Plant Circular RNA Database

Detail information of Os03g0340900_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os03g0340900_circ_g.3
					
						ID in PlantcircBase
						osa_circ_019726
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr3: 12699769-12702505  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os03g0340900						
					
						Parent gene annotation
						
							Similar to RSH1. (Os03t0340900-01)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os03g0340900_circ_g.2 						
					
						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
						Os03t0340900-01:9

General Information
CircRNA Name	Os03g0340900_circ_g.3
ID in PlantcircBase	osa_circ_019726
Alias	NA
Organism	Oryza sativa
Position	chr3: 12699769-12702505 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	Os03g0340900
Parent gene annotation	Similar to RSH1. (Os03t0340900-01)
Parent gene strand	+
Alternative splicing	Os03g0340900_circ_g.2
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	Os03t0340900-01:9

			
						 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  
						
							AAGAGGGGTTGTTTCAGGGCCTGTTCGTCCTGGAATATCAAGTGGAAGGAATTCAAATGGGAAA
GTGATATGTCTGAACAATACAGGCTTTGCTCTGAGGgttcgtgtaatcattgtgaaactggcag
acaggctgcataatatgcgtacactcacacatatgcctcagcacaagcaggtaaactcttgttc
cactgaaa

									
								

					

						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
						
							GTTCGTGTAATCATTGTGAAACTGGCAGACAGGCTGCATAATATGCGTACACTCACACATATGC
CTCAGCACAAGCAGGTAAACTCTTGTTCCACTGAAAATAATATCTGTCCGTAACTTAGTTTCTA
TTTTTATTGTAAGCACTCTCTTTGCAGTATGCCATTGCCATGGAGACACTGCAGGTTTTTGCAC
CCCTAGCTAAACTTCTCGGGATGTATCGAATAAAGGTATCTGATGATAAATCATCTTGAAATAT
AACTGTTATTTCTGTTTATTGTATAGACTAACTTCATTACTGCAGTGCTTTTATGTTATTGCTG
TGTTTGCTTACAAACATTTTGTACTACCATGCTGTTGTGTTTTTTCCAATAAAATTTATACTTC
TTTTTTAATGATAATTGTTTTCGTGTTTGCTTTTTTGATTTTAAAAACCTGTATTTCTGCTATA
ATTTGACCAGTAGACTTGTTTGTCCTGAACTTATTAGTAATATTAAGAAACAAGTCCATTTTAT
CCTTAAATATTGCTCAAGTTCAGAAATCTATGCTAAAATTTGGTATTTCACAACCGTGCAAAAA
CAACCTCCCTTGCTTAATTCACCAATTTTTCGTTGACTTGGTTTTCTGATTGCCAACTTTATGC
TGATGTGGCATACGAATCAGTAACAGCATAAAGTGATTCAGTTGTACAGATTGAAATATTCAGA
