCC
						
					

			
		

Sequences
Splice junction sequence	CATGCCGGGATCGACGACGCCGCCGGCGTTGGCGCCATGGATGAGGGCCTCCTCCAGCTCGCCG AAGTAGGCAGCTGCCGCGGCAGCAGGCTGGAAGTCCcttgtcatggtctcctcctccgtgcagc tgctgctgctggtggtgctggagctgatgctgctgctgaaagcttggggaggcagcagcgaggc ctggcttg
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: 496 Transcript exons: 37186147-37186416,37186695-37186795,37187193-37187317 CTTGTCATGGTCTCCTCCTCCGTGCAGCTGCTGCTGCTGGTGGTGCTGGAGCTGATGCTGCTGC TGAAAGCTTGGGGAGGCAGCAGCGAGGCCTGGCTTGTAGCTGTAATCATCAGTGGTCACCATCA TGACCTCCTGCCCCGGCTGCTGCTGCTGGTGCTGGTGCTCGGAGGAGGCCCTGATACTCGCTGG GGACACCAACTCCATCTGCGGCATTGTGTTCTGGGCTGAGCTCGAGTCAGTGGTGCTCCCGACT GACTGCGAATTCCCACTGTGTAGCTGCTGTTGCTGCCTCATTGGCCATGAAGGGAAGATCTCCA GCGTGGGGGGCCTGGCCGCGAGATATCCTGCCGTCGCTGCCGCTGCCGCCGACTTGCTGTGCAC GTCGGCTCTGATCATGCCGGGATCGACGACGCCGCCGGCGTTGGCGCCATGGATGAGGGCCTCC TCCAGCTCGCCGAAGTAGGCAGCTGCCGCGGCAGCAGGCTGGAAGTCC
Genomic sequence	CTTGTCATGGTCTCCTCCTCCGTGCAGCTGCTGCTGCTGGTGGTGCTGGAGCTGATGCTGCTGC TGAAAGCTTGGGGAGGCAGCAGCGAGGCCTGGCTTGTAGCTGTAATCATCAGTGGTCACCATCA TGACCTCCTGCCCCGGCTGCTGCTGCTGGTGCTGGTGCTCGGAGGAGGCCCTGATACTCGCTGG GGACACCAACTCCATCTGCGGCATTGTGTTCTGGGCTGAGCTCGAGTCAGTGGTGCTCCCGACT GACTGCGAATTCCCCTGTTCAGCCATTAATTGAGGCAGCGAGAGACAACAGTGAGCGGTCGGTA AGCATGAGATTAATGTGCTCTGAATCATCTCTCAGTCTCTCTCTCTCTTTCTCTCTCTGCTCGT GGTGATGCGAACCAAGAGCCAAGAACAACAGCGGCAACAGTGTCGTCTCGATCTCTTTTCTTGG GTTCAGCGATGAGCAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGGGGAAGAAGAAGAC GATGAATGAATGATCATGGGAAGCGCGTCCATTTACACTGTGTAGCTGCTGTTGCTGCCTCATT GGCCATGAAGGGAAGATCTCCAGCGTGGGGGGCCTGGCCGCGAGATATCCTGCCGTCGCTGCCG CTGCCGCCGCTGCATGCATACAAAGAGAATTAAAAAGCCCGCCCTCATCGATTCCTACTACTGC TACCCTGTTCATCTCTCTCTCTCTCTCCAACAAGGCTACAGAGAAACAGGAGAGAGAAGCTGCT ACTGGTAAATCGCCAATAGTGTGTAGGTGAAGCCGAGCTGGAGGACATGCTTGATCATGTTTCC ATCTTTGTGGCATCGGCATCTCGCCATTTATGCGGCGCCAACAACAATTTCTCTCTCTCTGTGC ATGTGGCCGGCCACTGTGTGCTGGATCGCAAAAGGCGAGGCATGTCTCGCCATGTGTGGCAATC GGACAAGGTTTGGAGAGACACCGAAACATCGATGCAGAGAAAGAGAGAGAGAGAAAACAAGAAA GAAAGAAGAAAATTTGGCTTACACTTGCTGTGCACGTCGGCTCTGATCATGCCGGGATCGACGA CGCCGCCGGCGTTGGCGCCATGGATGAGGGCCTCCTCCAGCTCGCCGAAGTAGGCAGCTGCCGC GGCAGCAGGCTGGAAGTCC

