Plant Circular RNA Database

Detail information of Os01g0856500_circ_g.6

			
						 General Information
					
						CircRNA Name
						Os01g0856500_circ_g.6
					
						ID in PlantcircBase
						osa_circ_004870
					
						Alias
						Os_ciR3554
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr1: 37002304-37002769  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, KNIFE, PcircRNA_finder, find_circ
					
						Parent gene
						
							Os01g0856500						
					
						Parent gene annotation
						
							Auxin transporter, Primary root and root hair elongation, Cd str
ess response (Os01t0856500-01);Amino acid transporter, transmemb
rane domain containing protein. (Os01t0856500-02);Splicing varia
nt with unknown function (Os01t0856500-03);Similar to auxin tran
sporter-like protein 1. (Os01t0856500-04)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os01g0856500_circ_g.2 Os01g0856500_circ_g.3 Os01g0856500_circ_g.4 Os01g0856500_circ_g.5 						
					
						Support reads
						2/13
					
						Tissues
						root/shoot, root, anther, pistil
					
						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
						Os01t0856500-01:1
Os01t0856500-04:1
Os01t0856500-02:1
Os01t0856500-03:1

General Information
CircRNA Name	Os01g0856500_circ_g.6
ID in PlantcircBase	osa_circ_004870
Alias	Os_ciR3554
Organism	Oryza sativa
Position	chr1: 37002304-37002769 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, KNIFE, PcircRNA_finder, find_circ
Parent gene	Os01g0856500
Parent gene annotation	Auxin transporter, Primary root and root hair elongation, Cd str ess response (Os01t0856500-01);Amino acid transporter, transmemb rane domain containing protein. (Os01t0856500-02);Splicing varia nt with unknown function (Os01t0856500-03);Similar to auxin tran sporter-like protein 1. (Os01t0856500-04)
Parent gene strand	+
Alternative splicing	Os01g0856500_circ_g.2 Os01g0856500_circ_g.3 Os01g0856500_circ_g.4 Os01g0856500_circ_g.5
Support reads	2/13
Tissues	root/shoot, root, anther, pistil
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	Os01t0856500-01:1 Os01t0856500-04:1 Os01t0856500-02:1 Os01t0856500-03:1

			
						 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  
						
							CATCAACTCCGCCGTCGGCGCGCTCCTCGTCAGCTTCACCGTCTACATCATCCCGGCACTCGCC
CACATCCTCACCTACCGTACGGCCTCCGCGCGCATGggagatcatgcacgcgatgtggaaaccg
gccaagttcaagtacatctacctgctggcgacgctgtacgtgttcacgctgacgctgccgtcgg
cgtcggcc

									
								

					

						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: 231
Transcript exons: 37002304-37002449,37002685-37002769
GGAGATCATGCACGCGATGTGGAAACCGGCCAAGTTCAAGTACATCTACCTGCTGGCGACGCTG
TACGTGTTCACGCTGACGCTGCCGTCGGCGTCGGCCATGTACTGGGCGTTCGGGGACGAGCTGC
TGACCCACTCCAACGCCTCGGCGCGCTCCTCGTCAGCTTCACCGTCTACATCATCCCGGCACTC
GCCCACATCCTCACCTACCGTACGGCCTCCGCGCGCATG
Transcript length: 239
Transcript exons: 37002304-37002452,37002680-37002769
GGAGATCATGCACGCGATGTGGAAACCGGCCAAGTTCAAGTACATCTACCTGCTGGCGACGCTG
TACGTGTTCACGCTGACGCTGCCGTCGGCGTCGGCCATGTACTGGGCGTTCGGGGACGAGCTGC
TGACCCACTCCAACGCCTTCTGCCGTCGGCGCGCTCCTCGTCAGCTTCACCGTCTACATCATCC
CGGCACTCGCCCACATCCTCACCTACCGTACGGCCTCCGCGCGCATG
Transcript length: 466
Transcript exons: 37002304-37002769
GGAGATCATGCACGCGATGTGGAAACCGGCCAAGTTCAAGTACATCTACCTGCTGGCGACGCTG
TACGTGTTCACGCTGACGCTGCCGTCGGCGTCGGCCATGTACTGGGCGTTCGGGGACGAGCTGC
TGACCCACTCCAACGCCTTCTCGCTGCTGCCCAAGACCGGGTGGCGCGACGCGGCGGTGATACT
GATGCTGATCCACCAGTTCATCACGTTCGGGTTCGCGTGCACGCCGCTCTACTTCGTGTGGGAG
AAGGTGATCGGCATGCACGACACCAAGAGCATCTGCCTCAGGGCGCTCGCGCGGCTCCCCATCG
TCGTCCCCATCTGGTTCCTCGCCATCATCTTCCCCTTCTTCGGCCCCATCAACTCCGCCGTCGG
CGCGCTCCTCGTCAGCTTCACCGTCTACATCATCCCGGCACTCGCCCACATCCTCACCTACCGT
ACGGCCTCCGCGCGCATG
						
