Plant Circular RNA Database

Detail information of Os01g0653800_circ_g.4

			
						 General Information
					
						CircRNA Name
						Os01g0653800_circ_g.4
					
						ID in PlantcircBase
						osa_circ_002947
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr1: 26456676-26458016  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os01g0653800						
					
						Parent gene annotation
						
							Similar to predicted protein. (Os01t0653800-01);WD40 repeat-like
 domain containing protein. (Os01t0653800-02);Similar to Peptida
se S8 and S53, subtilisin, kexin, sedolisin; WD40-like. (Os01t06
53800-03)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os01g0653800_circ_g.5 Os01g0653800_circ_g.6 						
					
						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
						Os01t0653800-01:1
Os01t0653800-03:2
Os01t0653800-02:2

General Information
CircRNA Name	Os01g0653800_circ_g.4
ID in PlantcircBase	osa_circ_002947
Alias	NA
Organism	Oryza sativa
Position	chr1: 26456676-26458016 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	Os01g0653800
Parent gene annotation	Similar to predicted protein. (Os01t0653800-01);WD40 repeat-like domain containing protein. (Os01t0653800-02);Similar to Peptida se S8 and S53, subtilisin, kexin, sedolisin; WD40-like. (Os01t06 53800-03)
Parent gene strand	-
Alternative splicing	Os01g0653800_circ_g.5 Os01g0653800_circ_g.6
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	Os01t0653800-01:1 Os01t0653800-03:2 Os01t0653800-02:2

			
						 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  
						
							TGCAGCCGCCCGACTCTGAGCTTCTCTTGCTTTCATTTCTTCTTTCCTCTTTTTTGTTTCAATG
TCAATGGCAGCCACACCCGCATCAACAAAGACACACctgtcaacgagccatagaactccatctc
tgacaccaaccacaacaaggggtccaataggtcttttctgctcaggagggaagcgggttactgc
aacagata

									
								

					

						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: 435
Transcript exons: 26456676-26456923,26457830-26458016
CTGTCAACGAGCCATAGAACTCCATCTCTGACACCAACCACAACAAGGGGTCCAATAGGTCTTT
TCTGCTCAGGAGGGAAGCGGGTTACTGCAACAGATACCCCTCCTCCAGCAACAGCAACTTCAGC
ATATCTTCTATCATCCAATTCTTTCTGAAACACTGAATCTTCTCCATCTAACTTTGATTGCTTT
GGCACTATAAATGGGGGTATAGATGGAGCATACTGAAAGGAGGCTAACCGAACAACCTGCAACA
TTGGAGGTCTTAAAGCTATTTTCTCAGAAGTGGTAGTCTTGGGGCCTTCAACTGTAATAAGAGC
CAAATCTCCATGCTCTGCAGCCGCCCGACTCTGAGCTTCTCTTGCTTTCATTTCTTCTTTCCTC
TTTTTTGTTTCAATGTCAATGGCAGCCACACCCGCATCAACAAAGACACAC
						
					

						Genomic sequence
						
							CTGTCAACGAGCCATAGAACTCCATCTCTGACACCAACCACAACAAGGGGTCCAATAGGTCTTT
TCTGCTCAGGAGGGAAGCGGGTTACTGCAACAGATACCCCTCCTCCAGCAACAGCAACTTCAGC
ATATCTTCTATCATCCAATTCTTTCTGAAACACTGAATCTTCTCCATCTAACTTTGATTGCTTT
GGCACTATAAATGGGGGTATAGATGGAGCATACTGAAAGGAGGCTAACCGAACAACCTGAGAAA
TGTACAGAGTAATTAAAAATAATGATGACTTGTTCCAAATGAGATAAATATCCACACACAATAA
TTGATATACTCCCTCCATTAACATATGTAATAGTGAATGGTTTGACTTGTGCATGATTTCCATA
TTGATTTTTTCCCATTAACAGTATATTGCCAATAACTACAAAACCAAGTTCAAATGAGATACTT
TCAAATATGGACCCAATGACACCCATAAAAAAATGAGATATAAAAATAACATTGCCAGGATTTT
TTAAATAACAGCCCACTAACCAATAATGAATGCTTTACTAGATTAACTATGCGTATCCTGAAGA
GAGTTCACCGCTCATCTGATTGACATCGCAGCCCACTAACCATTAATGAGAATGCTTACTTTAC
TATTTGAACTACACGTATCCTGGAGATGGGTTAACAGTCAGATGTAAAACGCCAGGTTACACCT
GATCAAATTTTGAAAAAAAGAGAACTCTGATTCACAGAAGGAGAAGATTCAACAGGACTGTAGC
TGAGGGGAGTTGATTCTTTTCTTTTTGCAAGGTGATAATTAAAGGCTAGGAATCCAAATAATTG
TGGATGTGAAAATAAAAGGGATCATAGTAAGCAAACACAATCTCTTCCTAAAAGATGGAACAGG
GAAATAACAATTATGTTCATCAAAAAAACCCAACGAGACTGCATCAATCCAACGGCCACTATAT
ACAAATAAGTGCAAATAGGAAATCCATACAACTACGAAGAGAAGCTTCAAATACATGGGGATAC
ATTTCAATCATGTAAAGTAATAAATTCCGTATTACTGAAACTGACTTCAAATAACATTAGAAGA
ACACAAAAGAAAACAGTATATAAGTAGAAACGGTACAAAAGAAATCAAGAATGTAGAAAACTGT
ACCTGCAACATTGGAGGTCTTAAAGCTATTTTCTCAGAAGTGGTAGTCTTGGGGCCTTCAACTG
TAATAAGAGCCAAATCTCCATGCTCTGCAGCCGCCCGACTCTGAGCTTCTCTTGCTTTCATTTC
TTCTTTCCTCTTTTTTGTTTCAATGTCAATGGCAGCCACACCCGCATCAACAAAGACACAC
						