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_010952 						
					
						PMCS
						0.274828466

Conservation Information
Conserved circRNAs	osi_circ_010952
PMCS	0.274828466

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							37187255-37186274(+)
37187222-37186387(-)
37186261-37186387(-)
						
						Potential amino acid sequence
						
							MDEGLLQLAEVGSCRGSRLEVPCHGLLLRAAAAAGGAGADAAAESLGRQQRGLACSCNHQWSPS
*(+)
MIRADVHSKSAAAAATAGYLAARPPTLEIFPSWPMRQQQQLHSGNSQSVGSTTDSSSAQNTMPQ
MELVSPASIRASSEHQHQQQQPGQEVMMVTTDDYSYKPGLAAASPSFQQQHQLQHHQQQQLHGG
GDHDKGLPACCRGSCLLRRAGGGPHPWRQRRRRRRSRHDQSRRAQQVGGSGSDGRISRGQAPHA
GDLPFMANEAATAATQWEFAVSREHH*(-)
MITATSQASLLPPQAFSSSISSSTTSSSSCTEEETMTRDFQPAAAAAAYFGELEEALIHGANAG
GVVDPGMIRADVHSKSAAAAATAGYLAARPPTLEIFPSWPMRQQQQLHSGNSQSVGSTTDSSSA
QNTMPQMELVSPASIRASSEHQHQQQQPGQEVMMVTTDDYSYKPGLAAASPSFQQQHQLQHHQQ
QQLHGGGDHDKGLPACCRGSCLLRRAGGGPHPWRQRRRRRRSRHDQSRRAQQVGGSGSDGRISR
GQAPHAGDLPFMANEAATAATQWEFAVSREHH*(-)
						
						Sponge-miRNAs
						
							osa-miR444a-3p.1 osa-miR3979-5p 						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	37187255-37186274(+) 37187222-37186387(-) 37186261-37186387(-)
Potential amino acid sequence	MDEGLLQLAEVGSCRGSRLEVPCHGLLLRAAAAAGGAGADAAAESLGRQQRGLACSCNHQWSPS (+) MIRADVHSKSAAAAATAGYLAARPPTLEIFPSWPMRQQQQLHSGNSQSVGSTTDSSSAQNTMPQ MELVSPASIRASSEHQHQQQQPGQEVMMVTTDDYSYKPGLAAASPSFQQQHQLQHHQQQQLHGG GDHDKGLPACCRGSCLLRRAGGGPHPWRQRRRRRRSRHDQSRRAQQVGGSGSDGRISRGQAPHA GDLPFMANEAATAATQWEFAVSREHH(-) MITATSQASLLPPQAFSSSISSSTTSSSSCTEEETMTRDFQPAAAAAAYFGELEEALIHGANAG GVVDPGMIRADVHSKSAAAAATAGYLAARPPTLEIFPSWPMRQQQQLHSGNSQSVGSTTDSSSA QNTMPQMELVSPASIRASSEHQHQQQQPGQEVMMVTTDDYSYKPGLAAASPSFQQQHQLQHHQQ QQLHGGGDHDKGLPACCRGSCLLRRAGGGPHPWRQRRRRRRSRHDQSRRAQQVGGSGSDGRISR GQAPHAGDLPFMANEAATAATQWEFAVSREHH*(-)
Sponge-miRNAs	osa-miR444a-3p.1 osa-miR3979-5p
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ye et al., 2015;Ye et al., 2016;Chu et al., 2017

circRNA

Detail information of Os01g0859500_circ_g.6

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