					

						Genomic sequence
						
							GGAGATCATGCACGCGATGTGGAAACCGGCCAAGTTCAAGTACATCTACCTGCTGGCGACGCTG
TACGTGTTCACGCTGACGCTGCCGTCGGCGTCGGCCATGTACTGGGCGTTCGGGGACGAGCTGC
TGACCCACTCCAACGCCTTCTCGCTGCTGCCCAAGACCGGGTGGCGCGACGCGGCGGTGATACT
GATGCTGATCCACCAGTTCATCACGTTCGGGTTCGCGTGCACGCCGCTCTACTTCGTGTGGGAG
AAGGTGATCGGCATGCACGACACCAAGAGCATCTGCCTCAGGGCGCTCGCGCGGCTCCCCATCG
TCGTCCCCATCTGGTTCCTCGCCATCATCTTCCCCTTCTTCGGCCCCATCAACTCCGCCGTCGG
CGCGCTCCTCGTCAGCTTCACCGTCTACATCATCCCGGCACTCGCCCACATCCTCACCTACCGT
ACGGCCTCCGCGCGCATG
						
					

			
		

Sequences
Splice junction sequence	CATCAACTCCGCCGTCGGCGCGCTCCTCGTCAGCTTCACCGTCTACATCATCCCGGCACTCGCC CACATCCTCACCTACCGTACGGCCTCCGCGCGCATGggagatcatgcacgcgatgtggaaaccg gccaagttcaagtacatctacctgctggcgacgctgtacgtgttcacgctgacgctgccgtcgg cgtcggcc
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: 231 Transcript exons: 37002304-37002449,37002685-37002769 GGAGATCATGCACGCGATGTGGAAACCGGCCAAGTTCAAGTACATCTACCTGCTGGCGACGCTG TACGTGTTCACGCTGACGCTGCCGTCGGCGTCGGCCATGTACTGGGCGTTCGGGGACGAGCTGC TGACCCACTCCAACGCCTCGGCGCGCTCCTCGTCAGCTTCACCGTCTACATCATCCCGGCACTC GCCCACATCCTCACCTACCGTACGGCCTCCGCGCGCATG Transcript length: 239 Transcript exons: 37002304-37002452,37002680-37002769 GGAGATCATGCACGCGATGTGGAAACCGGCCAAGTTCAAGTACATCTACCTGCTGGCGACGCTG TACGTGTTCACGCTGACGCTGCCGTCGGCGTCGGCCATGTACTGGGCGTTCGGGGACGAGCTGC TGACCCACTCCAACGCCTTCTGCCGTCGGCGCGCTCCTCGTCAGCTTCACCGTCTACATCATCC CGGCACTCGCCCACATCCTCACCTACCGTACGGCCTCCGCGCGCATG Transcript length: 466 Transcript exons: 37002304-37002769 GGAGATCATGCACGCGATGTGGAAACCGGCCAAGTTCAAGTACATCTACCTGCTGGCGACGCTG TACGTGTTCACGCTGACGCTGCCGTCGGCGTCGGCCATGTACTGGGCGTTCGGGGACGAGCTGC TGACCCACTCCAACGCCTTCTCGCTGCTGCCCAAGACCGGGTGGCGCGACGCGGCGGTGATACT GATGCTGATCCACCAGTTCATCACGTTCGGGTTCGCGTGCACGCCGCTCTACTTCGTGTGGGAG AAGGTGATCGGCATGCACGACACCAAGAGCATCTGCCTCAGGGCGCTCGCGCGGCTCCCCATCG TCGTCCCCATCTGGTTCCTCGCCATCATCTTCCCCTTCTTCGGCCCCATCAACTCCGCCGTCGG CGCGCTCCTCGTCAGCTTCACCGTCTACATCATCCCGGCACTCGCCCACATCCTCACCTACCGT ACGGCCTCCGCGCGCATG
Genomic sequence	GGAGATCATGCACGCGATGTGGAAACCGGCCAAGTTCAAGTACATCTACCTGCTGGCGACGCTG TACGTGTTCACGCTGACGCTGCCGTCGGCGTCGGCCATGTACTGGGCGTTCGGGGACGAGCTGC TGACCCACTCCAACGCCTTCTCGCTGCTGCCCAAGACCGGGTGGCGCGACGCGGCGGTGATACT GATGCTGATCCACCAGTTCATCACGTTCGGGTTCGCGTGCACGCCGCTCTACTTCGTGTGGGAG AAGGTGATCGGCATGCACGACACCAAGAGCATCTGCCTCAGGGCGCTCGCGCGGCTCCCCATCG TCGTCCCCATCTGGTTCCTCGCCATCATCTTCCCCTTCTTCGGCCCCATCAACTCCGCCGTCGG CGCGCTCCTCGTCAGCTTCACCGTCTACATCATCCCGGCACTCGCCCACATCCTCACCTACCGT ACGGCCTCCGCGCGCATG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_010944 hvu_circ_000018 zma_circ_007737 zma_circ_001454 
osi_circ_015536 osi_circ_008779 						
					