TTTGTTGTTGTTGATTTGGATGCAATGTCATCAATTACACCTCCCTCGGATATTTTAGAAGTCA
ACTTTTCACCTCAGAATGAGACATCCAAGCCCCAAAACAGTTAAAATCTAACCATCGTTTTATC
CACTTTATGGTTTTAATGGTGGTTTTGGAGAGTTAAAAGAACATAATGTACTTCCAAAGTTCAG
GGGCCAAAGAAATCAATTCCCCTTAATCTTATGACTGTACGAGATATTTTCATAGTAGTATTTT
GTAGTTCAAGGACCAAAGGAAAAAAAATCCAGTTCAAGGACCAAAGGAAAAAAAATCCCTTTAT
CTTATGAATAGAAGGGGTGGTTTCATACTGGTGTTTTCTGTCAGTCTTAGAAAGGTCTCCTCTG
TAGTTCGTTGCATTGTGAGAATGTCGATGTGTTTCTTATGAAGCTTATCATAGCTTCTGGTACT
TTGCCTGGGTCCATTTGACCAGTTGCTCTTATTCTTGTAGTCTGAGCTAGAATATCTGTCCTTC
ATGTACATGAATCCTGGTGATTTCGCTGAACTAAAGAAAAGAGTTGAGGACCTCTACAAGGCCC
ATGAACAAGAATTGGAAGAGGTACTTTGTTTTTGCTATTGCACTTTGATTTGCATTCTACTCTG
AATGAGATTCATTATAATTTTTGAATTACAGGCAAATCAAATCTTAGGGGAAAAGATTGCTGAG
GATCAATTTCTTGATCTTGTTAGTGTTGAAACACAAGTGCGTTCAGTCTGCAAAGAACTCTACA
GGTAGAGCACACATGATGTCTTATTAATTAAAAATAAGTATTATCTTGAACCTTCACTTCCACT
TTAATACTACCCCTGCCTAGTGATATACTGTTGGTATAAACTTGGTTTAGCTTATTTGTTTACA
CTACTTACAAATGCAATTCATATTAGAGCACAATGAATTTCCTCACAAATTTCTTTAGTTATAT
CTTTGTAAAAAAGTGGATATTTGTTTTCACTACTTTGTCAATTTGCTTACACAACATCATTAAA
TAGTGTGGTACAGTTACAGACTGATTGACGTTTTCTGCTGCAAAATCCTTTTTTTCTTCTCATT
CACATTTTGCACCTAAAAAGGTGATCAACAATTATTTTTGCATTATTCATTACCAAGTTTGAAA
TAGGTGGCAAAAGTGTTTTCTTAGGCAGATTATTTATCATTTGGTCATATTGCAGCATTTATAA
AACTGCGCTGAAGTCCAAGAGTTCAATAAATGAGATAAATCAGGTTGCACAGGTATGATTTTCC
TATGTCAGATAAGTTGCCTAGCTTTATCATTTTAACGAATAACTTATTCTCTGAAAAGTATTGT
GTTTCTATATTATTCAGCTGCGGATCATCATAAAGCCAAAATCCTGCAATGGTGTGGGGCCATT
GTGCACTGCACAACAGGTATAACATTACAAGTGTAACATACCATCTTTTCTGTATGAAATTAAA
ATTTACTAATGTGTAAATATGCTCAATCCACTGATGCGCAAGCATTCAATTCATTTCAGATCTG
CTACCATGTCCTTGGTCTTGTTCATGGTATCTGGACACCTATACCTCAAGCTGTGAGTTATCTG
CTTTCCTTATTCATTATAATTTTTACCTCTTTTGATTTTGCCATTTCTAAAAGCCAGCTGTATA
GGTGAAAGATTACATTGCAACCCCAAAGCCTAATGGATACCAAAGTCTACACACGACAGTGATA
CCATTTCTGAATGAGAGTATGTTCCATTTGGAAGTTCAGGTAATGTTGGCTTAGCTGCCTGCCA
TTTAGCTAAATTCATACTACAAACTCTCAAGCATGTGCTCATTCTAATGCAAGTTTCACTTTAT
GTTCCTACTGTATTGCAGATAAGAACAGAGGATATGGATCTCATAGCAGAAAGAGGCATTGCTG
CGCACTACAGTGGAAGAGGGGTTGTTTCAGGGCCTGTTCGTCCTGGAATATCAAGTGGAAGGAA
TTCAAATGGGAAAGTGATATGTCTGAACAATACAGGCTTTGCTCTGAGG
						
					

			
		