					

			
		

Sequences
Splice junction sequence	TGCAGCCGCCCGACTCTGAGCTTCTCTTGCTTTCATTTCTTCTTTCCTCTTTTTTGTTTCAATG TCAATGGCAGCCACACCCGCATCAACAAAGACACACctgtcaacgagccatagaactccatctc tgacaccaaccacaacaaggggtccaataggtcttttctgctcaggagggaagcgggttactgc aacagata
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: 435 Transcript exons: 26456676-26456923,26457830-26458016 CTGTCAACGAGCCATAGAACTCCATCTCTGACACCAACCACAACAAGGGGTCCAATAGGTCTTT TCTGCTCAGGAGGGAAGCGGGTTACTGCAACAGATACCCCTCCTCCAGCAACAGCAACTTCAGC ATATCTTCTATCATCCAATTCTTTCTGAAACACTGAATCTTCTCCATCTAACTTTGATTGCTTT GGCACTATAAATGGGGGTATAGATGGAGCATACTGAAAGGAGGCTAACCGAACAACCTGCAACA TTGGAGGTCTTAAAGCTATTTTCTCAGAAGTGGTAGTCTTGGGGCCTTCAACTGTAATAAGAGC CAAATCTCCATGCTCTGCAGCCGCCCGACTCTGAGCTTCTCTTGCTTTCATTTCTTCTTTCCTC TTTTTTGTTTCAATGTCAATGGCAGCCACACCCGCATCAACAAAGACACAC
Genomic sequence	CTGTCAACGAGCCATAGAACTCCATCTCTGACACCAACCACAACAAGGGGTCCAATAGGTCTTT TCTGCTCAGGAGGGAAGCGGGTTACTGCAACAGATACCCCTCCTCCAGCAACAGCAACTTCAGC ATATCTTCTATCATCCAATTCTTTCTGAAACACTGAATCTTCTCCATCTAACTTTGATTGCTTT GGCACTATAAATGGGGGTATAGATGGAGCATACTGAAAGGAGGCTAACCGAACAACCTGAGAAA TGTACAGAGTAATTAAAAATAATGATGACTTGTTCCAAATGAGATAAATATCCACACACAATAA TTGATATACTCCCTCCATTAACATATGTAATAGTGAATGGTTTGACTTGTGCATGATTTCCATA TTGATTTTTTCCCATTAACAGTATATTGCCAATAACTACAAAACCAAGTTCAAATGAGATACTT TCAAATATGGACCCAATGACACCCATAAAAAAATGAGATATAAAAATAACATTGCCAGGATTTT TTAAATAACAGCCCACTAACCAATAATGAATGCTTTACTAGATTAACTATGCGTATCCTGAAGA GAGTTCACCGCTCATCTGATTGACATCGCAGCCCACTAACCATTAATGAGAATGCTTACTTTAC TATTTGAACTACACGTATCCTGGAGATGGGTTAACAGTCAGATGTAAAACGCCAGGTTACACCT GATCAAATTTTGAAAAAAAGAGAACTCTGATTCACAGAAGGAGAAGATTCAACAGGACTGTAGC TGAGGGGAGTTGATTCTTTTCTTTTTGCAAGGTGATAATTAAAGGCTAGGAATCCAAATAATTG TGGATGTGAAAATAAAAGGGATCATAGTAAGCAAACACAATCTCTTCCTAAAAGATGGAACAGG GAAATAACAATTATGTTCATCAAAAAAACCCAACGAGACTGCATCAATCCAACGGCCACTATAT ACAAATAAGTGCAAATAGGAAATCCATACAACTACGAAGAGAAGCTTCAAATACATGGGGATAC ATTTCAATCATGTAAAGTAATAAATTCCGTATTACTGAAACTGACTTCAAATAACATTAGAAGA ACACAAAAGAAAACAGTATATAAGTAGAAACGGTACAAAAGAAATCAAGAATGTAGAAAACTGT ACCTGCAACATTGGAGGTCTTAAAGCTATTTTCTCAGAAGTGGTAGTCTTGGGGCCTTCAACTG TAATAAGAGCCAAATCTCCATGCTCTGCAGCCGCCCGACTCTGAGCTTCTCTTGCTTTCATTTC TTCTTTCCTCTTTTTTGTTTCAATGTCAATGGCAGCCACACCCGCATCAACAAAGACACAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.241058141

