Plant Circular RNA Database

Detail information of Os07g0258400_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os07g0258400_circ_g.3
					
						ID in PlantcircBase
						osa_circ_033346
					
						Alias
						Os_ciR5590
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr7: 8968062-8968534  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, circseq_cup, find_circ
					
						Parent gene
						
							Os07g0258400						
					
						Parent gene annotation
						
							OsNramp1 (Integral membrane protein). (Os07t0258400-01);Similar 
to Metal transporter. (Os07t0258400-02);Integral membrane protei
n, Metal ion transport (Os07t0258400-03)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os07g0258400_circ_g.1 Os07g0258400_circ_g.2 Os07g0258400_circ_g.4 Os07g0258400_circ_g.5 Os07g0258400_circ_g.6 Os07g0258400_circ_g.7 Os07g0258400_circ_g.8 Os07g0258400_circ_g.9 Os07g0258400_circ_g.10 Os07g0258400_circ_g.11 Os07g0258400_circ_g.12 						
					
						Support reads
						3/3/7
					
						Tissues
						root/root/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
						Os07t0258400-01:2
Os07t0258400-02:2
Os07t0258400-03:2

General Information
CircRNA Name	Os07g0258400_circ_g.3
ID in PlantcircBase	osa_circ_033346
Alias	Os_ciR5590
Organism	Oryza sativa
Position	chr7: 8968062-8968534 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, circseq_cup, find_circ
Parent gene	Os07g0258400
Parent gene annotation	OsNramp1 (Integral membrane protein). (Os07t0258400-01);Similar to Metal transporter. (Os07t0258400-02);Integral membrane protei n, Metal ion transport (Os07t0258400-03)
Parent gene strand	+
Alternative splicing	Os07g0258400_circ_g.1 Os07g0258400_circ_g.2 Os07g0258400_circ_g.4 Os07g0258400_circ_g.5 Os07g0258400_circ_g.6 Os07g0258400_circ_g.7 Os07g0258400_circ_g.8 Os07g0258400_circ_g.9 Os07g0258400_circ_g.10 Os07g0258400_circ_g.11 Os07g0258400_circ_g.12
Support reads	3/3/7
Tissues	root/root/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	Os07t0258400-01:2 Os07t0258400-02:2 Os07t0258400-03:2

			
						 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  
						
							CTCCGGTTAATGAGGTCCTTCAAGGATTATTCATCCCCAGGCTCAGTGGGCCCGGTGCCACAGG
AGACTCCATTGCCCTTCTTGGGGCTCTTGTAATGCCttataggtacaggatttgctttcaacct
tttgttccacataccagtgtggaccggggttctcattgctggctctagcacgcttcttcttctt
ggactgca

									
								

					

						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: 222
Transcript exons: 8968062-8968148,8968400-8968534
TTATAGGTACAGGATTTGCTTTCAACCTTTTGTTCCACATACCAGTGTGGACCGGGGTTCTCAT
TGCTGGCTCTAGCACGCTTCTTCAGGGTGCTTCTTCGTGGAGATGAGCATAGTCAAGCCTCCGG
TTAATGAGGTCCTTCAAGGATTATTCATCCCCAGGCTCAGTGGGCCCGGTGCCACAGGAGACTC
CATTGCCCTTCTTGGGGCTCTTGTAATGCC
Transcript length: 292
Transcript exons: 8968062-8968171,8968353-8968534
TTATAGGTACAGGATTTGCTTTCAACCTTTTGTTCCACATACCAGTGTGGACCGGGGTTCTCAT
TGCTGGCTCTAGCACGCTTCTTCTTCTTGGACTGCAAAGATATGGGGTAAGGAAACTGGAGGTT
GTGGTCGCGCTATTGGTGTTTGTCATGGCAGGGTGCTTCTTCGTGGAGATGAGCATAGTCAAGC
CTCCGGTTAATGAGGTCCTTCAAGGATTATTCATCCCCAGGCTCAGTGGGCCCGGTGCCACAGG
AGACTCCATTGCCCTTCTTGGGGCTCTTGTAATGCC
Transcript length: 292
Transcript exons: 8968062-8968534
TTATAGGTACAGGATTTGCTTTCAACCTTTTGTTCCACATACCAGTGTGGACCGGGGTTCTCAT
TGTTGGCTCTAGCACGCTTCTTCTTCTTGGACTGCAAAGATATGGGGTAAGGAAACTGGAGGTT
GTGGTCGCGCTATTGGTGTTTGTCATGGCAGGGTGCTTCTTCGTGGAGATGAGCATAGTCAAGC
CTCCGGTTAATGAGGTCCTTCAAGGATTATTCATCCCCAGGCTCAGTGGGCCCGGTGCCACAGG
AGACTCCATTGCCCTTCTTGGGGCTCTTGTAATGCC
						
					