Sequences
Splice junction sequence	AAGAGGGGTTGTTTCAGGGCCTGTTCGTCCTGGAATATCAAGTGGAAGGAATTCAAATGGGAAA GTGATATGTCTGAACAATACAGGCTTTGCTCTGAGGgttcgtgtaatcattgtgaaactggcag acaggctgcataatatgcgtacactcacacatatgcctcagcacaagcaggtaaactcttgttc cactgaaa
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	GTTCGTGTAATCATTGTGAAACTGGCAGACAGGCTGCATAATATGCGTACACTCACACATATGC CTCAGCACAAGCAGGTAAACTCTTGTTCCACTGAAAATAATATCTGTCCGTAACTTAGTTTCTA TTTTTATTGTAAGCACTCTCTTTGCAGTATGCCATTGCCATGGAGACACTGCAGGTTTTTGCAC CCCTAGCTAAACTTCTCGGGATGTATCGAATAAAGGTATCTGATGATAAATCATCTTGAAATAT AACTGTTATTTCTGTTTATTGTATAGACTAACTTCATTACTGCAGTGCTTTTATGTTATTGCTG TGTTTGCTTACAAACATTTTGTACTACCATGCTGTTGTGTTTTTTCCAATAAAATTTATACTTC TTTTTTAATGATAATTGTTTTCGTGTTTGCTTTTTTGATTTTAAAAACCTGTATTTCTGCTATA ATTTGACCAGTAGACTTGTTTGTCCTGAACTTATTAGTAATATTAAGAAACAAGTCCATTTTAT CCTTAAATATTGCTCAAGTTCAGAAATCTATGCTAAAATTTGGTATTTCACAACCGTGCAAAAA CAACCTCCCTTGCTTAATTCACCAATTTTTCGTTGACTTGGTTTTCTGATTGCCAACTTTATGC TGATGTGGCATACGAATCAGTAACAGCATAAAGTGATTCAGTTGTACAGATTGAAATATTCAGA TTTGTTGTTGTTGATTTGGATGCAATGTCATCAATTACACCTCCCTCGGATATTTTAGAAGTCA ACTTTTCACCTCAGAATGAGACATCCAAGCCCCAAAACAGTTAAAATCTAACCATCGTTTTATC CACTTTATGGTTTTAATGGTGGTTTTGGAGAGTTAAAAGAACATAATGTACTTCCAAAGTTCAG GGGCCAAAGAAATCAATTCCCCTTAATCTTATGACTGTACGAGATATTTTCATAGTAGTATTTT GTAGTTCAAGGACCAAAGGAAAAAAAATCCAGTTCAAGGACCAAAGGAAAAAAAATCCCTTTAT CTTATGAATAGAAGGGGTGGTTTCATACTGGTGTTTTCTGTCAGTCTTAGAAAGGTCTCCTCTG TAGTTCGTTGCATTGTGAGAATGTCGATGTGTTTCTTATGAAGCTTATCATAGCTTCTGGTACT TTGCCTGGGTCCATTTGACCAGTTGCTCTTATTCTTGTAGTCTGAGCTAGAATATCTGTCCTTC ATGTACATGAATCCTGGTGATTTCGCTGAACTAAAGAAAAGAGTTGAGGACCTCTACAAGGCCC ATGAACAAGAATTGGAAGAGGTACTTTGTTTTTGCTATTGCACTTTGATTTGCATTCTACTCTG AATGAGATTCATTATAATTTTTGAATTACAGGCAAATCAAATCTTAGGGGAAAAGATTGCTGAG GATCAATTTCTTGATCTTGTTAGTGTTGAAACACAAGTGCGTTCAGTCTGCAAAGAACTCTACA GGTAGAGCACACATGATGTCTTATTAATTAAAAATAAGTATTATCTTGAACCTTCACTTCCACT TTAATACTACCCCTGCCTAGTGATATACTGTTGGTATAAACTTGGTTTAGCTTATTTGTTTACA CTACTTACAAATGCAATTCATATTAGAGCACAATGAATTTCCTCACAAATTTCTTTAGTTATAT CTTTGTAAAAAAGTGGATATTTGTTTTCACTACTTTGTCAATTTGCTTACACAACATCATTAAA TAGTGTGGTACAGTTACAGACTGATTGACGTTTTCTGCTGCAAAATCCTTTTTTTCTTCTCATT CACATTTTGCACCTAAAAAGGTGATCAACAATTATTTTTGCATTATTCATTACCAAGTTTGAAA TAGGTGGCAAAAGTGTTTTCTTAGGCAGATTATTTATCATTTGGTCATATTGCAGCATTTATAA AACTGCGCTGAAGTCCAAGAGTTCAATAAATGAGATAAATCAGGTTGCACAGGTATGATTTTCC TATGTCAGATAAGTTGCCTAGCTTTATCATTTTAACGAATAACTTATTCTCTGAAAAGTATTGT GTTTCTATATTATTCAGCTGCGGATCATCATAAAGCCAAAATCCTGCAATGGTGTGGGGCCATT GTGCACTGCACAACAGGTATAACATTACAAGTGTAACATACCATCTTTTCTGTATGAAATTAAA ATTTACTAATGTGTAAATATGCTCAATCCACTGATGCGCAAGCATTCAATTCATTTCAGATCTG CTACCATGTCCTTGGTCTTGTTCATGGTATCTGGACACCTATACCTCAAGCTGTGAGTTATCTG CTTTCCTTATTCATTATAATTTTTACCTCTTTTGATTTTGCCATTTCTAAAAGCCAGCTGTATA GGTGAAAGATTACATTGCAACCCCAAAGCCTAATGGATACCAAAGTCTACACACGACAGTGATA CCATTTCTGAATGAGAGTATGTTCCATTTGGAAGTTCAGGTAATGTTGGCTTAGCTGCCTGCCA TTTAGCTAAATTCATACTACAAACTCTCAAGCATGTGCTCATTCTAATGCAAGTTTCACTTTAT GTTCCTACTGTATTGCAGATAAGAACAGAGGATATGGATCTCATAGCAGAAAGAGGCATTGCTG CGCACTACAGTGGAAGAGGGGTTGTTTCAGGGCCTGTTCGTCCTGGAATATCAAGTGGAAGGAA TTCAAATGGGAAAGTGATATGTCTGAACAATACAGGCTTTGCTCTGAGG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.142620573

