Plant Circular RNA Database

Detail information of Os01g0276800_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os01g0276800_circ_g.3
					
						ID in PlantcircBase
						osa_circ_001314
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr1: 9707451-9709041  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os01g0276800						
					
						Parent gene annotation
						
							Mannose-6-phosphate receptor, binding domain containing protein.
 (Os01t0276800-01);Similar to predicted protein. (Os01t0276800-0
2);Hypothetical conserved gene. (Os01t0276800-03);Similar to pre
dicted protein. (Os01t0276800-04);Similar to predicted protein. 
(Os01t0276800-05)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os01g0276800_circ_g.1 Os01g0276800_circ_g.2 						
					
						Support reads
						1
					
						Tissues
						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
						Os01t0276800-03:3
Os01t0276800-01:4
Os01t0276800-02:3

General Information
CircRNA Name	Os01g0276800_circ_g.3
ID in PlantcircBase	osa_circ_001314
Alias	NA
Organism	Oryza sativa
Position	chr1: 9707451-9709041 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	Os01g0276800
Parent gene annotation	Mannose-6-phosphate receptor, binding domain containing protein. (Os01t0276800-01);Similar to predicted protein. (Os01t0276800-0 2);Hypothetical conserved gene. (Os01t0276800-03);Similar to pre dicted protein. (Os01t0276800-04);Similar to predicted protein. (Os01t0276800-05)
Parent gene strand	-
Alternative splicing	Os01g0276800_circ_g.1 Os01g0276800_circ_g.2
Support reads	1
Tissues	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	Os01t0276800-03:3 Os01t0276800-01:4 Os01t0276800-02:3

			
						 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  
						
							TTACCACAGATACCATCATTCACTCGCGACGAGAAGATCGTGATGGGAGAATGCCCAGCATTCT
GGCAGTAGAACTTCCCCTCCGGGCACGCCGATGTCCctgctcaacagatgactcgctttctggt
gtgtgattgtcatggctcgtggcatgtccatcatgatgttcagctacctgtattcatcatcaaa
aacaaaat

									
								

					

						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
						
							CTGCTCAACAGATGACTCGCTTTCTGGTGTGTGATTGTCATGGCTCGTGGCATGTCCATCATGA
TGTTCAGCTACCTGTATTCATCATCAAAAACAAAATAATATAAATATCTCTTTATGGCATTGAG
CTACCTAGTTGTGCAGTAAGTTCCTACAATTCATAAGTGAGGAACTGAGGATTAGTACAGCATA
GTATCATATGTTACCACAGTGATGATCATTTTTATGTTCTTTATGACTAACCATTACTGGTAAA
TTGTGGGGAAAAAGGTTATAAATAGCATTGATGGAACATCCAGTTGCTAGGATACATGGGGACT
ATCCGTTCTTGATGTATGTATGTATGCATATGGTATCTCTGTTAAGAAGGCAGTTTAATGGTTC
AGATCATCTAGCCCAAAACCTAAAATGAAGCCAACAATTTGAGGCTTTAAGTGCCACCAAGAAA
CTTAAGGTTCTGCACAATTATGACATAAATCCTGTACTTTTCGATAAACCATTGTTACAAAACT
CTGTAGAACATTGATTTATCTTCTTATGTGAATCATTTTGCGATAAAAATGCACTGAAACCATT
GGAAGGATGGTAGTTCTCTCCCAAAGCATAGTAATTTCATGAGTATACAACACATAGCTGCACC
CTATTAGACGTGTCAACATGCTAACACCAGCTTAACTCGATTCAAGATATTAATGGTGAGGATG
AAGAGTTCATCAGACAAAGGTATATATGGCAATCTAACAGATATATAGAAAGAATGCTAACCTT
GCTCTCATCTTCTTGCACAGTTTCATGATTTTCCTGAGAATCTACCTCCTGAGAGGCATCTGAC
GCTTTCTTTTCATCAGCAGCTTGCTTTTCGGCTTCTTCCTTCATCCTCTTTTCTTCCTTTTCTT
TTCTTAAGCGTTCCTCTTCCTCTGCCTTCTCTATCAATTTCTTTTGTTCTGCACAACATGAGAA
GTCATAGTTTAACACAAAATAAACTATCCATTGAAAATTAGCAGCGCCAACAGCATTTCCCAAC
ATAACATTCTTTGGTAAATGACTCAAGACAAACCGCCACGAAGAGCACACCTGTGAGCTTGTCA
ACAAGGCCTTGTAGTATTTTCTCTTCACCCTTCAGTTTCGCTAGCTCTGCCTCGTCTTTAGCAA
ATGCCACTTTTGCCTTTTGAATTTCCTGATTTCGAATAACAACTCCGCTTTTATATGTAGCTAC
TTTTTTCTTCAATTTATCCCTTGCCGCTTTACCAGCCTCCCAGCACGTATTCTTGCAAGTGACA
TTGCTATCATACTCATCACTCCCGTCGCAGCAATCTAAGAGGCAGCGACAAACACATATGGGTA
ATTAGAAAAAAATATAGCGGGAATTCCCTCAAGCACTATGTTTACGGAACAAAAGCACCCTAAT
CTCTAGCCTTACAATTGATTTTGTGTACATTTACTGTGTTTACATTTGAATGATACAGAGAATG
GCCACCGATTATAATCCTCTTACCACAGATACCATCATTCACTCGCGACGAGAAGATCGTGATG
GGAGAATGCCCAGCATTCTGGCAGTAGAACTTCCCCTCCGGGCACGCCGATGTCC
						