						Genomic sequence
						
							TTATAGGTACAGGATTTGCTTTCAACCTTTTGTTCCACATACCAGTGTGGACCGGGGTTCTCAT
TGCTGGCTCTAGCACGCTTCTTCTTCTTGGACTGCAAAGATATGGGGTAACCAACTATTTATGA
CTGGATATATGATAGATGTCTGTATAAAATGTTTTAATGAATGTCTAAACATCATTGTATTGTA
TTTGATCATTACTGTTTGGTCATTGTAAATGGTGGTCATTACAAATGGGTTTGTTGTTGAATTG
ACTTGTTTGCATTTTTCCTTCATCTATATAACTAGGTAAGGAAACTGGAGGTTGTGGTCGCGCT
ATTGGTGTTTGTCATGGCAGGGTGCTTCTTCGTGGAGATGAGCATAGTCAAGCCTCCGGTTAAT
GAGGTCCTTCAAGGATTATTCATCCCCAGGCTCAGTGGGCCCGGTGCCACAGGAGACTCCATTG
CCCTTCTTGGGGCTCTTGTAATGCC
						
					

			
		

Sequences
Splice junction sequence	CTCCGGTTAATGAGGTCCTTCAAGGATTATTCATCCCCAGGCTCAGTGGGCCCGGTGCCACAGG AGACTCCATTGCCCTTCTTGGGGCTCTTGTAATGCCttataggtacaggatttgctttcaacct tttgttccacataccagtgtggaccggggttctcattgctggctctagcacgcttcttcttctt ggactgca
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: 222 Transcript exons: 8968062-8968148,8968400-8968534 TTATAGGTACAGGATTTGCTTTCAACCTTTTGTTCCACATACCAGTGTGGACCGGGGTTCTCAT TGCTGGCTCTAGCACGCTTCTTCAGGGTGCTTCTTCGTGGAGATGAGCATAGTCAAGCCTCCGG TTAATGAGGTCCTTCAAGGATTATTCATCCCCAGGCTCAGTGGGCCCGGTGCCACAGGAGACTC CATTGCCCTTCTTGGGGCTCTTGTAATGCC Transcript length: 292 Transcript exons: 8968062-8968171,8968353-8968534 TTATAGGTACAGGATTTGCTTTCAACCTTTTGTTCCACATACCAGTGTGGACCGGGGTTCTCAT TGCTGGCTCTAGCACGCTTCTTCTTCTTGGACTGCAAAGATATGGGGTAAGGAAACTGGAGGTT GTGGTCGCGCTATTGGTGTTTGTCATGGCAGGGTGCTTCTTCGTGGAGATGAGCATAGTCAAGC CTCCGGTTAATGAGGTCCTTCAAGGATTATTCATCCCCAGGCTCAGTGGGCCCGGTGCCACAGG AGACTCCATTGCCCTTCTTGGGGCTCTTGTAATGCC Transcript length: 292 Transcript exons: 8968062-8968534 TTATAGGTACAGGATTTGCTTTCAACCTTTTGTTCCACATACCAGTGTGGACCGGGGTTCTCAT TGTTGGCTCTAGCACGCTTCTTCTTCTTGGACTGCAAAGATATGGGGTAAGGAAACTGGAGGTT GTGGTCGCGCTATTGGTGTTTGTCATGGCAGGGTGCTTCTTCGTGGAGATGAGCATAGTCAAGC CTCCGGTTAATGAGGTCCTTCAAGGATTATTCATCCCCAGGCTCAGTGGGCCCGGTGCCACAGG AGACTCCATTGCCCTTCTTGGGGCTCTTGTAATGCC
Genomic sequence	TTATAGGTACAGGATTTGCTTTCAACCTTTTGTTCCACATACCAGTGTGGACCGGGGTTCTCAT TGCTGGCTCTAGCACGCTTCTTCTTCTTGGACTGCAAAGATATGGGGTAACCAACTATTTATGA CTGGATATATGATAGATGTCTGTATAAAATGTTTTAATGAATGTCTAAACATCATTGTATTGTA TTTGATCATTACTGTTTGGTCATTGTAAATGGTGGTCATTACAAATGGGTTTGTTGTTGAATTG ACTTGTTTGCATTTTTCCTTCATCTATATAACTAGGTAAGGAAACTGGAGGTTGTGGTCGCGCT ATTGGTGTTTGTCATGGCAGGGTGCTTCTTCGTGGAGATGAGCATAGTCAAGCCTCCGGTTAAT GAGGTCCTTCAAGGATTATTCATCCCCAGGCTCAGTGGGCCCGGTGCCACAGGAGACTCCATTG CCCTTCTTGGGGCTCTTGTAATGCC

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_017686 						
					
						PMCS
						0.390637182

Conservation Information
Conserved circRNAs	osi_circ_017686
PMCS	0.390637182

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							8968396-8968134(+)
8968428-8968463(-)
						
						Potential amino acid sequence
						
							MAGCFFVEMSIVKPPVNEVLQGLFIPRLSGPGATGDSIALLGALVMPYRYRICFQPFVPHTSVD
RGSHCWL*(+)
MLISTKKHPAMTNTNSATTTSSFLTPYLCSPRRRSVLEPAMRTPVHTGMWNKRLKANPVPIRHY
KSPKKGNGVSCGTGPTEPGDE*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	8968396-8968134(+) 8968428-8968463(-)
Potential amino acid sequence	MAGCFFVEMSIVKPPVNEVLQGLFIPRLSGPGATGDSIALLGALVMPYRYRICFQPFVPHTSVD RGSHCWL(+) MLISTKKHPAMTNTNSATTTSSFLTPYLCSPRRRSVLEPAMRTPVHTGMWNKRLKANPVPIRHY KSPKKGNGVSCGTGPTEPGDE(-)
Sponge-miRNAs	NA
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 Os07g0258400_circ_g.3

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