Conservation Information
Conserved circRNAs	NA
PMCS	0.142620573

			
				
						 Functional Information
					

				
						Coding potential
						Y
					

						Potential coding position
						
							12699812-12702502(+)
12702476-12699806(+)
12699830-12702460(-)
12699784-12702399(-)
						
					

						Potential amino acid sequence
						
							MRTLTHMPQHKQYAIAMETLQVFAPLAKLLGMYRIKSELEYLSFMYMNPGDFAELKKRVEDLYK
AHEQELEEANQILGEKIAEDQFLDLVSVETQVRSVCKELYSIYKTALKSKSSINEINQVAQLRI
IIKPKSCNGVGPLCTAQQICYHVLGLVHGIWTPIPQAVKDYIATPKPNGYQSLHTTVIPFLNES
MFHLEVQIRTEDMDLIAERGIAAHYSGRGVVSGPVRPGISSGRNSNGKVICLNNTGFALRVRVI
IVKLADRLHNMRTLTHMPQHKQYAIAMETLQVFAPLAKLLGMYRIKSELEYLSFMYMNPGDFAE
LKKRVEDLYKAHEQELEEANQILGEKIAEDQFLDLVSVETQVRSVCKELYSIYKTALKSKSSIN
EINQVAQLRIIIKPKSCNGVGPLCTAQQICYHVLGLVHGIWTPIPQAVKDYIATPKPNGYQSLH
TTVIPFLNESMFHLEVQIRTEDMDLIAERGIAAHYSGRGVVSGPVRPGISSGRNSNGKVICLNN
TGFALRVRVIIVKLADRLHNMRTLTHMPQHKQYAIAMETLQVFAPLAKLLGMYRIKSELEYLSF
MYMNPGDFAELKKRVEDLYKAHEQELEEANQILGEKIAEDQFLDLVSVETQVRSVCKELYSIYK
TALKSKSSINEINQVAQLRIIIKPKSCNGVGPLCTAQQICYHVLGLVHGIWTPIPQAVKDYIAT
PKPNGYQSLHTTVIPFLNESMFHLEVQIRTEDMDLIAERGIAAHYSGRGVVSGPVRPGISSGRN
SNGKVICLNNTGFALRVRVIIVKLADRLHNMRTLTHMPQHKQYAIAMETLQVFAPLAKLLGMYR
IKSELEYLSFMYMNPGDFAELKKRVEDLYKAHEQELEEANQILGEKIAEDQFLDLVSVETQVRS
VCKELYSIYKTALKSKSSINEINQVAQLRIIIKPKSCNGVGPLCTAQQICYHVLGLVHGIWTPI
PQAVKDYIATPKPNGYQSLHTTVIPFLNESMFHLEVQIRTEDMDLIAERGIAAHYSGRGVVSGP
VRPGISSGRNSNGKVICLNNTGFALR(+)
MSEQYRLCSEGSCNHCETGRQAA*(+)
MCECTHIMQPVCQFHNDYTNPQSKACIVQTYHFPI*(-)
MITRTLRAKPVLFRHITFPFEFLPLDIPGRTGPETTPLPL*(-)
						