					

			
		

Sequences
Splice junction sequence	TTACCACAGATACCATCATTCACTCGCGACGAGAAGATCGTGATGGGAGAATGCCCAGCATTCT GGCAGTAGAACTTCCCCTCCGGGCACGCCGATGTCCctgctcaacagatgactcgctttctggt gtgtgattgtcatggctcgtggcatgtccatcatgatgttcagctacctgtattcatcatcaaa aacaaaat
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	CTGCTCAACAGATGACTCGCTTTCTGGTGTGTGATTGTCATGGCTCGTGGCATGTCCATCATGA TGTTCAGCTACCTGTATTCATCATCAAAAACAAAATAATATAAATATCTCTTTATGGCATTGAG CTACCTAGTTGTGCAGTAAGTTCCTACAATTCATAAGTGAGGAACTGAGGATTAGTACAGCATA GTATCATATGTTACCACAGTGATGATCATTTTTATGTTCTTTATGACTAACCATTACTGGTAAA TTGTGGGGAAAAAGGTTATAAATAGCATTGATGGAACATCCAGTTGCTAGGATACATGGGGACT ATCCGTTCTTGATGTATGTATGTATGCATATGGTATCTCTGTTAAGAAGGCAGTTTAATGGTTC AGATCATCTAGCCCAAAACCTAAAATGAAGCCAACAATTTGAGGCTTTAAGTGCCACCAAGAAA CTTAAGGTTCTGCACAATTATGACATAAATCCTGTACTTTTCGATAAACCATTGTTACAAAACT CTGTAGAACATTGATTTATCTTCTTATGTGAATCATTTTGCGATAAAAATGCACTGAAACCATT GGAAGGATGGTAGTTCTCTCCCAAAGCATAGTAATTTCATGAGTATACAACACATAGCTGCACC CTATTAGACGTGTCAACATGCTAACACCAGCTTAACTCGATTCAAGATATTAATGGTGAGGATG AAGAGTTCATCAGACAAAGGTATATATGGCAATCTAACAGATATATAGAAAGAATGCTAACCTT GCTCTCATCTTCTTGCACAGTTTCATGATTTTCCTGAGAATCTACCTCCTGAGAGGCATCTGAC GCTTTCTTTTCATCAGCAGCTTGCTTTTCGGCTTCTTCCTTCATCCTCTTTTCTTCCTTTTCTT TTCTTAAGCGTTCCTCTTCCTCTGCCTTCTCTATCAATTTCTTTTGTTCTGCACAACATGAGAA GTCATAGTTTAACACAAAATAAACTATCCATTGAAAATTAGCAGCGCCAACAGCATTTCCCAAC ATAACATTCTTTGGTAAATGACTCAAGACAAACCGCCACGAAGAGCACACCTGTGAGCTTGTCA ACAAGGCCTTGTAGTATTTTCTCTTCACCCTTCAGTTTCGCTAGCTCTGCCTCGTCTTTAGCAA ATGCCACTTTTGCCTTTTGAATTTCCTGATTTCGAATAACAACTCCGCTTTTATATGTAGCTAC TTTTTTCTTCAATTTATCCCTTGCCGCTTTACCAGCCTCCCAGCACGTATTCTTGCAAGTGACA TTGCTATCATACTCATCACTCCCGTCGCAGCAATCTAAGAGGCAGCGACAAACACATATGGGTA ATTAGAAAAAAATATAGCGGGAATTCCCTCAAGCACTATGTTTACGGAACAAAAGCACCCTAAT CTCTAGCCTTACAATTGATTTTGTGTACATTTACTGTGTTTACATTTGAATGATACAGAGAATG GCCACCGATTATAATCCTCTTACCACAGATACCATCATTCACTCGCGACGAGAAGATCGTGATG GGAGAATGCCCAGCATTCTGGCAGTAGAACTTCCCCTCCGGGCACGCCGATGTCC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.128487272

Conservation Information
Conserved circRNAs	NA
PMCS	0.128487272

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							9708993-9707481(+)
9707514-9708959(-)
9708328-9708963(-)
						
						Potential amino acid sequence
						
							MPSILAVELPLRARRCPCSTDDSLSGV*(+)
MMDMPRAMTITHQKASHLLSRDIGVPGGEVLLPECWAFSHHDLLVASE*(-)
MKEEAEKQAADEKKASDASQEVDSQENHETVQEDESKVAEHHDGHATSHDNHTPESESSVEQGH
RRARRGSSTARMLGILPSRSSRRE*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	9708993-9707481(+) 9707514-9708959(-) 9708328-9708963(-)
Potential amino acid sequence	MPSILAVELPLRARRCPCSTDDSLSGV(+) MMDMPRAMTITHQKASHLLSRDIGVPGGEVLLPECWAFSHHDLLVASE(-) MKEEAEKQAADEKKASDASQEVDSQENHETVQEDESKVAEHHDGHATSHDNHTPESESSVEQGH RRARRGSSTARMLGILPSRSSRRE*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os01g0276800_circ_g.3

Address

Any questions?

Supported by