						PMCS
						0.703265379

Conservation Information
Conserved circRNAs	osi_circ_010944 hvu_circ_000018 zma_circ_007737 zma_circ_001454 osi_circ_015536 osi_circ_008779
PMCS	0.703265379

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							37002312-37002380(+)
37002350-37002743(-)
						
						Potential amino acid sequence
						
							MHAMWKPAKFKYIYLLATLYVFTLTLPSASAMYWAFGDELLTHSNAFSLLPKTGWRDAAVILML
IHQFITFGFACTPLYFVWEKVIGMHDTKSICLRALARLPIVVPIWFLAIIFPFFGPINSAVGAL
LVSFTVYIIPALAHILTYRTASARMGDHARDVETGQVQVHLPAGDAVRVHADAAVGVGHVLGVR
GRAADPLQRLLAAAQDRVARRGGDTDADPPVHHVRVRVHAALLRVGEGDRHARHQEHLPQGARA
APHRRPHLVPRHHLPLLRPHQLRRRRAPRQLHRLHHPGTRPHPHLPYGLRAHGRSCTRCGNRPS
SSTSTCWRRCTCSR*(+)
MYLNLAGFHIACMISHARGGRTVGEDVGECRDDVDGEADEERADGGVDGAEEGEDDGEEPDGDD
DGEPRERPEADALGVVHADHLLPHEVERRAREPERDELVDQHQYHRRVAPPGLGQQREGVGVGQ
QLVPERPVHGRRRRQRQREHVQRRQQVDVLELGRFPHRVHDLPCARRPYGR*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	37002312-37002380(+) 37002350-37002743(-)
Potential amino acid sequence	MHAMWKPAKFKYIYLLATLYVFTLTLPSASAMYWAFGDELLTHSNAFSLLPKTGWRDAAVILML IHQFITFGFACTPLYFVWEKVIGMHDTKSICLRALARLPIVVPIWFLAIIFPFFGPINSAVGAL LVSFTVYIIPALAHILTYRTASARMGDHARDVETGQVQVHLPAGDAVRVHADAAVGVGHVLGVR GRAADPLQRLLAAAQDRVARRGGDTDADPPVHHVRVRVHAALLRVGEGDRHARHQEHLPQGARA APHRRPHLVPRHHLPLLRPHQLRRRRAPRQLHRLHHPGTRPHPHLPYGLRAHGRSCTRCGNRPS SSTSTCWRRCTCSR(+) MYLNLAGFHIACMISHARGGRTVGEDVGECRDDVDGEADEERADGGVDGAEEGEDDGEEPDGDD DGEPRERPEADALGVVHADHLLPHEVERRAREPERDELVDQHQYHRRVAPPGLGQQREGVGVGQ QLVPERPVHGRRRRQRQREHVQRRQQVDVLELGRFPHRVHDLPCARRPYGR(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

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

circRNA

Detail information of Os01g0856500_circ_g.6

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