Plant Circular RNA Database

Detail information of Os03g0628800_circ_g.1

			
						 General Information
					
						CircRNA Name
						Os03g0628800_circ_g.1
					
						ID in PlantcircBase
						osa_circ_020715
					
						Alias
						Os03circ20675/Os_ciR1433
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr3: 23990498-23991657  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, SMALT, Segemehl, find_circ
					
						Parent gene
						
							Os03g0628800						
					
						Parent gene annotation
						
							Similar to H1flk (Fragment). (Os03t0628800-01)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os03g0628800_circ_g.2 Os03g0628800_circ_g.3 Os03g0628800_circ_g.4 						
					
						Support reads
						2/13/3
					
						Tissues
						leaf/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  
						
							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
						Os03t0628800-01:2

General Information
CircRNA Name	Os03g0628800_circ_g.1
ID in PlantcircBase	osa_circ_020715
Alias	Os03circ20675/Os_ciR1433
Organism	Oryza sativa
Position	chr3: 23990498-23991657 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, SMALT, Segemehl, find_circ
Parent gene	Os03g0628800
Parent gene annotation	Similar to H1flk (Fragment). (Os03t0628800-01)
Parent gene strand	+
Alternative splicing	Os03g0628800_circ_g.2 Os03g0628800_circ_g.3 Os03g0628800_circ_g.4
Support reads	2/13/3
Tissues	leaf/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	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	Os03t0628800-01:2

			
						 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  
						
							TATGTTAATTAATTATATGCATATATATGCAGGCCTTGACCGTAGACTGTGGCACCGCCAGCAA
GAAGAAGCTAAGGAACCTCGTGTTGGAAGCTACAAGctaggcagatggggtttcaggacataaa
tgagtgcccacagctgtgcaaattagcaaataactacctcaagaggaccaagaattgcatggat
gacatcga

						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: 292
Transcript exons: 23990498-23990721,23991590-23991657
CTAGGCAGATGGGGTTTCAGGACATAAATGAGTGCCCACAGCTGTGCAAATTAGCAAATAACTA
CCTCAAGAGGACCAAGAATTGCATGGATGACATCGATGACTTCTTCGCAAATATCCTGGATTCG
GAGTCCCTTTATGTCAAGTTCATAGAAGAGTTGGATAAATGCATTCTTGGATATTTTGCGTTCC
ATTGGGACCATGCTACCGCTCTTATCAGCCAGGCCTTGACCGTAGACTGTGGCACCGCCAGCAA
GAAGAAGCTAAGGAACCTCGTGTTGGAAGCTACAAG
						
						Genomic sequence
						
							CTAGGCAGATGGGGTTTCAGGACATAAATGAGTGCCCACAGCTGTGCAAATTAGCAAATAACTA
CCTCAAGAGGACCAAGAATTGCATGGATGACATCGATGACTTCTTCGCAAATATCCTGGATTCG
GAGTCCCTTTATGTCAAGTTCATAGAAGAGTTGGATAAATGCATTCTTGGATATTTTGCGTTCC
ATTGGGACCATGCTACCGCTCTTATCAGCCAGGTATTTATTGTACCATGCGACAACTGGTTTTC
TGATTTTTTTTTCCTGGCCATTTACATGGAATTAAGTTTCACTTTTATATACAGTAAGTACTAC
TGGTATCCAAAGTTTACTTTGGAAAAAAAATTAATATTACCGTGTGGATGGTTGTTTCAAAAAA
ATATTATAACGTATGGACTACTCTTAACATTTGTATTACTCATTTAGGGTGTACTTATCACGTG
CACAACTAAAATTAATCAAAAGCACATGCATGTTCGATTATCGTGTGTAAGCACACGCTAACTG
CTTATATCCCTTGCAACATTAGTTAATTACGTGACTGACACTAACTATCCAAATTTATGATGTC
TATTTTCTTCAGTCCAATTTTTTTTCTGTCCAAATACCAGCCAAATAAAGTTAGAACAACATTA
ATTGGTCAACTCGCACATAAATTAACATGTTTAGCATAGCTTCTTCTTAATTAGTAATTCGTGT
TAGATTAGCAGCAGGCAGTTATTAATTAATCTCTTGAGAAAACAGCAAGGGTGAATCCAGAAAA
TTAATTAATATATATCCCGTGCACGTTCTATTTGTATCAATATTGGCGGATCGATCTGGAAGCA
AAGGGATTTTTAGGGAGACGTACGCACGTACATATATGTACGTGACAGAAAATTTATTCTTTTT
ACACAGAATTAATGAACACATTACTGCAGCTATAGTGTAATGGCAGTACTACCACTATATAGAT
TAATGGGCACATCTAGCATATACAGTACACGTACGTGCACATATATATCAACGTAACTGCCATA
ATTTTTCCATGAACTAATTAATATATCTCGTAGTATTATGTTAATTAATTATATGCATATATAT
GCAGGCCTTGACCGTAGACTGTGGCACCGCCAGCAAGAAGAAGCTAAGGAACCTCGTGTTGGAA
GCTACAAG