					

						Sponge-miRNAs
						
							NA						
					

						circRNA-miRNA-mRNA network
						 VISUALIZATION
					

						Potential function description
						NA
					

			
		

Functional Information
Coding potential	Y
Potential coding position	12699812-12702502(+) 12702476-12699806(+) 12699830-12702460(-) 12699784-12702399(-)
Potential amino acid sequence	MRTLTHMPQHKQYAIAMETLQVFAPLAKLLGMYRIKSELEYLSFMYMNPGDFAELKKRVEDLYK AHEQELEEANQILGEKIAEDQFLDLVSVETQVRSVCKELYSIYKTALKSKSSINEINQVAQLRI IIKPKSCNGVGPLCTAQQICYHVLGLVHGIWTPIPQAVKDYIATPKPNGYQSLHTTVIPFLNES MFHLEVQIRTEDMDLIAERGIAAHYSGRGVVSGPVRPGISSGRNSNGKVICLNNTGFALRVRVI IVKLADRLHNMRTLTHMPQHKQYAIAMETLQVFAPLAKLLGMYRIKSELEYLSFMYMNPGDFAE LKKRVEDLYKAHEQELEEANQILGEKIAEDQFLDLVSVETQVRSVCKELYSIYKTALKSKSSIN EINQVAQLRIIIKPKSCNGVGPLCTAQQICYHVLGLVHGIWTPIPQAVKDYIATPKPNGYQSLH TTVIPFLNESMFHLEVQIRTEDMDLIAERGIAAHYSGRGVVSGPVRPGISSGRNSNGKVICLNN TGFALRVRVIIVKLADRLHNMRTLTHMPQHKQYAIAMETLQVFAPLAKLLGMYRIKSELEYLSF MYMNPGDFAELKKRVEDLYKAHEQELEEANQILGEKIAEDQFLDLVSVETQVRSVCKELYSIYK TALKSKSSINEINQVAQLRIIIKPKSCNGVGPLCTAQQICYHVLGLVHGIWTPIPQAVKDYIAT PKPNGYQSLHTTVIPFLNESMFHLEVQIRTEDMDLIAERGIAAHYSGRGVVSGPVRPGISSGRN SNGKVICLNNTGFALRVRVIIVKLADRLHNMRTLTHMPQHKQYAIAMETLQVFAPLAKLLGMYR IKSELEYLSFMYMNPGDFAELKKRVEDLYKAHEQELEEANQILGEKIAEDQFLDLVSVETQVRS VCKELYSIYKTALKSKSSINEINQVAQLRIIIKPKSCNGVGPLCTAQQICYHVLGLVHGIWTPI PQAVKDYIATPKPNGYQSLHTTVIPFLNESMFHLEVQIRTEDMDLIAERGIAAHYSGRGVVSGP VRPGISSGRNSNGKVICLNNTGFALR(+) MSEQYRLCSEGSCNHCETGRQAA(+) MCECTHIMQPVCQFHNDYTNPQSKACIVQTYHFPI(-) MITRTLRAKPVLFRHITFPFEFLPLDIPGRTGPETTPLPL*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os03g0340900_circ_g.3

Address

Any questions?

Supported by