Conservation Information
Conserved circRNAs	NA
PMCS	0.241058141

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							26457979-26456828(+)
26457912-26456689(+)
26457954-26456678(-)
26456702-26457951(-)
						
						Potential amino acid sequence
						
							MSMAATPASTKTHLSTSHRTPSLTPTTTRGPIGLFCSGGKRVTATDTPPPATATSAYLLSSNSF
*(+)
MLCSRPTLSFSCFHFFFPLFCFNVNGSHTRINKDTPVNEP*(+)
MKAREAQSRAAAEHGDLALITVEGPKTTTSEKIALRPPMLQVVRLASFQYAPSIPPFIVPKQSK
LDGEDSVFQKELDDRRYAEVAVAGGGVSVAVTRFPPEQKRPIGPLVVVGVRDGVLWLVDRCVFV
DAGVAAIDIETKKRKEEMKAREAQSRAAAEHGDLALITVEGPKTTTSEKIALRPPMLQVVRLAS
FQYAPSIPPFIVPKQSKLDGEDSVFQKELDDRRYAEVAVAGGGVSVAVTRFPPEQKRPIGPLVV
VGVRDGVLWLVDRCVFVDAGVAAIDIETKKRKEEMKAREAQSRAAAEHGDLALITVEGPKTTTS
EKIALRPPMLQVVRLASFQYAPSIPPFIVPKQSKLDGEDSVFQKELDDRRYAEVAVAGGGVSVA
VTRFPPEQKRPIGPLVVVGVRDGVLWLVDRCVFVDAGVAAIDIETKKRKEEMKAREAQSRAAAE
HGDLALITVEGPKTTTSEKIALRPPMLQVVRLASFQYAPSIPPFIVPKQSKLDGEDSVFQKELD
DRRYAEVAVAGGGVSVAVTRFPPEQKRPIGPLVVVGVRDGVLWLVD(-)
MEFYGSLTGVSLLMRVWLPLTLKQKRGKKK*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	26457979-26456828(+) 26457912-26456689(+) 26457954-26456678(-) 26456702-26457951(-)
Potential amino acid sequence	MSMAATPASTKTHLSTSHRTPSLTPTTTRGPIGLFCSGGKRVTATDTPPPATATSAYLLSSNSF (+) MLCSRPTLSFSCFHFFFPLFCFNVNGSHTRINKDTPVNEP(+) MKAREAQSRAAAEHGDLALITVEGPKTTTSEKIALRPPMLQVVRLASFQYAPSIPPFIVPKQSK LDGEDSVFQKELDDRRYAEVAVAGGGVSVAVTRFPPEQKRPIGPLVVVGVRDGVLWLVDRCVFV DAGVAAIDIETKKRKEEMKAREAQSRAAAEHGDLALITVEGPKTTTSEKIALRPPMLQVVRLAS FQYAPSIPPFIVPKQSKLDGEDSVFQKELDDRRYAEVAVAGGGVSVAVTRFPPEQKRPIGPLVV VGVRDGVLWLVDRCVFVDAGVAAIDIETKKRKEEMKAREAQSRAAAEHGDLALITVEGPKTTTS EKIALRPPMLQVVRLASFQYAPSIPPFIVPKQSKLDGEDSVFQKELDDRRYAEVAVAGGGVSVA VTRFPPEQKRPIGPLVVVGVRDGVLWLVDRCVFVDAGVAAIDIETKKRKEEMKAREAQSRAAAE HGDLALITVEGPKTTTSEKIALRPPMLQVVRLASFQYAPSIPPFIVPKQSKLDGEDSVFQKELD DRRYAEVAVAGGGVSVAVTRFPPEQKRPIGPLVVVGVRDGVLWLVD(-) MEFYGSLTGVSLLMRVWLPLTLKQKRGKKK*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os01g0653800_circ_g.4

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