Sequences
Splice junction sequence	TATGTTAATTAATTATATGCATATATATGCAGGCCTTGACCGTAGACTGTGGCACCGCCAGCAA GAAGAAGCTAAGGAACCTCGTGTTGGAAGCTACAAGctaggcagatggggtttcaggacataaa tgagtgcccacagctgtgcaaattagcaaataactacctcaagaggaccaagaattgcatggat gacatcga
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: 292 Transcript exons: 23990498-23990721,23991590-23991657 CTAGGCAGATGGGGTTTCAGGACATAAATGAGTGCCCACAGCTGTGCAAATTAGCAAATAACTA CCTCAAGAGGACCAAGAATTGCATGGATGACATCGATGACTTCTTCGCAAATATCCTGGATTCG GAGTCCCTTTATGTCAAGTTCATAGAAGAGTTGGATAAATGCATTCTTGGATATTTTGCGTTCC ATTGGGACCATGCTACCGCTCTTATCAGCCAGGCCTTGACCGTAGACTGTGGCACCGCCAGCAA GAAGAAGCTAAGGAACCTCGTGTTGGAAGCTACAAG
Genomic sequence	CTAGGCAGATGGGGTTTCAGGACATAAATGAGTGCCCACAGCTGTGCAAATTAGCAAATAACTA CCTCAAGAGGACCAAGAATTGCATGGATGACATCGATGACTTCTTCGCAAATATCCTGGATTCG GAGTCCCTTTATGTCAAGTTCATAGAAGAGTTGGATAAATGCATTCTTGGATATTTTGCGTTCC ATTGGGACCATGCTACCGCTCTTATCAGCCAGGTATTTATTGTACCATGCGACAACTGGTTTTC TGATTTTTTTTTCCTGGCCATTTACATGGAATTAAGTTTCACTTTTATATACAGTAAGTACTAC TGGTATCCAAAGTTTACTTTGGAAAAAAAATTAATATTACCGTGTGGATGGTTGTTTCAAAAAA ATATTATAACGTATGGACTACTCTTAACATTTGTATTACTCATTTAGGGTGTACTTATCACGTG CACAACTAAAATTAATCAAAAGCACATGCATGTTCGATTATCGTGTGTAAGCACACGCTAACTG CTTATATCCCTTGCAACATTAGTTAATTACGTGACTGACACTAACTATCCAAATTTATGATGTC TATTTTCTTCAGTCCAATTTTTTTTCTGTCCAAATACCAGCCAAATAAAGTTAGAACAACATTA ATTGGTCAACTCGCACATAAATTAACATGTTTAGCATAGCTTCTTCTTAATTAGTAATTCGTGT TAGATTAGCAGCAGGCAGTTATTAATTAATCTCTTGAGAAAACAGCAAGGGTGAATCCAGAAAA TTAATTAATATATATCCCGTGCACGTTCTATTTGTATCAATATTGGCGGATCGATCTGGAAGCA AAGGGATTTTTAGGGAGACGTACGCACGTACATATATGTACGTGACAGAAAATTTATTCTTTTT ACACAGAATTAATGAACACATTACTGCAGCTATAGTGTAATGGCAGTACTACCACTATATAGAT TAATGGGCACATCTAGCATATACAGTACACGTACGTGCACATATATATCAACGTAACTGCCATA ATTTTTCCATGAACTAATTAATATATCTCGTAGTATTATGTTAATTAATTATATGCATATATAT GCAGGCCTTGACCGTAGACTGTGGCACCGCCAGCAAGAAGAAGCTAAGGAACCTCGTGTTGGAA GCTACAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_013340 						
					
						PMCS
						0.308752795

Conservation Information
Conserved circRNAs	osi_circ_013340
PMCS	0.308752795

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							23990665-23990521(+)
23990507-23990498(+)
						
						Potential amino acid sequence
						
							MHSWIFCVPLGPCYRSYQPGLDRRLWHRQQEEAKEPRVGSYKLGRWGFRT*(+)
MGFQDINECPQLCKLANNYLKRTKNCMDDIDDFFANILDSESLYVKFIEELDKCILGYFAFHWD
HATALISQALTVDCGTASKKKLRNLVLEATS*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	23990665-23990521(+) 23990507-23990498(+)
Potential amino acid sequence	MHSWIFCVPLGPCYRSYQPGLDRRLWHRQQEEAKEPRVGSYKLGRWGFRT(+) MGFQDINECPQLCKLANNYLKRTKNCMDDIDDFFANILDSESLYVKFIEELDKCILGYFAFHWD HATALISQALTVDCGTASKKKLRNLVLEATS(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

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

circRNA

Detail information of Os03g0628800_circ_g.1

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