Plant Circular RNA Database

Detail information of Os04g0280200_circ_g.1

			
						 General Information
					
						CircRNA Name
						Os04g0280200_circ_g.1
					
						ID in PlantcircBase
						osa_circ_023282
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr4: 11869398-11869737  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ie-circRNA							
									
						Identification method
						CIRCexplorer, circseq_cup
					
						Parent gene
						
							Os04g0280251						
					
						Parent gene annotation
						
							Hypothetical protein. (Os04t0280251-00)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							NA						
					
						Support reads
						4/4
					
						Tissues
						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
						Os04t0280200-01:2
Os04t0280251-00:2
Os04t0280200-01:2

General Information
CircRNA Name	Os04g0280200_circ_g.1
ID in PlantcircBase	osa_circ_023282
Alias	NA
Organism	Oryza sativa
Position	chr4: 11869398-11869737 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ie-circRNA
Identification method	CIRCexplorer, circseq_cup
Parent gene	Os04g0280251
Parent gene annotation	Hypothetical protein. (Os04t0280251-00)
Parent gene strand	-
Alternative splicing	NA
Support reads	4/4
Tissues	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	Os04t0280200-01:2 Os04t0280251-00:2 Os04t0280200-01:2

			
						 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  
						
							CGTGATCGTCTCCATGGAGGACTACCGCACGGTGGCCGGGGCCGACGACGGCAGCGACGTTGAC
GCCATCGACTTCGACGCCCTCGCTCGTAACCTCCAGtccttcgaccgcggcttctacctcctcg
tcaaggcgatccaggagctgcgtgagcgcaaggacggcctcgtcgtcaccgtcggcatcggcgg
gccaaccg

						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: 252
Transcript exons: 11869398-11869513,11869602-11869737
TCCTTCGACCGCGGCTTCTACCTCCTCGTCAAGGCGATCCAGGAGCTGCGTGAGCGCAAGGACG
GCCTCGTCGTCACCGTCGGCATCGGCGGGCCAACCGGCTCCGGCAAGACCAGCCTGGCGGAGAA
GGTGGCGTCGGTGCTGGGGTGCGTCGTGATCGTCTCCATGGAGGACTACCGCACGGTGGCCGGG
GCCGACGACGGCAGCGACGTTGACGCCATCGACTTCGACGCCCTCGCTCGTAACCTCCAG
						
						Genomic sequence
						
							TCCTTCGACCGCGGCTTCTACCTCCTCGTCAAGGCGATCCAGGAGCTGCGTGAGCGCAAGGACG
GCCTCGTCGTCACCGTCGGCATCGGCGGGCCAACCGGCTCCGGCAAGACCAGGTACGGGCCGCT
CCCCTCCTTCCCGCCGCGCGCTGGTTGCTGTTGCTGATTGGTGGTGGTGGTGTTGTGCACTTTG
TGCCGGGCGCAGCCTGGCGGAGAAGGTGGCGTCGGTGCTGGGGTGCGTCGTGATCGTCTCCATG
GAGGACTACCGCACGGTGGCCGGGGCCGACGACGGCAGCGACGTTGACGCCATCGACTTCGACG
CCCTCGCTCGTAACCTCCAG

Sequences
Splice junction sequence	CGTGATCGTCTCCATGGAGGACTACCGCACGGTGGCCGGGGCCGACGACGGCAGCGACGTTGAC GCCATCGACTTCGACGCCCTCGCTCGTAACCTCCAGtccttcgaccgcggcttctacctcctcg tcaaggcgatccaggagctgcgtgagcgcaaggacggcctcgtcgtcaccgtcggcatcggcgg gccaaccg
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: 252 Transcript exons: 11869398-11869513,11869602-11869737 TCCTTCGACCGCGGCTTCTACCTCCTCGTCAAGGCGATCCAGGAGCTGCGTGAGCGCAAGGACG GCCTCGTCGTCACCGTCGGCATCGGCGGGCCAACCGGCTCCGGCAAGACCAGCCTGGCGGAGAA GGTGGCGTCGGTGCTGGGGTGCGTCGTGATCGTCTCCATGGAGGACTACCGCACGGTGGCCGGG GCCGACGACGGCAGCGACGTTGACGCCATCGACTTCGACGCCCTCGCTCGTAACCTCCAG
Genomic sequence	TCCTTCGACCGCGGCTTCTACCTCCTCGTCAAGGCGATCCAGGAGCTGCGTGAGCGCAAGGACG GCCTCGTCGTCACCGTCGGCATCGGCGGGCCAACCGGCTCCGGCAAGACCAGGTACGGGCCGCT CCCCTCCTTCCCGCCGCGCGCTGGTTGCTGTTGCTGATTGGTGGTGGTGGTGTTGTGCACTTTG TGCCGGGCGCAGCCTGGCGGAGAAGGTGGCGTCGGTGCTGGGGTGCGTCGTGATCGTCTCCATG GAGGACTACCGCACGGTGGCCGGGGCCGACGACGGCAGCGACGTTGACGCCATCGACTTCGACG CCCTCGCTCGTAACCTCCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.432178725

Conservation Information
Conserved circRNAs	NA
PMCS	0.432178725

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							11869652-11869734(+)
						
						Potential amino acid sequence
						
							MEDYRTVAGADDGSDVDAIDFDALARNLQSFDRGFYLLVKAIQELRERKDGLVVTVGIGGPTGS
GKTSLAEKVASVLGCVVIVSMEDYRTVAGADDGSDVDAIDFDALARNLQSFDRGFYLLVKAIQE
LRERKDGLVVTVGIGGPTGSGKTSLAEKVASVLGCVVIVSMEDYRTVAGADDGSDVDAIDFDAL
ARNLQSFDRGFYLLVKAIQELRERKDGLVVTVGIGGPTGSGKTSLAEKVASVLGCVVIVSMEDY
RTVAGADDGSDVDAIDFDALARNLQ(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	11869652-11869734(+)
Potential amino acid sequence	MEDYRTVAGADDGSDVDAIDFDALARNLQSFDRGFYLLVKAIQELRERKDGLVVTVGIGGPTGS GKTSLAEKVASVLGCVVIVSMEDYRTVAGADDGSDVDAIDFDALARNLQSFDRGFYLLVKAIQE LRERKDGLVVTVGIGGPTGSGKTSLAEKVASVLGCVVIVSMEDYRTVAGADDGSDVDAIDFDAL ARNLQSFDRGFYLLVKAIQELRERKDGLVVTVGIGGPTGSGKTSLAEKVASVLGCVVIVSMEDY RTVAGADDGSDVDAIDFDALARNLQ(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

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

circRNA

Detail information of Os04g0280200_circ_g.1

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