Plant Circular RNA Database

Detail information of Os04g0252200_circ_g.1

			
						 General Information
					
						CircRNA Name
						Os04g0252200_circ_g.1
					
						ID in PlantcircBase
						osa_circ_023186
					
						Alias
						Os_ciR9738
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr4: 9893940-9898942  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRCexplorer, find_circ
					
						Parent gene
						
							Os04g0252200						
					
						Parent gene annotation
						
							Similar to CPSF160; nucleic acid binding. (Os04t0252200-01);Simi
lar to CPSF160; nucleic acid binding. (Os04t0252200-02)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os04g0252200_circ_g.2 Os04g0252200_circ_g.3 Os04g0252200_circ_g.4 Os04g0252200_circ_g.5 Os04g0252200_circ_g.6 Os04g0252200_circ_g.7 Os04g0252200_circ_g.8 Os04g0252200_circ_g.9 Os04g0252200_circ_g.10 Os04g0252200_circ_g.11 Os04g0252200_circ_g.12 Os04g0252200_circ_g.13 Os04g0252200_circ_g.14 Os04g0252200_circ_g.15 Os04g0252200_circ_g.16 Os04g0252200_circ_g.17 Os04g0252200_circ_g.18 						
					
						Support reads
						2/2
					
						Tissues
						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  
						
							CT-AC							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
						Os04t0252200-02:3

General Information
CircRNA Name	Os04g0252200_circ_g.1
ID in PlantcircBase	osa_circ_023186
Alias	Os_ciR9738
Organism	Oryza sativa
Position	chr4: 9893940-9898942 JBrowse»
Reference genome	IRGSP-1.0.38
Type	u-circRNA
Identification method	CIRCexplorer, find_circ
Parent gene	Os04g0252200
Parent gene annotation	Similar to CPSF160; nucleic acid binding. (Os04t0252200-01);Simi lar to CPSF160; nucleic acid binding. (Os04t0252200-02)
Parent gene strand	-
Alternative splicing	Os04g0252200_circ_g.2 Os04g0252200_circ_g.3 Os04g0252200_circ_g.4 Os04g0252200_circ_g.5 Os04g0252200_circ_g.6 Os04g0252200_circ_g.7 Os04g0252200_circ_g.8 Os04g0252200_circ_g.9 Os04g0252200_circ_g.10 Os04g0252200_circ_g.11 Os04g0252200_circ_g.12 Os04g0252200_circ_g.13 Os04g0252200_circ_g.14 Os04g0252200_circ_g.15 Os04g0252200_circ_g.16 Os04g0252200_circ_g.17 Os04g0252200_circ_g.18
Support reads	2/2
Tissues	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	CT-AC 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	Os04t0252200-02:3

			
						 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  
						
							AAGAGAACAGAAGCACACGTCCTCTAGCAGCTACATCCTCCCCAAGAACATAAGCAGTCCCAAT
GGCCAACAGGGTCTCATTTTCCTTGGTGGTTGTATTctgcacattcttatcagaatctgaagct
acaaggctcagcgtgcttccatcaattaagaactcagttgcaaagcaatcgagtgatccaaaat
cttttgcc

						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: 489
Transcript exons: 9893940-9894125,9898548-9898721,9898814-9898942
CTGCACATTCTTATCAGAATCTGAAGCTACAAGGCTCAGCGTGCTTCCATCAATTAAGAACTCA
GTTGCAAAGCAATCGAGTGATCCAAAATCTTTTGCCAGGAGACTCAATTGAGAACCTTGCTCTT
TCCAGCTCAGAAAATAAATGCTTTTATGAATATCACCAAACAAAACGAAGTTTTTGACAATGTT
CAGGCTCACAACATGCAAAGGGGCATCATAGAATGCAACAGCAGTCAATTCAGCACCAGTCCAC
TTGTTTAATGTGATCTTAGGACCAGAAGCTATCAGCAGATGACCTTGAAGAGACGCAACAGCTG
ATACAGCACCTTTACTCTCTTTTGAGTAGACTTCAGTGACCAGATTTTGAGAATTTTCACTTTT
CGTGAAAGAGAACAGAAGCACACGTCCTCTAGCAGCTACATCCTCCCCAAGAACATAAGCAGTC
CCAATGGCCAACAGGGTCTCATTTTCCTTGGTGGTTGTATT
						
						Genomic sequence
						
							TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

Sequences
Splice junction sequence	AAGAGAACAGAAGCACACGTCCTCTAGCAGCTACATCCTCCCCAAGAACATAAGCAGTCCCAAT GGCCAACAGGGTCTCATTTTCCTTGGTGGTTGTATTctgcacattcttatcagaatctgaagct acaaggctcagcgtgcttccatcaattaagaactcagttgcaaagcaatcgagtgatccaaaat cttttgcc
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: 489 Transcript exons: 9893940-9894125,9898548-9898721,9898814-9898942 CTGCACATTCTTATCAGAATCTGAAGCTACAAGGCTCAGCGTGCTTCCATCAATTAAGAACTCA GTTGCAAAGCAATCGAGTGATCCAAAATCTTTTGCCAGGAGACTCAATTGAGAACCTTGCTCTT TCCAGCTCAGAAAATAAATGCTTTTATGAATATCACCAAACAAAACGAAGTTTTTGACAATGTT CAGGCTCACAACATGCAAAGGGGCATCATAGAATGCAACAGCAGTCAATTCAGCACCAGTCCAC TTGTTTAATGTGATCTTAGGACCAGAAGCTATCAGCAGATGACCTTGAAGAGACGCAACAGCTG ATACAGCACCTTTACTCTCTTTTGAGTAGACTTCAGTGACCAGATTTTGAGAATTTTCACTTTT CGTGAAAGAGAACAGAAGCACACGTCCTCTAGCAGCTACATCCTCCCCAAGAACATAAGCAGTC CCAATGGCCAACAGGGTCTCATTTTCCTTGGTGGTTGTATT
Genomic sequence	TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.209789323

Conservation Information
Conserved circRNAs	NA
PMCS	0.209789323

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							9898906-9894051(+)
9893949-9898875(-)
						
						Potential amino acid sequence
						
							MANRVSFSLVVVFCTFLSESEATRLSVLPSIKNSVAKQSSDPKSFARRLN*(+)
MCRIQPPRKMRPCWPLGLLMFLGRM*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	9898906-9894051(+) 9893949-9898875(-)
Potential amino acid sequence	MANRVSFSLVVVFCTFLSESEATRLSVLPSIKNSVAKQSSDPKSFARRLN(+) MCRIQPPRKMRPCWPLGLLMFLGRM(-)
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 Os04g0252200_circ_g.1

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